U.S. patent application number 15/321595 was filed with the patent office on 2017-08-10 for plant-endophyte combinations and uses therefor.
The applicant listed for this patent is AIT AUSTRIAN INSTITUTE OF TECHNOLOGY GMBH, INDIGO AGRICULTURE, INC.. Invention is credited to Karen AMBROSE, Birgit MITTER, Milica PASTAR, Nikolaus PFAFFENBICHLER, Guenther REICHENBERGER, Angela SESSITSCH, Xuecheng ZHANG.
Application Number | 20170223967 15/321595 |
Document ID | / |
Family ID | 54929132 |
Filed Date | 2017-08-10 |
United States Patent
Application |
20170223967 |
Kind Code |
A1 |
MITTER; Birgit ; et
al. |
August 10, 2017 |
PLANT-ENDOPHYTE COMBINATIONS AND USES THEREFOR
Abstract
The disclosure provides materials and methods for conferring
improved plant traits or benefits on plants. The materials can
include a formulation comprising an exogenous endophytic bacterial
population, which can be disposed on an exterior surface of a seed
or seedling, typically in an amount effective to colonize the
plant. The formulations can include at least one member selected
from the group consisting of an agriculturally compatible carrier,
a tackifier, a microbial stabilizer, a fungicide, an antibacterial
agent, an herbicide, a nematicide, an insecticide, a plant growth
regulator, a rodenticide, and a nutrient.
Inventors: |
MITTER; Birgit; (Giesshubl,
AT) ; PASTAR; Milica; (Wien, AT) ; SESSITSCH;
Angela; (Vienna, AT) ; AMBROSE; Karen;
(Cambridge, MA) ; ZHANG; Xuecheng; (Brookline,
MA) ; REICHENBERGER; Guenther; (Vienna, AT) ;
PFAFFENBICHLER; Nikolaus; (Vienna, AT) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
AIT AUSTRIAN INSTITUTE OF TECHNOLOGY GMBH
INDIGO AGRICULTURE, INC. |
Vienna
Boston |
MA |
AT
US |
|
|
Family ID: |
54929132 |
Appl. No.: |
15/321595 |
Filed: |
June 26, 2015 |
PCT Filed: |
June 26, 2015 |
PCT NO: |
PCT/US15/38110 |
371 Date: |
December 22, 2016 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
14315804 |
Jun 26, 2014 |
9364005 |
|
|
15321595 |
|
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12N 1/20 20130101; A01N
63/10 20200101; G01N 33/0098 20130101; A01H 5/00 20130101; A01N
63/00 20130101 |
International
Class: |
A01N 63/00 20060101
A01N063/00; A01H 5/00 20060101 A01H005/00; C12N 1/20 20060101
C12N001/20 |
Claims
1. A seed or seedling of an agricultural plant having disposed on
an exterior surface of the seed or seedling a formulation
comprising an exogenous endophytic bacterial population consisting
essentially of an endophytic bacterium comprising a 16S rRNA
nucleic acid sequence at least 95% identical to a nucleic acid
sequence selected from the group consisting of SEQ ID NOs: 1-10,
wherein the exogenous endophytic bacterial population is disposed
on an exterior surface of the seed or seedling in an amount
effective to colonize the plant, the formulation further comprising
at least one member selected from the group consisting of an
agriculturally compatible carrier, a tackifier, a microbial
stabilizer, a fungicide, an antibacterial agent, an herbicide, a
nematicide, an insecticide, a plant growth regulator, a
rodenticide, and a nutrient.
2. The seed or seedling of claim 1, wherein the exogenous
endophytic bacterial population is disposed in an amount effective
to be detectable within a target tissue of the mature agricultural
plant selected from a fruit, a seed, a leaf, a stem, a shoot, a
flower, or a root, or portion thereof.
3. The seed or seedling of claim 2, wherein the exogenous
endophytic bacterial population is disposed in an amount effective
to be detectable in an amount of at least about 100 CFU of the
endophytic bacterial population per gram fresh weight of the target
tissue.
4. The seed or seedling of claim 1, comprising at least about 100
CFU per gram fresh weight of the exogenous endophytic bacterial
population on its exterior surface.
5. The seed or seedling of claim 1, wherein the agricultural plant
is a monocot.
6. The seed or seedling of claim 1, wherein the agricultural plant
is a corn plant.
7. The seed or seedling of claim 1, wherein the agricultural plant
is a dicot.
8. The seed or seedling of claim 1, wherein the exogenous
endophytic bacterial population is disposed on an exterior surface
in an amount effective to be detectable in an amount of at least
about 100 CFU in the mature agricultural plant.
9. The seed or seedling of claim 1, wherein the exogenous
endophytic bacterial population is disposed in an amount effective
to increase fruit or grain biomass or yield from the resulting
plant by at least 5% when compared with a reference agricultural
plant.
10. The seed or seedling of claim 1, wherein the exogenous
endophytic bacterial population is disposed in an amount effective
to increase the biomass of the agricultural plant or portion
thereof by at least 5% when compared with a reference agricultural
plant.
11. The seed or seedling of claim 1, wherein the exogenous
endophytic bacterial population is disposed in an amount effective
to increase the rate of seed germination when compared with a
reference agricultural plant.
12. The seed or seedling of claim 1, wherein the exogenous
endophytic bacterial population is disposed in an amount effective
to detectably induce production of auxin in the seed or
seedling.
13. The seed or seedling of claim 1, wherein the seed is a corn
seed, and wherein the formulation further comprises at least about
10,000 CFU of the exogenous endophytic bacterial population
consisting essentially of an endophytic bacterium comprising a 16S
rRNA nucleic acid sequence at least 95% identical to a nucleic acid
sequence selected from the group consisting of SEQ ID NOs: 1-10
disposed on the exterior surface of the seed, the formulation
comprising a microbial stabilizer.
14. The seed or seedling of claim 1, wherein the seed or seedling
is packaged in a container, wherein the container further comprises
a label describing said seeds or seedlings and/or said exogenous
endophytic bacterial population.
15. The seed or seedling of claim 14, wherein the container
comprises at least 1000 of said seeds or seedlings.
16. A method for preparing a seed or seedling comprising an
endophytic bacterial population, said method comprising applying to
a seed or seedling a formulation comprising an endophytic bacterial
population consisting essentially of an endophytic bacterium
comprising a 16S rRNA nucleic acid sequence at least 95% identical
to a nucleic acid sequence selected from the group consisting of
SEQ ID NOs: 1-10.
17. The method of claim 16, wherein the formulation further
comprises at least one member selected from the group consisting of
an agriculturally compatible carrier, a tackifier, a microbial
stabilizer, a fungicide, an antibacterial agent, an herbicide, a
nematicide, an insecticide, a plant growth regulator, a
rodenticide, and a nutrient.
18. The method of claim 16, wherein the endophytic bacterial
population is applied in an amount effective to be detectable
within a target tissue of the mature agricultural plant selected
from a fruit, a seed, a leaf, a stem, a shoot, a flower, or a root,
or portion thereof.
19. The method of claim 18, wherein the endophytic bacterial
population is applied in an amount effective to be detectable in an
amount of at least about 100 CFU of the endophytic bacterial
population per gram fresh weight of the target tissue.
20. The method of claim 16, wherein the seed is a monocot seed.
21. The method of claim 16, wherein the monocot seed is a corn
seed.
22. The method of claim 16, wherein the endophytic bacterial
population is applied in an amount effective to increase water use
efficiency of a plant grown from the seed by at least 5% when
compared with a reference agricultural plant grown under the same
conditions.
23. The method of claim 16, wherein the endophytic bacterial
population is applied in an amount effective to increase
photosynthetic rates of a plant grown from the seed by at least 8%
when compared with a reference agricultural plant grown under the
same conditions.
24. The method of claim 16, wherein the endophytic bacterial
population is applied in an amount effective to increase the
biomass of a plant, or plant part, grown from the seed under
abiotic-stress free conditions by at least 5% when compared with a
reference agricultural plant grown under the same conditions.
25. The method of claim 16, wherein the endophytic bacterial
population is applied in an amount effective to increase fruit or
grain biomass or yield from the resulting plant by at least 5% when
compared with a reference agricultural plant that was grown under
stress-free conditions.
26. The method of claim 16, wherein the endophytic bacterial
population is applied in an amount effective to increase the rate
of seed germination by at least 5% when compared with a reference
agricultural plant grown under the same conditions.
27. The method of claim 16, wherein the endophytic bacterial
population is applied in an amount effective to increase plant
height by at least 5% when compared with a reference agricultural
plant grown under the same conditions.
28. The method of 16, wherein the seed is a corn seed, and wherein
the formulation comprises at least about 1,000 CFU of the
endophytic bacterium applied on the exterior surface of the seed,
the formulation comprising a microbial stabilizer.
29. The method of claim 28, further comprising packaging the seeds
in a container, wherein the container further comprises a label
describing said seeds and/or said exogenous endophytic bacterial
population.
30. The method of claim 29, wherein the container comprises at
least 1000 of said seeds.
31. A method for conferring one or more fitness benefits to an
agricultural plant comprising: a. Providing a seed or seedling of
the plant; b. Contacting said seed or seedling with a formulation
comprising an exogenous endophytic bacterial population consisting
essentially of an endophytic bacterium comprising a 16S rRNA
nucleic acid sequence at least 95% identical to a nucleic acid
sequence selected from the group consisting of SEQ ID NOs: 1-10,
wherein the exogenous endophytic bacterial population is disposed
on an exterior surface of the seed or seedling in an amount
effective to colonize the mature plant, wherein the formulation
further comprises at least one member selected from the group
consisting of an agriculturally compatible carrier, a tackifier, a
microbial stabilizer, a fungicide, an antibacterial agent, an
herbicide, a nematicide, an insecticide, a plant growth regulator,
a rodenticide, and a nutrient; and c. Allowing the seed or seedling
to grow under conditions that permit the endophytic bacterium to
colonize the plant.
32. The method of claim 31, wherein the one or more of the fitness
benefits are selected from the group consisting of increased
germination, increased biomass, increased flowering time, increased
plant biomass, increased fruit or grain yield, increased biomass of
the fruit or cob, and increased drought tolerance.
33. A method for conferring one or more fitness benefits to a
monocot agricultural plant comprising: a. Providing a monocot seed
of the plant; b. Applying to an exterior surface of the monocot
seed a formulation comprising an exogenous endophytic bacterial
population consisting essentially of an endophytic bacterium
comprising a 16S rRNA nucleic acid sequence at least 99% identical
to a nucleic acid sequence selected from the group consisting of
SEQ ID NOs: 1-10, wherein the exogenous endophytic bacterial
population is applied to an exterior surface of the seed in an
amount effective to colonize the mature plant, wherein the
formulation further comprises at least one member selected from the
group consisting of an agriculturally compatible carrier, a
tackifier, a microbial stabilizer, a fungicide, an antibacterial
agent, an herbicide, a nematicide, an insecticide, a plant growth
regulator, a rodenticide, and a nutrient; and c. Allowing the seed
to grow under conditions that permit the endophytic bacterium to
colonize the plant.
34. The method of claim 33, wherein the one or more of the fitness
benefits is selected from the group consisting of increased
germination rate, shortened time before onset of flowering,
increased stomatal conductance, increased photosynthetic rates,
increased plant height, and increased drought tolerance as compared
to an agricultural plant grown under the same conditions.
35. The method of claim 33, wherein the one or more of the fitness
benefits is selected from the group consisting of increased
biomass, increased root biomass, increased leaf biomass, increased
fruit or grain yield, and increased biomass of the fruit or cob as
compared to an agricultural plant that was grown under stress-free
conditions.
36. The method of claim 33, wherein the seed is allowed to grow
under abiotic-stress free conditions and the one or more of the
fitness benefits is selected from the group consisting of increased
germination rate, increased biomass, shortened time before onset of
flowering, increased plant biomass, increased fruit or grain yield,
increased biomass of the fruit or cob, increased stomatal
conductance, increased photosynthetic rates, increased plant
height, and increased drought tolerance compared to a reference
agricultural plant grown under the same conditions.
37. A method of obtaining greater flowering uniformity in a
population of agricultural monocot plants comprising: a. Providing
a population of monocot seeds; b. Applying to an exterior surfaces
of the population of seeds a formulation comprising an exogenous
endophytic bacterial population consisting essentially of an
endophytic bacterium comprising a 16S rRNA nucleic acid sequence at
least 99% identical to a nucleic acid sequence selected from the
group consisting of SEQ ID NOs: 1-10, wherein the exogenous
endophytic bacterial population is applied on an exterior surface
of the seed in an amount effective to colonize the mature plant,
wherein the formulation further comprises at least one member
selected from the group consisting of an agriculturally compatible
carrier, a tackifier, a microbial stabilizer, a fungicide, an
antibacterial agent, an herbicide, a nematicide, an insecticide, a
plant growth regulator, a rodenticide, and a nutrient; and c.
Allowing the population of seeds to grow at least to the flowering
stage, wherein the population of plants has a reduction in the
standard deviation in the flowering time of at least 5% when
compared with a population of reference agricultural plants grown
under the same conditions.
38. A method for preparing a monocot seed comprising an endophytic
bacterial population, said method comprising applying to an
exterior surface of a monocot seed a formulation comprising an
endophytic bacterial population consisting essentially of an
endophytic bacterium comprising a 16S rRNA nucleic acid sequence at
least 99% identical to a nucleic acid sequence selected from the
group consisting of SEQ ID NOs: 1-10.
39. A method for treating seedlings, the method comprising: a)
contacting foliage or the rhizosphere of a plurality of
agricultural plant seedlings with a seed a formulation comprising
an endophytic bacterial population consisting essentially of an
endophytic bacterium comprising a 16S rRNA nucleic acid sequence at
least 99% identical to a nucleic acid sequence selected from the
group consisting of SEQ ID NOs: 1-10; and b) growing the contacted
seedlings.
40. The method of claim 38 or 39, wherein the contacting comprises
spraying, immersing, coating, encapsulating, or dusting the seeds
or seedlings with the formulation.
41. A method for modulating a plant trait comprising applying to
vegetation or an area adjacent the vegetation, a seed a formulation
comprising an endophytic bacterial population consisting
essentially of an endophytic bacterium comprising a 16S rRNA
nucleic acid sequence at least 99% identical to a nucleic acid
sequence selected from the group consisting of SEQ ID NOs: 1-10,
wherein the formulation is capable of providing a benefit to the
vegetation, or to a crop produced from the vegetation.
42. The method of claim 41, wherein the vegetation is dicot
seedlings.
43. The method of claim 41, wherein the vegetation is monocot
seedlings.
44. A method for modulating a plant trait comprising applying a
formulation to soil, the seed a formulation comprising an
endophytic bacterial population consisting essentially of an
endophytic bacterium comprising a 16S rRNA nucleic acid sequence at
least 99% identical to a nucleic acid sequence selected from the
group consisting of SEQ ID NOs: 1-10, wherein the formulation is
capable of providing a benefit to seeds planted within the soil, or
to a crop produced from plants grown in the soil.
45. The method of any of claim 16, 31, 33, 38, 39, 41, or 44,
wherein the endophytic bacterium is capable of exhibiting
production of an auxin, nitrogen fixation, production of an
antimicrobial, production of a siderophore, mineral phosphate
solubilization, production of a cellulase, production of a
chitinase, production of a xylanase, or production of acetoin.
46. The method of claim 46, wherein the bacterial endophyte
exhibits at least two of: production of an auxin, nitrogen
fixation, production of an antimicrobial, production of a
siderophore, mineral phosphate solubilization, production of a
cellulase, production of a chitinase, production of a xylanase, and
production of acetoin.
47. The method of any of claim 16, 31, 33, 38, 39, 41, or 44,
wherein the endophytic bacterium is capable of utilizing arabinose
as a substrate.
48. The method of any one of claim 16, 31, 33, 38, 39, 41, or 44,
wherein the bacterial endophyte is present at a concentration of at
least 10 2 CFU/seed on the surface of the seeds after
contacting.
49. The method of any one of claim 16, 31, 33, 38, 39, 41, or 44,
wherein the benefit is selected from the group consisting of:
increased root biomass, increased root length, increased height,
increased shoot length, increased leaf number, increased water use
efficiency, increased tolerance to low nitrogen stress, increased
nitrogen use efficiency, increased overall biomass, increase grain
yield, increased photosynthesis rate, increased tolerance to
drought, increased heat tolerance, increased salt tolerance,
increased resistance to nematode stress, increased resistance to a
fungal pathogen, increased resistance to a bacterial pathogen,
increased resistance to a viral pathogen, a detectable modulation
in the level of a metabolite, and a detectable modulation in the
proteome, relative to reference seeds or agricultural plants
derived from reference seeds.
50. The method of claim 49, wherein the benefit comprises at least
two benefits selected from the group consisting of: increased root
biomass, increased root length, increased height, increased shoot
length, increased leaf number, increased water use efficiency,
increased tolerance to low nitrogen stress, increased nitrogen use
efficiency, increased overall biomass, increase grain yield,
increased photosynthesis rate, increased tolerance to drought,
increased heat tolerance, increased salt tolerance, increased
resistance to nematode stress, increased resistance to a fungal
pathogen, increased resistance to a bacterial pathogen, increased
resistance to a viral pathogen, a detectable modulation in the
level of a metabolite, and a detectable modulation in the proteome,
relative to reference seeds or plants derived from reference
seeds.
51. The method of claim 50, wherein the benefit is increased
tolerance to low nitrogen stress or increased nitrogen use
efficiency, and the endophytic bacterium is non-diazotrophic.
52. The method of claim 50, wherein the benefit is increased
tolerance to low nitrogen stress or increased nitrogen use
efficiency, and the endophytic bacterium is diazotrophic.
53. A synthetic combination comprising a purified bacterial
population in association with a plurality of seeds or seedlings of
an agricultural plant, wherein the purified bacterial population
comprises a first bacterial endophyte capable of at least one of:
production of an auxin, nitrogen fixation, production of an
antimicrobial, production of a siderophore, mineral phosphate
solubilization, production of a cellulase, production of a
chitinase, production of a xylanase, utilization of arabinose as a
carbon source, and production of acetoin, or a combination of two
or more thereof, wherein the first bacterial endophyte comprises a
16S rRNA nucleic acid sequence at least 95% identical to a nucleic
acid sequence selected from the group consisting of SEQ ID NOs:
1-10, and wherein the bacterial endophyte is present in the
synthetic combination in an amount effective to provide a benefit
to the seeds or seedlings or the plants derived from the seeds or
seedlings.
54. The synthetic combination of claim 53, wherein the synthetic
combination is disposed within a packaging material selected from a
bag, box, bin, envelope, carton, or container.
55. The synthetic combination of claim 54, comprising 1000 seed
weight amount of seeds, wherein the packaging material optionally
comprises a dessicant, and wherein the synthetic combination
optionally comprises an anti-fungal agent.
56. The synthetic combination of claim 53, wherein the purified
bacterial population is localized on the surface of the seeds or
seedlings.
57. The synthetic combination of claim 53, wherein the first
bacterial endophyte is obtained from a plant species other than the
seeds or seedlings of the synthetic combination.
58. The synthetic combination of claim 53 wherein the first
bacterial endophyte is obtained from a plant cultivar different
from the cultivar of the seeds or seedlings of the synthetic
combination.
59. The synthetic combination of claim 53, wherein the first
bacterial endophyte is obtained from a plant cultivar that is the
same as the cultivar of the seeds or seedlings of the synthetic
combination.
60. The synthetic combination of claim 53, wherein the bacterial
population comprises two or more families of bacterial
endophytes.
61. The synthetic combination of claim 53, wherein the bacterial
population further comprises a second bacterial endophyte having an
16S nucleic acid sequence less than 95% identical to that of the
first bacterial endophyte.
62. The synthetic combination of claim 53, wherein the bacterial
population further comprises a second bacterial endophyte, wherein
the first and second bacterial endophytes are independently capable
of at least one of production of an auxin, nitrogen fixation,
production of an antimicrobial, production of a siderophore,
mineral phosphate solubilization, production of a cellulase,
production of a chitinase, production of a xylanase, utilization of
arabinose as a carbon source, or production of acetoin, or a
combination of two or more thereof.
63. The synthetic combination of claim 53, wherein the bacterial
population further comprises a second bacterial endophyte, wherein
the first and second bacterial endophytes are capable of
synergistically increasing at least one of: production of an auxin,
nitrogen fixation, production of an antimicrobial, production of a
siderophore, mineral phosphate solubilization, production of a
cellulase, production of a chitinase, production of a xylanase,
utilization of arabinose as a carbon source, or production of
acetoin, or a combination of two or more thereof, in an amount
effective to increase tolerance to drought relative to a reference
plant.
64. The synthetic combination of claim 53, wherein the first
bacterial endophyte is capable of at least two of: production of an
auxin, nitrogen fixation, production of an antimicrobial,
production of a siderophore, mineral phosphate solubilization,
production of a cellulase, production of a chitinase, production of
a xylanase, utilization of arabinose as a carbon source, and
production of acetoin.
65. The synthetic combination of claim 53, wherein the benefit is
selected from the group consisting of increased root biomass,
increased root length, increased height, increased shoot length,
increased leaf number, increased water use efficiency, increased
overall biomass, increase grain yield, increased photosynthesis
rate, increased tolerance to drought, increased heat tolerance,
increased salt tolerance, increased resistance to nematode stress,
increased resistance to a fungal pathogen, increased resistance to
a bacterial pathogen, increased resistance to a viral pathogen, a
detectable modulation in the level of a metabolite, and a
detectable modulation in the proteome relative to a reference
plant.
66. The synthetic combination of claim 53, wherein the benefit
comprises at least two benefits selected from the group consisting
of increased root biomass, increased root length, increased height,
increased shoot length, increased leaf number, increased water use
efficiency, increased tolerance to low nitrogen stress, increased
nitrogen use efficiency, increased overall biomass, increase grain
yield, increased photosynthesis rate, increased tolerance to
drought, increased heat tolerance, increased salt tolerance,
increased resistance to nematode stress, increased resistance to a
fungal pathogen, increased resistance to a bacterial pathogen,
increased resistance to a viral pathogen, a detectable modulation
in the level of a metabolite, and a detectable modulation in the
proteome, relative to a reference plant.
67. The synthetic combination of claim 53, wherein the combination
comprises seeds and the first bacterial endophyte is associated
with the seeds as a coating on the surface of the seeds.
68. The synthetic combination of claim 53, wherein the combination
comprises seedlings and the first bacterial endophyte is contacted
with the seedlings as a spray applied to one or more leaves and/or
one or more roots of the seedlings.
69. The synthetic combination of claim 53, wherein the synthetic
combination further comprises one or more additional bacterial
endophyte species.
70. The synthetic combination of claim 53, wherein the effective
amount is at least 1.times.10 3 CFU/per seed.
71. The synthetic combination of claim 53, wherein the combination
comprises seeds and the effective amount is from about 1.times.10 2
CFU/per seed to about 1.times.10 8 CFU/per seed.
72. An agricultural product comprising a 1000 seed weight amount of
a synthetic combination produced by the step of contacting a
plurality of agricultural plant seeds with a liquid formulation
comprising a bacterial population at a concentration of at least 1
CFU per agricultural plant seed, wherein at least 10% of the CFUs
present in the formulation are one or more bacterial endophytes,
wherein the purified bacterial population comprises a first
bacterial endophyte capable of at least one of: production of an
auxin, nitrogen fixation, production of an antimicrobial,
production of a siderophore, mineral phosphate solubilization,
production of a cellulase, production of a chitinase, production of
a xylanase, utilization of arabinose as a carbon source, and
production of acetoin, or a combination of two or more thereof,
wherein the first bacterial endophyte comprises a 16S rRNA nucleic
acid sequence at least 95% identical to a nucleic acid sequence
selected from the group consisting of SEQ ID NOs: 1-10, under
conditions such that the formulation is associated with the surface
of the seeds in a manner effective for the bacterial endophytes to
confer a benefit to the seeds or to a crop comprising a plurality
of agricultural plants produced from the seeds.
73. The agricultural product of claim 72, wherein the bacterial
endophytes are present in a concentration of from about 10 2 to
about 10 5 CFU/ml.
74. The agricultural product of claim 73, wherein the bacterial
endophytes are present in a concentration is from about 10 5 to
about 10 8 CFU/seed.
75. An agricultural formulation comprising a purified bacterial
population and an agriculturally acceptable carrier, the bacterial
population comprising a first bacterial endophyte capable of at
least one of: production of an auxin, nitrogen fixation, production
of an antimicrobial, production of a siderophore, mineral phosphate
solubilization, production of a cellulase, production of a
chitinase, production of a xylanase, utilization of arabinose as a
carbon source, and production of acetoin, or a combination of two
or more thereof, wherein the first bacterial endophyte comprises a
16S rRNA nucleic acid sequence at least 95% identical to a nucleic
acid sequence selected from the group consisting of SEQ ID NOs:
1-10, and wherein the first bacterial endophyte is present in an
amount effective to confer a benefit to an agricultural plant seed
to which the formulation is applied or to an agricultural plant
seedling to which the formulation is applied.
76. The agricultural formulation of claim 75, wherein the purified
bacterial population consists essentially of two or more species of
bacterial endophytes.
77. The agricultural formulation of claim 75, wherein the
formulation is a liquid and the bacterial concentration is from
about 10 3 to about 10 11 CFU/ml.
78. The agricultural formulation of claim 75, wherein the
formulation is a gel or powder and the bacterial concentration is
from about 10 3 to about 10 11 CFU/gm.
79. The agricultural product or formulation of claim 72 or 75,
wherein the benefit is selected from the group consisting of:
increased root biomass, increased root length, increased height,
increased shoot length, increased leaf number, increased water use
efficiency, increased tolerance to low nitrogen stress, increased
nitrogen use efficiency, increased overall biomass, increase grain
yield, increased photosynthesis rate, increased tolerance to
drought, increased heat tolerance, increased salt tolerance,
increased resistance to nematode stress, increased resistance to a
fungal pathogen, increased resistance to a bacterial pathogen,
increased resistance to a viral pathogen, a detectable modulation
in the level of a metabolite, and a detectable modulation in the
proteome relative to a reference plant, or a combination
thereof.
80. The agricultural product or formulation of claim 72 or 75,
wherein the bacterial population comprises two or more families of
bacterial endophytes.
81. The agricultural product or formulation of claim 72 or 75,
wherein the formulation further comprises a second bacterial
endophyte having a 16S nucleic acid sequence less than 95%
identical to that of the first bacterial endophyte.
82. The agricultural product or formulation of claim 72 or 75,
wherein the bacterial endophyte exhibits: production of auxin,
production of a siderophore, mineral phosphate solubilization,
production of a cellulase, production of a chitinase, production of
a xylanase, and production of acetoin, but not increase nitrogen
fixation relative to a reference plant.
83. The agricultural product or formulation of claim 72 or 75,
wherein the product or formulation comprises two or more bacterial
endophyte species.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Application
No.14/315,804, filed Jun. 26, 2014, which is hereby incorporated in
its entirety by reference.
SEQUENCE LISTING
[0002] The instant application contains a Sequence Listing which
has been submitted via EFS-Web and is hereby incorporated by
reference in its entirety. Said ASCII copy, created on Jun. 26,
2015, is named 29254_PCT_CRF_sequence_listing.txt, and is 22 KB in
size.
BACKGROUND
[0003] With limited arable land coupled with rising demand of a
steadily increasing human population that could reach 9 billion by
2050, food supply is a global challenge making production of
economically attractive and high quality food, free from
unacceptable levels of agrochemicals, a dire need.
[0004] Traditional plant breeding strategies to enhance plant
traits are relatively slow and inefficient. For example, breeding
plants for increased tolerance to abiotic stress requires abiotic
stress-tolerant founder lines for crossing with other germplasm to
develop new abiotic stress-resistant lines. Limited germplasm
resources for such founder lines and incompatibility in crosses
between distantly related plant species represent significant
problems encountered in conventional breeding. Breeding for stress
tolerance has often been inadequate given the incidence of stresses
and the impact that stresses have on crop yields in most
environments of the world.
SUMMARY OF THE INVENTION
[0005] The present invention is based on the systematic efforts to
discover endophytic bacterial species that have the potential to
greatly improve agricultural productivity. The endophytic bacterial
strains extensively characterized herein are able to confer onto
the host plant several key fitness benefits and, as such, offer the
possibility of improving yields of agricultural crops without the
need for time-consuming breeding efforts or genetic
modification.
[0006] In a first aspect, the present invention provides for an
agricultural plant or portion thereof comprising an exogenous
endophytic bacterial population disposed on an exterior surface of
the seed or seedling in an amount effective to colonize the plant,
and further comprising a formulation that comprises at least one
member selected from the group consisting of an agriculturally
compatible carrier, a tackifier, a microbial stabilizer, a
fungicide, an antibacterial agent, an herbicide, a nematicide, an
insecticide, a plant growth regulator, a rodenticide, and a
nutrient. The agricultural plant can be a mature plant. In other
cases, it can be a seedling. In still other cases, it can be a seed
of an agricultural plant. In one particular embodiment, the
agricultural plant is a seed or seedling.
[0007] In one embodiment, the endophytic bacterial population
consists essentially of an endophytic bacterium comprising a 16S
rRNA nucleic acid sequence at least 95%, at least 96%, at least
97%, at least 98%, at least 99%, or at least 99.5% identical to a
nucleic acid sequence selected from the group consisting of SEQ ID
NOs: 1-10.
[0008] In one particular embodiment, the endophytic bacterium is a
species of Agrobacterium, family Rhizobiaceae. In a particular
embodiment, the Agrobacterium species is identified on the basis of
its rDNA sequence, as outlined herein. In a particular embodiment,
the Agrobacterium species comprises a 16S rDNA sequence that is at
least 95% identical to SEQ ID NO: 1. In another embodiment, the
Agrobacterium species comprises a 16S rDNA sequence that is at
least 99% identical to SEQ ID NO: 1. In still another embodiment,
the Agrobacterium species comprises a 16S rDNA sequence that is
identical to SEQ ID NO: 1. In still another embodiment, the
Agrobacterium species is the isolate FA13.
[0009] In another embodiment, the endophytic bacterium is a species
of Pantoea, family Rhizobiaceae. In a particular embodiment, the
Pantoea species is identified on the basis of its rDNA sequence, as
outlined herein. In a particular embodiment, the Pantoea species
comprises a 16S rDNA sequence that is at least 95% identical to SEQ
ID NO: 2. In another embodiment, the Pantoea species comprises a
16S rDNA sequence that is at least 99% identical to SEQ ID NO: 2.
In still another embodiment, the Pantoea species comprises a 16S
rDNA sequence that is identical to SEQ ID NO: 2. In still another
embodiment, the Pantoea species is the isolate FF34.
[0010] In another embodiment, the endophytic bacterium is a species
of Sphingobium, family Rhizobiaceae. In a particular embodiment,
the Sphingobium species is identified on the ba1sis of its rDNA
sequence, as outlined herein. In a particular embodiment, the
Sphingobium species comprises a 16S rDNA sequence that is at least
95% identical to SEQ ID NO: 3. In another embodiment, the
Sphingobium species comprises a 16S rDNA sequence that is at least
99% identical to SEQ ID NO: 3. In still another embodiment, the
Sphingobium species comprises a 16S rDNA sequence that is identical
to SEQ ID NO: 3. In still another embodiment, the Sphingobium
species is the isolate FC42.
[0011] In another embodiment, the endophytic bacterium is a species
of Pseudomonas, family Pseudomonadaceae. In a particular
embodiment, the Pseudomonas species is identified on the basis of
its rDNA sequence, as outlined herein. In a particular embodiment,
the Pseudomonas species comprises a 16S rDNA sequence that is at
least 95% identical to SEQ ID NO: 4. In another embodiment, the
Pseudomonas species comprises a 16S rDNA sequence that is at least
99% identical to SEQ ID NO: 4. In still another embodiment, the
Pseudomonas species comprises a 16S rDNA sequence that is identical
to SEQ ID NO: 4. In still another embodiment, the Pseudomonas
species is the isolate FB12.
[0012] In another embodiment, the endophytic bacterium is a species
of Enterobacter, family Enterobacteriaceae. In a particular
embodiment, the Enterobacter species is identified on the basis of
its rDNA sequence, as outlined herein. In a particular embodiment,
the Enterobacter species comprises a 16S rDNA sequence that is at
least 95% identical to SEQ ID NO: 5. In another embodiment, the
Enterobacter species comprises a 16S rDNA sequence that is at least
99% identical to SEQ ID NO: 5. In still another embodiment, the
Enterobacter species comprises a 16S rDNA sequence that is
identical to SEQ ID NO: 5. In still another embodiment, the
Enterobacter species is the isolate FD17.
[0013] In another embodiment, the endophytic bacterium is a species
of Micrococcus, family Micrococcaceae. In a particular embodiment,
the Micrococcus species is identified on the basis of its rDNA
sequence, as outlined herein. In a particular embodiment, the
Micrococcus species comprises a 16S rDNA sequence that is at least
95% identical to SEQ ID NO: 6. In another embodiment, the
Micrococcus species comprises a 16S rDNA sequence that is at least
99% identical to SEQ ID NO: 6. In still another embodiment, the
Micrococcus species comprises a 16S rDNA sequence that is identical
to SEQ ID NO: 6. In still another embodiment, the Micrococcus
species is the isolate S2.
[0014] In another embodiment, the endophytic bacterium is a species
of Bacillus, family Bacillaceae. In a particular embodiment, the
Bacillus species is identified on the basis of its rDNA sequence,
as outlined herein. In a particular embodiment, the Bacillus
species comprises a 16S rDNA sequence that is at least 95%
identical to SEQ ID NO: 7. In another embodiment, the Bacillus
species comprises a 16S rDNA sequence that is at least 99%
identical to SEQ ID NO: 7. In still another embodiment, the
Bacillus species comprises a 16S rDNA sequence that is identical to
SEQ ID NO: 7. In still another embodiment, the Bacillus species is
the isolate S4.
[0015] In another embodiment, the endophytic bacterium is a species
of Pantoea, family Enterobacteriaceae. In a particular embodiment,
the Pantoea species is identified on the basis of its rDNA
sequence, as outlined herein. In a particular embodiment, the
Pantoea species comprises a 16S rDNA sequence that is at least 95%
identical to SEQ ID NO: 8. In another embodiment, the Pantoea
species comprises a 16S rDNA sequence that is at least 99%
identical to SEQ ID NO: 8. In still another embodiment, the Pantoea
species comprises a 16S rDNA sequence that is identical to SEQ ID
NO: 8. In still another embodiment, the Pantoea species is the
isolate S6.
[0016] In another embodiment, the endophytic bacterium is a species
of Acinetobacter, family Moraxellaceae. In a particular embodiment,
the Acinetobacter species is identified on the basis of its rDNA
sequence, as outlined herein. In a particular embodiment, the
Acinetobacter species comprises a 16S rDNA sequence that is at
least 95% identical to SEQ ID NO: 9. In another embodiment, the
Acinetobacter species comprises a 16S rDNA sequence that is at
least 99% identical to SEQ ID NO: 9. In still another embodiment,
the Acinetobacter species comprises a 16S rDNA sequence that is
identical to SEQ ID NO: 9. In still another embodiment, the
Acinetobacter species is the isolate S9.
[0017] In another embodiment, the endophytic bacterium is a species
of Paenibacillus, family Paenibacillaceae. In a particular
embodiment, the Paenibacillus species is identified on the basis of
its rDNA sequence, as outlined herein. In a particular embodiment,
the Paenibacillus species comprises a 16S rDNA sequence that is at
least 95% identical to SEQ ID NO: 10. In another embodiment, the
Paenibacillus species comprises a 16S rDNA sequence that is at
least 99% identical to SEQ ID NO: 10. In still another embodiment,
the Paenibacillus species comprises a 16S rDNA sequence that is
identical to SEQ ID NO: 10. In still another embodiment, the
Paenibacillus species is the isolate S10.
[0018] In certain cases, the endophytic bacterial population is
disposed in an amount effective to be detectable within a target
tissue of the mature agricultural plant selected from a fruit, a
seed, a leaf, or a root, or portion thereof.
[0019] In certain embodiments, the seed or seedling comprises at
least about 100 CFU, for example, at least about 200 CFU, at least
about 300 CFU, at least about 500 CFU, at least about 1,000 CFU, at
least about 3,000 CFU, at least about 10,000 CFU, at least about
30,000 CFU, at least about 100,000 CFU, at least about 10 6 CFU, or
more, of the endophytic bacterial population on its exterior
surface.
[0020] In another embodiment, the endophytic bacterial population
is disposed on an exterior surface or within a tissue of the seed
or seedling in an amount effective to be detectable in an amount of
at least about 100 CFU, for example, at least about 200 CFU, at
least about 300 CFU, at least about 500 CFU, at least about 1,000
CFU, at least about 3,000 CFU, at least about 10,000 CFU, at least
about 30,000 CFU, at least about 100,000 CFU or more per gram fresh
weight of the mature agricultural plant.
[0021] In another embodiment, the endophytic bacterial population
is disposed on the surface or within a tissue of the seed or
seedling in an amount effective to increase the biomass of the
fruit or cob from the resulting plant by at least 1%, at least 2%,
at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at
least 8%, at least 9%, or at least 10% when compared with a
reference agricultural plant.
[0022] In still another embodiment, the endophytic bacterial
population is disposed on the surface or within a tissue of the
seed or seedling in an amount effective to detectably colonize the
soil environment surrounding the mature agricultural plant when
compared with a reference agricultural plant.
[0023] In some cases, the endophytic bacterial population is
disposed in an amount effective to increase root biomass by at
least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at
least 6%, at least 7%, at least 8%, at least 9%, or at least 10%
when compared with a reference agricultural plant.
[0024] In some embodiments, the endophytic bacterial population is
disposed on the surface or within a tissue of the seed or seedling
in an amount effective to increase the rate of seed germination
when compared with a reference agricultural plant.
[0025] In another embodiment, the endophytic bacterial population
is disposed on the surface or within a tissue of the seed or
seedling in an amount effective to detectably induce production of
auxin in the seed or seedling.
[0026] In one embodiment, the endophytic bacterial population is
cultured prior to disposition on the seed or seedling. In one
embodiment, the endophytic bacterial population is cultured in a
synthetic or semi-synthetic medium prior to disposition on the seed
or seedling.
[0027] In certain cases, the endophytic bacterial population can be
modified. In one embodiment, the endophytic bacterial population is
genetically modified. In another embodiment, the endophytic
bacterial population is modified such that it has enhanced
compatibility with an antimicrobial agent when compared with an
unmodified control. The antimicrobial agent is an antibacterial
agent. Alternatively, the antimicrobial agent can be an antifungal
agent. In some cases, the modified endophytic bacterial population
exhibits at least 3 fold greater, for example, at least 5 fold
greater, at least 10 fold greater, at least 20 fold greater, at
least 30 fold greater or more resistance to the antimicrobial agent
when compared with an unmodified control. In one embodiment, the
antimicrobial agent is glyphosate.
[0028] The seed or seedling of the agricultural plant can be a
monocot. For example, it can be a corn seed or seedling.
Alternatively, it can be a wheat seed or seedling. In other
embodiments, it can be a barley seed or seedling. In still other
cases, it can be a rice seed or seedling.
[0029] In another embodiment, the seed or seedling is a dicot. For
example, it can be a cotton seed or seedling, a soy seed or
seedling, or a tomato seed or seedling.
[0030] In still another embodiment, the seed or seedling can be
derived from a transgenic plant. In another embodiment, the seed or
seedling can be a hybrid seed or seedling.
[0031] In one particular embodiment, the seed is a corn seed, and
further comprises at least about 10,000 CFU of the endophytic
bacterial population consisting essentially of an endophytic
bacterium comprising a 16S rRNA nucleic acid sequence that is at
least 95%, 96%, 97%, for example, at least 98%, at least 99%, at
least 99.5%, or 100% identical to a nucleic acid sequence selected
from the group consisting of SEQ ID NOs: 1-10 disposed on the
exterior surface of the seed, and further comprising a formulation
comprising a microbial stabilizer.
[0032] In another aspect, the invention provides for a
substantially uniform population of seeds comprising a plurality of
seeds described above. Substantial uniformity can be determined in
many ways. In some cases, at least 10%, for example, at least 20%,
at least 30%, at least 40%, at least 50%, at least 60%, at least
70%, at least 75%, at least 80%, at least 90%, at least 95% or more
of the seeds in the population, contains the endophytic bacterial
population in an amount effective to colonize the plant disposed on
the surface of the seeds. In other cases, at least 10%, for
example, at least 20%, at least 30%, at least 40%, at least 50%, at
least 60%, at least 70%, at least 75%, at least 80%, at least 90%,
at least 95% or more of the seeds in the population, contains at
least 100 CFU on its surface, for example, at least 200 CFU, at
least 300 CFU, at least 1,000 CFU, at least 3,000 CFU, at least
10,000 CFU, at least 30,000 CFU, at least 100,000 CFU, at least
300,000 CFU, or at least 1,000,000 CFU per seed or more.
[0033] In yet another aspect, the present invention provides for a
bag comprising at least 1,000 seeds as described herein above. The
bag further comprises a label describing the seeds and/or said
endophytic bacterial population.
[0034] In still another aspect of the present invention, a plant or
part or tissue of the plant, or progeny thereof is disclosed, which
is generated by growing the seed or seedling described herein
above.
[0035] In yet another aspect, disclosed are substantially uniform
populations of plants produced by growing a plurality of seeds,
seedlings, or progeny thereof. In some cases, at least 75%, at
least 80%, at least 90%, at least 95% or more of the plants in the
population comprise an amount of the endophytic bacterial
population effective to increase the root biomass of the plant by
at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at
least 6%, at least 7%, at least 8%, at least 9%, or at least 10%.
In other cases, at least 10%, for example at least 20%, at least
30%, at least 40%, at least 50%, at least 60%, at least 70%, at
least 75%, at least 80%, at least 90%, at least 95% or more of the
plants comprise a microbe population that is substantially
similar.
[0036] In yet another aspect of the present invention, disclosed is
an agricultural field comprising the population described above.
The field generally comprises at least 100 plants, for example, at
least 1,000 plants, at least 3,000 plants, at least 10,000 plants,
at least 30,000 plants, at least 100,000 plants or more in the
field. In certain cases, the population of plants occupies at least
about 100 square feet of space, and at least about 10%, for
example, at least 20%, at least 30%, at least 40%, at least 50%, at
least 60%, at least 70%, at least 80%, at least 90% or more than
90% of the population comprises an amount of the endophytic
bacterial population effective to increase the root biomass of the
plant by at least 1%, at least 2%, at least 3%, at least 4%, at
least 5%, at least 6%, at least 7%, at least 8%, at least 9%, or at
least 10%. In another embodiment, the population of plants occupies
at least about 100 square feet of space, wherein and at least about
10%, for example, at least 20%, at least 30%, at least 40%, at
least 50%, at least 60%, at least 70%, at least 80%, at least 90%
or more than 90% of the population comprises the microbe in
reproductive tissue. In another embodiment, the population of
plants occupies at least about 100 square feet of space, and at
least about 10%, for example, at least 20%, at least 30%, at least
40%, at least 50%, at least 60%, at least 70%, at least 80%, at
least 90% or more than 90% of the population comprises at least 100
CFUs, 1,000 CFUs, 10,000 CFUs, 100,000 CFUs or more of the
endophytic bacterial population.
[0037] In another aspect of the invention, provided are
preparations comprising a population of endophytic bacteria
described herein and further comprising at least one agent selected
from the group consisting of an agriculturally acceptable carrier,
a tackifier, a microbial stabilizer, a fungicide, an antibacterial
agent, an herbicide, a nematicide, an insecticide, a plant growth
regulator, a rodenticide, and a nutrient, and wherein the
population comprises an amount of endophytes sufficient to improve
an agronomic trait of the population of seeds. In one embodiment,
the endophytic bacterial population consists essentially of an
endophytic bacterium comprising a 16S rRNA nucleic acid sequence at
least 95% identical to a nucleic acid sequence selected from the
group consisting of SEQ ID NOs: 1-10.
[0038] In one embodiment, the preparation is substantially stable
at temperatures between about 4.degree. C. and about 45.degree. C.
for at least about seven days.
[0039] In another embodiment, the preparation is formulated to
provide at least 100 endophytes per seed, for example, at least 300
endophytes, at least 1,000 endophytes, at least 3,000 endophytes,
at least 10,000 endophytes, at least 30,000 endophytes, at least
100,000 endophytes, at least 300,000 endophytes, or at least
1,000,000 endophytes per seed.
[0040] In another embodiment, the preparation is formulated to
provide a population of plants that demonstrates a substantially
homogenous growth rate when introduced into agricultural
production.
[0041] In still another aspect, the present invention provides for
a method of producing a commodity plant product. The method
generally comprises obtaining a plant or plant tissue from the
agricultural plant comprising the endophytic bacteria as described
herein above, and producing the commodity plant product therefrom.
In certain cases, the commodity plant product is selected from the
group consisting of grain, flour, starch, seed oil, syrup, meal,
flour, oil, film, packaging, nutraceutical product, an animal feed,
a fish fodder, a cereal product, a processed human-food product, a
sugar or an alcohol and protein.
[0042] In a related aspect, the present invention provides for a
commodity plant product comprising a plant or part thereof and
further comprising the endophytic bacterial population or a portion
thereof in a detectable level.
[0043] In yet another aspect of the present invention, provided is
a method for preparing an agricultural plant or a portion thereof
comprising an endophytic bacterial population. The method generally
comprises applying to the seed or seedling a formulation comprising
an endophytic bacterial population consisting essentially of an
endophytic bacterium comprising a 16S rRNA nucleic acid sequence at
least 95% identical, for example, at least 96%, at least 97%, at
least 98% identical, at least 99% identical, at least 99.5%
identical, or 100% identical to a nucleic acid sequence selected
from the group consisting of SEQ ID NOs: 1-10. In one embodiment,
the formulation further comprises at least one member selected from
the group consisting of an agriculturally compatible carrier, a
tackifier, a microbial stabilizer, a fungicide, an antibacterial
agent, an herbicide, a nematicide, an insecticide, a plant growth
regulator, a rodenticide, and a nutrient. In some cases, the
agricultural plant can be a seedling. In other cases, the
agricultural plant can be a seed. In a particular embodiment, the
agricultural plant is a seed or a seedling. In another embodiment,
the method further comprises applying at least one member selected
from the group consisting of an agriculturally compatible carrier,
a tackifier, a microbial stabilizer, a fungicide, an antibacterial
agent, an herbicide, a nematicide, an insecticide, a plant growth
regulator, a rodenticide, and a nutrient.
[0044] In a final aspect, the present invention provides for a
method for conferring one or more fitness benefits to an
agricultural plant. The method generally comprises providing an
agricultural plant or portion thereof, contacting said plant or
portion thereof with a formulation comprising an exogenous
endophytic bacterial population consisting essentially of an
endophytic bacterium comprising a 16S rRNA nucleic acid sequence at
least 95% identical, for example, at at least 96%, at least 97%,
least 98% identical, at least 99% identical, at least 99.5%
identical, or 100% identical to a nucleic acid sequence selected
from the group consisting of SEQ ID NOs: 1-10, disposed on an
exterior surface in an amount effective to colonize the mature
plant, wherein the formulation further comprises at least one
member selected from the group consisting of an agriculturally
compatible carrier, a tackifier, a microbial stabilizer, a
fungicide, an antibacterial agent, an herbicide, a nematicide, an
insecticide, a plant growth regulator, a rodenticide, and a
nutrient, and allowing the seed or seedling to grow under
conditions that allow the endophytic bacterium to colonize the
plant. In some cases, the agricultural plant can be a seedling. In
other cases, the agricultural plant can be a seed. In a particular
embodiment, the agricultural plant is a seed or a seedling.
[0045] In one embodiment, the one or more of the fitness benefits
are selected from the group consisting of increased germination,
increased biomass, increased flowering time, increased biomass of
the fruit or grain, increased grain or fruit yield, and increased
drought tolerance.
DETAILED DESCRIPTION
BRIEF DESCRIPTION OF THE FIGURES
[0046] FIG. 1A show the increases in root biomass in maize plants
inoculated with the bacterial endophyte populations when compared
with uninoculated control plants.
[0047] FIG. 1B show the increases in shoot biomass in maize plants
inoculated with the bacterial endophyte populations when compared
with uninoculated control plants.
[0048] FIG. 1C show the increases in total biomass in maize plants
inoculated with the bacterial endophyte populations when compared
with uninoculated control plants.
[0049] FIG. 2 shows the increases in stomatal conductance in maize
plants inoculated with the bacterial endophyte populations when
compared with uninoculated control plants.
[0050] FIG. 3 shows the increase in photosynthetic rates in maize
plants inoculated with the bacterial endophyte populations when
compared with uninoculated control plants.
[0051] FIG. 4 shows the increases in PS II photochemical efficiency
(Fv/Fm) in maize plants inoculated with the bacterial endophyte
populations, when compared with uninoculated control plants.
[0052] FIG. 5 shows the increases in leaf area in maize plants
inoculated with the bacterial endophyte populations, when compared
with uninoculated control plants.
[0053] FIG. 6 shows the increases in chlorophyll content in maize
plants inoculated with the bacterial endophyte populations, when
compared with uninoculated control plants.
DEFINITIONS
[0054] A "synthetic combination" includes a combination of a host
plant and an endophyte. The combination may be achieved, for
example, by coating the surface of the seed of a plant, such as an
agricultural plant, or host plant tissues with an endophyte.
[0055] As used herein, an "agricultural seed" is a seed used to
grow a plant in agriculture (an "agricultural plant"). The seed may
be of a monocot or dicot plant, and is planted for the production
of an agricultural product, for example grain, food, fiber, etc. As
used herein, an agricultural seed is a seed that is prepared for
planting, for example, in farms for growing.
[0056] An "endophyte", or "endophytic microbe" includes an organism
capable of living within a plant or associated therewith. An
endophyte may refer to a bacterial or fungal organism that may
confer an increase in yield, biomass, resistance, or fitness in its
host plant. Endophytes may occupy the intracellular or
extracellular spaces of plant tissue, including the leaves, stems,
flowers, fruits, seeds, or roots. An endophyte can be a fungus, or
a bacterium. As used herein, the term "microbe" is sometimes used
to describe an endophyte.
[0057] In some embodiments, the invention contemplates the use of
microbes that are "exogenous" to a seed or plant. As used herein, a
microbe is considered exogenous to the seed or plant if the seed or
seedling that is unmodified (e.g., a seed or seedling that is not
treated with the endophytic bacterial population descried herein)
does not contain the microbe.
[0058] In other cases, the invention contemplates the synthetic
combinations of agricultural plants and an endophytic microbe
population, in which the microbe population is "heterologously
disposed" on the surface of or within a tissue of the agricultural
plant. As used herein, a microbe is considered "heterologously
disposed" on the surface or within a plant (or tissue) when the
microbe is applied or disposed on the plant in a number or within a
tissue in a number that is not found on that plant prior to
application of the microbe. As such, a microbe is deemed
heterologously disposed when applied on the plant that either does
not naturally have the microbe on its surface or within the
particular tissue to which the microbe is disposed, or does not
naturally have the microbe on its surface or within the particular
tissue in the number that is being applied. For the avoidance of
doubt, "heterologously disposed" contemplates use of microbes that
are "exogenous" to a seed or plant.
[0059] In some cases, the present invention contemplates the use of
microbes that are "compatible" with agricultural chemicals for
example, a fungicide, an anti-bacterial compound, or any other
agent widely used in agricultural which has the effect of
interfering with optimal growth of microbes. As used herein, a
microbe is "compatible" with an agricultural chemical, when the
microbe is modified or otherwise adapted to grow in, or otherwise
survive, the concentration of the agricultural chemical used in
agriculture. For example, a microbe disposed on the surface of a
seed is compatible with the fungicide metalaxyl if it is able to
survive the concentrations that are applied on the seed
surface.
[0060] "Biomass" means the total mass or weight (fresh or dry), at
a given time, of a plant tissue, plant tissues, an entire plant, or
population of plants, usually given as weight per unit area. The
term may also refer to all the plants or species in the community
(community biomass).
[0061] Some of the compositions and methods described herein
involve endophytic microbes in an amount effective to colonize a
plant. As used herein, a microbe is said to "colonize" a plant or
seed when it can exist in an endophytic relationship with the plant
in the plant environment, for example inside the plant or a part or
tissue thereof, including the seed.
[0062] Some compositions described herein contemplate the use of an
agriculturally compatible carrier. As used herein an
"agriculturally compatible carrier" is intended to refer to any
material, other than water, which can be added to a seed or a
seedling without causing/having an adverse effect on the seed, the
plant that grows from the seed, seed germination, or the like.
[0063] A "transgenic plant" includes a plant or progeny plant of
any subsequent generation derived therefrom, wherein the DNA of the
plant or progeny thereof contains an introduced exogenous DNA
segment not naturally present in a non-transgenic plant of the same
strain. The transgenic plant may additionally contain sequences
that are native to the plant being transformed, but wherein the
"exogenous" gene has been altered in order to alter the level or
pattern of expression of the gene, for example, by use of one or
more heterologous regulatory or other elements.
[0064] As used herein, a nucleic acid has "homology" or is
"homologous" to a second nucleic acid if the nucleic acid sequence
has a similar sequence to the second nucleic acid sequence. The
terms "identity", "percent sequence identity" or "identical" in the
context of nucleic acid sequences refer to the residues in the two
sequences that are the same when aligned for maximum
correspondence. There are a number of different algorithms known in
the art that can be used to measure nucleotide sequence identity.
For instance, polynucleotide sequences can be compared using FASTA,
Gap or Bestfit, which are programs in Wisconsin Package Version
10.0, Genetics Computer Group (GCG), Madison, Wis. FASTA provides
alignments and percent sequence identity of the regions of the best
overlap between the query and search sequences. Pearson, Methods
Enzymol. 183:63-98 (1990). The term "substantial homology" or
"substantial similarity," when referring to a nucleic acid or
fragment thereof, indicates that, when optimally aligned with
appropriate nucleotide insertions or deletions with another nucleic
acid (or its complementary strand), there is nucleotide sequence
identity in at least about 76%, 80%, 85%, or at least about 90%, or
at least about 95%, 96%, 97%, 98% or 99% of the nucleotide bases,
as measured by any well-known algorithm of sequence identity, such
as FASTA, BLAST or Gap, as discussed above.
[0065] The present invention is directed to methods and
compositions of bacterial endophytes, and plant-endophyte
combinations that confer a fitness benefit in agricultural
plants.
Bacterial Endophyte
[0066] In a first aspect, disclosed is a composition comprising a
pure culture of a bacterial endophyte.
[0067] In one embodiment, the endophytic bacterium is a species of
Agrobacterium. In a particular embodiment, the Agrobacterium
species is identified on the basis of its rDNA sequence, as
outlined herein. In a particular embodiment, the Agrobacterium
species comprises a 16S rDNA sequence that is at least 95%
identical to SEQ ID NO: 1. In another embodiment, the Agrobacterium
species comprises a 16S rDNA sequence that is at least 99%
identical to SEQ ID NO: 1. In still another embodiment, the
Agrobacterium species comprises a 16S rDNA sequence that is
identical to SEQ ID NO: 1. In still another embodiment, the
Agrobacterium species is the isolate FA13.
[0068] In another embodiment, the endophytic bacterium is a species
of Pantoea . In a particular embodiment, the Pantoea species is
identified on the basis of its rDNA sequence, as outlined herein.
In a particular embodiment, the Pantoea species comprises a 16S
rDNA sequence that is at least 95% identical to SEQ ID NO: 2. In
another embodiment, the Pantoea species comprises a 16S rDNA
sequence that is at least 99% identical to SEQ ID NO: 2. In still
another embodiment, the Pantoea species comprises a 16S rDNA
sequence that is identical to SEQ ID NO: 2. In still another
embodiment, the Pantoea species is the isolate FF34.
[0069] In another embodiment, the endophytic bacterium is a species
of Sphingobium . In a particular embodiment, the Sphingobium
species is identified on the basis of its rDNA sequence, as
outlined herein. In a particular embodiment, the Sphingobium
species comprises a 16S rDNA sequence that is at least 95%
identical to SEQ ID NO: 3. In another embodiment, the Sphingobium
species comprises a 16S rDNA sequence that is at least 99%
identical to SEQ ID NO: 3. In still another embodiment, the
Sphingobium species comprises a 16S rDNA sequence that is identical
to SEQ ID NO: 3. In still another embodiment, the Sphingobium
species is the isolate FC42.
[0070] In another embodiment, the endophytic bacterium is a species
of Pseudomonas. In a particular embodiment, the Pseudomonas species
is identified on the basis of its rDNA sequence, as outlined
herein. In a particular embodiment, the Pseudomonas species
comprises a 16S rDNA sequence that is at least 95% identical to SEQ
ID NO: 4. In another embodiment, the Pseudomonas species comprises
a 16S rDNA sequence that is at least 99% identical to SEQ ID NO: 4.
In still another embodiment, the Pseudomonas species comprises a
16S rDNA sequence that is identical to SEQ ID NO: 4. In still
another embodiment, the Pseudomonas species is the isolate
FB12.
[0071] In another embodiment, the endophytic bacterium is a species
ofEnterobacter. In a particular embodiment, the Enterobacter
species is identified on the basis of its rDNA sequence, as
outlined herein. In a particular embodiment, the Enterobacter
species comprises a 16S rDNA sequence that is at least 95%
identical to SEQ ID NO: 5. In another embodiment, the Enterobacter
species comprises a 16S rDNA sequence that is at least 99%
identical to SEQ ID NO: 5. In still another embodiment, the
Enterobacter species comprises a 16S rDNA sequence that is
identical to SEQ ID NO: 5. In still another embodiment, the
Enterobacter species is the isolate FD17.
[0072] In another embodiment, the endophytic bacterium is a species
of Micrococcus. In a particular embodiment, the Micrococcus species
is identified on the basis of its rDNA sequence, as outlined
herein. In a particular embodiment, the Micrococcus species
comprises a 16S rDNA sequence that is at least 95% identical to SEQ
ID NO: 6. In another embodiment, the Micrococcus species comprises
a 16S rDNA sequence that is at least 99% identical to SEQ ID NO: 6.
In still another embodiment, the Micrococcus species comprises a
16S rDNA sequence that is identical to SEQ ID NO: 6. In still
another embodiment, the Micrococcus species is the isolate S2.
[0073] In another embodiment, the endophytic bacterium is a species
of Bacillus. In a particular embodiment, the Bacillus species is
identified on the basis of its rDNA sequence, as outlined herein.
In a particular embodiment, the Bacillus species comprises a 16S
rDNA sequence that is at least 95% identical to SEQ ID NO: 7. In
another embodiment, the Bacillus species comprises a 16S rDNA
sequence that is at least 99% identical to SEQ ID NO: 7. In still
another embodiment, the Bacillus species comprises a 16S rDNA
sequence that is identical to SEQ ID NO: 7. In still another
embodiment, the Bacillus species is the isolate S4.
[0074] In another embodiment, the endophytic bacterium is a species
of Pantoea . In a particular embodiment, the Pantoea species is
identified on the basis of its rDNA sequence, as outlined herein.
In a particular embodiment, the Pantoea species comprises a 16S
rDNA sequence that is at least 95% identical to SEQ ID NO: 8. In
another embodiment, the Pantoea species comprises a 16S rDNA
sequence that is at least 99% identical to SEQ ID NO: 8. In still
another embodiment, the Pantoea species comprises a 16S rDNA
sequence that is identical to SEQ ID NO: 8. In still another
embodiment, the Pantoea species is the isolate S6.
[0075] In another embodiment, the endophytic bacterium is a species
of Acinetobacter. In a particular embodiment, the Acinetobacter
species is identified on the basis of its rDNA sequence, as
outlined herein. In a particular embodiment, the Acinetobacter
species comprises a 16S rDNA sequence that is at least 95%
identical to SEQ ID NO: 9. In another embodiment, the Acinetobacter
species comprises a 16S rDNA sequence that is at least 99%
identical to SEQ ID NO: 9. In still another embodiment, the
Acinetobacter species comprises a 16S rDNA sequence that is
identical to SEQ ID NO: 9. In still another embodiment, the
Acinetobacter species is the isolate S9.
[0076] In another embodiment, the endophytic bacterium is a species
of Paenibacillus. In a particular embodiment, the Paenibacillus
species is identified on the basis of its rDNA sequence, as
outlined herein. In a particular embodiment, the Paenibacillus
species comprises a 16S rDNA sequence that is at least 95%
identical to SEQ ID NO: 10. In another embodiment, the
Paenibacillus species comprises a 16S rDNA sequence that is at
least 99% identical to SEQ ID NO: 10. In still another embodiment,
the Paenibacillus species comprises a 16S rDNA sequence that is
identical to SEQ ID NO: 10. In still another embodiment, the
Paenibacillus species is the isolate S10.
[0077] In some cases, the endophytic microbe can be modified. For
example, the endophytic microbe can be genetically modified by
introduction of a transgene which stably integrates into the
bacterial genome. In another embodiment, the endophytic microbe can
be modified to harbor a plasmid or episome containing a transgene.
In still another embodiment, the microbe can be modified by
repeated passaging under selective conditions.
[0078] The microbe can be modified to exhibit altered
characteristics. In one embodiment, the endophytic microbe is
modified to exhibit increased compatibility with chemicals commonly
used in agriculture. Agricultural plants are often treated with a
vast array of agrichemicals, including fungicides, biocides
(anti-bacterial agents), herbicides, insecticides, nematicides,
rodenticides, fertilizers, and other agents. Many such agents can
affect the ability of an endophytic bacterium to grow, divide,
and/or otherwise confer beneficial traits to the plant.
[0079] In some cases, it can be important for the microbe to be
compatible with agrichemicals, particularly those with fungicidal
or antibacterial properties, in order to persist in the plant
although, as mentioned earlier, there are many such fungicidal or
antibacterial agents that do not penetrate the plant, at least at a
concentration sufficient to interfere with the microbe. Therefore,
where a systemic fungicide or antibacterial agent is used in the
plant, compatibility of the microbe to be inoculated with such
agents will be an important criterion.
[0080] In one embodiment, spontaneous isolates of microbes which
are compatible with agrichemicals can be used to inoculate the
plants according to the methods described herein. For example,
fungal microbes which are compatible with agriculturally employed
fungicides can be isolated by plating a culture of the microbes on
a petri dish containing an effective concentration of the
fungicide, and isolating colonies of the microbe that are
compatible with the fungicide. In another embodiment, a microbe
that is compatible with a fungicide is used for the methods
described herein. In still another embodiment, a microbe that is
compatible with an antibacterial compound is used for the methods
described herein. Fungicide compatible microbes can also be
isolated by selection on liquid medium. The culture of microbes can
be plated on petri dishes without any forms of mutagenesis;
alternatively, the microbes can be mutagenized using any means
known in the art. For example, microbial cultures can be exposed to
UV light, gamma-irradiation, or chemical mutagens such as
ethylmethanesulfonate (EMS) prior to selection on fungicide
containing media. Finally, where the mechanism of action of a
particular fungicide is known, the target gene can be specifically
mutated (either by gene deletion, gene replacement, site-directed
mutagenesis, etc.) to generate a microbe that is resilient against
that particular fungicide. It is noted that the above-described
methods can be used to isolate fungi that are compatible with both
fungistatic and fungicidal compounds.
[0081] It will also be appreciated by one skilled in the art that a
plant may be exposed to multiple types of fungicides or
antibacterial compounds, either simultaneously or in succession,
for example at different stages of plant growth. Where the target
plant is likely to be exposed to multiple fungicidal and/or
antibacterial agents, a microbe that is compatible with many or all
of these agrichemicals can be used to inoculate the plant. A
microbe that is compatible with several fungicidal agents can be
isolated, for example, by serial selection. A microbe that is
compatible with the first fungicidal agent is isolated as described
above (with or without prior mutagenesis). A culture of the
resulting microbe can then be selected for the ability to grow on
liquid or solid media containing the second antifungal compound
(again, with or without prior mutagenesis). Colonies isolated from
the second selection are then tested to confirm its compatibility
to both antifungal compounds.
[0082] Likewise, bacterial microbes that are compatible to biocides
(including herbicides such as glyphosate or antibacterial
compounds, whether bacteriostatic or bactericidal) that are
agriculturally employed can be isolated using methods similar to
those described for isolating fungicide compatible microbes. In one
embodiment, mutagenesis of the microbial population can be
performed prior to selection with an antibacterial agent. In
another embodiment, selection is performed on the microbial
population without prior mutagenesis. In still another embodiment,
serial selection is performed on a microbe: the microbe is first
selected for compatibility to a first antibacterial agent. The
isolated compatible microbe is then cultured and selected for
compatibility to the second antibacterial agent. Any colony thus
isolated is tested for compatibility to each, or both antibacterial
agents to confirm compatibility with these two agents.
[0083] The selection process described above can be repeated to
identify isolates of the microbe that are compatible with a
multitude of antifungal or antibacterial agents.
[0084] Candidate isolates can be tested to ensure that the
selection for agrichemical compatibility did not result in loss of
a desired microbial bioactivity. Isolates of the microbe that are
compatible with commonly employed fungicides can be selected as
described above. The resulting compatible microbe can be compared
with the parental microbe on plants in its ability to promote
germination.
Plant-Endophyte Combinations
[0085] In another aspect, the present invention provides for
combinations of endophytes and plants. In one embodiment, disclosed
is a seed or seedling of an agricultural plant comprising an
exogenous endophytic bacterial population that is disposed on an
exterior surface of or within the seed or seedling in an amount
effective to colonize the plant, and further comprising a
formulation that comprises at least one member selected from the
group consisting of an agriculturally compatible carrier, a
tackifier, a microbial stabilizer, a fungicide, an antibacterial
agent, an herbicide, a nematicide, an insecticide, a plant growth
regulator, a rodenticide, and a nutrient. In another embodiment,
the present invention discloses a seed or seedling of an
agricultural plant comprising an endophytic bacterial population
that is heterologously disposed on an exterior surface of or within
the seed or seedling in an amount effective to colonize the plant,
and further comprising a formulation that comprises at least one
member selected from the group consisting of an agriculturally
compatible carrier, a tackifier, a microbial stabilizer, a
fungicide, an antibacterial agent, an herbicide, a nematicide, an
insecticide, a plant growth regulator, a rodenticide, and a
nutrient.
[0086] The endophytic bacterial population consists essentially of
an endophytic bacterium described herein. In one embodiment, the
endophytic bacterium comprises a 16S rRNA nucleic acid sequence
that is at least 95% identical, for example, at least 96%, at least
97%, at least 98% identical to a nucleic acid sequence selected
from the group consisting of SEQ ID NOs: 1-10. In another
embodiment, the endophytic bacterium comprises a 16S rRNA nucleic
acid sequence that is at least 99% identical to a nucleic acid
sequence selected from the group consisting of SEQ ID NOs: 1-10. In
still another embodiment, the endophytic bacterium comprises a 16S
rRNA nucleic acid sequence that is identical to a nucleic acid
sequence selected from the group consisting of SEQ ID NOs:
1-10.
[0087] In one embodiment according to this aspect, disclosed is a
seed of an agricultural plant comprising an exogenous endophytic
bacterial population that is disposed on an exterior surface of or
within the seed in an amount effective to colonize the plant. The
bacterial population is considered exogenous to the seed if that
particular seed does not inherently contain the bacterial
population. Indeed, several of the endophytic microbes described
herein have not been detected, for example, in any of the corn
seeds sampled, as determined by highly sensitive methods.
[0088] In other cases, the present invention discloses a seed of an
agricultural plant comprising an endophytic bacterial population
that is heterologously disposed on an exterior surface of or within
the seed in an amount effective to colonize the plant. For example,
the endophytic bacterial population that is disposed on an exterior
surface or within the seed can be an endophytic bacterium that may
be associated with the mature plant, but is not found on the
surface of or within the seed. Alternatively, the endophytic
bacterial population can be found in the surface of, or within the
seed, but at a much lower number than is disposed.
[0089] In some embodiments, a purified endophytes population is
used that includes two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 15,
20, 25 or greater than 25) different endophytes, e.g., obtained
from different families of plant or fungus, or different genera of
plant or fungus, or from the same genera but different species of
plant or fungus.
[0090] The different endophytes can be obtained from the same
cultivar of agricultural plant (e.g., the same maize, wheat, rice,
or barley plant), different cultivars of the same agricultural
plant (e.g., two or more cultivars of maize, two or more cultivars
of wheat, two or more cultivars of rice, or two or more cultivars
of barley), or different species of the same type of agricultural
plant (e.g., two or more different species of maize, two or more
different species of wheat, two or more different species of rice,
or two or more different species of barley). In embodiments in
which two or more endophytes are used, each of the endophytes can
have different properties or activities, e.g., produce different
metabolites, produce different enzymes such as different hydrolytic
enzymes, confer different beneficial traits, or colonize different
elements of a plant (e.g., leaves, stems, flowers, fruits, seeds,
or roots). For example, one endophyte can colonize a first and a
second endophyte can colonize a tissue that differs from the first
tissue.
[0091] Combinations of endophytes can be selected by any one or
more of several criteria. In one embodiment, compatible endophytes
are selected. As used herein, "compatibility" refers to endophyte
populations that do not significantly interfere with the growth,
propagation, and/or production of beneficial substances of the
other. Incompatible endophyte populations can arise, for example,
where one of the populations produces or secrets a compound that is
toxic or deleterious to the growth of the other population(s).
Incompatibility arising from production of deleterious
compounds/agents can be detected using methods known in the art,
and as described herein elsewhere. Similarly, the distinct
populations can compete for limited resources in a way that makes
co-existence difficult.
[0092] In another embodiment, combinations are selected on the
basis of compounds produced by each population of endophytes. For
example, the first population is capable of producing siderophores,
and another population is capable of producing anti-fungal
compounds. In one embodiment, the first population of endophytes or
endophytic components is capable of a function selected from the
group consisting of auxin production, nitrogen fixation, production
of an antimicrobial compound, siderophore production, mineral
phosphate solubilization, cellulase production, chitinase
production, xylanase production, and acetoin production. In another
embodiment, the second population of endophytes or endophytic
component is capable of a function selected from the group
consisting of auxin production, nitrogen fixation, production of an
antimicrobial compound, siderophore production, mineral phosphate
solubilization, cellulase production, chitinase production,
xylanase production, and acetoin production. In certain
combinations, one of the endophytes is capable of using arabinose
as a carbon source. In still another embodiment, the first and
second populations are capable of at least one different
function.
[0093] In still another embodiment, the combinations of endophytes
are selected for their distinct localization in the plant after
colonization. For example, the first population of endophytes or
endophytic components can colonize, and in some cases
preferentially colonize, the root tissue, while a second population
can be selected on the basis of its preferential colonization of
the aerial parts of the agricultural plant. Therefore, in one
embodiment, the first population is capable of colonizing one or
more of the tissues selected from the group consisting of a root,
shoot, leaf, flower, and seed. In another embodiment, the second
population is capable of colonizing one or more tissues selected
from the group consisting of root, shoot, leaf, flower, and seed.
In still another embodiment, the first and second populations are
capable of colonizing a different tissue within the agricultural
plant.
[0094] In still another embodiment, combinations of endophytes are
selected for their ability to confer one or more distinct fitness
traits on the inoculated agricultural plant, either individually or
in synergistic association with other endophytes. Alternatively,
two or more endophytes induce the colonization of a third
endophyte. For example, the first population of endophytes or
endophytic components is selected on the basis that it confers
significant increase in biomass, while the second population
promotes increased drought tolerance on the inoculated agricultural
plant. Therefore, in one embodiment, the first population is
capable of conferring at least one trait selected from the group
consisting of thermal tolerance, herbicide tolerance, drought
resistance, insect resistance, fungus resistance, virus resistance,
bacteria resistance, male sterility, cold tolerance, salt
tolerance, increased yield, enhanced nutrient use efficiency,
increased nitrogen use efficiency, increased fermentable
carbohydrate content, reduced lignin content, increased antioxidant
content, enhanced water use efficiency, increased vigor, increased
germination efficiency, earlier or increased flowering, increased
biomass, altered root-to-shoot biomass ratio, enhanced soil water
retention, or a combination thereof. In another embodiment, the
second population is capable of conferring a trait selected from
the group consisting of thermal tolerance, herbicide tolerance,
drought resistance, insect resistance, fungus resistance, virus
resistance, bacteria resistance, male sterility, cold tolerance,
salt tolerance, increased yield, enhanced nutrient use efficiency,
increased nitrogen use efficiency, increased fermentable
carbohydrate content, reduced lignin content, increased antioxidant
content, enhanced water use efficiency, increased vigor, increased
germination efficiency, earlier or increased flowering, increased
biomass, altered root-to-shoot biomass ratio, and enhanced soil
water retention. In still another embodiment, each of the first and
second population is capable of conferring a different trait
selected from the group consisting of thermal tolerance, herbicide
tolerance, drought resistance, insect resistance, fungus
resistance, virus resistance, bacteria resistance, male sterility,
cold tolerance, salt tolerance, increased yield, enhanced nutrient
use efficiency, increased nitrogen use efficiency, increased
fermentable carbohydrate content, reduced lignin content, increased
antioxidant content, enhanced water use efficiency, increased
vigor, increased germination efficiency, earlier or increased
flowering, increased biomass, altered root-to-shoot biomass ratio,
and enhanced soil water retention.
[0095] The combinations of endophytes can also be selected based on
combinations of the above criteria. For example, the first
population of endophytes can be selected on the basis of the
compound it produces (e.g., its ability to fix nitrogen, thus
providing a potential nitrogen source to the plant), while the
second population can be selected on the basis of its ability to
confer increased resistance of the plant to a pathogen (e.g., a
fungal pathogen).
[0096] In some aspects of the present invention, it is contemplated
that combinations of endophytes can provide an increased benefit to
the host plant, as compared to that conferred by a single
endophyte, by virtue of additive effects. For example, one
endophyte strain that induces a benefit in the host plant may
induce such benefit equally well in a plant that is also colonized
with a different endophyte strain that also induces the same
benefit in the host plant. The host plant thus exhibits the same
total benefit from the plurality of different endophyte strains as
the additive benefit to individual plants colonized with each
individual endophyte of the plurality. In one example, a plant is
colonized with two different endophyte strains: one provides a
1.times. increase in biomass when associated with the plant, and
the other provides a 2.times. increase in biomass when associated
with a different plant. When both endophyte strains are associated
with the same plant, that plant would experience a 3.times.
(additive of 1.times.+2.times. single effects) increase in auxin
biomass. Additive effects are a surprising aspect of the present
invention, as non-compatibility of endophytes may result in a
cancelation of the beneficial effects of both endophytes.
[0097] In some aspects of the present invention, it is contemplated
that a combination of endophytes can provide an increased benefit
to the host plant, as compared to that conferred by a single
endophyte, by virtue of synergistic effects. For example, one
endophyte strain that induces a benefit in the host plant may
induce such benefit beyond additive effects in a plant that is also
colonized with a different endophyte strain that also induces that
benefit in the host plant. The host plant thus exhibits the greater
total benefit from the plurality of different endophyte strains
than would be expected from the additive benefit of individual
plants colonized with each individual endophyte of the plurality.
In one example, a plant is colonized with two different endophyte
strains: one provides a 1.times. increase in biomass when
associated with a plant, and the other provides a 2.times. increase
in biomass when associated with a different plant. When both
endophyte strains are associated with the same plant, that plant
would experience a 5.times. (greater than an additive of
1.times.+2.times. single effects) increase in biomass. Synergistic
effects are a surprising aspect of the present invention.
[0098] As shown in the Examples section below, the endophytic
bacterial populations described herein are capable of colonizing
the host plant. In certain cases, the endophytic bacterial
population can be applied to the plant, for example the plant seed,
or by foliar application, and successful colonization can be
confirmed by detecting the presence of the bacterial population
within the plant. For example, after applying the bacteria to the
seeds, high titers of the bacteria can be detected in the roots and
shoots of the plants that germinate from the seeds. In addition,
significant quantities of the bacteria can be detected in the
rhizosphere of the plants. Therefore, in one embodiment, the
endophytic microbe population is disposed in an amount effective to
colonize the plant. Colonization of the plant can be detected, for
example, by detecting the presence of the endophytic microbe inside
the plant. This can be accomplished by measuring the viability of
the microbe after surface sterilization of the seed or the plant:
endophytic colonization results in an internal localization of the
microbe, rendering it resistant to conditions of surface
sterilization. The presence and quantity of the microbe can also be
established using other means known in the art, for example,
immunofluorescence microscopy using microbe specific antibodies, or
fluorescence in situ hybridization (see, for example, Amann et al.
(2001) Current Opinion in Biotechnology 12:231-236, incorporated
herein by reference in its entirety). Alternatively, specific
nucleic acid probes recognizing conserved sequences from the
endophytic bacterium can be employed to amplify a region, for
example by quantitative PCR, and correlated to CFUs by means of a
standard curve.
[0099] In another embodiment, the endophytic microbe is disposed in
an amount effective to be detectable in the mature agricultural
plant. In one embodiment, the endophytic microbe is disposed in an
amount effective to be detectable in an amount of at least about
100 CFU, at least about 200 CFU, at least about 300 CFU, at least
about 500 CFU, at least about 1,000 CFU, at least about 3,000 CFU,
at least about 10,000 CFU, at least about 30,000 CFU, at least
about 100,000 CFU or more in the mature agricultural plant.
[0100] In some cases, the endophytic microbe is capable of
colonizing particular tissue types of the plant. In one embodiment,
the endophytic microbe is disposed on the seed or seedling in an
amount effective to be detectable within a target tissue of the
mature agricultural plant selected from a fruit, a seed, a leaf, or
a root, or portion thereof. For example, the endophytic microbe can
be detected in an amount of at least about 100 CFU, at least about
200 CFU, at least about 300 CFU, at least about 500 CFU, at least
about 1,000 CFU, at least about 3,000 CFU, at least about 10,000
CFU, at least about 30,000 CFU, at least about 100,000 CFU or more,
in the target tissue of the mature agricultural plant.
[0101] In some cases, the microbes disposed on the seed or seedling
can be detected in the rhizosphere. This may be due to successful
colonization by the endophytic microbe, where certain quantities of
the microbe is shed from the root, thereby colonizing the
rhizosphere. In some cases, the rhizosphere-localized microbe can
secrete compounds (such as siderophores or organic acids) which
assist with nutrient acquisition by the plant. Therefore, in
another embodiment, the endophytic microbe is disposed on the
surface of the seed in an amount effective to detectably colonize
the soil environment surrounding the mature agricultural plant when
compared with a reference agricultural plant. For example, the
microbe can be detected in an amount of at least 100 CFU/g DW, for
example, at least 200 CFU/g DW, at least 500 CFU/g DW, at least
1,000 CFU/g DW, at least 3,000 CFU/g DW, at least 10,000 CFU/g DW,
at least 30,000 CFU/g DW, at least 100,000 CFU/g DW, at least
300,000 CFU/g DW, or more, in the rhizosphere.
[0102] The endophytic bacterial populations described herein are
also capable of providing many fitness benefits to the host plant.
As shown in the Examples section, endophyte-inoculated plants
display increased seed germination, increased vigor, increased
biomass (e.g., increased root or shoot biomass), increased
photochemical efficiency. Therefore, in one embodiment, the
endophytic bacterial population is disposed on the surface or
within a tissue of the seed or seedling in an amount effective to
increase the biomass of the plant, or a part or tissue of the plant
grown from the seed or seedling. The increased biomass is useful in
the production of commodity products derived from the plant. Such
commodity products include an animal feed, a fish fodder, a cereal
product, a processed human-food product, a sugar or an alcohol.
Such products may be a fermentation product or a fermentable
product, one such exemplary product is a biofuel. The increase in
biomass can occur in a part of the plant (e.g., the root tissue,
shoots, leaves, etc.), or can be an increase in overall biomass.
Increased biomass production, such an increase meaning at least
about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or greater
than 100% when compared with a reference agricultural plant. Such
increase in overall biomass can be under relatively stress-free
conditions. In other cases, the increase in biomass can be in
plants grown under any number of abiotic or biotic stresses,
including drought stress, salt stress, heat stress, cold stress,
low nutrient stress, nematode stress, insect herbivory stress,
fungal pathogen stress, bacterial pathogen stress, and viral
pathogen stress. In one particular embodiment, the endophytic
bacterial population is disposed in an amount effective to increase
root biomass by at least 1%, at least 2%, at least 3%, at least 4%,
at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, or
at least 10%, for example, at least 20%, at least 30%, at least
40%, at least 50%, at least 60%, at least 75%, at least 100%, or
more, when compared with a reference agricultural plant.
[0103] In another embodiment, the endophytic bacterial population
is disposed on the surface or within a tissue of the seed or
seedling in an amount effective to increase the rate of seed
germination when compared with a reference agricultural plant. For
example, the increase in seed germination can be at least 1%, at
least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at
least 7%, at least 8%, at least 9%, or at least 10%, for example,
at least 20%, at least 30%, at least 40%, at least 50%, at least
60%, at least 75%, at least 100%, or more, when compared with a
reference agricultural plant.
[0104] In other cases, the endophytic microbe is disposed on the
seed or seedling in an amount effective to increase the average
biomass or yield of the fruit or cob from the resulting plant by at
least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at
least 6%, at least 7%, at least 8%, at least 9%, or at least 10%,
for example, at least 15%, at least 20%, at least 30%, at least
40%, at least 50%, at least 75%, at least 100% or more, when
compared with a reference agricultural plant.
[0105] As highlighted in the Examples section, plants inoculated
with the endophytic bacterial population also show an increase in
overall plant height. Therefore, in one embodiment, the present
invention provides for a seed comprising an endophytic bacterial
population which is disposed on the surface or within a tissue of
the seed or seedling in an amount effective to increase the height
of the plant. For example, the endophytic bacterial population is
disposed in an amount effective to result in an increase in height
of the agricultural plant such that is at least 1%, at least 2%, at
least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at
least 8%, at least 9%, or at least 10% greater, for example, at
least 20% greater, at least 30% greater, at least 40% greater, at
least 50% greater, at least 60% greater, at least 70% greater, at
least 80% greater, at least 90% greater, at least 100% greater, at
least 125% greater, at least 150% greater or more, when compared
with a reference agricultural plant, the plant. Such increase in
height can be under relatively stress-free conditions. In other
cases, the increase in height can be in plants grown under any
number of abiotic or biotic stresses, including drought stress,
salt stress, heat stress, cold stress, low nutrient stress,
nematode stress, insect herbivory stress, fungal pathogen stress,
bacterial pathogen stress, and viral pathogen stress.
[0106] The host plants inoculated with the endophytic bacterial
population also show dramatic improvements in their ability to
utilize water more efficiently. Water use efficiency is a parameter
often correlated with drought tolerance. Water use efficiency (WUE)
is a parameter often correlated with drought tolerance, and is the
CO2 assimilation rate per water transpired by the plant. An
increase in biomass at low water availability may be due to
relatively improved efficiency of growth or reduced water
consumption. In selecting traits for improving crops, a decrease in
water use, without a change in growth would have particular merit
in an irrigated agricultural system where the water input costs
were high. An increase in growth without a corresponding jump in
water use would have applicability to all agricultural systems. In
many agricultural systems where water supply is not limiting, an
increase in growth, even if it came at the expense of an increase
in water use also increases yield.
[0107] When soil water is depleted or if water is not available
during periods of drought, crop yields are restricted. Plant water
deficit develops if transpiration from leaves exceeds the supply of
water from the roots. The available water supply is related to the
amount of water held in the soil and the ability of the plant to
reach that water with its root system. Transpiration of water from
leaves is linked to the fixation of carbon dioxide by
photosynthesis through the stomata. The two processes are
positively correlated so that high carbon dioxide influx through
photosynthesis is closely linked to water loss by transpiration. As
water transpires from the leaf, leaf water potential is reduced and
the stomata tend to close in a hydraulic process limiting the
amount of photosynthesis. Since crop yield is dependent on the
fixation of carbon dioxide in photosynthesis, water uptake and
transpiration are contributing factors to crop yield. Plants which
are able to use less water to fix the same amount of carbon dioxide
or which are able to function normally at a lower water potential
have the potential to conduct more photosynthesis and thereby to
produce more biomass and economic yield in many agricultural
systems. An increased water use efficiency of the plant relates in
some cases to an increased fruit/kernel size or number.
[0108] Therefore, in one embodiment, the plants described herein
exhibit an increased water use efficiency when compared with a
reference agricultural plant grown under the same conditions. For
example, the plants grown from the seeds comprising the endophytic
bacterial population can have at least 1% higher WUE, for example,
at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at
least 6%, at least 7%, at least 8%, at least 9%, or at least 10%
higher, at least 20% higher, at least 30% higher, at least 40%
higher, at least 50% higher, at least 60% higher, at least 70%
higher, at least 80% higher, at least 90% higher, at least 100%
higher WUE than a reference agricultural plant grown under the same
conditions. Such an increase in WUE can occur under conditions
without water deficit, or under conditions of water deficit, for
example, when the soil water content is less than or equal to 60%
of water saturated soil, for example, less than or equal to 50%,
less than or equal to 40%, less than or equal to 30%, less than or
equal to 20%, less than or equal to 10% of water saturated soil on
a weight basis.
[0109] In a related embodiment, the plant comprising the endophytic
bacterial endophyte can have at least 1%, at least 2%, at least 3%,
at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at
least 9%, or at least 10% higher relative water content (RWC), for
example, at least least 20% higher, at least 30% higher, at least
40% higher, at least 50% higher, at least 60% higher, at least 70%
higher, at least 80% higher, at least 90% higher, at least 100%
higher RWC than a reference agricultural plant grown under the same
conditions.
[0110] The endophytes described herein may also confer to the plant
an increased ability to grow in nutrient limiting conditions, for
example by solubilizing or otherwise making available to the plants
macronutrients or micronutrients that are complexed, insoluble, or
otherwise in an unavailable form. In one embodiment, a plant is
inoculated with an endophyte that confers increased ability to
liberate and/or otherwise provide to the plant with nutrients
selected from the group consisting of phosphate, nitrogen,
potassium, iron, manganese, calcium, molybdenum, vitamins, or other
micronutrients. Such a plant can exhibit increased growth in soil
containing limiting amounts of such nutrients when compared with
reference agricultural plant. Differences between the
endophyte-associated plant and reference agricultural plant can be
measured by comparing the biomass, or other physical parameters
described above, of the two plant types grown under limiting
conditions. Therefore, in one embodiment, the plant containing the
endophyte able to confer increased tolerance to nutrient limiting
conditions exhibits a difference in a physiological parameter that
is at least about 5% greater, for example at least about 5%, at
least about 8%, at least about 10%, at least about 15%, at least
about 20%, at least about 25%, at least about 30%, at least about
40%, at least about 50%, at least about 60%, at least about 75%, at
least about 80%, at least about 80%, at least about 90%, or at
least 100%, at least about 200%, at least about 300%, at least
about 400% or greater than a reference agricultural plant grown
under the same conditions of nutrient stress. In another
embodiment, the plant containing the endophyte is able to grown
under nutrient stress conditions while exhibiting no difference in
the physiological parameter compared to a plant that is grown
without nutrient stress. In some embodiments, such a plant will
exhibit no difference in the physiological parameter when grown
with 2-5% less nitrogen than average cultivation practices on
normal agricultural land, for example, at least 5-10% less
nitrogen, at least 10-15% less nitrogen, at least 15-20% less
nitrogen, at least 20-25% less nitrogen, at least 25-30% less
nitrogen, at least 30-35% less nitrogen, at least 35-40% less
nitrogen, at least 40-45% less nitrogen, at least 45-50% less
nitrogen, at least 50-55% less nitrogen, at least 55-60% less
nitrogen, at least 60-65% less nitrogen, at least 65-70% less
nitrogen, at least 70-75% less nitrogen, at least 80-85% less
nitrogen, at least 85-90% less nitrogen, at least 90-95% less
nitrogen, or less, when compared with crop plants grown under
normal conditions during an average growing season. In some
embodiments, the microbe capable of providing nitrogen-stress
tolerance to a plant is diazotrophic. In other embodiments, the
microbe capable of providing nitrogen-stress tolerance to a plant
is non-diazotrophic.
[0111] Many of the microbes described herein are capable of
producing the plant hormone auxin indole acetic acid (IAA) when
grown in culture. Auxin may play a key role in altering the
physiology of the plant, including the extent of root growth.
Therefore, in another embodiment, the endophytic bacterial
population is disposed on the surface or within a tissue of the
seed or seedling in an amount effective to detectably induce
production of auxin in the agricultural plant. For example, the
increase in auxin production can be at least 1%, at least 2%, at
least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at
least 8%, at least 9%, or at least 10%, for example, at least 20%,
at least 30%, at least 40%, at least 50%, at least 60%, at least
75%, at least 100%, or more, when compared with a reference
agricultural plant. In one embodiment, the increased auxin
production can be detected in a tissue type selected from the group
consisting of the root, shoot, leaves, and flowers.
[0112] In another embodiment, the endophytic bacterial population
of the present invention can cause a detectable modulation in the
amount of a metabolite in the plant or part of the plant. Such
modulation can be detected, for example, by measuring the levels of
a given metabolite and comparing with the levels of the metabolite
in a reference agricultural plant grown under the same
conditions.
Plants Useful for the Present Invention
[0113] The methods and compositions according to the present
invention can be deployed for any seed plant species.
Monocotyledonous as well as dicotyledonous plant species are
particularly suitable. The methods and compositions are preferably
used with plants that are important or interesting for agriculture,
horticulture, for the production of biomass used in producing
liquid fuel molecules and other chemicals, and/or forestry.
[0114] Thus, the invention has use over a broad range of plants,
preferably higher plants pertaining to the classes of Angiospermae
and Gymnospermae. Plants of the subclasses of the Dicotylodenae and
the Monocotyledonae are particularly suitable. Dicotyledonous
plants belong to the orders of the Aristochiales, Asterales,
Batales, Campanulales, Capparales, Caryophyllales, Casuarinales,
Celastrales, Cornales, Diapensales, Dilleniales, Dipsacales,
Ebenales, Ericales, Eucomiales, Euphorbiales, Fabales, Fagales,
Gentianales, Geraniales, Haloragales, Hamamelidales, Middles,
Juglandales, Lamiales, Laurales, Lecythidales, Leitneriales,
Magniolales, Malvales, Myricales, Myrtales, Nymphaeales,
Papeverales, Piperales, Plantaginales, Plumb aginales,
Podostemales, Polemoniales, Polygalales, Polygonales, Primulales,
Proteales, Rafflesiales, Ranunculales, Rhamnales, Rosales,
Rubiales, Salicales, Santales, Sapindales, Sarraceniaceae,
Scrophulariales, Theales, Trochodendrales, Umbellales, Urticales,
and Violates. Monocotyledonous plants belong to the orders of the
Alismatales, Arales, Arecales, Bromeliales, Commelinales,
Cyclanthales, Cyperales, Eriocaulales, Hydrocharitales, Juncales,
Lilliales, Najadales, Orchidales, Pandanales, Poales, Restionales,
Triuridales, Typhales, and Zingiberales. Plants belonging to the
class of the Gymnospermae are Cycadales, Ginkgoales, Gnetales, and
Pinales.
[0115] Suitable species may include members of the genus
Abelmoschus, Abies, Acer, Agrostis, Allium, Alstroemeria, Ananas,
Andrographis, Andropogon, Artemisia, Arundo, Atropa, Berberis,
Beta, Bixa, Brassica, Calendula, Camellia, Camptotheca, Cannabis,
Capsicum, Carthamus, Catharanthus, Cephalotaxus, Chrysanthemum,
Cinchona, Citrullus, Coffea, Colchicum, Coleus, Cucumis, Cucurbita,
Cynodon, Datura, Dianthus, Digitalis, Dioscorea, Elaeis, Ephedra,
Erianthus, Erythroxylum, Eucalyptus, Festuca, Fragaria, Galanthus,
Glycine, Gossypium, Helianthus, Hevea, Hordeum, Hyoscyamus,
Jatropha, Lactuca, Linum, Lolium, Lupinus, Lycopersicon,
Lycopodium, Manihot, Medicago, Mentha, Miscanthus, Musa, Nicotiana,
Oryza, Panicum, Papaver, Parthenium, Pennisetum, Petunia, Phalaris,
Phleum, Pinus, Poa, Poinsettia, Populus, Rauwolfia, Ricinus, Rosa,
Saccharum, Salix, Sanguinaria, Scopolia, Secale, Solanum, Sorghum,
Spartina, Spinacea, Tanacetum, Taxus, Theobroma, Triticosecale,
Triticum, Uniola, Veratrum, Vinca, Vitis, and Zea.
[0116] The methods and compositions of the present invention are
preferably used in plants that are important or interesting for
agriculture, horticulture, biomass for the production of biofuel
molecules and other chemicals, and/or forestry. Non-limiting
examples include, for instance, Panicum virgatum (switchgrass),
Sorghum bicolor (sorghum, sudangrass), Miscanthus giganteus
(miscanthus), Saccharum sp. (energycane), Populus balsamifera
(poplar), Zea mays (corn), Glycine max (soybean), Brassica napus
(canola), Triticum aestivum (wheat), Gossypium hirsutum (cotton),
Oryza sativa (rice), Helianthus annuus (sunflower), Medicago sativa
(alfalfa), Beta vulgaris (sugarbeet), Pennisetum glaucum (pearl
millet), Panicum spp., Sorghum spp., Miscanthus spp., Saccharum
spp., Erianthus spp., Populus spp., Secale cereale (rye), Salix
spp. (willow), Eucalyptus spp. (eucalyptus), Triticosecale spp.
(triticum-wheat X rye), Bamboo, Carthamus tinctorius (safflower),
Jatropha curcas (Jatropha), Ricinus communis (castor), Elaeis
guineensis (oil palm), Phoenix dactylifera (date palm),
Archontophoenix cunninghamiana (king palm), Syagrus romanzoffiana
(queen palm), Linum usitatissimum (flax), Brassica juncea, Manihot
esculenta (cassava), Lycopersicon esculentum (tomato), Lactuca
saliva (lettuce), Musa paradisiaca (banana), Solanum tuberosum
(potato), Brassica oleracea (broccoli, cauliflower,
brusselsprouts), Camellia sinensis (tea), Fragaria ananassa
(strawberry), Theobroma cacao (cocoa), Coffea arabica (coffee),
Vitis vinifera (grape), Ananas comosus (pineapple), Capsicum annum
(hot & sweet pepper), Allium cepa (onion), Cucumis melo
(melon), Cucumis sativus (cucumber), Cucurbita maxima (squash),
Cucurbita moschata (squash), Spinacea oleracea (spinach), Citrullus
lanatus (watermelon), Abelmoschus esculentus (okra), Solanum
melongena (eggplant), Papaver somniferum (opium poppy), Papaver
orientale, Taxus baccata, Taxus brevifolia, Artemisia annua,
Cannabis saliva, Camptotheca acuminate, Catharanthus roseus, Vinca
rosea, Cinchona officinalis, Coichicum autumnale, Veratrum
californica, Digitalis lanata, Digitalis purpurea, Dioscorea spp.,
Andrographis paniculata, Atropa belladonna, Datura stomonium,
Berberis spp., Cephalotaxus spp., Ephedra sinica, Ephedra spp.,
Erythroxylum coca, Galanthus wornorii, Scopolia spp., Lycopodium
serratum (Huperzia serrata), Lycopodium spp., Rauwolfia serpentina,
Rauwolfia spp., Sanguinaria canadensis, Hyoscyamus spp., Calendula
officinalis, Chrysanthemum parthenium, Coleus forskohlii, Tanacetum
parthenium, Parthenium argentatum (guayule), Hevea spp. (rubber),
Mentha spicata (mint), Mentha piperita (mint), Bixa orellana,
Alstroemeria spp., Rosa spp. (rose), Dianthus caryophyllus
(carnation), Petunia spp. (petunia), Poinsettia pulcherrima
(poinsettia), Nicotiana tabacum (tobacco), Lupinus albus (lupin),
Uniola paniculata (oats), Hordeum vulgare (barley), and Lolium spp.
(ryegrass).
[0117] The methods described herein can also be used with
genetically modified plants, for example, to yield additional trait
benefits to a plant. For example, a genetically modified plant
which is, by means of the transgene, optimized with respect to a
certain trait, can be further augmented with additional trait
benefits conferred by the newly introduced microbe. Therefore, in
one embodiment, a genetically modified plant is contacted with a
microbe.
Formulations/Seed Coating Compositions
[0118] In some embodiments, the present invention contemplates
seeds comprising a endophytic bacterial population, and further
comprising a formulation. The formulation useful for these
embodiments generally comprise at least one member selected from
the group consisting of an agriculturally compatible carrier, a
tackifier, a microbial stabilizer, a fungicide, an antibacterial
agent, an herbicide, a nematicide, an insecticide, a plant growth
regulator, a rodenticide, and a nutrient.
[0119] In some cases, the endophytic bacterial population is mixed
with an agriculturally compatible carrier. The carrier can be a
solid carrier or liquid carrier. The carrier may be any one or more
of a number of carriers that confer a variety of properties, such
as increased stability, wettability, or dispersability. Wetting
agents such as natural or synthetic surfactants, which can be
nonionic or ionic surfactants, or a combination thereof can be
included in a composition of the invention. Water-in-oil emulsions
can also be used to formulate a composition that includes the
endophytic bacterial population of the present invention (see, for
example, U.S. Pat. No. 7,485,451, which is incorporated herein by
reference in its entirety). Suitable formulations that may be
prepared include wettable powders, granules, gels, agar strips or
pellets, thickeners, and the like, microencapsulated particles, and
the like, liquids such as aqueous flowables, aqueous suspensions,
water-in-oil emulsions, etc. The formulation may include grain or
legume products, for example, ground grain or beans, broth or flour
derived from grain or beans, starch, sugar, or oil.
[0120] In some embodiments, the agricultural carrier may be soil or
plant growth medium. Other agricultural carriers that may be used
include fertilizers, plant-based oils, humectants, or combinations
thereof. Alternatively, the agricultural carrier may be a solid,
such as diatomaceous earth, loam, silica, alginate, clay,
bentonite, vermiculite, seed cases, other plant and animal
products, or combinations, including granules, pellets, or
suspensions. Mixtures of any of the aforementioned ingredients are
also contemplated as carriers, such as but not limited to, pesta
(flour and kaolin clay), agar or flour-based pellets in loam, sand,
or clay, etc. Formulations may include food sources for the
cultured organisms, such as barley, rice, or other biological
materials such as seed, plant parts, sugar cane bagasse, hulls or
stalks from grain processing, ground plant material or wood from
building site refuse, sawdust or small fibers from recycling of
paper, fabric, or wood. Other suitable formulations will be known
to those skilled in the art.
[0121] In one embodiment, the formulation can comprise a tackifier
or adherent. Such agents are useful for combining the bacterial
population of the invention with carriers that can contain other
compounds (e.g., control agents that are not biologic), to yield a
coating composition. Such compositions help create coatings around
the plant or seed to maintain contact between the microbe and other
agents with the plant or plant part. In one embodiment, adherents
are selected from the group consisting of: alginate, gums,
starches, lecithins, formononetin, polyvinyl alcohol, alkali
formononetinate, hesperetin, polyvinyl acetate, cephalins, Gum
Arabic, Xanthan Gum, Mineral Oil, Polyethylene Glycol (PEG),
Polyvinyl pyrrolidone (PVP), Arabino-galactan, Methyl Cellulose,
PEG 400, Chitosan, Polyacrylamide, Polyacrylate, Polyacrylonitrile,
Glycerol, Triethylene glycol, Vinyl Acetate,
[0122] Gellan Gum, Polystyrene, Polyvinyl, Carboxymethyl cellulose,
Gum Ghatti, and polyoxyethylene-polyoxybutylene block copolymers.
Other examples of adherent compositions that can be used in the
synthetic preparation include those described in EP 0818135, CA
1229497, WO 2013090628, EP 0192342, WO 2008103422 and CA 1041788,
each of which is incorporated herein by reference in its
entirety.
[0123] The formulation can also contain a surfactant. Non-limiting
examples of surfactants include nitrogen-surfactant blends such as
Prefer 28 (Cenex), Surf-N(US), Inhance (Brandt), P-28 (Wilfarm) and
Patrol (Helena); esterified seed oils include Sun-It II (AmCy), MSO
(UAP), Scoil (Agsco), Hasten (Wilfarm) and Mes-100 (Drexel); and
organo-silicone surfactants include Silwet L77 (UAP), Silikin
(Terra), Dyne-Amic (Helena), Kinetic (Helena), Sylgard 309
(Wilbur-Ellis) and Century (Precision). In one embodiment, the
surfactant is present at a concentration of between 0.01% v/v to
10% v/v. In another embodiment, the surfactant is present at a
concentration of between 0.1% v/v to 1% v/v.
[0124] In certain cases, the formulation includes a microbial
stabilizer. Such an agent can include a desiccant. As used herein,
a "desiccant" can include any compound or mixture of compounds that
can be classified as a desiccant regardless of whether the compound
or compounds are used in such concentrations that they in fact have
a desiccating effect on the liquid inoculant. Such desiccants are
ideally compatible with the bacterial population used, and should
promote the ability of the microbial population to survive
application on the seeds and to survive desiccation. Examples of
suitable desiccants include one or more of trehalose, sucrose,
glycerol, and methylene glycol. Other suitable desiccants include,
but are not limited to, non reducing sugars and sugar alcohols
(e.g., mannitol or sorbitol). The amount of desiccant introduced
into the formulation can range from about 5% to about 50% by
weight/volume, for example, between about 10% to about 40%, between
about 15% and about 35%, or between about 20% and about 30%.
[0125] In some cases, it is advantageous for the formulation to
contain agents such as a fungicide, an antibacterial agent, an
herbicide, a nematicide, an insecticide, a plant growth regulator,
a rodenticide, and a nutrient. Such agents are ideally compatible
with the agricultural seed or seedling onto which the formulation
is applied (e.g., it should not be deleterious to the growth or
health of the plant). Furthermore, the agent is ideally one which
does not cause safety concerns for human, animal or industrial use
(e.g., no safety issues, or the compound is sufficiently labile
that the commodity plant product derived from the plant contains
negligible amounts of the compound).
[0126] In the liquid form, for example, solutions or suspensions,
the endophytic bacterial populations of the present invention can
be mixed or suspended in aqueous solutions. Suitable liquid
diluents or carriers include aqueous solutions, petroleum
distillates, or other liquid carriers.
[0127] Solid compositions can be prepared by dispersing the
endophytic bacterial populations of the invention in and on an
appropriately divided solid carrier, such as peat, wheat, bran,
vermiculite, clay, talc, bentonite, diatomaceous earth, fuller's
earth, pasteurized soil, and the like. When such formulations are
used as wettable powders, biologically compatible dispersing agents
such as non-ionic, anionic, amphoteric, or cationic dispersing and
emulsifying agents can be used.
[0128] The solid carriers used upon formulation include, for
example, mineral carriers such as kaolin clay, pyrophyllite,
bentonite, montmorillonite, diatomaceous earth, acid white soil,
vermiculite, and pearlite, and inorganic salts such as ammonium
sulfate, ammonium phosphate, ammonium nitrate, urea, ammonium
chloride, and calcium carbonate. Also, organic fine powders such as
wheat flour, wheat bran, and rice bran may be used. The liquid
carriers include vegetable oils such as soybean oil and cottonseed
oil, glycerol, ethylene glycol, polyethylene glycol, propylene
glycol, polypropylene glycol, etc.
[0129] In one particular embodiment, the formulation is ideally
suited for coating of the endophytic microbial population onto
seeds. The endophytic bacterial populations described in the
present invention are capable of conferring many fitness benefits
to the host plants. The ability to confer such benefits by coating
the bacterial populations on the surface of seeds has many
potential advantages, particularly when used in a commercial
(agricultural) scale.
[0130] The endophytic bacterial populations herein can be combined
with one or more of the agents described above to yield a
formulation suitable for combining with an agricultural seed or
seedling. The bacterial population can be obtained from growth in
culture, for example, using a synthetic growth medium. In addition,
the microbe can be cultured on solid media, for example on petri
dishes, scraped off and suspended into the preparation. Microbes at
different growth phases can be used. For example, microbes at lag
phase, early-log phase, mid-log phase, late-log phase, stationary
phase, early death phase, or death phase can be used.
[0131] The formulations comprising the endophytic bacterial
population of the present invention typically contains between
about 0.1 to 95% by weight, for example, between about 1% and 90%,
between about 3% and 75%, between about 5% and 60%, between about
10% and 50% in wet weight of the bacterial population of the
present invention. It is preferred that the formulation contains at
least about 10.sup.3 per ml of formulation, for example, at least
about 10.sup.4, at least about 10.sup.5, at least about 10.sup.6,
at least 10.sup.7 CFU, at least 10.sup.8 CFU per ml of
formulation.
[0132] As described above, in certain embodiments, the present
invention contemplates the use of endophytic bacteria that are
heterologously disposed on the plant, for example, the seed. In
certain cases, the agricultural plant may contain bacteria that are
substantially similar to, or even genetically indistinguishable
from, the bacteria that are being applied to the plant. It is noted
that, in many cases, the bacteria that are being applied is
substantially different from the bacteria already present in
several significant ways. First, the bacteria that are being
applied to the agricultural plant have been adapted to culture, or
adapted to be able to grow on growth media in isolation from the
plant. Second, in many cases, the bacteria that are being applied
are derived from a clonal origin, rather than from a heterologous
origin and, as such, can be distinguished from the bacteria that
are already present in the agricultural plant by the clonal
similarity. For example, where a microbe that has been inoculated
by a plant is also present in the plant (for example, in a
different tissue or portion of the plant), or where the introduced
microbe is sufficiently similar to a microbe that is present in
some of the plants (or portion of the plant, including seeds), it
is still possible to distinguish between the inoculated microbe and
the native microbe by distinguishing between the two microbe types
on the basis of their epigenetic status (e.g., the bacteria that
are applied, as well as their progeny, would be expected to have a
much more uniform and similar pattern of cytosine methylation of
its genome, with respect to the extent and/or location of
methylation).
Population of Seeds
[0133] In another aspect, the invention provides for a
substantially uniform population of seeds comprising a plurality of
seeds comprising the endophytic bacterial population, as described
herein above. Substantial uniformity can be determined in many
ways. In some cases, at least 1%, at least 2%, at least 3%, at
least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at
least 9%, or at least 10%, for example, at least 20%, at least 30%,
at least 40%, at least 50%, at least 60%, at least 70%, at least
75%, at least 80%, at least 90%, at least 95% or more of the seeds
in the population, contains the endophytic bacterial population in
an amount effective to colonize the plant disposed on the surface
of the seeds. In other cases, at least 1%, at least 2%, at least
3%, at least 4%, at least 5%, at least 6%, at least 7%, at least
8%, at least 9%, or at least 10%, for example, at least 20%, at
least 30%, at least 40%, at least 50%, at least 60%, at least 70%,
at least 75%, at least 80%, at least 90%, at least 95% or more of
the seeds in the population, contains at least 100 CFU on its
surface, for example, at least 200 CFU, at least 300 CFU, at least
1,000 CFU, at least 3,000 CFU, at least 10,000 CFU, at least 30,000
CFU, at least 100,000 CFU, at least 300,000 CFU, or at least
1,000,000 CFU per seed or more.
[0134] In a particular embodiment, the population of seeds is
packaged in a bag or container suitable for commercial sale. Such a
bag contains a unit weight or count of the seeds comprising the
endophytic bacterial population as described herein, and further
comprises a label. In one embodiment, the bag or container contains
at least 1,000 seeds, for example, at least 5,000 seeds, at least
10,000 seeds, at least 20,000 seeds, at least 30,000 seeds, at
least 50,000 seeds, at least 70,000 seeds, at least 80,000 seeds,
at least 90,000 seeds or more. In another embodiment, the bag or
container can comprise a discrete weight of seeds, for example, at
least 1 lb, at least 2 lbs, at least 5 lbs, at least 10 lbs, at
least 30 lbs, at least 50 lbs, at least 70 lbs or more. The bag or
container comprises a label describing the seeds and/or said
endophytic bacterial population. The label can contain additional
information, for example, the information selected from the group
consisting of: net weight, lot number, geographic origin of the
seeds, test date, germination rate, inert matter content, and the
amount of noxious weeds, if any. Suitable containers or packages
include those traditionally used in plant seed commercialization.
The invention also contemplates other containers with more
sophisticated storage capabilities (e.g., with microbiologically
tight wrappings or with gas-or water-proof containments).
[0135] In some cases, a sub-population of seeds comprising the
endophytic bacterial population is further selected on the basis of
increased uniformity, for example, on the basis of uniformity of
microbial population. For example, individual seeds of pools
collected from individual cobs, individual plants, individual plots
(representing plants inoculated on the same day) or individual
fields can be tested for uniformity of microbial density, and only
those pools meeting specifications (e.g., at least 80% of tested
seeds have minimum density, as determined by quantitative methods
described elsewhere) are combined to provide the agricultural seed
sub-population.
[0136] The methods described herein can also comprise a validating
step. The validating step can entail, for example, growing some
seeds collected from the inoculated plants into mature agricultural
plants, and testing those individual plants for uniformity. Such
validating step can be performed on individual seeds collected from
cobs, individual plants, individual plots (representing plants
inoculated on the same day) or individual fields, and tested as
described above to identify pools meeting the required
specifications.
Population of Plants/Agricultural Fields
[0137] A major focus of crop improvement efforts has been to select
varieties with traits that give, in addition to the highest return,
the greatest homogeneity and uniformity. While inbreeding can yield
plants with substantial genetic identity, heterogeneity with
respect to plant height, flowering time, and time to seed, remain
impediments to obtaining a homogeneous field of plants. The
inevitable plant-to-plant variability are caused by a multitude of
factors, including uneven environmental conditions and management
practices. Another possible source of variability can, in some
cases, be due to the heterogeneity of the microbial population
inhabit the plants. By providing endophytic bacterial populations
onto seeds and seedlings, the resulting plants generated by
germinating the seeds and seedlings have a more consistent
microbial composition, and thus are expected to yield a more
uniform population of plants.
[0138] Therefore, in another aspect, the invention provides a
substantially uniform population of plants. The population
comprises at least 100 plants, for example, at least 300 plants, at
least 1,000 plants, at least 3,000 plants, at least 10,000 plants,
at least 30,000 plants, at least 100,000 plants or more. The plants
are grown from the seeds comprising the endophytic bacterial
population as described herein. The increased uniformity of the
plants can be measured in a number of different ways.
[0139] In one embodiment, there is an increased uniformity with
respect to the microbes within the plant population. For example,
in one embodiment, a substantial portion of the population of
plants, for example at least 1%, at least 2%, at least 3%, at least
4%, at least 5%, at least 6%, at least 7%, at least 8%, at least
9%, or at least 10%, at least 20%, at least 30%, at least 40%, at
least 50%, at least 60%, at least 70%, at least 75%, at least 80%,
at least 90%, at least 95% or more of the seeds or plants in a
population, contains a threshold number of the endophytic bacterial
population. The threshold number can be at least 100 CFU, for
example at least 300 CFU, at least 1,000 CFU, at least 3,000 CFU,
at least 10,000 CFU, at least 30,000 CFU, at least 100,000 CFU or
more, in the plant or a part of the plant. Alternatively, in a
substantial portion of the population of plants, for example, in at
least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at
least 6%, at least 7%, at least 8%, at least 9%, or at least 10%,
at least 20%, at least 30%, at least 40%, at least 50%, at least
60%, at least 70%, at least 75%, at least 80%, at least 90%, at
least 95% or more of the plants in the population, the endophytic
bacterial population that is provided to the seed or seedling
represents at least 1%, at least 2%, at least 3%, at least 4%, at
least 5%, at least 6%, at least 7%, at least 8%, at least 9%, or at
least 10%, least 20%, at least 30%, at least 40%, at least 50%, at
least 60%, at least 70%, at least 80%, at least 90%, at least 95%,
at least 99%, or 100% of the total microbe population in the
plant/seed.
[0140] In another embodiment, there is an increased uniformity with
respect to a physiological parameter of the plants within the
population. In some cases, there can be an increased uniformity in
the height of the plants when compared with a population of
reference agricultural plants grown under the same conditions. For
example, there can be a reduction in the standard deviation in the
height of the plants in the population of at least 1%, at least 2%,
at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at
least 8%, at least 9%, or at least 10%, at least 15%, at least 20%,
at least 30%, at least 40%, at least 50%, at least 60% or more,
when compared with a population of reference agricultural plants
grown under the same conditions. In other cases, there can be a
reduction in the standard deviation in the flowering time of the
plants in the population of at least 1%, at least 2%, at least 3%,
at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at
least 9%, or at least 10%, at least 15%, at least 20%, at least
30%, at least 40%, at least 50%, at least 60% or more, when
compared with a population of reference agricultural plants grown
under the same conditions.
Commodity Plant Product
[0141] The present invention provides a commodity plant product, as
well as methods for producing a commodity plant product, that is
derived from a plant of the present invention. As used herein, a
"commodity plant product" refers to any composition or product that
is comprised of material derived from a plant, seed, plant cell, or
plant part of the present invention. Commodity plant products may
be sold to consumers and can be viable or nonviable. Nonviable
commodity products include but are not limited to nonviable seeds
and grains; processed seeds, seed parts, and plant parts;
dehydrated plant tissue, frozen plant tissue, and processed plant
tissue; seeds and plant parts processed for animal feed for
terrestrial and/or aquatic animal consumption, oil, meal, flour,
flakes, bran, fiber, paper, tea, coffee, silage, crushed of whole
grain, and any other food for human or animal consumption; and
biomasses and fuel products; and raw material in industry.
Industrial uses of oils derived from the agricultural plants
described herein include ingredients for paints, plastics, fibers,
detergents, cosmetics, lubricants, and biodiesel fuel. Soybean oil
may be split, inter-esterified, sulfurized, epoxidized,
polymerized, ethoxylated, or cleaved. Designing and producing
soybean oil derivatives with improved functionality and improved
oliochemistry is a rapidly growing field. The typical mixture of
triglycerides is usually split and separated into pure fatty acids,
which are then combined with petroleum-derived alcohols or acids,
nitrogen, sulfonates, chlorine, or with fatty alcohols derived from
fats and oils to produce the desired type of oil or fat. Commodity
plant products also include industrial compounds, such as a wide
variety of resins used in the formulation of adhesives, films,
plastics, paints, coatings and foams.
[0142] In some cases, commodity plant products derived from the
plants, or using the methods of the present invention can be
identified readily. In some cases, for example, the presence of
viable endophytic microbes can be detected using the methods
described herein elsewhere. In other cases, particularly where
there are no viable endophytic microbes, the commodity plant
product may still contain at least a detectable amount of the
specific and unique DNA corresponding to the microbes described
herein. Any standard method of detection for polynucleotide
molecules may be used, including methods of detection disclosed
herein.
[0143] Throughout the specification, the word "comprise," or
variations such as "comprises" or "comprising," will be understood
to imply the inclusion of a stated integer or group of integers but
not the exclusion of any other integer or group of integers.
[0144] Although the present invention has been described in detail
with reference to examples below, it is understood that various
modifications can be made without departing from the spirit of the
invention. For instance, while the particular examples below may
illustrate the methods and embodiments described herein using a
specific plant, the principles in these examples may be applied to
any agricultural crop. Therefore, it will be appreciated that the
scope of this invention is encompassed by the embodiments of the
inventions recited herein and the specification rather than the
specific examples that are exemplified below. All cited patents and
publications referred to in this application are herein
incorporated by reference in their entirety.
EXAMPLES
Example 1
Phenotypic and Physiological Characterization of Microbes
[0145] Bacterial strains from overnight cultures in tryptic soy
broth were streaked on tryptic soy agar (TSA) plates and incubated
at 30.degree. C. After 24 h, the color and shape of colonies were
noted. Cell motility and colony shape were observed under light
microscope (Nikon, Japan). The pH limits for bacterial growth was
determined by adjusting the pH of the growth media to values
between 5 and 12 in triplicates. Bacterial growth on different salt
concentrations was tested in TSA medium containing 1-6% NaCl.
Furthermore, the ability of the microbes to grow in
methanol/ethanol as sole carbon source was analyzed by replacing
the glucose with either methanol or ethanol.
[0146] Aggregate formation of bacterial strains can positively
affect their dispersal and survival in the plant environment and
adsorption to plant roots. The extent of aggregation formation was
measured in six replicates following the method of Madi and Henis
(1989) Plant Soil 115:89-98 (incorporated herein by reference) with
some modifications. Aliquots of liquid culture containing
aggregates were transferred to glass tubes and allowed to stand for
30 min. Aggregates settled down to the bottom of each tubes, and
the suspension was mostly composed free of cells. The turbidity of
each suspension was measured at 540 nm (ODs) with a microplate
reader (Synergy 5; BioTek Instrument Inc., Winooski, USA). Cultures
were then dispersed with a tissue homogenizer for 1 min and the
total turbidity (OD) was measured. The percentage of aggregation
was estimated as follows:
% aggregation=(ODt-ODs).times.100/ODt
[0147] Motility assays (swimming, swarming and twitching) were
performed following the methods of Rashid and Kornberg (2000). Swim
plates (LB media contained 0.3% agarose) were inoculated in
triplicates with bacteria from an overnight culture on TSA agar
plates grown at 30.degree. C. with a sterile toothpick. For
swarming, plates (NB media contained 0.5% agar and glucose) were
inoculated with a sterile toothpick. Twitch plates (LB broth
containing 1% Difco granular agar) were stab inoculated with a
sharp toothpick to the bottom of petri dish from an overnight grown
culture in TSA agar plates.
[0148] Biofilm formation was analyzed using overnight grown
bacterial culture in 96 well microtiter plates by staining with 1%
crystal violet (CV) for 45 min. To quantify the amount of biofilm,
CV was destained with 200 .mu.l of 100% ethanol. The absorbance of
150 .mu.l of the destained CV, which was transferred into a new
microtiter plate was measured at 595 nm (modified from Djordjevic
et al. 2002, Appl Environ Microbiol 68:2950-2958, incorporated
herein by reference). The phenotypic characters of the strains are
shown in Table 1.
TABLE-US-00001 TABLE 1 Phenotypic characteristics of the strains:
Agrobacterium sp. Sphinogobium sp. Pseudomonas sp. Enterobacter sp.
Characteristics (FA13) Pantoea sp. (FF34) (FC42) (FB12) (FD17)
Phenotypic and hysiological characterization Colony Gray Yellow
Yellow Gray Creamy color white Colony Round Round Round Round Round
morphology Gram n.d. n.d. n.d. n.d. n.d. reaction Bacterial growth
conditions* Temperature 4.degree. C. n.d. n.d. n.d. n.d. n.d.
42.degree. C. n.d. n.d. n.d. n.d. n.d. NaCl 2% + + + + + 6% - + - -
+ pH 5 + + + + + 12 + - - + + Motility/chemotaxis.dagger-dbl.
Swimming + + - ++ +++ Swarming - - - - + Twitching + + - + +
Biofilm formation OD (600 nm) 0.92 .+-. 0.04 0.59 .+-. 0.02 0.95
.+-. 0.08 0.57 .+-. 0.08 0.95 .+-. 0.04 Biofilm 0.23 .+-. 0.02 0.22
.+-. 0.03 0.08 .+-. 0.01 0.08 .+-. 0.04 0.83 .+-. 0.06 (595 nm)
Aggregate 35.91 .+-. 2.57 26.07 .+-. 0.88 32.61 .+-. 2.13 36.38
.+-. 1.48 40.22 .+-. 1.99 stability (%) Acinetobacter sp.
Paenibacillus sp. Characteristics Micrococus sp. S2 Bacillus sp. S4
Pantoea sp. S6 S9 S10 Phenotypic and hysiological characterization
Colony Creamy Off- Yellow White Creamy color white white Colony
Round Round Round Round Round morphology Gram + + - - - reaction
Bacterial growth conditions* Temperature 4.degree. C. - + + + +
42.degree. C. - - - - - NaCl 2% + + + + + 6% + + + - + pH 5 + + + +
+ 12 + - + - + Motility/chemotaxis.dagger-dbl. Swimming - - + - ++
Swarming - - ++ - + Twitching - + + - + Biofilm formation OD (600
nm) 0.92 .+-. 0.04 0.59 .+-. 0.02 0.95 .+-. 0.08 0.57 .+-. 0.08
0.95 .+-. 0.04 Biofilm 0.23 .+-. 0.02 0.22 .+-. 0.03 0.08 .+-. 0.01
0.08 .+-. 0.04 0.83 .+-. 0.06 (595 nm) Aggregate 35.91 .+-. 2.57
26.07 .+-. 0.88 32.61 .+-. 2.13 36.38 .+-. 1.48 40.22 .+-. 1.99
stability (%)
Biochemical Characterization
[0149] Biochemical tests such as oxidase, catalase, gelatin
hydrolysis and casein hydrolysis of the selected strains were
performed. Oxidase and catalase activities were tested with 1%
(w/v) tetramethyl-p-phenylene diamine and 3% (v/v) hydrogen
peroxide solution, respectively. Gelatin and casein hydrolysis was
performed by streaking bacterial strains onto a TSA plates from the
stock culture. After incubation, trichloroacetic acid (TCA) was
applied to the plates and made observation immediately for a period
of at least 4 min (Medina and Baresi 2007, J Microbiol Methods
69:391-393, incorporated herein by reference). A summary of the
biochemical characteristics of the strains is shown below in Table
2:
TABLE-US-00002 TABLE 2 Biochemical Characterization of Endophytic
Bacteria Biochemical characterization* Pantoea Agrobacterium sp.
Sphinogobium Pseudomonas Enterobacter Micrococus Bacillus Pantoea
Acinetobacter Paenibacillus sp.(FA13) (FF34) sp. (FC42) sp. (FB12)
sp. (FD17) sp. S2 sp. S4 sp. S6 sp. S9 sp. S10 Catalase + + + + + +
+ + + + Oxidase - - - + - - + - - + Casein - - - + - + + - - -
Gelatin - + - + + + - + - - Meth- + - - + - + - - + + anol Ethanol
+ - - + - + - - + +
Quantification of Auxin Production
[0150] Auxin production by bacterial isolates both in the presence
and absence of L-tryptophan (L-TRP) was determined colormetrically
and expressed as IAA equivalent (Sarwar et al. 1992, Plant Soil
147:207-215, incorporated herein by reference). Two days old
bacterial cells grown (28.degree. C. at 180 rpm) in tryptic soy
broth supplemented with 1% L-TRP solution were harvested by
centrifugation (10, 000 g for 10 min). Three mL of the supernatants
were mixed with 2 mL Salkowski's reagent (12 g L.sup.-1 FeCl.sub.3
in 429 ml L.sup.-1 H.sub.2SO.sub.4). The mixture was incubated at
room temperature for 30 min for colour development and absorbance
at 535 nm was measured using spectrophotometer. Auxin concentration
produced by bacterial isolates was determined using standard curves
for IAA prepared from serial dilutions of 10-100 .mu.g
mL.sup.-1.
TABLE-US-00003 TABLE 3 Production of Indole Acetic Acid by
Endophytic Bacteria Agrobacterium Pantoea Sphinogobium Pseudomonas
Enterobacter Characteristics sp. (FA13) sp. (FF34) sp. (FC42) sp.
(FB12) sp. (FD17) without L-TRP 1.74 .+-. 0.18 10.33 .+-. 0.35 4.89
.+-. 0.78 1.63 .+-. 0.65 7.54 .+-. 1.02 with L-TRP 16.13 .+-. 1.05
95.34 .+-. 2.14 38.41 .+-. 1.78 7.26 .+-. 1.05 12.30 .+-. 0.98
[0151] As shown in Table 3 above, strains FA13, FF34, FC42, FB12
and FD17 were all shown to produce auxin (ranging from 1.63 to
10.33 .mu.g ml.sup.-1 in the absence of L-tryptophan), and the
level of auxin production was greatly enhanced by the presence of
L-tryptophan in the growth medium (at least 7.26 .mu.g
ml.sup.-1).
Assays for Phosphorus Solubilization and Siderophore Production
[0152] Bacterial strains were evaluated for their ability to
solubilize phosphates (organic/inorganic P). Aliquots (10 .mu.L) of
overnight bacterial growth culture in tryptic soy broth were spot
inoculated onto NBRI-PBP (Mehta and Nautiyal 2001) and
calcium/sodium phytate agar medium (Rosado et al. 1998).
Solubilization of organic/inorganic phosphates was detected by the
formation of a clear zone around the bacterial growth spot.
Phosphate solubilization activity was also determined by
development of clear zone around bacterial growth on Pikovskaya
agar medium (Pikovskaya 1948, Mikrobiologiya 17:362-370,
incorporated herein by reference). Bacterial isolates were assayed
for siderophores production on the Chrome azurol S (CAS) agar
medium described by Schwyn and Neilands (1987), Curr Microbiol
43:57-58 (incorporated herein by reference) as positive for
siderophore production.
Assays for Exopolysaccharide, NH.sub.3 and HCN Production
[0153] For exopolysaccharide (EPS) activity (qualitative), strains
were grown on Weaver mineral media enriched with glucose and
production of EPS was assessed visually (modified from Weaver et
al. 1975, Arch Microbiol 105:207-216, incorporated herein by
reference). The EPS production was monitored as floc formation
(fluffy material) on the plates after 48 h of incubation at 28
.+-.2.degree. C. Strains were tested for the production of ammonia
(NH.sub.3) in peptone water as described by Cappuccino and Sherman
(1992), Biochemical activities of microorganisms. In: Microbiology,
A Laboratory Manual. The Benjamin/Cummings Publishing Co.
California, USA, pp 125-178, incorporated herein by reference. The
bacterial isolates were screened for the production of hydrogen
cyanide (HCN) by inoculating King's
[0154] B agar plates amended with 4.4 g L.sup.-1 glycine (Lorck
1948, Physiol Plant 1:142-146, incorporated herein by reference).
Filter paper (Whatman no. 1) saturated with picrate solution (2%
Na.sub.2CO.sub.3 in 0.5% picric acid) was placed in the lid of a
petri plate inoculated with bacterial isolates. The plates were
incubated at 28.+-.2.degree. C. for 5 days. HCN production was
assessed by the colour change of yellow filter paper to reddish
brown.
Assays for Poly-Hydroxybutyrate (PHB) and n-Acyl-Homoserine Lactone
(AHL) Production
[0155] The bacterial isolates were tested for PHB production
(qualitative) following the viable colony staining methods using
Nile red and Sudan black B (Juan et al. 1998 Appl Environ Microbiol
64:4600-4602; Spiekermann et al. 1999, Arch Microbiol 171:73-80,
each of which is incorporated by reference). The LB plates with
overnight bacterial growth were flooded with 0.02% Sudan black B
for 30 min and then washed with ethanol (96%) to remove excess
strains from the colonies. The dark blue coloured colonies were
taken as positive for PHB production. Similarly, LB plates amended
with Nile red (0.5 .mu.L mL.sup.-1) were exposed to UV light (312
nm) after appropriate bacterial growth to detect PHB production.
Colonies of PHA-accumulating strains showed fluoresce under
ultraviolet light. The bacterial strains were tested for AHL
production following the method modified from Cha et al. (1998),
Mol Plant-Microbe Interact 11:1119-1129 (incorporated herein by
reference). The LB plates containing 40 .sub.iug m1.sup.-1 X-Gal
were plated with reporter strains (A. tumefaciens NTL4.pZLR4). The
LB plates were spot inoculated with 10 .mu.L of bacterial culture
and incubated at 28.+-.2.degree. C. for 24 h. Production of AHL
activity is indicated by a diffuse blue zone surrounding the test
spot of culture. Agrobacterium tumefaciens NTLI (pTiC58.DELTA.accR)
was used as positive control and plate without reporter strain was
considered as negative control.
TABLE-US-00004 TABLE 4 Various Biochemical Properties of Endophytic
Bacteria Agrobacterium sp. Sphinogobium sp. Pseudomonas sp.
Enterobacter sp. Characteristics.sup..dagger. (FA13) Pantoea sp.
(FF34) (FC42) (FB12) (FD17) P-solubilization (inorganic/organic P)
Ca.sub.3(PO.sub.4).sub.2 - ++ - + +++ CaHPO.sub.4 - ++ - + +++
Ca-phytate - ++ - ++ +++ Na-phytate - ++ - ++ +++ Exopolysaccharide
++ - + - + N.sub.2-fixation + + - - + HCN production - - - + -
NH.sub.3 production + + + + + Siderophore +++ + + ++ +++ production
AHL - - - + - PHB - + - + + Acinetobacter sp. Paenibacillus sp.
Characteristics.sup..dagger. Micrococus sp. S2 Bacillus sp. S4
Pantoea sp. S6 S9 S10 P-solubilization (inorganic/organic P)
Ca.sub.3(PO.sub.4).sub.2 - - + - + CaHPO.sub.4 - - + - + Ca-phytate
- - + - + Na-phytate - - + - + Exopolysaccharide - - - - +
N.sub.2-fixation - - + - - HCN production - - - - - NH.sub.3
production + + + + + Siderophore n.d. - n.d. - + production AHL - -
+ - + PHB + - + - -
[0156] As shown above, the bacteria described herein exhibit
varying degrees of phosphate utilization. For example, strains
FF34, FB12, FD17, S6, and S10 were capable of hydrolyzing
Ca.sub.3(PO.sub.4).sub.2, CaHPO.sub.4, Ca-phytate and Na-phytate.
These strains, therefore, may be effective for increasing phosphate
availability for host plants under conditions of limiting
concentrations of soluble phosphate in the soil.
[0157] Siderophores are small, high-affinity iron chelating
compounds secreted by microorganisms such as bacteria, fungi and
grasses. siderophores. They bind to the available form of iron
Fe.sup.3 in the rhizosphere, thus making it unavailable to the
phytopathogens and protecting the plant health (Ahmad et al. 2008,
Microbiol Res 163:173-181, incorporated herein by reference).
Siderophores are known for mobilizing Fe and making it available to
the plant. Several of the strains, including FA13, FF34, FC42,
FB12, FD17 and S10 were found to produce significant levels of
siderophore when tested in agar medium containing Chrom azurol S
(CAS). Therefore, in one embodiment, the strains described above
are effective in increasing iron availability to the host
plant.
[0158] The ability of bacterial strains to utilize or metabolize
different nitrogen sources was evaluated. Interestingly, four of
the strains tested (FA13, FF34, FD17, and S6) were capable of
growing in nitrogen-free medium, demonstrating their ability to fix
nitrogen. Therefore, in one embodiment, these strains can be
provided in an amount effective to increase nitrogen utilization in
a host plant.
[0159] Bacterial survival and colonization in the plant environment
are necessary for plant growth and yield. Recently, Z niga and
colleagues (2013), Mol Plant-Microbe Interact 26:546-553
(incorporated herein by reference) described that the cell-to-cell
communication (QS) system mediated by AHL is implicated in
rhizosphere competence and colonization of Arabidopsis thaliana by
B. phytofirmans PsJN. Motility, aggregate stability, and biofilm
formation are important traits for root surface colonization
(Danhorn and Fuqua 2007, Annu Rev Microbiol 61:401-422,
incorporated herein by reference). Three strains (FB12, S6 and S10)
were found to produce AHL. It should be noted, however, that the
bacteria described here may have other communication systems.
Aggregation and biofilm formation were common traits in all tested
strains. In the case of motility, six strains (FA13, FF34, FB12,
FD17, S6 and S10) were positive for swimming, while FD17, S6 and
S10 also showed swarming. Therefore, in one embodiment, the seeds
are provided with an amount of these strains in an amount effective
to produce detectable levels of AHL. In another embodiment, seeds
of an agricultural plant are provided with an amount of the
bacterial endophyte population effective to form biofilms.
[0160] Bacteria were tested for production of exopolysaccharide
(EPS) and poly-hydroxybutyrate (PHB). Bacterial EPS and PHB have
been shown to provide protection from such environmental insults as
desiccation, predation, and the effects of antibiotics (Gasser et
al. 2009, FEMS Microbiol Ecol 70:142-150; Staudt et al. 2012, Arch
Microbiol 194:197-206, each of which is incorporated by reference).
They can also contribute to bacterial aggregation, surface
attachment, and plant--microbe symbiosis (Laus et al. 2005, Mol
Plant-Microbe Interact 18:533-538, incorporated herein by
reference). Five strains (FF34, FB12, FD17, S2 and S6) showed PHB
production, while FA13, FC42, FD17 and S10 were found to produce
EPS. Therefore, in another embodiment, seeds of an agricultural
plant are provided with an amount of the bacterial endophyte
population effective to improve desiccation tolerance in the host
plant.
[0161] Volatile compounds such as ammonia and HCN produced by a
number of rhizobacteria were reported to play an important role in
biocontrol (Brimecombe et al. 2001, In: Pinton R, Varanini Z,
Nannipieri P (Eds.) The Rhizosphere, Marcel Dekker, New York, pp
95-140, incorporated herein by reference). Production of ammonia
was commonly detected in all selected isolates. In contrast, only
Pseudomonas sp. strain FB12 was able to produce HCN. Among the
strains tested, only FB12 was able to produce HCN.
Enzyme Hydrolyzing Activities
[0162] Bacterial hydrolyzing activities due to amylase, cellulase,
chitinase, hemolytic, lipase, pectinase, protease and xylanase were
screened on diagnostic plates after incubation at 28.degree. C.
Amylase activity was determined on agar plates following the
protocol Mannisto and Haggblom (2006), Syst Appl Microbiol
29:229-243, incorporated herein by reference. Formation of opaque
halo around colonies was used as an indication of lipase activity.
Cellulase and xylanase activities were assayed on plates containing
(per liter) 5 g of carboxymethyl cellulose or birch wood xylan, 1 g
of peptone and 1 g of yeast extract. After 10 days of incubation,
the plates were flooded with gram's iodine staining and washing
with 1M NaCl to visualize the halo zone around the bacterial growth
(modified from Teather and Wood 1982, Appl Environ Microbiol
43:777-780, incorporated herein by reference). Chitinase activity
of the isolates was determined as zones of clearing around colonies
following the method of Chemin et al. (1998) J Bacteriol
180:4435-4441 (incorporated herein by rereference). Hemolytic
activity was determined by streaking bacterial isolates onto
Cloumbia 5% sheep blood agar plates. Protease activity was
determined using 1% skimmed milk agar plates, while lipase activity
was determined on peptone agar medium. Formation of halo zone
around colonies was used as indication of activity (Smibert and
Krieg 1994, In: Gerhardt P, Murray R, Wood W, Krieg N (Eds) Methods
for General and Molecular Bacteriology, ASM Press, Washington, DC,
pp 615-640, incorporated herein by reference). Pectinase activity
was determined on nutrient agar supplemented with 5 g L.sup.-1
pectin. After 1 week of incubation, plates were flooded with 2%
hexadecyl trimethyl ammonium bromide solution for 30 min. The
plates were washed with 1M NaCl to visualize the halo zone around
the bacterial growth (Mateos et al. 1992, Appl Environ Microbiol
58:1816-1822, incorporated herein by reference).
TABLE-US-00005 TABLE 5 Enzyme Activities from Endophytic Bacteria
Characteristics Agrobacterium sp. (FA13) Pantoea sp. (FF34)
Sphinogobium sp. (FC42) Pseudomonas sp. (FB12) Enterobacter sp.
(FD17) Enzyme hydrolyzing activity.sup..dagger-dbl. Amylase - - - -
- Cellulase + - + + ++ Chitinase - - - + + Hemolytic + + - + +
Lipase ++ + + +++ ++ Pectinase - + - + + Phosphatase - ++ - ++ +++
Protease - - - - - Xylanase + - +++ + ++ Characteristics Micrococus
sp. S2 Bacillus sp. S4 Pantoea sp. S6 Acinetobacter sp. S9
Paenibacillus sp. S10 Enzyme hydrolyzing activity.sup..dagger-dbl.
Amylase - - - - + Cellulase + + - - + Chitinase - + - - - Hemolytic
n.d. n.d. n.d. n.d. n.d. Lipase - + + + + Pectinase - - + - +
Phosphatase - - + - + Protease + + - - - Xylanase + + + - +
[0163] All strains showed lipase activity, while only S10 produced
amylase activity. S2 and S4 produced significant protease activity.
Pectinase and phosphatase activity was observed with strains FF34,
FB12, FD17, S6 and S10. All strains were positive for cellulase
and/or xylanase except strains FF34 and S9. Chitinase was produced
by FB12, FD17 and S4 strains, while all strains tested except for
FC42 showed hemolytic activity.
Antagonistic Activities Against Plant Pathogenic Bacteria, Fungi
and Oomycetes
[0164] The antagonistic activities of bacterial isolates were
screened against plant pathogenic bacteria (Agrobacterium
tumefaciens, Pseudomonas syringae, Streptococcus pneumoniae), fungi
(Fusarium caulimons, Fusarium graminarium, Fusarium oxysporum,
Fusarium solani, Rhizoctonia solani, Thielaviopsis basicola) and
oomycetes (Phytophthora infestans, Phytophthora citricola,
Phytophthora cominarum). For antibacterial assays, the bacterial
isolates and pathogen were cultivated in tryptic soy broth at
30.degree. C. for 24 h. The bacterial isolates were spot-inoculated
(10 .mu.L aliquots) on TSA plates pre-seeded with 100 .mu.L tested
pathogen. The plates were incubated at 28.degree. C. for 48 h and
clear zones of inhibition were recorded.
[0165] Antagonistic activity of the bacterial isolates against
fungi and oomycetes was tasted by the dual culture technique on
potato dextrose agar (PDA) and yeast malt agar (YMA) media (Dennis
and Webster 1971, Trans Brit Mycol Soc 57:25-39, incorporated
herein by reference). A small disk (5 mm) of target
fungus/oomycetes was placed in the center of petri dishes of both
media. Aliquots of 10 .mu.L of overnight bacterial cultures grown
in tryptic soy broth were spotted 2 cm away from the center. Plates
were incubated for 14 days at 24.degree. C. and zones of inhibition
were scored.
TABLE-US-00006 TABLE 6 Antimicrobial Activity by Endophytic
Bacteria Characteristics Agrobacterium sp. (FA13) Pantoea sp.
(FF34) Sphinogobium sp. (FC42) Pseudomonas sp. (FB12) Enterobacter
sp. (FD17) Anti-bacterial activity A. tumefaciens - - - ++ + E.
Coli n.d. n.d. n.d. n.d. n.d. P. syringae - - - +++ + S. aureus - -
- + - Anti-fungal activity F. caulimons ++ + + ++ +++ F.
graminarium + + + + ++ F. oxysporum + ++ + ++ ++ F. solani ++ + ++
++ +++ R. solani + + + ++ ++ T. basicola + + + ++ + Anti-oomycete
activity P. infestans + + + ++ ++ P. citricola + + + ++ +++ P.
cominarum + + + ++ ++ Characteristics Micrococus sp. S2 Bacillus
sp. S4 Pantoea sp. S6 Acinetobacter sp. S9 Paenibacillus sp. S10
Anti-bacterial activity A. tumefaciens - + - - + E. Coli + + - - +
P. syringae - + - - + S. aureus + + + + + Anti-fungal activity F.
caulimons - + + - + F. graminarium - - + + + F. oxysporum + + + - -
F. solani - + - - + R. solani + + + + + T. basicola - + + - +
Anti-oomycete activity P. infestans - - + - - P. citricola - - + +
+ P. cominarum - + + + +
Auxin, Acetoin, and Siderophore Assays for S4, S9 and S10
[0166] For the auxin assay, 1 .mu.l of overnight-grown cultures of
endophytic bacterial strains were inoculated into 750 .mu.l of R2A
broth supplemented with L-TRP (5 mM) in 2-mL 96 well culture
plates. The plates were sealed with a breathable membrane and
incubated at 23 C. with constant shaking at 200 rpm for 4 days.
After 4 days, 100 .mu.L of each culture was transferred to a 96
well plate. 25 .mu.L of Salkowski reagent (1 mL of FeC13 0.5 M
solution to 50 mL of 35% HC104) was added into each well and the
plates were incubated in the dark for 30 minutes before taking
picture and measuring 540 nm obsorption using the SpectraMax M5
plate reader (Molecular Devices).
[0167] For acetoin measurements, microbial strains were cultured as
described above in R2A broth supplemented with 5% glucose. After 4
days, 100 .mu.L of each culture was transferred to a 96 well plate
and mixed with 25 .mu.L Barritt's Reagents (See Example 3) and 525
nm absorption was measured.
[0168] For siderophore measurements, microbial strains were
cultured as described above in R2A broth. After 3 days of
incubation at 28.degree. C. without shaking, to each well was added
100 ul of 0-CAS preparation without gelling agent [Perez-Miranda et
al. (2007), J Microbiol Methods 70: 127-131, incorporated herein by
reference]. Again using the cleaned glassware, 1 liter of 0-CAS
overlay was made by mixing 60.5 mg of Chrome azurol S (CAS), 72.9
mg of hexadecyltrimethyl ammonium bromide (HDTMA), 30.24 g of
finely crushed Piperazine-1,4-bis-2-ethanesulfonic acid (PIPES)
with 10 ml of 1 mM FeC13.6H2O in 10 mM HCl solvent. The PIPES had
to be finely powdered and mixed gently with stirring (not shaking)
to avoid producing bubbles, until a dark blue colour was achieved.
15 minutes after adding the reagent to each well, color change was
scored by looking for purple halos (catechol type siderophores) or
orange colonies (hydroxamate siderophores) relative to the deep
blue of the O-Cas.
[0169] The results of the auxin, acetoin and siderophore assays are
presented in Table 7.
TABLE-US-00007 TABLE 7 Production of auxin, acetoin and siderophore
by endophytic bacteria S4 S9 S10 auxin ++ ++ + acetoin - - +++
siderophore ++ ++ +++
Substrate use by endophytic bacteria S4, S9 and S10
[0170] In addition to determining whether the bacterial strains
produce auxin, acetoin, and siderophores, the ability of the
various strains to grow on various substrates was determined.
Liquid cultures of bacteria were first sonicated to achieve
homogeneity. 1 mL culture of each strain was harvested by
centrifugation for 10 minutes at 4500 RPM and subsequently washed
three times with sterile distilled water to remove any traces of
residual media. Bacterial samples were resuspended in sterile
distilled water to a final OD590 of 0.2. Measurements of absorbance
were taken using a SpectraMax M microplate reader (Molecular
Devices, Sunnyvale, Calif.).
[0171] Sole carbon substrate assays were done using BIOLOG
Phenotype MicroArray (PM) 1 and 2A MicroPlates (Hayward, Calif.).
An aliquot of each bacterial cell culture (2.32 mL) were inoculated
into 20 mL sterile IF-0a GN/GP Base inoculating fluid (IF-0), 0.24
mL 100.times.Dye F obtained from BIOLOG, and brought to a final
volume of 24 mL with sterile distilled water. Negative control PM1
and PM2A assays were also made similarly minus bacterial cells to
detect abiotic reactions. An aliquot of fungal culture (0.05 mL) of
each strain were inoculated into 23.95 mL FF-IF medium obtained
from BIOLOG. Bacterial cell suspensions were stirred in order to
achieve uniformity. One hundred microliters of the bacterial cell
suspension was added per well using a multichannel pipettor to the
96-well BIOLOG PM1 and PM2A MicroPlates that each contained 95
carbon sources and one water-only (negative control) well.
[0172] MicroPlates were sealed in paper surgical tape (Dynarex,
Orangeburg, N.Y.) to prevent plate edge effects, and incubated
stationary at 24.degree. C. in an enclosed container for 70 hours.
Absorbance at 590 nm was measured for all MicroPlates at the end of
the incubation period to determine carbon substrate utilization for
each strain and normalized relative to the negative control (water
only) well of each plate (Garland and Mills, 1991; Barua et al.,
2010; Siemens et al., 2012; Blumenstein et al., 2015). The
bacterial assays were also calibrated against the negative control
(no cells) PM1 and PM2A MicroPlates data to correct for any biases
introduced by media on the colorimetric analysis (Borglin et al.,
2012). Corrected absorbance values that were negative were
considered as zero for subsequent analysis (Garland and Mills,
1991; Blumenstein et al., 2015) and a threshold value of 0.1 and
above was used to indicate the ability of a particular bacterial
strain to use a given carbon substrate (Barua et al., 2010;
Blumenstein et al., 2015). Additionally, bacterial MicroPlates were
visually examined for the irreversible formation of violet color in
wells indicating the reduction of the tetrazolium redox dye to
formazan that result from cell respiration (Garland and Mills,
1991).
[0173] The results of these assays are shown in Tables 8 (BIOLOG
PM1 MicroPlates) and 9 (BIOLOG PM2A MicroPlates).
TABLE-US-00008 TABLE 8 Substrate utilization of certain endophytic
strains as determined by BIOLOG PM1 MicroPlates. substrate SYM260
SYM290 SYM292 D-Serine NO NO YES D-Glucose-6-Phosphate NO NO NO
L-Asparagine YES NO NO L-glutamine NO NO NO Glycyl-L-Aspartic acid
NO NO NO Glycyl-L-Glutamic acid YES NO NO Glycyl-L-Proline NO NO NO
L-Arabinose YES YES YES D-Sorbitol NO NO NO D-Galactonic
acid-.gamma.-lactone NO NO NO D-Aspartic acid NO NO NO m-Tartaric
acid NO NO NO Citric acid YES NO YES Tricarballylic acid NO NO NO
p-Hydroxy Phenyl acetic acid NO NO NO N-Acetyl-D-Glucosamine NO YES
YES Glycerol YES YES YES D-L-Malic acid YES YES YES D-Glucosaminic
acid NO NO NO D-Glucose-1-Phosphate NO NO NO m-Inositol YES NO YES
L-Serine YES NO NO m-Hydroxy Phenyl Acetic acid NO NO NO
D-Saccharic acid YES NO YES L-Fucose NO YES NO D-Ribose NO YES YES
1,2-Propanediol YES YES NO D-Fructose-6-Phosphate NO NO NO
D-Threonine NO YES NO L-Threonine YES YES NO Tyramine NO NO YES
Succinic acid NO NO NO D-Glucuronic acid NO NO NO Tween 20 YES YES
NO Tween 40 YES YES NO Tween 80 YES YES NO Fumaric acid YES YES YES
L-Alanine YES YES YES D-Psicose NO NO NO D-Galactose NO YES YES
D-Gluconic acid YES YES YES L-Rhamnose NO YES YES a-Keto-Glutaric
acid YES NO YES a-Hydroxy Glutaric acid-.gamma.-lactone YES NO NO
Bromo succinic acid YES NO YES L-Alanyl-Glycine YES YES YES
L-Lyxose NO NO NO L-Aspartic acid YES NO YES D-L-a-Glycerol
phosphate YES NO NO D-Fructose NO YES YES a-Keto-Butyric acid NO NO
NO a-Hydroxy Butyric acid YES YES NO Propionic acid YES YES YES
Acetoacetic acid YES YES YES Glucuronamide NO YES NO L-Proline YES
NO YES D-Xylose YES YES YES Acetic acid YES YES YES
a-Methyl-D-Galactoside NO YES YES .beta.-Methyl-D-glucoside YES YES
YES Mucic acid YES NO YES N-acetyl-.beta.-D-Mannosamine YES YES YES
Pyruvic acid YES YES YES D-Alanine NO YES NO L-Lactic acid YES NO
YES a-D-Glucose NO YES YES a-D-Lactose NO YES YES Adonitol NO NO NO
Glycolic acid YES NO NO Mono Methyl Succinate YES YES YES
L-Galactonic-acid-.gamma.-lactone YES YES YES D-Trehalose NO YES
YES Formic acid YES NO YES Maltose YES YES YES Lactulose NO YES YES
Maltotriose YES YES YES Glyoxylic acid YES NO YES Methyl Pyruvate
YES YES YES D-Galacturonic acid YES NO YES D-Mannose NO NO YES
D-Mannitol YES YES YES D-Melibiose NO YES YES Sucrose NO YES YES
2-Deoxy adenosine YES NO YES D-Cellobiose YES YES YES D-Malic acid
YES NO YES Phenylethyl-amine NO NO NO Dulcitol NO YES NO L-Glutamic
acid NO NO NO Thymidine YES YES YES Uridine YES YES YES Adenosine
YES YES YES Inosine NO NO YES L-Malic acid YES NO YES
TABLE-US-00009 TABLE 9 Substrate utilization of certain endophytic
strains as determined by BIOLOG PM2A MicroPlates. substrate SYM260
SYM290 SYM292 Negative control N/A N/A N/A N-acetyl-D-Galactosamine
NO NO NO Gentiobiose YES YES YES D-Raffinose YES YES YES Capric
acid NO NO NO D-lactic acid methyl ester NO NO NO Acetamide NO NO
NO L-Ornithine YES NO NO Chondrointin sulfate C YES NO NO
N-acetyl-neuraminic acid NO NO NO L-glucose NO NO NO Salicin YES
YES YES Caproic acid YES NO YES Malonic acid YES NO NO
L-Alaninamide NO YES NO L-Phenylalanine YES NO NO a-Cyclodextrin NO
YES YES .beta.-D-allose NO NO YES Lactitol NO YES YES
Sedoheptulosan NO NO NO Citraconic acid NO NO NO Melibionic acid
YES NO NO N-Acetyl-L-Glutamic acid YES NO YES L-Pyroglutamic acid
YES NO YES .beta.-Cyclodextrin NO YES YES Amygdalin NO YES YES
D-Melezitose NO YES YES L-Sorbose NO NO NO Citramalic acid YES NO
YES Oxalic acid NO NO NO L-Arginine YES NO NO L-Valine YES NO YES
.alpha.-Cyclodextrin NO YES YES D-arabinose NO YES YES Maltitol NO
YES YES Stachyose YES YES YES D-Glucosamine YES YES YES Oxalomalic
acid YES YES YES Glycine NO NO NO D,L-Carnitine NO NO NO Dextrin
YES YES YES D-arabitol NO NO YES a-Methyl-D-Glucoside NO YES YES
D-Tagatose NO YES NO 2-Hydroxy benzoic acid NO NO NO Quinic acid NO
NO NO L-Histidine YES YES NO Sec-Butylamine NO NO NO Gelatin YES
YES YES L-arabitol NO NO NO .beta.-Methyl-D-Galactoside NO YES YES
Turanose NO YES YES 4-Hydroxy benzoic acid NO NO NO
D-Ribono-1,4-Lactone NO NO NO L-Homoserine NO NO NO D,L-Octopamine
NO NO NO Glycogen YES YES YES Arbutin NO YES YES 3-Methyl Glucose
NO NO YES Xylitol NO NO YES .beta.-Hydroxy butyric acid YES NO NO
Sebacic acid YES NO NO Hydroxy-L-Proline YES NO YES Putrescine YES
NO NO Inulin YES YES YES 2-Deoxy-D-Ribose NO NO YES
.beta.-Methyl-D-Glucuronic acid NO NO YES N-Acetyl-D-glucosaminitol
NO NO NO .gamma.-Hydroxy butyric acid YES NO NO Sorbic acid NO NO
NO L-Isoleucine YES NO YES Dihydroxy acetone NO NO YES Laminarin NO
YES YES i-Erythritol NO NO NO a-Methyl-D-Mannoside NO NO NO
.gamma.-amino butyric acid YES NO NO a-Keto-valeric acid YES NO NO
Succinamic acid NO NO NO L-Leucine NO NO YES 2,3-Butanediol YES NO
NO Mannan NO NO NO D-Fucose NO NO NO .beta.-Methyl-D-Xyloside NO
YES YES d-amino valeric acid YES NO NO Itaconic acid YES NO YES
D-Tartaric acid NO NO NO L-Lysine YES NO NO 2,3-Butanone NO NO NO
Pectin NO YES YES 3-0-.beta.-D-Galactopyranosyl-D- NO NO YES
arabinose Palatinose NO YES YES Butyric acid YES NO NO
5-Keto-D-Gluconic acid NO NO NO L-Tartaric acid NO NO NO
L-Methionine NO NO NO
Example 2
Effect of Endophytic Strains on Maize Germination
[0174] Inoculants of the selected strains were prepared in 50 mL
tryptic soy broth in 100 mL Erlenmeyer flasks and incubated at
28.+-.2.degree. C. for 48 h in the orbital shaking incubator (VWR
International, GmbH) at 180 r min.sup.-1. The optical density of
the broth was adjusted to 0.5 measured at 600 nm using
spectrophotometer (Gene Quant Pro, Gemini BV, The Netherlands) to
obtain a uniform population of bacteria (10.sup.8-10.sup.9
colony-forming units (CFU) mL.sup.-1) in the broth at the time of
inoculation. More scientifically, harvested bacterial cells could
be resuspended in the phosphate buffered saline. The inoculum
density adjusts using a spectrophotometer to achieve population
density (Pillay and Nowak 1997, Can J Microbiol 43:354-361,
incorporated herein by reference).
[0175] Maize seeds were surface-sterilized with 70% ethanol (3
min), treated with 5% NaOHCl for 5 min, and followed by washing 3
times with sterile distilled water (1 min each time). The efficacy
of surface sterilization was checked by plating seed, and aliquots
of the final rinse onto LB plates. Samples were considered to be
successfully sterilized when no colonies were observed on the LB
plates after inoculation for 3 days at 28.degree. C.
Surface-disinfected seeds of different maize cultivars (Helmi,
Morignon, Pelicon, Peso and Cesor) were immersed in the bacterial
suspensions for 30 min. The bacterized seeds were deposited onto
soft water-agar plates (0.8%, w/v agar) and plates were placed in
the dark at room temperature (24.+-.2.degree. C.). After 96 hrs the
percentage of germinated seeds was scored. Surface-sterilized
seeds, but not bacterized (treated in tryptic soy broth), served as
the germination control.
[0176] Inoculation of maize seeds with endophytic bacteria
increased the germination rate of all cultivars by 20-40% compared
to the un-inoculated control. Maximum increase was observed by
inoculation with strain FD17 (40%) in maize cv. Morignon followed
by strains FF34, FA13, FB12 and FC42 (data not shown).
[0177] In other experiments, seeds of different cultivars of Maize
(Palazzo & die Samba), and Tomato (Red Pear and Gartenfreund)
were used to test for promotion of germination. The results,
provided below in Table 10, show that virtually all strains show a
marked increase in germination rates. For maize, Palazzo seeds
inoculated with the strains FA13, FF34, S2, S6, S9 and S10 show
greater than 90% germination after four days, as did die Samba
seeds inoculated with FF34 and S9 seeds. For tomato, Red Pear seeds
inoculated with the strains FB12, FF34, S6 and S10 showed 90% or
greater germination rate after 12 days.
TABLE-US-00010 TABLE 10 Germination rate of maize and tomato seeds
inoculated with endophytes Maize Germination Rate Tomato
Germination Rate (4 Days) (12 days) Maize Tomato Maize "die "Red
Tomato Strain "Palazzo" Samba" Pear" "Gartenfreund" Neg. 73.3%
73.3% 33.3% 50.0% control FA13 100.0% 86.7% 83.3% 60.0% FB12 83.3%
76.7% 96.7% 53.3% FC42 86.7% 86.7% 76.7% 80.0% FD17 76.7% 66.7%
43.3% 46.7% FF34 93.3% 93.3% 96.7% 50.0% S2 93.3% 70.0% 70.0% 60.0%
S4 70.0% 86.7% 76.7% 66.7% S6 90.0% 80.0% 100.0% 70.0% S9 96.7%
96.7% 60.0% 53.3% S10 93.3% 80.0% 90.0% 76.7%
Example 3
In vitro Screening of Efficient Strains on Maize Plants
[0178] A growth chamber experiment was conducted on maize to screen
the selected strains for their growth promoting activity under
gnotobiotic conditions. We used specially designed glass tubes with
beaded rim (Duran group, DURAN GmbH, Mainz, Germany) for the
experiment. The glass tubes were covered with lid to generate fully
axenic conditions (no exposure to any environmental factors).
Bacterial inoculant production and seed treatment were done as
described above. As control, seeds were treated with sterilized
tryptic soy broth. Treated seeds were placed onto water-agar plates
for germination. After 5 days, germinated seedlings (3-5 cm long)
were transferred in the sterilized glass tubes containing
sterilized 20 ml MS (Murashige and Skoog) medium (Duchefa
Biochemie, The Netherlands) (4.8 g L.sup.-1) and placed at
25.+-.2.degree. C. set at a 16 h light and 8 h dark period, with a
light intensity of 350 .mu.mol M.sup.-2 s.sup.-1. Data regarding
shoot/root length and biomass were recorded after 24 days.
Colonization of inoculant strains was scored by re-isolation of
endophytes. One g of plant shoot was homogenized with a pestle and
mortar in 4 ml of 0.9% (w/v) NaCl solution. The number of
cultivable endophytes in maize shoot, expressed in CFU per gram
(fresh weight), was determined by spreading serial dilution up to
10.sup.-4 (0.1 mL) of homogenized surface-sterilized plant material
onto TSA (DIFCO Laboratories, Detroit, Mich.) agar medium. Four
replicates for each treatment were spread on the agar plates and
incubated for 5 days at 28.degree. C. Twenty colonies per treatment
were randomly selected and their identity with the inoculant strain
was confirmed by restriction fragment length polymorphism (RFLP)
analysis of the 16S-23S rRNA intergenic spacer (IGS) region (Reiter
et al. 2001, Appl Environ Microbiol 68:2261-2268, incorporated
herein by reference).
[0179] All strains significantly increased the seedling growth
compared to the control. As shown in FIGS. 1A-1C, all strains
significantly promoted biomass production, with increases in both
root, shoot or overall biomass. Though responses were variable, the
strains generally increased root and shoot length in all three
cultivars of maize tested.
[0180] Next, colonization of plants was tested for all bacterial
strains. As shown in Table 11, strains FA13, FF34, FC42, FB12 and
FD17 successfully colonized corn plants, showing successful
colonization of the various strains, as detected in the shoot
tissue of various cultivars of maize. The amount of detectable
bacteria in the shoot tissue varied, ranging from
1.58.times.10.sup.4 in FB12-inoculated Helmi cultivar, to
1.83.times.10.sup.7 CFU found in Peso cultivars inoculated with
FF34. Therefore, the microbes described herein, when contacted with
seeds of plants, are capable of colonizing the plant as detectable,
in this case, in the shoot tissue. Furthermore, colonization of
Kolea, Mazurka and DaSilvie cultivars of maize by strains S2, S4,
S6, S9 and S10 was confirmed by isolating bacterial cells from
homogenates of surface sterilized shoot tissue of plants grown from
inoculated seeds on tryptic soy agar plates for two days on
28.degree. C. and testing the identity of colonies with IGS region
sequencing to confirm the presence of the microbe. S2, S4, S6, S9
and S10 strains were successfully recovered from the tissues of
these cultivars (data not shown).
TABLE-US-00011 TABLE 11 Colonization of Maize Plants by Endophytic
Bacteria Strains Helmi Peso Pelicon Morignon Cesor FA13 1.95
.times. 10.sup.5 1.16 .times. 10.sup.7 1.2 .times. 10.sup.4 1.21
.times. 10.sup.6 3.31 .times. 10.sup.6 FF34 2.66 .times. 10.sup.6
1.83 .times. 10.sup.7 1.21 .times. 10.sup.5 4.13 .times. 10.sup.6
9.1 .times. 10.sup.6 FC42 4.63 .times. 10.sup.5 1.37 .times.
10.sup.6 2.00 .times. 10.sup.4 8.24 .times. 10.sup.6 1.07 .times.
10.sup.5 FB12 1.58 .times. 10.sup.4 1.94 .times. 10.sup.7 1.12
.times. 10.sup.5 1.46 .times. 10.sup.6 9.38 .times. 10.sup.5 FD17
1.92 .times. 10.sup.6 2.60 .times. 10.sup.7 1.44 .times. 10.sup.7
2.93 .times. 10.sup.7 1.73 .times. 10.sup.6
Stomatal Conductance and Photosynthesis Rates
[0181] Maize plants inoculated with the strains described herein
were tested for photosynthesis and stomatal conductance. As shown
in FIG. 2, maize plants inoculated with the strains display an
increase in stomatal conductance when compared with uninoculated
controls (ranging from a 36% to 49% increase), with S2, S6, S9
strains displaying the highest level of conductance. Therefore,
there is an appreciable increase in stomatal conductance conferred
by the bacterial of the present invention.
[0182] Strain-inoculated maize plants were also tested for
photosynthetic rates. As shown in FIG. 3, all strains conferred
increased photosynthesis rates when compared with control plants in
all three maize cultivars tested (DaSilvie, Mazurka, and Kolea
cultivars; average of three cultivars shown), with an increase
ranging from 17% over controls (for S9 and S10 strains) to over 23%
over controls (S6 strain). Therefore, the endophytic bacterial
strains described above confer increased photosynthesis rates on
the host plants.
Example 4
Net-House Experiment
[0183] On the basis of the results from tests performed under
axenic conditions in Example 3, strain FD17 was selected for
further evaluation in a pot trial, in which plants were grown in
large containers exposed to natural environmental conditions.
[0184] Maize plants were grown in soil collected from agricultural
(maize) fields in Fischamend, Lower Austria, Austria. The soil was
silty clay loam and had the following characteristics: 12% sand,
61% silt, 27% clay, pH 6.5, 3.3% total carbon, 0.18% total
nitrogen, 0.13 mg g.sup.-1 available phosphorus, 0.066 mg g.sup.-1
extractable potassium.
[0185] Surface-disinfected seeds of two maize cultivars (Morignon
and Peso) were immersed in bacterial suspension (prepared as
described above) for 1 h. For the un-inoculated control, seeds were
treated with sterilized tryptic soy broth. Seeds were sown in a
plastic tray (wiped with ethanol) and 12 days old seedlings were
transferred into containers filled with 45 kg soil (2 plants in
each container) and placed in a net-house and exposed to natural
environmental conditions.
[0186] Weather conditions i.e. precipitation, temperature and
relative humidity were recorded by `Zentralanstalt fur Meteorologie
and Geodynamik` (ZAMG) during the crop growth period and described
in FIGS. 1A-1C. There were three replicates and the pots were
arranged in a completely randomized design. Recommended dose of NPK
fertilizers (160-100-60 kg ha.sup.-1) were applied in each
container and tap water was applied to the container for irrigation
whenever needed.
[0187] Data of photochemical efficiency of PSII was recorded at
flowering stage using handy PEA (Hansatech Instruments Ltd.
England) in the mid of July where day time temperature varied from
30-35.degree. C. The PSII efficiency in terms of F.sub.v/F.sub.m
was calculated from the data. Growth and yield contributing
parameters were recorded at maturity. The plants were harvested 140
days after planting. FIG. 4 shows the PS II efficiency of maize
plants inoculated with the bacterial endophyte populations
described herein.
[0188] Maize plants inoculated with the bacterial endophytes S2,
S4, S6, S9, S10 and FD17 were tested for increased leaf area. As
shown in FIG. 5, and in Table 12, all the tested strains increased
the leaf area significantly over the controls.
[0189] Similarly, maize plants inoculated with the strains showed a
dramatic increase in chlorophyll content (FIG. 6) over control
plants, with the highest levels found in S6 inoculated plants.
[0190] Table 12 below shows the effect of FD17 inoculation on the
physiology, growth parameters and yield of two maize cultivars
grown in field soil and exposed to natural climatic conditions.
Inoculation with strain FD17 led to a significant increase in leaf
area of both cultivars (20% and 13%, respectively). Similarly,
biomass (leaf dry weight) was increased by 27% and 23% in the
cultivars Peso and Morignon, respectively, as compared to the
control. In addition, root and plant dry biomass and plant height
were significantly enhanced, as was the average cob weight (35% and
42% increase in Peso and Morignon, respectively, as compared to
control). The FD17 strain also significantly affected other plant
physiological characteristics: for example, there was a significant
increase in chlorophyll fluorescence (up to a 9% in the Peso
cultivar) and a shortened time before onset of flowering (up to 10
days in cultivar Peso).
TABLE-US-00012 TABLE 12 Effect of inoculation with endophytic
strain FD17 on physiology, growth parameters and yield of two maize
cultivars grown in pots in field soil and exposed to natural
climatic conditions (net house experiment) Treatment Peso Morignon
Un- Inoculated Un- Inoculated Parameters inoculated with FD17
inoculated with FD17 Fv/Fm 0.69 0.75 0.73 0.79 Time to onset of
65.33 55 70.67 66.33 flowering (days) Plant height (cm) 192.33 208
196.69 213.68 No. of leaves plant 12.33 14 13.17 14.67 Leaf area
(cm.sup.2) 494.26 556.27 512.39 617.11 Leaf dry weight (g) 22.21
28.16 28.09 34.56 Plant dry biomass (g) 114.18 153.77 160.46 223.14
Root dry biomass (g) 17.26 24.34 19.73 28.28 Cob weight (g) 115.28
155.83 123.71 176.23
[0191] Rhizosphere and endophytic colonization of roots, stems and
leaves by the inoculant strain were determined by plate counting
using TSA plates. Root, stem and leave samples were washed, surface
sterilized (as described above) and used for inoculant strain
recovery (colonization). For this, samples were crushed in 0.9%
(w/v) NaCl solution, shaked with a pulsifier (Microgen Bioproducts
Ltd., UK) for 30 sec and different dilutions were spread on TSA
plates. Bacterial colonies were counted after 4 days of incubation
at 28.+-.2.degree. C. The selected colonies were identified and
confirmed by IGS region-based RFLP analysis.
[0192] The ability of strain FD17 to colonize various tissues of
the host plant, as well as the rhizosphere surrounding the plant,
was examined. As shown in Table 13 below, seeds of two different
maize cultivars inoculated with the FD17 strain resulted in
effective, detectable colonization in the root, shoot and leaf
interior. Therefore, the seeds were treated with an amount of the
endophytic bacterium that is sufficient to colonize the leaf, root,
and shoot tissues. Surprisingly, the rhizosphere also had
significant levels of detectable FD17. This suggests that the
beneficial effects of endophytic bacterial strains such as FD17
could be exerting effects externally to the plant. As described
elsewhere, the bacteria described herein are capable of producing
compounds which allow increased availability of limiting nutrients
such as phosphate and iron. The strains could be present on the
surface of the seeds in an amount sufficient to efficiently
colonize the plant, but also the surrounding rhizosphere. The
presence of significant amounts of detectable bacteria in the
rhizosphere raises the interesting possibility that the seeds can
be treated with the microbes either on its surface or inside the
seed in an amount sufficient to alter the rhizosphere of the plant,
thereby altering the soil around the plant, and rendering it more
hospitable for the plant.
TABLE-US-00013 TABLE 13 Colonization of strain FD17 in rhizosphere
root, stem and leaves of two maize cultivars (wire-house
experiment) Plant compartment Rhizosphere Root interior Shoot
interior Leaf interior (cfu g.sup.-1 (cfu g.sup.-1 (cfu g.sup.-1
(cfu g.sup.-1 Maize cv. dry wt) dry wt) dry wt) dry wt) Peso 4.07
.times. 10.sup.4 3.39 .times. 10.sup.4 1.63 .times. 10.sup.3 1.16
.times. 10.sup.2 Morignon 9.85 .times. 10.sup.4 8.59 .times.
10.sup.4 3.72 .times. 10.sup.3 6.23 .times. 10.sup.2
Statistical Analyses
[0193] The data of plant growth parameters and colonization were
subjected to analyses of variance. The means were compared by Least
Significant Difference (LSD) test (p<0.05) to detect statistical
significance among treatment (Steel et al. 1997, Principles and
procedures of statistics: A biometrical approach. 3rd ed.
McGraw-Hill Book Int. Co., Singapore, incorporated herein by
reference). All of the statistical analyses were conducted using
SPSS software version 19 (IBM SPSS Statistics 19, USA).
Example 5
Field Trials in Austria
Methods:
[0194] Four varieties of maize were grown at two locations in
Austria. Six replicate plots were sown for each treatment and
variety combination. Control plots were planted with formulation
treated seeds (20 mM phosphate buffer pH 7, 3% sucrose, 1% sodium
alginate).
[0195] Seeds were sown in a rainfed field in plots arranged in a
randomized complete block design. Leaf color was visually assessed
at one of the two locations and ranked from 1-3 light green to dark
green. Both male and female flowering was visually rated from 0-2
(0=not visible, 1=flower visible, 2=fully developed flower). Corn
was hand harvested over 4 m of interior rows. Kernel weight per and
kernel moisture per plot were recorded as well as the number of
ears harvested per plot. Yield was calculated as kernel weight per
plot divided by the number of ears harvested and adjusted for
moisture content to a storage moisture of 14% (i.e. dry kernel
weight per ear in g).
[0196] Results: As shown in Table 14, no treatment related
differences were evident for seedling emergence, LAI, color, height
and female flower development. A slight increase in male flower
development was recorded. No treatment related differences were
evident for yield measured as dry kernels per ear in g.
TABLE-US-00014 TABLE 14 Rainfed trials in Austria. Field trial
metrics aggregated over both locations and all varieties. Units:
Color (ratings scale 1-3), Flowering (ratings scale, 0 = not
visible, 1 = flower visible, 2 = fully developed flower), yield
(dry kernels per ear in g) Male Female Treatment Color Flower
Flower Yield Formulation 1.79 1.47 1.14 155.46 control S2 1.95 1.54
1.12 153.83 S6 1.79 1.52 1.06 155.17 S9 1.95 1.61 1.04 155.49 S10
1.87 1.52 1.14 153.29 FD17 1.83 1.5 1.02 151.76
Example 6
Field Trials in the US on Maize
Methods:
[0197] Two varieties of maize were grown at one location in the
United States in an irrigated trial. Six replicate plots were sown
for each treatment and variety combination. Control plots were
planted for formulation treated seeds (20 mM phosphate buffer pH 7,
3% sucrose, 1% sodium alginate).
[0198] Seeds were sown in an irrigated field in plots of 10 by 40
ft arranged in a randomized complete block design with a JD 7100
cone seeder and box seeder planters respectively. Four rows were
planted per plot with a row spacing of 30 inches. Seeding density
at was 35,000 seeds per acre. The interior 2 rows were harvested by
combine and 10 individual ears were hand harvested from exterior
rows. Grain yield per plot, grain moisture, and test weight were
assessed. Yield was adjusted for grain moisture content to a
storage moisture of 14% (i.e. dry bushels per acre for combine
harvest and dry kernels per ear in g for hand harvest).
[0199] Results:
[0200] As shown in Table 15, S4, S10, FD17 showed positive impacts
on hand harvest yield of up to 10 g per ear. None of the treatments
showed a difference when harvested by combine.
TABLE-US-00015 TABLE 15 Field trial metrics aggregated over both
varieties. Units: Hand harvest yield (dry kernels per ear in g),
Combine yield (dry bushels per acre). Hand harvest Combine
Treatment yield yield Formulation 106.58 104.66 control S2 101.40
95.79 S4 116.04 99.29 S6 101.68 104.58 S9 109.16 104.30 S10 113.34
95.28 FD17 113.99 101.40
Example 7
Field Trials in the US on Spring Wheat
Methods:
[0201] One variety of spring wheat were grown at one location in
the United States. Six replicate plots were sown for each treatment
and variety combination. Control plots were planted for formulation
treated seeds (20 mM phosphate buffer pH 7, 3% sucrose, 1% sodium
alginate).
[0202] Seeds were sown with a great plains drill in either
irrigated or rainfed field in plots of 10 by 40 ft arranged in a
randomized complete block design. 7 rows were planted per plot with
a row spacing of 17 inches and a seeding density was 60 pounds per
acre for rainfed. Wheat was harvested by combine over the entire
plot area. Grain yield per plot, grain moisture, and test weight
were assessed. Yield was adjusted for grain moisture content to a
storage moisture of 13% (i.e. dry bushels per acre).
[0203] Results: The combine yield results are shown in Table 16.
S6, S10 and S4 showed slight positive trends up to 2 bushels per
acre, while S9 showed a statistically significant yield increase of
2 bushels per acre or 4 bushels per acre compared to the
formulation controls respectively.
TABLE-US-00016 TABLE 16 Units: Combine yield (dry bushels per
acre). Treatment Yield Formulation 40.64 control S2 39.99 S4 41.10
S6 41.23 S9 42.76* S10 41.07 FD17 38.63
Example 8
Field Trials in Argentina on Maize
Methods:
[0204] Two varieties of maize were grown at one location in
Argentina. Ten replicate plots were sown for each treatment and
variety combination. Control plots were planted for formulation
treated seeds (20 mM phosphate buffer pH 7, 3% sucrose, 1% sodium
alginate).
[0205] Seeds were sown with a cone planter in a drip irrigated
field. The field was located in an extremely arid environment and
received irrigation targeted at 80% of evapotranspiration in order
to create a managed water stress environment designed to reduce
yield by around 20%. Plots were 5.times.3 m in size and arranged in
rectangular blocks in a randomized complete block design. Four rows
were planted per plot with a row spacing of 70 cm and an in-row
seed spacing of 15 cm. Above and belowground biomass were assessed
for 10 plants per plot one month after sowing. The date at which
50% of the plants per plot reached flowering was visually assessed.
The interior two rows were harvested by combine. Grain yield per
plot, grain moisture and test weight were assessed. Yield was
adjusted for grain moisture content to a storage moisture of 14%
(i.e. dry bushels per acre).
[0206] Results:
[0207] In this trial with moderate water stress, S4 and S9 showed a
positive impact on aboveground biomass up to 30 g compared to the
formulation control (Table 17). S4 showed a positive increase in
belowground biomass compared to the formulation control up to 6 g.
S4, S9 and S10 showed a positive increase in yield compared to the
formulation controls of up to 19 bushels per acre.
TABLE-US-00017 TABLE 17 Managed moderate water stress trial. Units:
Biomass (g), Combine yield (dry bushels per acre). Aboveground
Belowground Treatment biomass biomass Yield Formulation 477.90
55.62 152.38 control S4 503.60 61.23 163.80 S9 486.20 56.24 171.19*
S10 466.70 57.25 163.89
Sequence CWU 1
1
1011355DNAAgrobacterium sp. 1atagcagtcg acgccccgca ggggagtggc
agacgggtga gtaacgcgtg ggaacatacc 60ctttcctgcg gaatagctcc gggaaactgg
aattaatacc gcatacgccc tacgggggaa 120agatttatcg gggaaggatt
ggcccgcgtt ggattagcta gttggtgggg taaaggccta 180ccaaggcgac
gatccatagc tggtctgaga ggatgatcag ccacattggg actgagacac
240ggcccaaact cctacgggag gcagcagtgg ggaatattgg acaatgggcg
caagcctgat 300ccagccatgc cgcgtgagtg atgaaggcct tagggttgta
aagctctttc accggagaag 360ataatgacgg tatccggaga agaagccccg
gctaacttcg tgccagcagc cgcggtaata 420cgaagggggc tagcgttgtt
cggaattact gggcgtaaag cgcacgtagg cggatattta 480agtcaggggt
gaaatcccag agctcaactc tggaactgcc tttgatactg ggtatcttga
540gtatggaaga ggtaagtgga attccgagtg tagaggtgaa attcgtagat
attcggagga 600acaccagtgg cgaaggcggc ttactggtcc attactgacg
ctgaggtgcg aaagcgtggg 660gagcaaacag gattagatac cctggtagtc
cacgccgtaa acgatgaatg ttagccgtcg 720ggcagtatac tgttcggtgg
cgcagctaac gcattaaaca ttccgcctgg ggagtacggt 780cgcaagatta
aaactcaaag gaattgacgg gggcccgcac aagcggtgga gcatgtggtt
840taattcgaag caacgcgcag aaccttacca gctcttgaca ttcggggttt
gggcagtgga 900gacattgtcc ttcagttagg ctgggcccag aacaggtgct
gcatggctgt cgtcagctcg 960tgtcgtgaga tgttgggtta agtcccgcaa
cgagcgcaac cctcgccctt agttgccagc 1020atttagttgg gcactctaag
gggactgccg gtgataagcc gagaggaagg tggggatgac 1080gtcaagtcct
catggccctt acgggctggg ctacacacgt gctacaatgg tggtgacagt
1140gggcagcgag acagcgatgt cgagctaatc tccaaaagcc atctcagttc
ggattgcact 1200ctgcaactcg agtgcatgaa gttggaatcg ctagtaatcg
cagatcagca tgctgcggtg 1260aatacgttcc cgggccttgt acacaccgcc
cgtcacacca tgggagttgg ttttacccga 1320aggtagtgcg ctaaccgcaa
ggaggcagct atcca 135521388DNAPantoea sp. 2ccatgcagtc ggacggtagc
acagataagc ttgctccttg ggtgacgagt ggcggacggg 60tgagtaatgt ctggggatct
gcccgataga gggggataac cactggaaac ggtggctaat 120accgcataac
gtcgcaagac caaagagggg gaccttcggg cctctcacta tcggatgaac
180ccatatggga ttatctagta ggcggggtaa tggcccacct aggcgacgat
ccctagctgg 240tctgagagga tgaccagcca cactggaact gagacacggt
ccagactcct acgggaggca 300gcagtgggga atattgcaca atgggcgcaa
gcctgatgca cccatgccgc gtgtatgaag 360aaggccttcg ggttgtaaag
tactttcagc ggggaggaag gcgacggggt taataaccct 420gtcgattgac
gttacccgca gaagacgcac cggctaactc cgtgccagca gccgcggtaa
480tacggagggt gcaagcgtta atcggaatta ctgggcgtaa agcgcacgca
ggcggtctgt 540taagtcacat gtgaaatccc ccgggcttaa cctgggaact
gcatttgaaa ctggcaggct 600tgagtcttgt agaggggggt agaattcctg
gtgtagcggt gaaatgcgta gagatctgga 660cgaataccgg tggcgatcgc
ggccccctgg acaaagactg acgctcacgt gcgaaagcgt 720ggggagcaaa
ctcgattaca taccctggta gtccacgccg taaacgatgt cgacttggag
780gttgttccct tgaggagtgg cttccggagc taacgcgtta agtcgaccgc
ctggggagta 840cggccgcaag gttaaaactc aaatgaattg acgggggccc
gcacaagcgg tggagcatgt 900ggtttaattc gatgcaacgc gaagaacctt
acctactctt gacatccagc gaatttagca 960gagatgcttt ggtgccttcg
ggaacgctga gacaggtgct gcatggctgt cgtcagctcg 1020tgttgtgaaa
tgttgggtta agtcccgcaa cgagcgcaac ccttatcctt tgttgccagc
1080gattcggtcg ggaactcaaa ggagactgcc ggtgataaac cggaggaagg
tggggatgac 1140gtcaagtcat catggccctt acgagtaggg ctacacacgt
gctacaatgg cgcatacaaa 1200gagaagcgac ctcgcgagag caagcggacc
tcacaaagtg cgtcgtagtc cggatcggag 1260tctgcaactc gactccgtga
agtcggaatc gctagtaatc gtggatcaga atgccacggt 1320gaatacgttc
ccgggccttg tacacaccgc ccgtcacacc atgggagtgg gttgcaaaag 1380aagtagtt
138831313DNASphingomonas sp. 3catgcagtcg acgagccttt cggggctagt
ggcgcacggg tgcgtaacgc gtgggaatct 60gcccttgggt tcggaataac gtcgggaaac
tgacgctaat accggatgat gacgtaagtc 120caaagattta tcgcccaggg
atgagcccgc gtaggattag ctagttggtg aggtaaaggc 180tcaccaaggc
gacgatcctt agctggtctg agaggatgat cagccacact gggactgaga
240cacggcccag actcctacgg gaggcagcag tagggaatat tggacaatgg
gggcaaccct 300gatccagcaa tgccgcgtga gtgatgaagg ccttagggtt
gtaaagctct tttacccggg 360atgataatga atacggaggg ggctagcgtt
gttcggaatt actgggcgta aagcgcacgt 420aggcggcgat ttaagtcaga
ggtgaaagcc cggggctcaa cccccggaat agcctttgag 480actggattgc
ttgaacatcg gagaggtgag tggaattccg agtgtagagg tgaaatttcg
540tagatattcg gaagaacacc agtggcgaag gcggctcact ggacgattgt
tgacgctgag 600gtgcgaaagc gtggggagca aacaggatta gatacccctg
gtagtccacg ccgtaaacga 660tgataactag ctgctggggc tcatggagtt
tcggtggcgc agctaacgca ttaagttatc 720cgcctgggga gtacggtcgc
aagattaaaa ctcaaaggaa ttgacggggg cctgcacaag 780cggtggagca
tgtggtttaa ttcgaagcaa cgcgcagaac cttaccaacg tttgacatcc
840ctatcgcgga tcgtggagac actttccttc agttcggctg gataggtgac
aggtgctgca 900tggctgtcgt cagctcgtgt cgtgagaata cttgggttaa
gtcccgcaac gagcgcaacc 960ctcgccttta gttgccatca tttagttggg
tactctaaag gaaccgccgg tgataagccg 1020gaggaaggtg gggatgacgt
caagtcctca tggcccttac gcgttgggct acacacgtgc 1080tacaatggcg
actacagtgg gcagccactc cgcgaggagg agctaatctc caaaagtcgt
1140ctcagttcgg attgttctct gcaactcgag agcatgaagg cggaatcgct
agtaatcgcg 1200gatcagcatg ccgcggtgaa tacgttccca ggccttgtac
acaccgcccg tcacaccatg 1260ggagttggtt tcacccgaag gctgtgcgct
aaccgcaagg aggcagcaga cca 131341422DNAPseudomonas sp. 4acacatgcag
tcgagcggta gagaggtgct tgcacctctt gagagcggcg gacgggtgag 60taaagcctag
gaatctgcct ggtagtgggg gataacgctc ggaaacggac gctaataccg
120catacgtcct acgggagaaa gcaggggacc ttcgggcctt gcgctatcag
atgagcctag 180gtcggattag ctagttggtg aggtaatggc tcaccaaggc
gacgatccgt aactggtctg 240agaggatgat cagtcacact ggaactgaga
cacggtccag actcctacgg gaggcagcag 300tggggaatat tggacaatgg
gcgaaagcct gatccagcca tgccgcgtgt gtgaagaagg 360tcttcggatt
gtaaagcact ttaagttggg aggaagggca ttaacctaat acgttagtgt
420tttgacgtta ccgacagaat aagcaccggc taactctgtg ccagcagccg
cggtaataca 480gagggtgcaa gcgttaatcg gaattactgg gcgtaaagcg
cgcgtaggtg gttcgttaag 540ttggatgtga aatccccggg ctcaacctgg
gaactgcatt caaaactgtc gagctagagt 600atggtagagg gtggtggaat
ttcctgttgt agcggtgaaa tgcgtgatac agatatagga 660aggaacacca
gtggcgaagg cgacccacct ggactgatac tgacactgag gtgcgaaagc
720gtggggagca aacaggatta gataccctgg gtagtccacg cccgtaaacg
atgtcaacta 780gccgttggga gccttgagct cttagtggcg cagctaacgc
attaagttga ccgcctgggg 840agtacggccg caaggttaaa actcaaatga
attgacgggg gcccgcacaa gcggtggagc 900atgtggttta attcgaagca
acgcgaagta ccttaccagg ccttgacatc ctatgaactt 960tccagagatg
gattggtgcc ttcgggaaca ttgagacagg tgctgcatgg ctgtcgtcag
1020ctcgtgtcgt gagatgttgg gttaagtccc gtaacgagcg caacccttgt
ccttagttac 1080cagcacgtaa tggtgggcac tctaaggaga ctgccggtga
caaaccggag gaaggtgggg 1140atgacgtcaa gtcatcatgg cccttacggc
ctgggctaca cacgtgctac aatggtcggt 1200acagagggtt gccaagccgc
gaggtggagc taatcccaca aaaccgatcg tagtccggat 1260cgcagtctgc
aactcgactg cgtgaagtcg gaatcgctag taatcgcgaa tcagaatgtc
1320gcggtgaata cgttcccggg ccttgtacac accgcccgtc acaccatggg
agtgggttgc 1380accagaagta gctagtctaa ccttcggggg gacggtacca cg
142251352DNAEnterobacter sp. 5agtaatgtct gggaaactgc ctgatggagg
gggataacta ctggaaacgg tagctaatac 60cgcataacgt cgcaagacca aagaggggga
ccttcgggcc tcttgccatc agatgtgccc 120agatgggatt agctagtagg
tggggtaacg gctcacctag gcgacgatcc ctagctggtc 180tgagaggatg
accagccaca ctggaactga gacacggtcc agactcctac gggaggcagc
240agtggggaat attgcacaat gggcgcaagc ctgatgcagc catgccgcgt
gtatgaagaa 300ggccttcggg ttgtaaagta ctttcagcgg ggaggaaggt
gttgtggtta ataaccgcag 360caattgacgt tacccgcaga agaagcaccg
gctaactccg tgccagcagc cgcggtaata 420cggagggtgc aagcgttaat
cggaattact gggcgtaaag cgcacgcagg cggtctgtca 480agtcggatgt
gaaatccccg ggctcaacct gggaactgca ttcgaaactg gcaggctaga
540gtcttgtaga ggggggtaga attccaggtg tagcggtgaa atgcgtagag
atctggagga 600ataccggtgg cgaagggcgg ccccctggac aaagactgac
gctcaggtgc gaaagcgtgg 660ggagcaaaca ggattagata cccctggtag
tccacgccgt aaacgatgtc gacttggagg 720ttgtgccctt gaggcgtggc
ttccggagct aacgcgttaa gtcgaccgcc tggggagtac 780ggccgcaagg
ataaaacctt aatgaattga cgggggcccg cacaagcggt ggagcatgtg
840gtttaattcg atgcaacgcg aagaaccttt gctactcttg acatccagag
aactttccag 900agatggattg gtgccttcgg gaactctgag acaggtgctg
catggctgtc gtcagctcgt 960gttgtgaaat gttgggttaa gtcccgcaac
gagcgcaacc cttatccttt gttgccagcg 1020gtccggccgg gaactcaaag
gagactgcca gtgataaact ggaggaaggt ggggatgacg 1080tcaagtcatc
atggccctta cgagtagggc tacacacgtg ctacaatggc gcatacaaag
1140agaagcgaac tcgcgagagc aagcggacct cataaagtgc gtcgtagtcc
ggattggagt 1200ctgcaactcg actccatgaa gtcggaatcg ctagtaatcg
tagatcagaa tgctacggtg 1260aatacgttcc cgggccttgt acacaccgcc
cgtcacacca tgggagtggg ttgcaaaaga 1320agtaggtagc ttaaccttcg
ggagggcgct ac 135261394DNAMicrococcus sp. 6gcatgcagtc gacgatgaag
cccagcttgc tgggtggatt agtggcgaac gggtgagtaa 60cacgtgagta acctgccctt
aactctggga taagcctggg aaactgggtc taataccgga 120tatgagcgcc
taccgcatgg tgggtgttgg aaagatttat cggttttgga tggactcgcg
180gcctatcagc ttgttggtga ggtaatggct caccaaggcg acgacgggta
gccggcctga 240gagggtgacc ggccacactg ggactgagac acggcccaga
ctcctacggg aggcagcagt 300ggggaatatt gcacaatggg cgaaagcctg
atgcagcgac gccgcgtgag ggatgacggc 360cttcgggttg taaacctctt
tcagtaggga agaagcgaaa gtgacggtac ctgcagaaga 420agcaccggct
aactacgtgc cagcagccgc ggtaatacgt agggtgcgag cgttatccgg
480aattattggg cgtaaagagc tcgtaggcgg tttgtcgcgt ctgtcgtgaa
agtccggggc 540ttaaccccgg atctgcggtg ggtacgggca gactagagtg
cagtagggga gactggaatt 600cctggtgtag cggtggaatg cgcagatatc
aggaggaaca ccgatggcga aggcaggtct 660ctgggctgta actgacgctg
aggagcgaaa gcatggggag cgaacaggat tagataccct 720ggtagtccat
gccgtaaacg ttgggcacta ggtgtgggga ccattccacg gtttccgcgc
780cgcagctaac gcattaagtg ccccgcctgg ggagtacggc cgcaaggcta
aaactcaaag 840gaattgacgg gggcccgcac aagcggcgga gcatgcggat
taattcgatg caacgcgaag 900tagcttacca aggcttgaca tgtactcgat
cggcgtagag atacggtttc ccgttagggg 960cgggttctgt ggtggtgcat
ggttgtcgtc agctcgtgtc gtgagatgtt gggttaagtc 1020ccgcaacgag
cgcaaccctc gttccatgtt gccagcacgt cgtggtgggg actcatggga
1080gactgccggg gtcaactcgg aggaaggtga ggacgacgtc aaatcatcat
gccccttatg 1140tcttgggctt cacgcatgct acaatggccg gtacaatggg
ttgcgatact gtgaggtgga 1200gctaatccca aaaagccggt ctcagttcgg
attggggtct gcaactcgac cccatgaagt 1260cggagtcgct agtaatcgca
gatcagcaac gctgcggtga atacgttccc gggccttgta 1320cacaccgccc
gtcaagtcac gaaagttggt aacacccgaa gccggtggcc taacccttgt
1380ggggggagcc gtac 139471421DNABacillus sp. 7atgcagtcga gcgaatcgat
gggagcttgc tccctgagat tagcggcgga cgggtgagta 60acacgtgggc aacctgccta
taagactggg ataacttcgg gaaaccggag ctaataccgg 120atacgttctt
ttctcgcatg agagaagatg gaaagacggt ttacgctgtc acttatagat
180gggcccgcgg cgcattagct agttggtgag gtaatggctc accaaggcga
cgatgcgtag 240ccgacctgag agggtgatcg gccacactgg gactgagaca
cggcccagac tcctacggga 300ggcagcagta gggaatcttc cgcaatggac
gaaagtctga cggagcaacg ccgcgtgaac 360gaagaaggcc ttcgggtcgt
aaagttctgt tgttagggaa gaacaagtac cagagtaact 420gctggtacct
tgacggtacc taaccagaaa gccacggcta actacgtgcc agcagccgcg
480gtaatacgta ggtggcaagc gttgtccgga attattgggc gtaaagcgcg
cgcaggtggt 540tccttaagtc tgatgtgaaa gcccacggct caaccgtgga
gggtcattgg aaactgggga 600acttgagtgc agaagaggaa agtggaattt
ccaagtgtag cggtgaaatg cgtagagatt 660tggaggaaca ccagtggcga
aggcgacttt ctggtctgta actgacactg aggcgcgaaa 720gcgtggggag
caaacaggat tagataccct ggtagtccac gccgtaaacg atgagtgcta
780agtgttagag ggtttccgcc ctttagtgct gcagctaacg cattaagcac
tccgcctggg 840gagtacggcc gcaaggctga aactcaaagg aattgacggg
ggcccgcaca agcggtggag 900catgtggttt aattcgaacg atcccgttct
accttaccag gtgatgacat cctctgacaa 960ccctagagat agggctttcc
ccttcggggg acagagtgac aggtggtgca tggttgtcgt 1020cagctcgtgt
cgtgagatgt tgggttaagt cccgcaacga gcgcaaccct tgatcttagt
1080tgccagcatt cagttgggca ctctaaggtg actgccggtg acaaaccgga
ggaaggtggg 1140gatgacgtca aatcatcatg ccccttatga cctgggctac
acacgtgcta caatggatgg 1200tacaaagggc tgcaaacctg cgaaggtaag
cgaatcccat aaagccattc tcagttcgga 1260ttgcaggctg caactcgcct
gcatgaagcc ggaatcgcta gtaatcgcgg atcagcatgc 1320cgcggtgaat
acgttcccgg gccttgtaca caccgcccgt cacaccacga gagtttgtaa
1380cacccgaagt cggtgaggta accttcatgg agccagccgc c
142181419DNAPantoea sp. 8ccatgcagtc ggacggtagc acagaggagc
ttgctcctcg ggtgacgagt ggcggacggg 60tgagtaatgt ctggggatct gcccgataga
gggggataac cactggaaac ggtggctaat 120accgcaaaac gtcgcaagac
caaagagggg gaccttcggg cctctcacta tcggatgaac 180ccagatggga
ttagctagta ggcggggtaa cggcccacct aggcgacgat ccctagctgg
240tctgagagga tgaccagcca cactggaact gagacacggt ccagactcct
acgggaggca 300gcagtgggga atattgcaca atgggcgcaa gcctgatgca
gccatgccgc gtgtatgaag 360aaggccttcg ggttgtaaag tactttcagc
ggggaggaag gcgatgtggt taataaccgc 420gtcgattgac gttacccgca
gaagaagcac cggctaactc cgtgccagca gccgcggtaa 480tacggagggt
gcaagcgtta atcggaatta ctgggcgtaa agcgcacgca ggcggtctgt
540taagtcagat gtgaaatccc cgggcttaac ctgggaactg catttgaaac
tggcaggctt 600gagtctcgta gaggggggta gaatttccag gtgtagcggt
gaaatgcgta gagatctgga 660ggaataccgg tggcgaaggc ggccccctgg
acgaagactg acgctcaggt gcgaaagcgt 720ggggagcaaa caggattaga
taccctggta gtccacgccg taaacgatgt cgacttggag 780gttgttccct
tgaggagtgg cttccggagc taacgcgtta agtcgaccgc ctggggagta
840cggccgcaag gattaaactc aaatgaattg acgggggccc gcacaagcgg
tggagcatgt 900ggtttaattc gatgcaacgc gaagaaccat acctactctt
gacatccaga gaacttagca 960gagatgcttt ggtgccttcg ggaactctga
gacaggtgct gcatggctgt cgtcagctcg 1020tgttgtgaaa tgttgggtta
agtcccgcaa cgagcgcaac ccttatcctt tgttgccagc 1080gattcggtcg
ggaactcaaa ggagactgcc ggtgataaac cggaggaagg tggggatgac
1140gtcaagtcat catggccctt acgagtaggg ctacacacgt gctacaatgg
cgcatacaaa 1200gagaagcgac ctcgcgagag caagcggacc tcataaagtg
cgtcgtagtc cggatcggag 1260tctgcaactc gactccgtga agtcggaatc
gctagtaatc gtggatcaga atgccacggt 1320gaatacgttc ccgggccttg
tacacaccgc ccgtcacacc atgggagtgg gttgcaaaag 1380aagtaggcta
gcttaacctt cgggagggcg ctaccactt 141991420DNAAcinetobacter sp.
9cacatgcagt cgagcgggga gagtagcttg ctacttgacc tagcggcgga cgggtgagta
60atgcttagga atctgcctat tagtggggga caacatctcg aaagggatgc taataccgca
120tacgtcctac gggagaaagc aggggacctt cgggccttgc gctaatagat
gagcctaagt 180cggattagct agttggtggg gtaaaggcct accaaggcga
cgatctgtag cgggtctgag 240aggatgatcc gccacactgg gactgagaca
cggcccagac tcctacggga ggcagcagtg 300gggaatattg gacaatgggg
ggaaccctga tccagccatg ccgcgtgtgt gaagaaggcc 360ttttggttgt
aaagcacttt aagcgaggag gaggctaccg agattaatac tcttggatag
420tggacgttac tcgcagaata agcaccggct aactctgtgc cagcagccgc
ggtaatacag 480agggtgcaag cgttaatcgg atttactggg cgtaaagcgc
gcgtaggtgg ccaattaagt 540caaatgtgaa atccccgagc ttaacttggg
aattgcattc gatactggtt ggctagagta 600tgggagagga tggtagaatt
ccaggtgtag cggtgaaatg cgtagagatc tggaggaata 660ccgatggcga
aggcagccat ctggcctaat actgacactg aggtgcgaaa gcatggggag
720caaacaggat tagataccct ggtagtccat gccgtaaacg atgtctacta
gccgttgggg 780cctttgctgg ctttagtggc gcagctaacg cgataagtag
accgcctggg gagtacggtc 840gcaagactaa aactcaaatg aattgacggg
ggcccgcaca agcggtggag catgtggttt 900aattcgatgc aacgcgaagt
agcttacctg gtcttgacat agtatcttct ttccagagat 960ggattggtgc
cttcgggaac ttacatacag gtgctgcatg gctgtcgtca gctcgtgtcg
1020tgagatgttg ggttaagtcc cgcaacgagc gcaacccttt tccttatttg
ccagcgggtt 1080aagccgggaa ctttaaggat actgccagtg acaaactgga
ggaaggcggg gacgacgtca 1140agtcatcatg gcccttacga ccagggctac
acacgtgcta caatggtcgg tacaaagggt 1200tgctacctcg cgagaggatg
ctaatctcaa aaagccgatc gtagtccgga ttggagtctg 1260caactcgact
ccatgaagtc ggaatcgcta gtaatcgcgg atcagaatgc cgcggtgaat
1320acgttcccgg gccttgtaca caccgcccgt cacaccatgg gagtttgttg
caccagaagt 1380agggtaggtc cttaacgtct aagggaggac gctaccacgg
1420101436DNAPaenibacillus sp. 10atacatgcag tcgagcggac ttgcatgaga
agcttgcttc tctgatggtt agcggcggac 60gggtgagtaa cacgtaggca cctgccctca
agcttgggac aactaccgga aacggtagct 120aataccgaat agttgttttc
ttctcctgaa gaaaactgga aagacggagc aatctgtcac 180ttggggatgg
gcctgcggcg cattagctag ttggtggggt aacggctcac caaggcgacg
240atgcgtagcc gacctgagag ggtgatcggc cacactggga ctgagacacg
gcccagactc 300ctacgggagg cagcagtagg gaatcttccg caatgggcga
aagcctgacg gagcaatgcc 360gcgtgagtga tgaaggtttt cggatcgtaa
agctctgttg ccagggaaga acgcttggga 420gagtaactgc tctcaaggtg
acggtacctg agaagaaagc cccggctaac tacgtgccag 480cagccgcggt
aatacgtagg gggcaagcgt tgtccggaat tattgggcgt aaagcgcgcg
540caggcggtca tttaagtctg gtgtttaatc ccggggctca accccggatc
gcactggaaa 600ctgggtgact tgagtgcaga agaggagagt ggaattccac
gtgtagcggt gaaatgcgta 660gatatgtgga ggaacaccag tggcgaagcg
cgactctctg ggctgtaact gacgctgagg 720cgcgaaagcg tggggagcaa
acaggattag ataccctggt agtccacgcc gtaaacgatg 780agtgctaggt
gttaggggtt tcgataccct tggtgccgaa gttaacacat taagcactcc
840gcctggggag tacggtcgca agactgaaac tcaaaggaat tgacggggac
ccgcacaagc 900agtggagtat gtggttttat tcgaagcaac gcgaagaacc
ttaccaggtc ttgacatccc 960tctgaccggt acagagatgt acctttcctt
cgggacagag gagacaggtg gtgcatggtt 1020gtcgtcagct cgtgtcgtga
gatgttgggt taagtcccgc aacgagcgca acccttgatc 1080ttagttgcca
gcacttcggg tgggcactct aaggtgactg ccggtgacaa accggaggaa
1140ggtggggatg acgtcaaatc atcatgcccc ttatgacctg ggctacacac
gtactacaat 1200ggccggtaca acgggctgtg aagccgcgag gtggaacgaa
tcctaaaaag ccggtctcag 1260ttcggattgc aggctgcaac tcgcctgcat
gaagtcggaa ttgctagtaa tcgcggatca 1320gcatgccgcg gtgaatacgt
tcccgggtct tgtacacacc gcccgtcaca ccacgagagt 1380ttataacacc
cgaagtcggt ggggtaaccg caaggagcca gccgccgaag gtgatc 1436
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