U.S. patent application number 10/527076 was filed with the patent office on 2006-10-26 for method for isolating and culturing unculturable microorganisms.
Invention is credited to Shaul Geresh, Shimona Geresh, Ariel Kushmaro.
Application Number | 20060240506 10/527076 |
Document ID | / |
Family ID | 29596481 |
Filed Date | 2006-10-26 |
United States Patent
Application |
20060240506 |
Kind Code |
A1 |
Kushmaro; Ariel ; et
al. |
October 26, 2006 |
Method for isolating and culturing unculturable microorganisms
Abstract
The invention provides a method for isolating and culturing a
previously unculturable microorganism, which comprises: (i)
collecting a sample from an environmental source; (ii)
counting/estimating the number of microorganisms in the sample;
(iii) diluting the sample in an appropriate medium; (iv) adding a
gelating agent such as to entrap one or more microorganisms within
a sphere of the gelating agent; (v) coating the spheres containing
the entrapped microorganism(s) with a natural or synthetic polymer
to form a polymeric membrane; (vi) incubating the coated spheres in
the original environment for an appropriate time; (vii) cutting the
spheres and scanning for microorganisms colonies; and (viii)
isolating the microorganisms, and repeating steps (iii) to (vii)
until a pure clone of said previously unculturable microorganism is
obtained.
Inventors: |
Kushmaro; Ariel; (Nir-Zvi,
IL) ; Geresh; Shimona; (Omer, IL) ; Geresh;
Shaul; (Omer, IL) |
Correspondence
Address: |
BROWDY AND NEIMARK, P.L.L.C.;624 NINTH STREET, NW
SUITE 300
WASHINGTON
DC
20001-5303
US
|
Family ID: |
29596481 |
Appl. No.: |
10/527076 |
Filed: |
September 3, 2003 |
PCT Filed: |
September 3, 2003 |
PCT NO: |
PCT/IL03/00725 |
371 Date: |
January 23, 2006 |
Current U.S.
Class: |
435/34 ;
435/252.1 |
Current CPC
Class: |
C12N 1/00 20130101 |
Class at
Publication: |
435/034 ;
435/252.1 |
International
Class: |
C12Q 1/04 20060101
C12Q001/04; C12N 1/20 20060101 C12N001/20 |
Foreign Application Data
Date |
Code |
Application Number |
Sep 9, 2002 |
IL |
151660 |
Claims
1. A method for isolating and culturing a previously unculturable
microorganism, which comprises: (i) collecting a sample from an
environmental source; (ii) counting/estimating the number of
microorganisms in the sample; (iii) diluting the sample in an
appropriate medium; (iv) adding a gelating agent such as to entrap
one or more microorganisms within a sphere of the gelating agent;
(v) coating the spheres containing the entrapped microorganism(s)
with a natural or synthetic polymer to form a polymeric membrane;
(vi) incubating the coated spheres in the original environment for
an appropriate time; (vii) cutting the spheres and scanning for
microorganisms colonies; and (viii) isolating the microorganisms,
and repeating steps (iii) to (vii) until a pure clone of said
previously unculturable microorganism is obtained.
2. A method according to claim 1 wherein said environmental source
is a terrestrial, aquatic or marine source.
3. A method according to claim 1 wherein said appropriate medium of
(iii) is a medium compatible with the environment from which the
sample has been collected.
4. A method according to claim 1 wherein said gelating agent is a
natural, semi-synthetic or synthetic gelating agent selected from
agar, alginate, carrageenans, gum Arabic, guar gum, traganth gum,
xanthan gum, propyleneglycolalginate, and mycrocrystalline
cellulose.
5. A method according to claim 1 wherein said gelating agent sphere
of (iv) has a size from 0.1 mm or less to about 5 mm.
6. A method according to claim 1 wherein said natural or synthetic
polymer for coating the spheres containing the microorganism(s) is
a natural or synthetic transparent or opaque polymer selected from
the group consisting of a polysulfone, an alginate, an epoxy resin,
a polyacrylamide, silica gel polysulfone, alginate and epoxy
resin.
7. A microorganism isolated by the method according to claim 1.
8. A microorganism according to claim 7 consisting of a
bacterium.
9. A library of microorganisms according to claim 7.
10. A method for genomic characterization of previously
unculturable microorganisms, which comprises: (i) collecting a
sample from an environmental source; (ii) counting/estimating the
number of microorganisms in the sample; (iii) diluting the sample
in an appropriate medium; (iv) adding a gelating agent such as to
entrap one or more microorganisms within a sphere of the gelating
agent; (v) coating the spheres containing the entrapped
microorganism(s) with a natural or synthetic polymer to form a
polymeric membrane; (vi) incubating the coated spheres in the
original environment for an appropriate time; (vii) cutting the
spheres and extracting the microorganisms by chemical lysis using
an agent for extraction of genomic DNA; (viii) processing the total
genomic DNA to establish the restriction fragment length
polymorphism (RFLP) pattern of the microorganisms; (ix) analyzing
the RFLP patterns to identify unique clones that are submitted to
sequence analysis; and (x) identifying the microorganisms by
comparison of these sequences with sequences available at the
GenBank database.
11. A method according to claim 10 wherein the microorganisms are
isolated from a marine source, which comprises: (i) collecting a
sample from a marine source; (ii) counting/estimating the number of
microorganisms in the sample; (iii) diluting the sample in sterile
seawater; (iv) adding a gelating agent such as to entrap one or
more microorganisms within a sphere of the gelating agent; (v)
coating the spheres containing the entrapped microorganism(s) with
a natural or synthetic polymer to form a polymeric membrane; (vi)
incubating the coated spheres in an aquarium containing seawater
for an appropriate time; (vii) cutting the spheres and extracting
the microorganisms by chemical lysis using an agent for extraction
of genomic DNA; (viii) processing the total genomic DNA to
establish the restriction fragment length polymorphism (RFLP)
pattern of the microorganisms; (ix) analyzing the RFLP patterns to
identify unique clones that are submitted to sequence analysis; and
(x) identifying the microorganisms by comparison of these sequences
with sequences available at the GenBank database.
12. A bacterium characterized or identified by the method according
to claim 11.
13. A method according to claim 11 wherein the marine source is
coral mucus.
14. A bacterium isolated from coral mucus identified by the method
of claim 13 and characterized by partial 16S rDNA sequence selected
from the group consisting of SEQ ID NO:3, SEQ ID NO:4, and SEQ ID
NO:5.
15. A method according to claim 10 wherein said environmental
source is a soil source.
16. A bacterium isolated from soil identified by the method
according to claim 15 and characterized by partial 16S rDNA
sequences selected from the group consisting of the pair of
sequences of SEQ ID NO:6 and SEQ ID NO:7, and SEQ ID NO:8 and SEQ
ID NO:9.
17. (canceled)
18. A method according to claim 1 wherein said gelating agent
sphere of (iv) has a size of 1-2 mm in diameter.
19. A library of microorganisms according to claim 8.
Description
FIELD OF THE INVENTION
[0001] The present invention relates to a method for isolating and
culturing novel "uncultivable" microorganisms.
BACKGROUND OF THE INVENTION
[0002] Cultured microorganisms are the most common source of
antibiotics and other medicinal agents. However, only a small
percentage (less than 1%) of the viable bacteria in soil can be
cultured on known nutrient media using current techniques such as
petri dishes (Handelsman et al. 1998; Amann et al. 1995). The other
99% of uncultured/uncultivable microorganisms, with their genetic
and biochemical diversity, may emerge as a major source of new
natural chemical structures that may be useful for humans, for
example as drugs.
[0003] The exploration of previously uncultured microorganisms for
the discovery of new useful natural products is now being carried
out in several laboratories. The main approach involves genomics
techniques such as the approach designated metagenomics for the
analysis of the collective genomes of the microorganisms in the
soil community. According to this approach, DNA in large segments
is cloned directly from soil into a culturable host and a
sequence-based and functional genomic analysis is conducted on it.
The intention is the isolation of new signals, new secondary
metabolites that might have utility for humans, and the
reconstruction of an entire genome of an uncultured organism.
[0004] Molecular microbial ecology represents a recent development
in research methods. It consists of utilizing techniques of
molecular biology to investigate the ecology of microorganisms, and
offers new tools to facilitate the detection and identification of
microorganisms in the environment.
[0005] Molecular microbial ecology allowed the development of tools
to address a central dogma of microbial ecology: an inability to
cultivate more than a small proportion (0.1-1%) of the bacteria
that can be visualized by direct count procedures (Head et al.,
1998). Thus, the identification of bacteria by molecular methods
represents an indispensable addition to the traditional methods
based on the analyses of morphological and physiological
characteristics. Among these culture-independent new techniques,
the technique based on direct sequencing seems to be the most
effective. It consists in sequencing a specific region of the
bacterial chromosome, namely the bacterial 16S rDNA region, and in
comparing this sequence with known sequences stored in data banks.
All microorganisms possess at least one copy of the genes coding
for the ribosomal RNA (rRNA), which are indispensable in any cells
for the biosynthesis of proteins. Within these genes, the 16S rDNA
region is principally used for the determination of the genus and
the species of bacteria. By using this approach, it could be
determined in many environmental samples the predominance of many
different uncultured species. It might be feasible that the yet
uncultured types of bacteria might be grown under laboratory
conditions if just the right nutrients are found (Amann et al.
1995; Felske et al. 1999).
[0006] Recently, Kaeberlein et al. (2002, and published US Patent
Applications Nos. 2003/0059866 and 2003/0059867) disclosed a new
method for isolating and growing uncultivable microorganisms in
pure culture in a simulated natural environment using a diffusion
chamber. Microorganisms were separated from intertidal marine
sediment particles, serially diluted, mixed with warm agar made
with seawater, and placed in the diffusion chamber. The membranes
allowed exchange of chemicals between the chamber and the
environment, but restricted movement of cells. After the first
membrane was affixed to the base of the chamber, the agar with
microorganisms was poured in, and the top was sealed with another
membrane (See FIG. 1, Kaeberlein et al., 2002' and FIG. 1a, US
Patent Application No. 2003/0059866). The diffusion chamber
consists of a stainless steel washer (70 mm o.d., 33 mm i.d., 3 mm
in thickness) sandwiched between two 0.03-.mu.m pore-size
polycarbonate membranes. The membranes were glued to the washer
forming the inner space filled with test microorganisms in
semi-solid agar. The sealed chambers were placed on the surface of
the sediment collected from the tidal flat and kept in a marine
aquarium. Colonies of representative marine microorganisms were
isolated in pure culture. These isolates did not grow on artificial
media alone but formed colonies in the presence of other
microorganisms.
[0007] Zengler et al. (2002) disclose a universal method that
provides access to the immense reservoir of untapped microbial
diversity. They utilized a technique that combines encapsulation of
cells in gel microdroplets (using the OneCell System technology)
for massively parallel microbial cultivation under low nutrient
flux conditions, followed by flow cytometry to detect microdroplets
containing microbial microcolonies.
[0008] In summary, most microorganisms in the environment have been
overlooked as yet due to their resistance to cultivation on
artificial media. The cultured microorganisms represent only a
small fraction of natural microbial communities and hence the
microbial diversity in terms of species richness and species
abundance is grossly underestimated. Our understanding of microbial
diversity is not represented by the cultured fraction of the
microbial community (Wintzingerode et al., 1997).
SUMMARY OF THE INVENTION
[0009] It is an object of the present invention to provide a method
for isolating and culturing previously unculturable
microorganism.
[0010] In one preferred embodiment of the invention, the sample is
collected from an environmental source and diluted in an
appropriate medium after counting/estimating the number of
microorganisms in the sample. A gelating agent is then added such
as to entrap one or more microorganisms within a sphere of the
gelating agent. The spheres containing the entrapped
microorganism(s) are then coated with a natural or synthetic
polymer to form a polymeric membrane. The coated spheres with the
entrapped microorganisms are incubated in the original environment
and, after an appropriate time, are cut and scanned for
microorganisms colonies. The microorganisms are isolated and
subjected one or more times to the steps of dilution in an
appropriate medium, entrapping in a gelating agent, coating of the
spheres containing the entrapped microorganisms, incubation of the
coated spheres, cutting the spheres and scanning for microorganisms
colonies, until a pure clone of said previously unculturable
microorganism is obtained.
[0011] The present invention further provides a library of
microorganisms obtained by the method of the invention, wherein
each of the microorganisms was isolated from a sphere as
described.
[0012] The present invention still further provides a method for
screening and identification of new drugs and other substances of
commercial interest in the pharmaceutical, chemical, biotechnology
and other industries as well as in the agriculture, which comprises
cultivating a previously unculturable microorganism or screening a
library of previously unculturable microorganisms, and isolating
and identifying compounds having biological or other activity of
interest.
BRIEF DESCRIPTION OF THE DRAWINGS
[0013] FIG. 1 depicts a schematic drawing of an agar sphere coated
with a polymeric membrane.
[0014] FIG. 2 is a scanning electron microscopy photograph showing
an agar sphere coated with a polysulfone membrane as obtained in
Example 1 hereinafter.
[0015] FIG. 3 is a photograph (.times.1000) of microcolony of an
unidentified rod-shaped bacterium obtained from soil as described
in Example 3 hereinafter.
DETAILED DESCRIPTION OF THE INVENTION
[0016] The present invention relates to a method for isolation and
culture of microorganisms suitable for microorganisms from any
environmental source.
[0017] According to one aspect, the present invention relates to a
method for isolating and culturing a previously unculturable
microorganism, which comprises: [0018] (i) collecting a sample from
an environmental source; [0019] (ii) counting/estimating the number
of microorganisms in the sample; [0020] (iii) diluting the sample
in an appropriate medium; [0021] (iv) adding a gelating agent such
as to entrap one or more microorganisms within a sphere of the
gelating agent; [0022] (v) coating the spheres containing the
entrapped microorganism(s) with a natural or synthetic polymer to
form a polymeric membrane; [0023] (vi) incubating the coated
spheres in the original environment for an appropriate time; [0024]
(vii) cutting the spheres and scanning for microorganisms colonies;
and [0025] (viii) isolating the microorganisms, and repeating steps
(iii) to (vii) until a pure clone of said previously unculturable
microorganism is obtained.
[0026] According to the invention, an environmental sample is
collected and the number of bacteria is counted/estimated by
microscopic observation, namely, all cells are counted in a large
square: 12 cells (in practice, several squares are counted and the
numbers averaged). The sample is diluted 1/10 in an appropriate
medium, 1 ml of the broth is transferred to a tube, diluted again
to 1/10.sup.2, 1 ml thereof is transferred to another tube, and the
dilution steps are repeated until about 1/10.sup.6, when
approximately one bacterium will be entrapped in the gelating agent
sphere. The gelating agent sphere is coated with a polymeric
membrane and incubated in the environment for weeks to months. At
the end of the incubation period, the coated sphere is cut, the
bacterium is then isolated, cultured in the sphere, and subjected
to molecular biology techniques.
[0027] The environmental source from which the samples are
collected may be any terrestrial, aquatic or marine source such as
soil, biofilms, sediments (e.g. coral or other marine sediments,
aquifer sediments and the like), waste waters and the like. The
sample is suspended in its natural or other appropriate medium, and
is divided, for example, into 1-ml tubes, and each divisional
sample is then subjected to counting/estimation of the number of
microorganisms by well-known techniques, for example by DAPI
(4',6-diamidino-2-phenylindole) staining of the cells and direct
microscopic count of the DAPI-stained cells.
[0028] In the next step, the samples are diluted as necessary in an
appropriate medium. As used herein, an "appropriate medium" is
intended to mean a medium compatible with the environment from
which the sample has been collected with respect to
physico-chemical parameters such as pH, salinity, temperature,
oxygen concentration, and the like. The medium may be sterile
water, sterile saline, sterile water containing suitable
ingredients for compatibility with the environmental source, and
the like. For example, a sample collected from a marine source will
have the salinity corresponding to the marine source and the salt
concentration will be higher if the sample is originated from the
Dead Sea. When the sample is collected from soil, the medium may be
sterile water.
[0029] The next step consists in the addition of a gelating agent
as a matrix to the diluted samples. Any suitable natural,
semi-synthetic or synthetic gelating agent may be used such as, but
not limited to, agar, alginate, carrageenans, gum Arabic, guar gum,
traganth gum, xanthan gum, propyleneglycolalginate, and
mycrocrystalline cellulose.
[0030] In one preferred embodiment, the gelating agent is agar.
Preferably, the diluted samples are mixed with warm (40-50.degree.
C.) autoclaved agar (0.7-2%) such as to entrap preferably one, or
more, microorganisms within a sphere of the gelating agent. The
agar spheres can be obtained by dripping agar droplets into cold
mineral oil. The sphere size of 0.1 mm or less, up to 5 mm,
preferably up to 2-3 mm, in diameter, can be determined by the
nozzle diameter and dripping rate.
[0031] The gelating agent spheres containing the entrapped
microorganism(s) are then coated with a natural or synthetic
polymer such as, but not limited to, a polysulfone, an alginate, an
epoxy resin, polyacrylamide, silica gel and the like, such as to
form a multilayered membrane. Polysulfone resin of average m.w.
35000, Na-alginate, and epoxy resin such as Epikote 255 have been
disclosed before for biomass entrapment for different applications
(Ferguson et al., 1989; Blanco et al., 1999) and can be used
according to the invention.
[0032] For coating, the polymer is first dissolved in a suitable
solvent the dried gelating agent spheres containing the entrapped
microorganism are introduced into the polymer solution, and are
then transferred into a medium that enables coating of the spheres
by several layers of the polymer, thus forming the desired spheres
coated by the polymeric membrane. In one embodiment, agar spheres
containing one or more microorganisms are immersed into a solution
of polysulfone in dimethylformamide (DMF) and transferred to water
in order to obtain the desired polymeric coating. The polymeric
membrane allows exchange of chemicals between the sphere and the
environment, but restrict movement of cells. The polymer can be
opaque, but preferably it is transparent such that the colonies
inside the sphere can be seen.
[0033] The next step consists in the incubation of the polymeric
coated gelating agent spheres containing one or more microorganisms
in the environment from which the original sample has been
collected, for an appropriate time. This is the alternative to
cultivate such microorganisms that cannot grow in known growth
media for microorganisms. The incubation in the environment can
take from days to months. When the sample is collected from a
marine source, the incubation may be carried out in a container,
e.g., aquarium, containing water with the degree of salinity of the
marine source. When the sample is collected from soil, the
incubation may be carried out in containers, e.g. pots, filled with
the same soil material.
[0034] After the incubation, the spheres are cut and placed on a
glass slide and covered with a coverslip, and the entire volume of
agar is scanned for microbial colonies at magnification of
400.times. and 1,000.times.. The microorganisms are then isolated
into pure culture by successive re-inoculation of individual
colonies into new spheres followed by incubation in the
environment, by repetition of steps (iii) to (vii) as many times as
necessary, until a pure clone of the previously unculturable
microorganism is obtained.
[0035] After incubation in the environment, previously uncultured
microorganisms can be isolated and then subjected to molecular
biology and genomics techniques, and/or cultured for the production
of bioactive materials. Libraries can be construed composed of
microorganisms, each isolated from a separate sphere, and can be
used for identification of new biologically active compounds, even
without identification and characterization of the microorganisms.
When the identified biologically active compound is a small organic
molecule, its structure can be determined by known methods, it is
then synthesized, the biological activity is ascertained and it can
then be formulated in pharmaceutical or veterinary
compositions.
[0036] The method of the present invention allows
isolation/identification of new types of microorganisms, such as
bacteria, previously considered as unculturable, and the
establishment of libraries of "uncultivable" microorganisms useful
for the drug discovery and biotechnology industries. The method
enables exploration of new natural products from previously
uncultured microorganisms New genes might be obtained from the
previously uncultivable microbial communities, and new biologically
active materials such as proteins, enzymes and antibiotics of
utility to humans may be discovered.
[0037] According to the invention, metagenomics techniques can be
used to address the genetic structure and functional composition of
a sample irrespective of whether the microorganism can be cultured.
Molecular methodologies such as PCR of select molecular targets can
be used to discover genes with useful properties. Microbial
communities can be profiled by techniques well known in the art.
Cloning and sequencing of molecular targets such as 16S rDNA enable
identification of indigenous and novel organisms.
[0038] In one embodiment of the invention, cells or extracts from
unculturable microorganisms are subjected to analysis by 16S RNA
gene sequencing. Ribosomal RNA genes from the samples,
microcolonies or cultures are amplified by PCR by using specific
16S RNA oligonucleotide primers for bacteria. After cloning the PCR
products, the inserts are screened by their restriction patterns
(RFLP--restriction fragment length polymorphism). The clones are
submitted to sequence analysis and compared with known 16S RNA
genes using, for example, the online GenBank database
(hhtp://ncbi.nlm.nih.gov/GenBank). In this way, it can be
determined whether or not the microorganism represents a new
species/genus.
[0039] The present invention further provides a method for genomic
characterization of previously unculturable microorganisms, which
comprises: (i) collecting a sample from an environmental source;
(ii) counting/estimating the number of microorganisms in the
sample; (iii) diluting the sample in an appropriate medium; (iv)
adding a gelating agent such as to entrap one or more
microorganisms within a sphere of the gelating agent; (v) coating
the spheres containing the entrapped microorganism(s) with a
natural or synthetic polymer to form a polymeric membrane; (vi)
incubating the coated spheres in the original environment for an
appropriate time; (vii) cutting the spheres and extracting the
microorganisms by chemical lysis using an agent for extraction of
genomic DNA; (viii) processing the total genomic DNA to establish
the restriction fragment length polymorphism (RFLP) pattern of the
microorganisms; (ix) analyzing the RFLP patterns to identify unique
clones that are submitted to sequence analysis; and (x) identifying
the microorganisms by comparison of these sequences with sequences
available at the GenBank database.
[0040] In one preferred embodiment, a method is provided wherein
the microorganisms are isolated from a marine source, which
comprises: (i) collecting a sample from a marine source; (ii)
counting/estimating the number of microorganisms in the sample;
(iii) diluting the sample in sterile seawater; (iv) adding a
gelating agent such as to entrap one or more microorganisms within
a sphere of the gelating agent; (v) coating the spheres containing
the entrapped microorganism(s) with a natural or synthetic polymer
to form a polymeric membrane; (vi) incubating the coated spheres in
an aquarium containing seawater for an appropriate time; (vii)
cutting the spheres and extracting the microorganisms by chemical
lysis using an agent for extraction of genomic DNA; (viii)
processing the total genomic DNA to establish the restriction
fragment length polymorphism (RFLP) pattern of the microorganisms;
(ix) analyzing the RFLP patterns to identify unique clones that are
submitted to sequence analysis; and (x) identifying the
microorganisms by comparison of these sequences with sequences
available at the GenBank database.
[0041] In a preferred embodiment of the present invention, the
microorganism is a bacterium isolated from a marine source
consisting of coral mucus. According to this embodiment, extracts
from unculturable microorganisms from Red Sea coral mucus were
amplified by PCR using the specific 16S RNA oligonucleotide primers
for bacteria of SEQ ID NO:1 (forward primer, 8F) and SEQ ID NO:2
(reverse primer, 1512 R).
[0042] The most abundant sequence (70%) in this Red Sea coral mucus
sample corresponded to the partial 16S rDNA sequence characterized
by the SEQ ID NO: 3 (1,428 bp), and represent the Bacteria
(domain), Proteobacteria (phylum), Betaproteobacteria (class),
Burkholderiales (order), Alcaligenaceae (family), Alcaligenes
(genus).
[0043] The next most abundant clone (20%) in the Red Sea coral
mucus sample corresponded to the partial 16S rDNA sequence
characterized by the SEQ ID NO:4 (1,382 bp), and represent the
Bacteria (domain), Proteobacteria (phylum), Alphaproteobacteria
(class), Rhodobacteriales (order), Rhodobacteraceae (family),
Roseobacter (genus) or Ruegeria (genus) or unclassified
(genus).
[0044] The less abundant clone (10%) in the Red Sea coral mucus
sample corresponded to the partial 16S rDNA sequence characterized
by the SEQ ID NO: 5 (1,483 bp), and represent the Bacteria
(domain), Proteobacteria (phylum), Gammaproteobacteria (class),
Endobacteriales (order) or Verrucomicrobiales (order).
[0045] In another embodiment of the present invention, the
microorganism is isolated from a soil sample. According to this
embodiment, a clone from a library constructed from unculturable
soil bacteria from the soil of the Halutza region, Negev, Israel,
was amplified by PCR using the specific 16S RNA oligonucleotide
primers for bacteria of SEQ ID NO:1 (forward primer, 8F) and SEQ ID
NO:2 (reverse primer, 1512 R).
[0046] The most abundant clone in the Halutza soil bacteria
corresponded to the partial 16S rDNA sequences characterized by the
SEQ ID NO: 6 (730 bases, by direct 8F primer) and SEQ ID NO: 7 (689
bases, by reverse 1512R primer) and represent the Proteobacteria
(phylum), Betaproteobacteria (class), Burkholderiales (order),
Alcaligenaceae (family), Alcaligenes (genus).
[0047] The next most abundant clone in this sample of Halutza soil
bacteria corresponded to the partial 16S rDNA sequences
characterized by the SEQ ID NO:8 (651 bases, by direct 8F primer)
and SEQ ID NO: 9 (886 bases, by reverse 1512R primer) and represent
the Proteobacteria (phylum), Gammaproteobacteria (class),
Pseudomonadales (order), Pseudomonadaceae (family), Pseudomonas
(genus).
[0048] In another aspect, the present invention relates to a
previously uncultured microorganism isolated by the method of the
present invention. The microorganism may be a eukaryote, e.g. a
fungus, or a prokaryote, e.g., a bacterium. In a preferred
embodiment, the microorganism is a bacterium. In most preferred
embodiments, the bacterium is the bacterium isolated from soil
depicted in FIG. 3, or it is a bacterium comprising the partial 16S
rDNA nucleic acid sequences selected from the group consisting of
SEQ ID NO:3, SEQ ID NO:4, and SEQ ID NO:5, or the pair of 16S rDNA
sequences consisting of SEQ ID NO:6 and NO:7, or SEQ ID NO:8 and
NO:9.
[0049] In a further aspect, the present invention relates to a
library of previously uncultured microorganisms obtained by the
method of the invention and to the use of said library for the
discovery of new biologically active agents including, but not
being limited, to new antibiotics, enzymes, biocatalysts,
genes.
[0050] It is further envisaged to construct BAC, cosmid and small
insert libraries from diverse environmental samples and then
subject the libraries to a screening for novel genes, proteins and
small molecules exhibiting activities of interest. For example, 16S
rRNA gene clone libraries can be formed from mixed colonies of
microorganisms and screened.
[0051] The colonies of microorganisms can also be screened for
antibiotic activity by contacting diluted samples with a strain of
interest and studying the influence on its growth. Colonies of
unculturable microorganisms that produce compounds with antibiotic
activity will inhibit growth of strains. Said compounds can then be
isolated, purified, analyzed and either synthesized for use as
antibiotic or used as a model for further drug discovery.
[0052] Libraries of test extracts of the microorganisms can also be
tested for activity by automated highthrouput biochemical or
biological assays using, for example, a panel of test
microorganisms to test antibiotic activity, or a panel of enzymes
or antibodies to find compounds that affect their activities.
[0053] The invention will now be illustrated by the following
non-limiting Examples.
EXAMPLES
Example 1
Laboratory Scale Wastewater Bioreactor
[0054] An environmental sample was obtained from laboratory scale
wastewater bioreactor (waste water from Ramat Hovav Toxic Waste
Dumping Site, Negev, Israel) and estimated for microorganism number
by DAPI-staining and microscope direct counting (10.sup.8-10.sup.9
cell/mL). The sample was diluted 8- and 9-fold with water in order
to entrap approximately one microorganism in one agar sphere.
[0055] The diluted samples were mixed with warm (50.degree. C.)
autoclaved agar (DIFCO) (900 .mu.l agar per 100 .mu.l diluted
sample, final concentration 1.5% agar). Agar spheres of
approximately 1-2 mm in diameter containing the entrapped
microorganism(s) were formed by dripping droplets of the mixture
into cold mineral oil.
[0056] A solution of 10% polysulfone of m.w. ca. 35,000
(Sigma-Aldrich, Product No. 42,830-2) in DMF was prepared and used
to coat the dried agar spheres containing the entrapped
microorganism(s). For this purpose, the agar spheres were
introduced into the polymer solution, and then transferred into
water in order to obtain the desired polymeric membrane. FIG. 2 is
a photograph of such a coated agar sphere.
[0057] The polysulfone-coated agar spheres containing the entrapped
microorganism(s) were then incubated for 3 weeks in a wastewater
bioreactor. At the end of the incubation, the agar spheres were cut
and placed between a glass slide and a coverslip, and the entire
volume of agar was scanned for microbial colonies at magnification
of 400.times. and 1000.times..
[0058] In the spheres, we could see development of isolated
colonies of bacteria and fungi presumably uncultivable, since
experiments to grow them in ordinary agar plates were not
successful and no bacterial growth was observed.
Example 2
Microbial Communities Inhabiting Coral Mucus
[0059] Mucus of coral heads from the Red Sea was sampled by
collecting ca. 1 ml.sup.-1 in a sterile disposable 50-ml
polypropylene centrifuge tube. Mucus bacteria were counted directly
under phase microscopy. Mucus was diluted by sterile seawater and
placed on marine agar for culturable colony forming units (CFU).
Several dilutions (10.sup.-7, 10.sup.-6, 10.sup.-5 and 10.sup.-4)
were mixed with 2% marine agar in ratio 1 to 1 and agar spheres
were coated with polysulphone and incubated in a seawater aquarium
containing corals for several weeks. Agar spheres of approximately
1-2 mm in diameter containing the entrapped microorganism(s) were
formed by dripping droplets of the mixture into cold mineral
oil.
[0060] A solution of 10% polysulfone of m.w. ca. 35,000
(Sigma-Aldrich, Product No. 42,830-2) in DMF was prepared and used
to coat the dried agar spheres containing the entrapped
microorganism(s). For this purpose, the agar spheres were
introduced into the polymer solution, and then transferred into
water in order to obtain the desired polymeric membrane.
[0061] The polysulfone-coated agar spheres containing the entrapped
microorganism(s) were then incubated for 3 weeks in a seawater
aquarium containing corals. At the end of the incubation, the agar
spheres were cut and placed between a glass slide and a coverslip,
and the entire volume of agar was scanned for microbial colonies at
magnification of 400.times. and 1000.times..
[0062] In the spheres, we could see development of isolated
colonies of bacteria presumably uncultivable, since experiments to
grow them in ordinary agar plates were not successful and no
bacterial growth was observed.
[0063] Agar spheres including unculturable bacteria were extracted
by chemical lysis protocol using CTAB solution
(hexadecyltrimethylammonium bromide, Sigma H-5882) for genomic DNA.
The total DNA was amplified with a Mastercycler gradient
thermocycler (Eppendorf, Westbury, N.Y.) by PCR using specific 16S
rRNA primers for bacteria [forward primer, 8F (5'-GGATCCAGACTTT
GAT(C/T)(A/C)TGGCTCAG--SEQ ID NO:1) and reverse primer, 1512R (5'
GTGAAGCTTA CGG(C/T)TAGCTTGTTACGACTT--SEQ ID NO:2)]. Primers used in
the PCR amplifications were obtained from Sigma-Genosys. Reaction
mixtures included a 12.5 .mu.l ReddyMix (PCR Master mix containing
1.5 mM MgCl.sub.2 and 0.2 mM concentration of each deoxynucleoside
triphosphate) (ABgene, Surrey, UK), a 1 pmol each of the forward
and reverse primers, 1 .mu.l of the sample preparation, and water
to bring the total volume to 25 .mu.l. An initial denaturation-hot
start of 4 min at 95.degree. C. was followed by 30 cycles of the
following incubation pattern: 94.degree. C. for 20 sec, 56.degree.
C. for 20 sec, and 72.degree. C. for 105 sec. A final soak at
72.degree. C. for 20 min concluded the reaction.
[0064] PCR products were purified by electrophoresis through a 0.8%
agarose gel (Sigma), stained with ethidium bromide, and visualized
on a UV transilluminator. The approximately 1,500-bp heterologous
ribosomal DNA (rDNA) product was excised from the gel, and the DNA
was purified from the gel slice by using the QIAquick gel
extraction kit (Qiagen, Germany). The gel-purified PCR product was
cloned into the pDrive vector by QIAgen PCR cloning kit (Qiagen,
Germany) and transformed into calcium chloride-competent XL MRF' E.
coli cells. Plasmid DNA was isolated from individual clones by
QIAprep Spin Miniprep kit (Qiagen, Germany).
[0065] Aliquots from a subset of the samples of purified plasmid
DNA were digested with 5 U of the restriction enzyme EcoRI for more
than 4 h at 37.degree. C., and the digested product was separated
by electrophoresis on a 1% agarose gel. After staining with
ethidium bromide, the bands were visualized on a UV
transilluminator and the RFLP (restriction fragment length
polymorphism) patterns were analyzed to select clones containing
the appropriately sized insert. Plasmid DNA from these clones was
then digested with the six-base recognition site enzymes SphI,
SalI, EcoRV, BamHI, HindIII, NotI, XbaI and XhoI (Sigma) under the
conditions described above. The digest products were then separated
by electrophoresis on a 1% agarose gel, stained with ethidium
bromide, and the RFLP patterns were used to identify unique clones
to be submitted for sequence analysis.
[0066] Three additional internal primers were designed for
completed sequencing of the clones. Sequence reactions were
performed on the plasmid templates by using an ABI 3700 capillary
sequencer. The rDNA sequences were first compared with those in the
GenBank database with the basic local alignment search tool (BLAST)
network service through San-Diego Supercomputer Center (SDSC). From
the alignments created by this search, the orientation of each
cloned 16S rRNA gene could be determined and a rough phylogenetic
association was established. Each sequence was analyzed using the
CHIMERA CHECK program (version 2.7) available at the Ribosomal
Database Project.
[0067] Clone library constructed from agar spheres (10 colonies)
inoculated by mucus, revealed three different patterns by RFLP by
ratio 7 to 2 to 1. Representative DNA from each group was partial
sequenced by using direct (8F) and reversed (1512R) primers.
Microorganism identification was based on comparison of these
sequences with the GenBank database and exhibited high
division-level diversity of bacterial sequences.
[0068] The most abundant clone (70%) is characterized by partial
16S rDNA sequence of SEQ ID NO:3 that represents Bacteria (domain),
Proteobacteria (phylum), Betaproteobacteria (class),
Burkholderiales (order), Alcaligenaceae (family), Alcaligenes
(genus). The next most abundant clone (20%) is characterized by
partial 16S rDNA sequence of SEQ ID NO:4 that represents Bacteria
(domain), Proteobacteria (phylum), Alphaproteobacteria (class),
Rhodobacteriales (order), Rhodobacteraceae (family), Roseobacter
(genus) or Ruegeria (genus) or unclassified (genus). The less
abundant clone (10%) in the Red Sea coral mucus sample is
characterized by partial 16S rDNA sequence of SEQ ID NO:5 that
represents Bacteria (domain), Proteobacteria (phylum),
Gammaproteobacteria (class), Endobacteriales (order) or
Verrucomicrobiales (order).
Example 3
Microbial Communities Inhabiting Soil
[0069] A sample was collected from the soil of the Halutza region,
Negev, Israel, and processed as described in Example 2. The medium
was sterile tapwater and the incubation of the polysulfone-coated
agar spheres was carried out in pots filled with soil material from
the Halutza region. A clone library constructed from agar spheres
(10 colonies) inoculated with the soil bacteria was incubated for 3
weeks, analyzed as described above and revealed two different
patterns by RFLP by ratio 9 to 1. DNA from two clones were
partially sequenced by using direct (8F) and reversed (1512R)
primers and microorganism identification was based on comparison of
these sequences with the GenBank database.
[0070] The most abundant sequence (90%) of this sample of soil
bacteria is characterized by partial 16S rDNA sequences of SEQ ID
NO:9 and SEQ ID NO:10, that represent Proteobacteria (phylum),
Betaproteobacteria (class), Burkholderiales (order), Alcaligenaceae
(family), Alcaligenes (genus). The less abundant (10%) clone is
characterized by partial 16S rDNA sequences of SEQ ID NO:11 and SEQ
ID NO:12, that represent Proteobacteria (phylum),
Gammaproteobacteria (class), Pseudomonadales (order),
Pseudomonadaceae (family), Pseudomonas (genus).
[0071] FIG. 3 is a photograph (.times.1000) of a microcolony of an
unidentified rod-shaped bacterium obtained in purified form from
the Halutza soil.
REFERENCES
[0072] Amann, R. I., Ludwig, W. and Schleifer, K-H. (1995)
Phylogenetic identification and in situ detection of individual
microbial cells without cultivation. Microbiol. Rev. 59, 143-169.
[0073] Blanco A., Sanz B., Llama J. M., Serra L. M. (1999).
Biosorption of heavy metals to immobilised Phormidium laminosum
biomass. Journal of Biotechnology 69: 227-240. [0074] Felske A.,
Wolterink A., van Lis R., W. M. de Vos, A. D. L. Akkermans. (2000).
Searching for predominant soil bacteria: 16S rDNA cloning versus
strain cultivation. FEMS Microbiology Ecology 30:137-145. [0075]
Ferguson C. R., Peterson M. R., Jeffers T. H. (1989). Removal of
metal contaminants from waste waters using biomass immobilized in
polysulfone beads. In: Scheiner, B. J., Doyle, F. M., Kawatras, S.
K. (Eds.), Biotechnology in Minerals and Metal Processing. Society
of Mining Engineers, Littleton, Colo., pp. 193-199. [0076]
Handelsman J., Rondo R. M., Brady F. S., Clardy J., Goodman M. R.
(1998). Molecular biological access to the chemistry of unknown
soil microbes: a new frontier for natural products. Chem. Biol.
5(10):245-249. [0077] Head I. M., Saunders J. R., Pickup R. W.
(1998). Microbial Evolution, Diversity, and Ecology: A Decade of
Ribosomal RNA Analysis of Uncultivated Microorganisms. Microb Ecol
35:1-21. [0078] Kaeberlein T., Lewis K., Epstein S. (2002).
Isolating "uncultivable" microorganisms in pure culture in a
simulated natural environment. Science 296: 1127-1129. [0079]
Spring S., Schulze R., Overmann J., Schleifer K. (2000).
Identification and characterization of ecologically significant
prokaryotes in the sediment of freshwater lakes: molecular and
cultivation studies. FEMS Microbiology Reviews 24:573-590. [0080]
Wintzingerode F., Goebel U., Stackebrandt E. (1997). Determination
of microbial diversity in environmental samples: pitfalls of
PCR-based rRNA analysis. FEMS Microbiology Reviews 21:213-229.
[0081] Zengler K., Toledo G., Rappe{acute over ( )} M., Elkins J.,
Mathur J. E., Short J. M., and Keller M. (2002). Cultivating the
uncultured. PNAS 99 (24): 15681-15686.
Sequence CWU 0
0
SEQUENCE LISTING <160> NUMBER OF SEQ ID NOS: 9 <210>
SEQ ID NO 1 <211> LENGTH: 26 <212> TYPE: DNA
<213> ORGANISM: Artificial Sequence <220> FEATURE:
<223> OTHER INFORMATION: Synthetic <220> FEATURE:
<221> NAME/KEY: misc_feature <222> LOCATION: (17)..(18)
<223> OTHER INFORMATION: y (residue 17) is c or t, m (residue
18) is a or c <400> SEQUENCE: 1 ggatccagac tttgatymtg gctcag
26 <210> SEQ ID NO 2 <211> LENGTH: 30 <212> TYPE:
DNA <213> ORGANISM: Artificial Sequence <220> FEATURE:
<223> OTHER INFORMATION: Synthetic <220> FEATURE:
<221> NAME/KEY: misc_feature <222> LOCATION: (14)..(14)
<223> OTHER INFORMATION: y (residue 14) is c or t <400>
SEQUENCE: 2 gtgaagctta cggytagctt gttacgactt 30 <210> SEQ ID
NO 3 <211> LENGTH: 1428 <212> TYPE: DNA <213>
ORGANISM: Bacterium-partial 16S rDNA of unknown species from Red
Sea coral mucus <400> SEQUENCE: 3 agtcgaacgg cagcgcgaga
gagcttgctt ttttggcggc gagtggcgga cgggtgagta 60 atatatcgga
acgtgcccag tagcggggga taactactcg aaagagtggc taataccgca 120
tacgccctac gggggaaagg gggggatcgc aagacctctc actattggag cggccgatat
180 cggattagct agttggtggg gtaaaggctc accaaggcaa cgatccgtag
ctggtttgag 240 aggacgacca gccacactgg gactgagaca cggcccagac
tcctacggga ggcagcagtg 300 gggaattttg gacaatgggg gaaaccctga
tccagccatc ccgcgtgtat gatgaaggcc 360 ttcgggttgt aaagtacttt
tggcagagaa gaaaaggtat cccctaatac gggatactgc 420 tgacggtatc
tgcagaataa gcaccggcta actacgtgcc agcagccgcg gtaatacgta 480
gggtgcaagc gttaatcgga attactgggc gtaaagcgtg tgtaggcggt tcggaaagaa
540 agatgtgaaa tcccaggggc tcaaccttgg aactgcattt ttaactgccg
agctagagta 600 tgtcagaggg gggtagccat tccacgtgta gcagtgaaat
gcgtagatat gtggaggaat 660 accgatggcg aaggccgccc cctgggataa
tactgacgct cagacacgaa agcgtgggga 720 gcaaacagga ttagataccc
tggtagtcca cgccctaaac gatgtcaact agctgttggg 780 gccgttaggc
cttagtagcg cagctaacgc gtgaagttga ccgcctgggg agtacggtcg 840
caagattaaa actcaaagga attgacgggg acccgcacaa gcggtggatg atgtggatta
900 attcgatgca acgcgaaaaa ccttacctac ccttgacatg tctggaaagc
cgaagagatt 960 tggccgtgct cgcaagagaa ccggaacaca ggtgctgcat
ggctgtcgtc agctcgtgtc 1020 gtgagatgtt gggttaagtc ccgcaacgag
cgcaaccctt gtcattagtt gctacgcaag 1080 agcactctaa tgagactgcc
ggtgacaaac cggaggaagg tggggatgac gtcaagtcct 1140 catggccctt
atgggtaggg cttcacacgt catacaatgg tcgggacaga gggtcgccaa 1200
cccgcgaggg ggagccaatc tcagaaaccc gatcgtagtc cggatcgcag tctgcaactc
1260 gactgcgtga agtcggaatc gctagtaatc gcggatcaga atgtcgcggt
gaatacgttc 1320 ccgggtcttg tacacaccgc ccgtcacacc atgggagtgg
gtttcaccag aagtaggtag 1380 cctaaccgta aggagggcgc ttaccacggt
gggaatcatg actgggag 1428 <210> SEQ ID NO 4 <211>
LENGTH: 1382 <212> TYPE: DNA <213> ORGANISM:
Bacterium-partial 16S rDNA of unknown species from Red Sea coral
mucus <400> SEQUENCE: 4 gaagaccgct ggcggcaggc ctagcacatg
caagtcgagc gcaccttcgg gtgagcggcg 60 gacgggttag taacgcgtgg
gaacgtaccc agatctgcgg aatagccact ggaaacggtg 120 agtaataccg
catacgccct tcgggggaaa gatttatcgg atttggatcg gcccgcgtta 180
gattagatag ttggtggggt aatggcctac caagtctacg atctatagct ggttttagag
240 gatgatcagc aacactggga ctgagacacg gcccagactc ctacgggagg
cagcagtggg 300 gaatcttgga caatgggcgc aagcctgatc cagccatgcc
gcgtgagtga tgaaggccct 360 agggtcgtaa agctctttcg ccagggaaga
taatgacggt acctggtaaa gaaaccccgg 420 ctaactccgt gccagcagcc
gcggtaatac ggagggggtt agcgttgttc ggaattactg 480 ggcgtaaagc
gcgcgtaggc ggactattaa gtcgagggtg aaatcccggg gctcaacccc 540
ggaactgcct tcgatactgg tagtcttgag gtcgagagag gtgagtggaa ctccgagtgt
600 agaggtgaaa ttcgtagata ttcggaagaa caccagtggc gaaggcggct
cactggctcg 660 atactgacgc tgaggtgcga aagtgtgggg agcaaacagg
attagatacc ctggtagtcc 720 acaccgtaaa cgatgaatgc cagtcgtcgg
gtagcatgct attcggtgac acacctaacg 780 gattaagcat tccgcctggg
gagtacggtc gcaagattaa aactcaaagg aattgacggg 840 ggcccgcaca
agcggtggag catgtggttt aattcgaagc aacgcgcaga accttaccaa 900
cccttgacat cccgtgaccg ctggagagat ccagtttccc ttcggggcac ggtgacaggt
960 gctgcatggc tgtcgtcagc tcgtgtcgtg agatgttcgg ttaagtccgg
caacgagcgc 1020 aactcacacc cttagttgcc agcctttagt gggcactcta
ggggaactgc ccgtgataag 1080 cgggaggaag gtgtggatga cgtcaagtcc
tcatggccct tacgggttgg gctacacacg 1140 tgctacaatg gcatctacag
tgggttaatc ccaaaaagat gtctcagttc ggattgtcgt 1200 ctgcaactcg
acggcatgaa gtcggaatcg ctagtaatcg cgtaacagca tgacgcggtg 1260
aatacgttcc cgggccttgt acacaccgcc cgtcacacca tgggagttgg gtctacccga
1320 aggccgtgcg ctaacttttg aggcagcggg gccacggtag gctcagcgag
tggggtgtcc 1380 cc 1382 <210> SEQ ID NO 5 <211> LENGTH:
1483 <212> TYPE: DNA <213> ORGANISM: Bacterium- partial
16S rDNA of unknown species from Red Sea coral mucus <400>
SEQUENCE: 5 tgacgctggc ggcgtggttc agactccaag tcgaacggga ctctttaact
agcttgctat 60 ttaaagatga gagtggcgaa cgggtgcgta acacgtaaag
aacctaccct tatgtctggg 120 atagcccacc gaaaggtgga ttaataccgg
atgtgatctc tcttctcatg aagagaatat 180 taaagctggg gaccttcggg
cctggcgcat aaggagggct ttgcggccta tcagcttgtt 240 ggtgaggtaa
cggctcacca aggctaagac gggtagctgg tctgagagga tgatcagcca 300
cactggaact tagacacggt ccagacacct acgggtggca gcagtttcga atctttcaca
360 atgggcgaaa gcctgatgga gcaacgccgc gtgggggatg aaggccttcg
ggttgtaaac 420 ccctgtcacc aaggataaaa cgctatctat taatactagg
tagcctgatg taacttggag 480 aggaaggagt ggctaactct gtgccagcag
ccgcggtaat acagagactc caggcgttat 540 tcggattcac tgggcgtaaa
gggtgcgcag gcggtcagat gtgtcaggtg tgaaatactg 600 cagcttaact
gtagaactgc acttgaaact atttgactag agtatcggag aggtaagcgg 660
aattccaggt gtagcagtga aatgcgtaga tatctggagg aacaccaatg gcgaaggcag
720 cttactggac gattactgac gctcaggcac gaaagcatgg ggagcgaaag
ggattagata 780 cccctgtagt ccatgccgta aacgttgttc actaactgtt
ggaggattcg accccttcag 840 cggccaagct aacgcgataa gtgaaccgcc
tgaggactac ggccgcaagg ctaaaactca 900 aaggaattga cgggggcctg
cacaagcggt ggagcatgtg gcttaattcg atgcaacgcg 960 aagaacctta
cctaggcttg acatgtggac gaccggggca gagatgccct ttctcttcgg 1020
agcggctaca caggtgctgc atggctgtcg tcagctcgtg tcgtgagatg tttggttaag
1080 tccagcaacg agcgcaaccc ctgccactag ttgccagcat ttagttgggg
actctagtgg 1140 gacaaactct ctctgagagt gggaaggtgg ggacgacgtc
aagtcagtat ggcccttacg 1200 tctagggctg cacacgtgct acaatgcccg
gtacagaggg acgcaatacc gcgaggtgga 1260 gcaaatcctt aaagccgggc
ccagttcaga ttggagtctg caactcgact ccatgaagtt 1320 ggaatcgcta
gtaatggcgc atcagctacg gcgccgtgaa tacgttccca ggccttgtac 1380
acaccgcccg tcacgttatg gaagcccggt cttgccccga agtatgttag ctaacccctt
1440 gtgggtggcg atgtcctaag gtgaggctgg taactggaac gaa 1483
<210> SEQ ID NO 6 <211> LENGTH: 730 <212> TYPE:
DNA <213> ORGANISM: Bacterium-16S rDNA of unknown species of
bacterium from Negev soil <400> SEQUENCE: 6 atgccacgct
agcgggatgc tttacacatg caagtcgaac ggcagcgcga gagagcttgc 60
tctcttggcg gcgagtggcg gacgggtgag taatatatcg gaacgtgccc agtagcgggg
120 gataactact cgaaagagtg gctaataccg catacgccct acgggggaaa
gggggggatc 180 gcaagacctc tcactattgg agcggccgat atcggattag
ctagttggtg gggtaaaggc 240 tcaccaaggc aacgatccgt agctggtttg
agaggacgac cagccacact gggactgaga 300 cacggcccag actcctacgg
gaggcagcag tggggaattt tggacaatgg gggaaaccct 360 gatccagcca
tcccgcgtgt atgatgaagg ccttcgggtt gtaaagtact tttggcagag 420
aagaaaaggt atcccctaat acgggatact gctgacggta tctgcagaat aagcaccggc
480 taactacgtg ccagcagccg cggtaatacg tagggtgcaa gcgttaatcg
gaattactgg 540 gcgtaaagcg tgtgtaggcg gttcggaaag aaagatgtga
aatcccaggg ctcaaccttg 600 gaactgcatt tttaactgcc gagctagagt
atgtcagagg ggggtagaat tccacgtgta 660 gcagtgagat gcgtagatat
gtggaggaat accgatggcg aagcagcccc ctgggatata 720
ctgacgctca 730 <210> SEQ ID NO 7 <211> LENGTH: 689
<212> TYPE: DNA <213> ORGANISM: Bacterium-16S rDNA of
unknown species of bacterium from Negev soil <400> SEQUENCE:
7 cccccagtct gattcccacc gtggtaagcg ccctccttac ggttaggcta cctacttctg
60 gtgaaaccca ctcccatggt gtgacgggcg gtgtgtacaa gacccgggaa
cgtattcacc 120 gcgacattct gatccgcgat tactagcgat tccgacttca
cgcagtcgag ttgcagactg 180 cgatccggac tacgatcggg tttctgagat
tggctccccc tcgcgggttg gcgaccctct 240 gtcccgacca ttgtatgacg
tgtgaagccc tacccataag ggccatgagg acttgacgcc 300 atccccacct
tcctccggtt tgtcaccggc agtctcatta gagtgctctt gcgtagcaac 360
taatgacaag ggttgcgctc gttgcgggac ttaacccaac atctcacgac acgagctgac
420 gacagccatg cagcacctgt gttccggctc tcttgcgagc acggccaaat
ctcttcggct 480 ttccagatat gtcaagggta ggtaaggttt ttcgcgttgc
atcgaattaa tccacatcat 540 ccaccgcttg tgcgggtccc cgtcaattcc
tttgagtttt aatcttgcga ccgtactccc 600 caggcggtca acttcacgcg
ttagctgcgc tactaaggcc taacggcccc aacagctagt 660 tgacatcgtt
tagggcgtgg actaccagg 689 <210> SEQ ID NO 8 <211>
LENGTH: 651 <212> TYPE: DNA <213> ORGANISM:
Bacterium-16S rDNA of unknown species of bacterium from Negev soil
<400> SEQUENCE: 8 ggatgaacgc tggcggcagg cctaacacat gcaagtcgag
cggtagagag aagcttgctt 60 ctcttgagag cggcggacgg gtgagtaatg
cctaggaatc tgcctggtag tgggggataa 120 cgttcggaaa cggacgctaa
taccgcatac gtcctacggg agaaagcagg ggaccttcgg 180 gccttgcgct
atcagatgag cctaggtcgg attagctagt tggtggggta atggctcacc 240
aaggcgacga tccgtaactg gtctgagagg atgatcagtc acactggaac tgagacacgg
300 tccagactcc tacgggaggc agcagtgggg aatattggac aatgggcgaa
agcctgatcc 360 agccatgccg cgtgtgtgaa gaaggtcttc ggattgtaaa
gcactttaag ttgggaggaa 420 gggttgtaga ttaatactct gcaattttga
cgttaccgac agaataagca ccggctaact 480 ctgtgccagc agccgcggta
atacagaggg tgcaagcgtt aatcggaatt actgggcgta 540 aagcgcgcgt
aggtggttag ttaaagttgg gatgtgaaat ccccgggctc aaccctggga 600
actgcattca aaactgactg actagggtat ggtagagggt ggtggaattt c 651
<210> SEQ ID NO 9 <211> LENGTH: 686 <212> TYPE:
DNA <213> ORGANISM: Bacterium-16S rDNA of unknown species of
bacterium from Negev soil <400> SEQUENCE: 9 cccccagtca
tgattacacc gtggtaaccg tcctcccgaa ggttagacta gctacttctg 60
gtgcaaccca ctcccatggt gtgacgggcg gtgtgtacaa ggcccgggaa cgtattcacc
120 gcgacattct gattcgcgat tactagcgat tccgacttca cgcagtcgag
ttgcagactg 180 cgatccggac tacgatcggt tttgtgggat tagctccacc
tcgcggcttg gcaaccctct 240 gtaccgacca ttgtagcacg tgtgtagccc
aggccgtaag ggccatgatg acttgacgtc 300 atccccacct tcctccggtt
tgtcaccggc agtctcctta gagtgcccac cattacgtgc 360 tggtaactaa
ggacaagggt tgcgctcgtt acgggactta acccaacatc tcacgacacg 420
agctgacgac agccatgcag cacctgtctc aatgttcccg aaggcaccaa tctatctcta
480 gaaagttcat tggatgtcaa ggcctggtaa ggttcttcgc gttgcttcga
attaaaccac 540 atgctccacc gcttgtgcgg gcccccgtca attcatttga
gttttaacct tgcggccgta 600 ctccccaggc ggtcaactta atgcgttagc
tgcgccacta agagctcaag gctcccaacg 660 gctagttgac atcgtttacg gcgtgg
686
* * * * *