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Applied and Environmental Microbiology, September 2003, p. 5248-5254, Vol. 69, No. 9
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.9.5248-5254.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Isolation of Strains Belonging to the Cosmopolitan Polynucleobacter necessarius Cluster from Freshwater Habitats Located in Three Climatic Zones
Martin W. Hahn*
Institute for Limnology, Austrian Academy of Sciences, A-5310 Mondsee, Austria
Received 14 April 2003/
Accepted 24 June 2003

ABSTRACT
More than 40 bacterial strains belonging to the cosmopolitan
Polynucleobacter necessarius cluster (
Betaproteobacteria) were
isolated from a broad spectrum of freshwater habitats located
in three climatic zones. Sequences affiliated with the freshwater
P. necessarius cluster are among the most frequently detected
in studies on bacterial diversity in freshwater ecosystems.
Despite this frequent detection with culture-independent techniques
and the cosmopolitan occurrence of members affiliated with this
cluster, no isolates have been reported thus far. The isolated
strains have been obtained from lakes, ponds, and rivers in
central Europe, the People's Republic of China, and East Africa
by use of the filtration-acclimatization method. The 16S rRNA
gene sequences of the isolates are 98.8 to 100% identical to
reference sequences obtained by various authors by use of culture-independent
methods. The isolates, aerobic heterotrophs, grew on a wide
range of standard complex media and formed visible colonies
on agar plates. Thus, the previous lack of isolates cannot be
explained by a lack of appropriate media. Most of the isolates
possess, under a wide range of culture conditions, very small
cells (<0.1 µm
3), even when grown in medium containing
high concentrations of organic substances. Thus, these strains
are obligate ultramicrobacteria. The obtained strains have a
C-shaped cell morphology which is very similar to that of recently
isolated ultramicrobacterial Luna cluster strains (
Actinobacteria)
and the SAR11 cluster strains (
Alphaproteobacteria).

INTRODUCTION
In recent years, diversity studies employing culture-independent
methods have strongly expanded the knowledge about the phylogenetic
composition of freshwater bacterioplankton (
7,
15,
32). In a
comparative study, Zwart and colleagues (
32) identified 34 putative
phylogenetic clusters of bacteria which seem to contain typical
freshwater inhabitants. Seventy percent of these clusters were
reported to contain no cultivated representatives. Each of the
other clusters contained usually only a few cultivated strains,
which are far from covering the whole range of diversity represented
by the available environmental sequences. Zwart and coauthors
also analyzed a set of 14 diversity studies for the detection
of each of the 34 putative freshwater clusters. All of these
analyzed studies have used random cloning of 16S rRNA genes.
One of the most frequently detected putative clusters was the
betaproteobacterial
Polynucleobacter necessarius cluster (the
ACK-1 cluster [
14], or the beta II cluster [
7]). This cluster
was discovered by Hirons and colleagues in a study on diversity
of bacterioplankton in the Adirondack mountain lakes (
14). Meanwhile,
more than 100 environmental 16S rRNA gene sequences affiliated
with the
P. necessarius cluster have been deposited in the public
databases during the past eight years. Most of the sequences
are partial sequences of cloned genes. The sequences have been
obtained from a broad spectrum of lakes and river ecosystems
widely distributed over the northern hemisphere, as well as
from one lake in the southern hemisphere. This set of ecosystems
included, for instance, the arctic Toolik Lake (
2,
5), the antarctic
Sombre Lake (
19), the predominately acidic Adirondack mountain
lakes (
14,
18), the deep oligotrophic Lake Baikal (
7,
24), and
rivers ranging from oligotrophic to eutrophic (
4,
22,
23,
32).
Only one published
P. necessarius cluster sequence has been
obtained from a nonsurface freshwater system (
20). This short
sequence was obtained in an investigation on the bacterial diversity
in boreholes along a tunnel 626 m below ground surface. No
P. necessarius cluster sequences have been reported from freshwater
sediments or marine or soil systems.
Pernthaler and colleagues applied a cluster-specific probe for detection of P. necessarius cluster members in the acidic Lake Fuchskuhle by way of fluorescence in situ hybridization. Up to 50% of the bacterioplankton consisted of bacteria affiliated with the P. necessarius cluster (3a).
No pure-culture isolates affiliated with the P. necessarius cluster have been reported thus far. Bruns and colleagues systematically studied the influence of signal compounds (e.g., cyclic AMP) and different incubation conditions on the culturability of freshwater bacterioplankton (3). They grew diluted samples of bacterioplankton in synthetic medium and analyzed the obtained mixed cultures by 16S rRNA gene fingerprinting techniques. Analysis of sequences obtained from the fingerprints demonstrated that they successfully enriched members of the P. necessarius cluster in their mixed cultures.
The species after which the P. necessarius cluster was named is an obligate endosymbiont of the hypotrichous ciliate Euplotes aediculatus (13, 28). This bacterium was never grown in pure culture but was described as a species in 1987 (13). The type strain of this species is still growing as an endosymbiont in a ciliate culture.
In this paper, the first isolation and cultivation of strains affiliated with the P. necessarius cluster is reported, and insights into the ecology of this group of representative freshwater bacteria are presented.

MATERIALS AND METHODS
Sampling sites.
Samples from nine ecologically contrasting freshwater habitats
located in three climatic zones were processed in order to isolate
representative freshwater bacteria (Table
1). Samples taken
from Lake Mondsee were immediately processed after sampling.
All of the other samples were transported to the laboratory
in sealed tubes and processed within a few days after sampling.
All treatments after sampling were carried out under aseptic
conditions.
Isolation and maintenance of strains.
For isolation, the filtration-acclimatization method was used
(
12). Briefly, 5 to 10 ml of sample was filtered through 0.2-µm-pore-size
filters (Minisart syringe filters; Sartorius, Göttingen,
Germany). Subsamples of 100 µl of filtrate were transferred
to wells of sterile 24-well cell culture plates and diluted
with 900 µl of sterile inorganic basal medium (
12). One
to four culture plates were set up per sample. The bacteria
contained in the filtrated subsamples were stepwise acclimatized
to higher substrate concentrations. Therefore, each well received
stepwise-increasing doses of NSY (nutrient broth, soytone, yeast
extract) medium (
12). In most of the isolation experiments performed,
screening of wells for growth of bacteria was done by dropping
5-µl samples of the cultures onto agar plates with concentrations
of NSY of 3 g liter
-1 (hereafter referred to as 3-g liter
-1 NSY agar plates) and subsequently incubating the plates at room
temperature. In a few isolation experiments, the wells were
screened microscopically before plating of samples onto agar
plates (
12). In all of the experiments, samples of colonies
grown on plates were suspended in inorganic basal medium, stained
with DAPI (4',6'-diamidino-2-phenylindole [Sigma]; 0.1 mg ml
-1 final concentration), and screened by epifluorescence microscopy
for the presence of small C-shaped cells. Positive colonies
were subcultured in liquid 3-g liter
-1 NSY medium and plated
again onto NSY agar plates. This procedure was repeated until
pure cultures were established. Pure cultures were preserved
by deep freezing (3 g-liter
-1 NSY medium plus 10% glycerol and
storage at -70°C).
Sequencing of 16S rRNA genes and phylogenetic analysis.
Amplification and sequencing of the 16S rRNA genes of the isolates were performed as described previously (12), but PCR products were sequenced by MWG-Biotech (Ebersberg, Germany). The program BLAST (http://www.ncbi.nlm.nih.gov/BLAST/; 1) was used to find all publicly available sequences closely related to the sequences obtained from the isolates, as well as all sequences affiliated with the P. necessarius cluster. Therefore, complete and partial sequences of the isolates and other members of the cluster were submitted for comparison. Self-owned as well as publicly available reference sequences were aligned by using the ARB software package (http://www.arb-home.de; 30). For construction of phylogenetic trees, the aligned sequences were exported to other programs. Neighbor-joining trees were constructed with the software Mega version 2.1 (http://www.megasoftware.net; 17). Evolutionary distances were corrected for multiple substitutions according to the algorithm of Jukes and Cantor (16). Maximum likelihood trees were constructed with the software Treefinder (written by G. Jobb; http://www.treefinder.de).
Growth of isolates on various complex media.
Ten different complex media were used in order to reveal the range of media which support growth of the isolates. The media used for this purpose were Bacto Yeast Extract, Bacto Peptone, soytone peptone, Bacto Tryptic Soy Broth (without dextrose), Bacto Luria-Bertani Broth, Bacto Nutrient Broth, R2A agar (Remel), standard method agar (Remel), eugonic broth (Remel), and Bacto Brain Heart Infusion (Becton Dickinson). Unless stated otherwise, media were purchased from Difco. For better comparability, all media were adjusted to substrate concentrations of 3 g liter-1 and agar concentrations of 1.5%. The test was restricted to a subset of 10 isolates representing almost all of the isolated 16S rRNA genotypes. Ten microliters of precultures (liquid 3-g liter-1 NSY medium) were spread onto the agar plates by use of an inoculating loop, and the plates were incubated at room temperature (ca. 20°C) for 10 days. Incubation of the isolates on 3-g liter-1 NSY agar plates served as a positive control for bacterial growth. Formation of visible colonies within 10 days was assessed as support of growth by a particular medium.
Determination of bacterial growth rates.
For a subset of 10 isolates, the growth rates in liquid 3-g liter-1 NSY medium were determined by measurement of the optical density at 575 nm during growth at a constant temperature of 20°C.
Determination of bacterial cell sizes.
The cell sizes of several isolates grown under various culture conditions were determined as described previously (12).
Nucleotide sequence accession numbers.
The nearly complete 16S rRNA gene sequences of the 25 isolates were deposited in the EMBL nucleotide sequence database under the accession numbers AJ550649 to AJ550673.

RESULTS
Isolation of strains.
Forty-five strains with partial 16S rRNA gene sequences affiliated
with the
P. necessarius cluster were isolated from 12 samples
obtained from nine habitats (Table
1). In the cases in which
coisolates obtained from the same water samples shared identical
partial (ca. 500-bp) sequences, only one representative was
included in further sequencing. The remaining 25 isolates (Table
2) represent 11 different 16S rRNA genotypes (Fig.
1). All of
the 25 isolates sharing identical sequences were isolated either
from different habitats or from samples from the same habitat
(Lake Mondsee) taken on different dates.
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TABLE 2. Isolates affiliated with the P. necessarius cluster and partial or nearly complete environmental 16S rRNA gene sequences with highest similarities
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In total, six samples taken from Lake Tai hu at three different
locations have been processed, but despite the large number
of samples it was possible to isolate only a single strain belonging
to the
P. necessarius cluster. In the case of all six samples,
large filamentous bacteria occurred in the majority of the 144
established enrichment cultures. These filamentous bacteria
are able to overgrow
P. necessarius cluster strains, as well
as other ultramicrobacteria (
12). The same filamentous morphotypes
also occurred in cultures inoculated with samples taken from
other habitats. These bacteria occurred with lower frequencies
in the other enrichment cultures than in the enrichment cultures
obtained from Lake Tai hu samples. Therefore, isolation experiments
with the other investigated samples were more successful in
terms of the number of
P. necessarius cluster isolates obtained
than the trials with the Lake Tai hu samples.
All isolated strains possess a C-shaped morphology and small cells (Fig. 2). The strains formed tiny, nonpigmented, convex colonies with entire margins on NSY agar plates. In comparison to most of the isolates usually growing on NSY plates inoculated with lake water, the tested strains grew slowly and formed only small colonies (
1 mm after 10 days of incubation). A few isolates never grew to colony size (>0.1 mm), which strongly complicated the handling of single colonies.
Cell sizes of the isolated strains.
During the isolation procedure, the established enrichment cultures
were screened microscopically for the presence of small C-shaped
cells. During this process, no C-shaped cells larger than 0.1
µm
3 were observed. All finally isolated strains possessed
small cells when grown in low-substrate-concentration media.
Most isolates even kept this small cell size when growing exponentially
in a medium with high substrate concentrations (Table
3; Fig.
3).
Growth on various complex media.
The 10 tested strains grew on a wide range of complex media
(Table
3). Each of the 10 tested complex media supported the
growth of at least a few strains, and the majority of the media
supported the growth of most tested strains. Best results were
obtained with NSY, R2A, Luria-Bertani, and peptone agar (Table
3).
16S rRNA gene phylogeny.
The phylogenetic analysis of the 16S rRNA gene sequences obtained from the isolated strains revealed that all isolates are more closely related to uncultured bacteria than to any bacterial strain previously obtained from pure cultures (Table 2). Some of the isolates share identical sequences with uncultured bacteria, and sequences of most of the isolates differ in only a few nucleotide positions from sequences obtained by culture-independent techniques. The closest related previously described species is the obligate endosymbiont P. necessarius (96 to 99% similarity), and the closest related bacteria available as pure cultures are Ralstonia basilensis (93 to 94% similarity), R. campinensis (93 to 94% similarity), and R. paucula (93 to 94% similarity) (8, 29).
The minimum sequence similarity within the whole P. necessarius cluster is 95.7%. The whole P. necessarius cluster can be subdivided into four subclusters (labeled A, B, C, and D) which contain sequences separated from the other sequences by sequence similarities of
98% (Fig. 1). Sequence similarities between members of subclusters C and D are in the range of 96.4 to 97.8%. Subcluster A contains only one sequence long enough to be considered in the phylogenetic tree shown in Fig. 1. In analysis with data sets including shorter sequences, other sequences clustered within subcluster A, and results from bootstrap analysis supported this subcluster (data not shown). Furthermore, other shorter sequences clearly clustered within the subclusters B, C, and D. The subclusters were consistent in the neighbor-joining tree (Fig. 1), the maximum likelihood tree (data not shown), and in a minimum evolution tree published by Zwart and colleagues (32). On the other hand, all three trees show some differences in the branching orders. Analysis with larger data sets including shorter sequences indicated that more than the four described major subclusters may exist. All described subclusters contain several environmental sequences, but all isolates analyzed thus far fall into two of the four subclusters. Both of these subclusters contain identical sequences obtained from isolates originating from distantly located ecosystems (Fig. 1). On the other hand, sequences obtained from organisms inhabiting the same ecosystem are affiliated with different subclusters or occur in part at different positions within the same subclusters. For instance, eight strains were isolated from Lake Mondsee, which represent four different genotypes distributed over subclusters C and D.

DISCUSSION
Isolation.
Given the observed cosmopolitan distribution of
P. necessarius cluster bacteria, the occurrence in a broad spectrum of freshwater
habitats, the expected significant contribution to freshwater
bacterioplankton, and the ability of isolates to form visible
colonies on agar plates, it is highly surprising that isolation
of strains belonging to this cluster has not been reported before.
Clearly, the previous lack of isolates cannot be explained by
a lack of suitable media supporting the growth of these bacteria.
With certainty, there have been many research projects which
included plating of freshwater samples onto diverse solid media.
When isolates obtained in such projects have been screened microscopically,
the
P. necessarius cluster members should have attracted attention
because of their unusually small cells and their unusual morphology.
Thus, the previous lack of isolates clearly indicates that members
of this cluster are not readily cultivable.
I assume that one crucial step in the isolation of these bacteria is the acclimatization procedure. The applied slow transition from the low environmental substrate concentrations to the high concentrations of standard microbiological media may enable the bacteria to acclimatize their physiology to the artificial conditions existent in these media. Another crucial step, at least in the case of culturing in liquid media, seems to be the exclusion of strains able to overgrow the slowly growing P. necessarius cluster members in the cultures.
The filtration-acclimatization method employed in this study has been recently developed and employed for the isolation of ultramicrobial Actinobacteria from freshwater (12). Interestingly, only one isolate (MWH-VicM1) affiliated with the P. necessarius cluster has been obtained during this previous isolation effort. On the other hand, only a few pure cultures of members of the actinobacterial Luna-1 and Luna-2 clusters were obtained in the study presented here. The two series of isolation experiments differ in only two seemingly minor points. In the first series, screening of cell culture plate wells was performed by spreading diluted samples onto agar plates, while in the second set of isolation efforts, undiluted samples were dropped onto the plates and incubated without spreading. Secondly, the first series of isolation experiments included samples taken at in situ temperatures of <10°C, while all samples used in the second series of isolation efforts were taken at in situ temperatures of >10°C. Both series of isolation efforts, however, included several samples taken from Lake Mondsee, which is inhabited by both groups of freshwater ultramicrobacteria. Currently it is not clear which factors caused the markedly different results of the two series of isolation efforts.
Phylogenetic structure of the P. necessarius cluster.
The phylogenetic analyses presented by others (32) as well as that in this study clearly show that the P. necessarius cluster is organized into at least four different subclusters. The sequence dissimilarities separating these subclusters may indicate that these subclusters represent different species. Isolates belonging to subclusters C and D, however, have similar morphologies and cell sizes. Likewise, the investigated strains belonging to the two subclusters do not show any consistent differences in growth on the 10 complex media (Table 3). Further detailed studies may reveal that strains belonging to different subclusters differ in physiological and ecological traits.
Ecology of the P. necessarius cluster bacteria.
All investigated isolates affiliated with the P. necessarius cluster can be characterized as aerobic heterotrophic bacteria with small cells. The only other well-investigated representative of the P. necessarius cluster is the obligate endosymbiont P. necessarius which was found in cytoplasmic vesicles of the hypotrichous ciliate Euplotes aediculatus but has never been cultured in pure culture (13, 28). This endosymbiont is closely related to the isolates (Fig. 1) but is distinctively different in morphology (slightly curved rods versus C-shaped cells) and cell size. Cell volumes of all the isolates are <0.2 µm3 (Table 3) while the endosymbiotic strain possesses larger cell volumes of 0.2 to 0.5 µm3 (calculated from data from reference 6). Furthermore, P. necessarius cells stained with DNA-specific dyes show usually 3 to 9, but in some cases up to 12, intensely stained and regularly spaced dots. Some of the isolates affiliated with subcluster C also show such nucleoid-like structures when stained with DAPI. In contrast to those of the endosymbiont P. necessarius, almost all cells of these strains show only a single nucleoid, but in cases of dividing stages two nucleoid-like structures have been observed. All of these differences between the endosymbiont and the isolates, as well as the small sample volumes (
10 ml) used for isolation experiments, the filtration step (with 0.2-µm-pore-size filters) applied during the isolation process, and the observed occurrence of high numbers of free-living cells affiliated with the P. necessarius cluster by in situ hybridization (3a), indicate that it is highly unlikely that the isolates are endosymbionts of planktonic ciliates. Thus, it is much more likely that the P. necessarius cluster represents an important fraction of the free-living freshwater bacterioplankton. On the other hand, it seems that a free-living ancestor of the endosymbiont P. necessarius successfully invaded a ciliate cell and subsequently adapted to the life strategy of an obligate endosymbiont.
A highly important ecological trait which is shared by almost all isolated P. necessarius cluster members is their small (ultramicrosize) cell size (<0.1 µm3), which is even retained under favorable growth conditions (Fig. 2). In this trait, all of the isolates differ markedly from the obligate endosymbiont P. necessarius, as well as from the large-celled R. basilesis, R. campinensis, and R. paucula (8), which are the closest known relatives of the P. necessarius cluster. In the case of free-living, non-particle-associated pelagic bacteria, this trait seems to be one of the prerequisites necessary for establishing populations contributing large fractions to total bacterioplankton. Larger cells are often disadvantageous in the interaction with bacterivorous predators (9, 10, 27). In some cases, large bacterial morphotypes, e.g., bacterial filaments, may receive protection against grazing by some groups of predators (11, 26), but the only way to minimize vulnerability to grazing by all predators seems to be the possession of small cells. This appears to be one of the reasons for the dominance of small bacterial cells in marine and freshwater bacterioplankton.
Interestingly, the P. necessarius cluster isolates share their C-shaped morphology and ultramicrosize with isolates affiliated with the ubiquitous marine SAR11 cluster (21), as well as with actinobacterial Luna cluster members (12). This C-shaped morphology may be a specific adaptation to planktonic life or may provide advantages in the interaction with predators. In a previous experiment with one strain affiliated with the Luna-2 cluster which possesses such a C-shaped cell morphology, a complete protection against grazing by a nanoflagellate was observed (12).
The occurrence of bacteria of the P. necessarius cluster is not restricted to specific types of freshwater ecosystems or to certain climatic zones. They occur in acidic (e.g., Adirondack mountain lakes [14]) and alkaline (e.g., Lake Mondsee and Lake Tai Hu [Table 2]) lakes; they were detected in large lakes (e.g., Lake Baikal [7, 24]) and in small artificial ponds (e.g., Tiger Hill pond in the People's Republic of China [Table 2]); they were observed in arctic (e.g., Toolik Lake [2, 5]), temperate (e.g., Fuchskuhle [7]), and tropical (e.g., Lake Victoria [Table 2]) habitats. Furthermore, they inhabit freshwater ecosystems covering almost the whole range of trophic statuses. The range spans from oligotrophic (e.g., Toolik Lake) over oligomesotrophic (e.g., Lake Mondsee) and eutrophic (e.g., Lake Loosdrecht [32]) to hypertrophic (Lake Tai Hu, Meiling Bay [Table 2]) freshwater ecosystems. Furthermore, the cluster has been detected in several running water systems (e.g., Columbia River [4], Weser River [23], and Yangtze River [22] [Table 2]). On the other hand, there are a few lakes in which the P. necessarius cluster has not been detected (e.g., Crater Lake [31], Lake Gossenköllesee [7], and Lake IJssel [32]). Currently, it is not known whether this lack of detection was caused by low numbers of P. necessarius members combined with methodological limitations or whether this bacterial group is really absent in these lakes. Some of these lakes have very large surface-to-catchment-area ratios and sparse coverage of the catchment areas with vegetation. Thus, import of allochthonous organic substances can be assumed to play only a minor role in these ecosystems. Pernthaler and colleagues observed a higher relative abundance of P. necessarius cluster bacteria in that half of the artificially divided Lake Fuchskuhle which has higher concentrations of humic substances (3a). Both the observation from Lake Fuchskuhle and the lack of detection in lakes with low impact of the catchment areas on the availability of organic carbon in the water columns may indicate that the P. necessarius cluster bacteria utilize allochthonous humic substances. Besides this hypothesis, the currently available data do not indicate that the P. necessarius cluster has a preference for specific types of freshwater ecosystems. When detailed in situ data on abundance and potential seasonal fluctuations of the cluster members become available, it may turn out that the whole cluster or single subgroups prevail in some types of ecosystems more successfully than in others.

ACKNOWLEDGMENTS
I am grateful to Peter Stadler and Matthias Pöckl for their
skillful lab assistance, to Qinglong L. Wu for guiding and assisting
me during sampling of habitats in the People's Republic of China,
to Grace Ssanyu Asiyo, Kampala, Uganda, for water samples from
Lake Victoria, and to Pan Hongxi (NIGLAS) and Liselotte Eisl
for their chemical analysis of samples. Doris and Axel Pitt,
Avrilly, France, enabled the sampling of Canal de Roanne à
Digoin with the research vessel
Bateaux Bleu. Michael Schauer
is acknowledged for providing valuable comments on an earlier
version of the manuscript. Sampling of sites in the People's
Republic of China was made possible by the Chinese Academy of
Sciences, the Nanjing Institute of Geography & Limnology
(NIGLAS), and the Austrian Academy of Sciences.
This study was supported by the Austrian Science Fund (project P15655).

FOOTNOTES
* Mailing address: Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria. Phone: 43 6232 3125-29. Fax: 43 6232 3578. E-mail:
martin.hahn{at}oeaw.ac.at.


REFERENCES
1 - Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.[Abstract/Free Full Text]
2 - Bahr, M., J. E. Hobbie, and M. L. Sogin. 1996. Bacterial diversity in an arctic lake: a freshwater SAR11 cluster. Aquat. Microb. Ecol. 11:271-277.
3 - Bruns, A., U. Nubel, H. Cypionka, and J. Overmann. 2003. Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton. Appl. Environ. Microbiol. 69:1980-1989.[Abstract/Free Full Text]
3 - Burkert, U., J. Pernthaler, F. Warnecke, D. Babenzien, E. Zwirnmann, and R. Amann. Members of a readily enriched ß-proteobacterial clade are common in the surface waters of a humic lake. Appl. Environ. Microbiol., in press.
4 - Crump, B. C., E. V. Armbrust, and J. A. Baross. 1999. Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean. Appl. Environ. Microbiol. 65:3192-3204.[Abstract/Free Full Text]
5 - Crump, B. C., G. W. Kling, M. Bahr, and J. E. Hobbie. 2003. Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Appl. Environ. Microbiol. 69:2253-2268.[Abstract/Free Full Text]
6 - Esteve, I., and N. Gaju. 1999. Bacterial symbioses. Predation and mutually beneficial associations. Int. Microbiol. 2:81-86.[Medline]
7 - Glöckner, F. O., E. Zaichikov, N. Belkova, L. Denissova, J. Pernthaler, A. Pernthaler, and R. Amann. 2000. Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of Actinobacteria. Appl. Environ. Microbiol. 66:5053-5065.[Abstract/Free Full Text]
8 - Goris, J., P. De Vos, T. Coenye, B. Hoste, D. Janssens, H. Brim, L. Diels, M. Mergeay, K. Kersters, and P. Vandamme. 2001. Classification of metal-resistant bacteria from industrial biotopes as Ralstonia campinensis sp. nov., Ralstonia metallidurans sp. nov. and Ralstonia basilensis Steinle et al. 1998 emend. Int. J. Syst. Evol. Microbiol. 51:1773-1782.[Abstract]
9 - Hahn, M. W., and M. G. Höfle. 1999. Flagellate predation on a bacterial model community: interplay of size-selective grazing, specific bacterial cell size, and bacterial community composition. Appl. Environ. Microbiol. 65:4863-4872.[Abstract/Free Full Text]
10 - Hahn, M. W., and M. G. Höfle. 2001. Grazing of protozoa and its effect on populations of aquatic bacteria. FEMS Microbiol. Ecol. 35:113-121.[CrossRef][Medline]
11 - Hahn, M. W., E. R. B. Moore, and M. G. Höfle. 1999. Bacterial filament formation, a defense mechanism against flagellate grazing, is growth rate controlled in bacteria of different phyla. Appl. Environ. Microbiol. 65:25-35.[Abstract/Free Full Text]
12 - Hahn, M. W., H. Lünsdorf, Q. L. Wu, M. Schauer, M. G. Höfle, J. Boenigk, and P. Stadler. 2003. Isolation of novel ultramicrobacteria classified as Actinobacteria from five freshwater habitats in Europe and Asia. Appl. Environ. Microbiol. 69:1442-1451.[Abstract/Free Full Text]
13 - Heckmann, K., and H. J. Schmidt. 1987. Polynucleobacter necessarius gen. nov., sp. nov., an obligately endosymbiotic bacterium living in the cytoplasm of Euplotes aediculatus. Int. J. Syst. Bacteriol. 37:456-457.[Abstract/Free Full Text]
14 - Hirons, W. D., E. A. Methé, S. A. Nierzwickibauer, and J. P. Zehr. 1997. Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences. Appl. Environ. Microbiol. 63:2957-2960.[Abstract]
15 - Höfle, M. G., H. Haas, and K. Dominik. 1999. Seasonal dynamics of bacterioplankton community structure in a eutrophic lake as determined by 5S rRNA analysis. Appl. Environ. Microbiol. 65:3164-3174.[Abstract/Free Full Text]
16 - Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. N. Munro (ed.), Mammalian protein metabolism, vol. 3. Academic Press, New York, N.Y.
17 - Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.[Abstract/Free Full Text]
18 - Methé, B. A., W. D. Hiorns, and J. P. Zehr. 1998. Contrasts between marine and freshwater bacterial community compositionanalyses of communities in Lake George and six other Adirondack lakes. Limnol. Oceanogr. 43:368-374.
19 - Pearce, D. A., C. J. van der Gast, B. Lawley, and J. C. Ellis-Evans. 2003. Bacterioplankton community diversity in a maritime antarctic lake, determined by culture-dependent and culture-independent techniques. FEMS Microbiol. Ecol. 45:59-70.[CrossRef]
20 - Pedersen, K., J. Arlinger, S. Ekendahl., and L. Hallbeck. 1996. 16S rRNA gene diversity of attached and unattached bacteria in boreholes along the access tunnel to the Aespoe hard rock laboratory, Sweden. FEMS Microbiol. Ecol. 19:249-262.[CrossRef]
21 - Rappé, M. S., S. A. Connon, K. L. Vergin, and S. J. Giovannoni. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630-633.[CrossRef][Medline]
22 - Sekiguchi, H., M. Watanabe, T. Nakahara, B. Xu, and H. Uchiyama. 2002. Succession of bacterial community structure along the Changjiang River determined by denaturing gradient gel electrophoresis and clone library analysis. Appl. Environ. Microbiol. 68:5142-5150.[Abstract/Free Full Text]
23 - Selje, N., and M. Simon. 2003. Composition and dynamics of particle-associated and free-living bacterial communities in the Weser estuary, Germany. Aquat. Microb. Ecol. 30:221-237.[CrossRef]
24 - Semenova, E. A., and K. D. Kuznedelov. 1998. A study of the biodiversity of Baikal picoplankton by comparative analysis of 16S rRNA gene 5'-terminal regions. Mol. Biol. 32:754-760.
25 - Simek, K., J. Pernthaler, M. G. Weinbauer, K. Hornak, J. R. Dolan, J. Nedoma, M. Masin, and R. Amann. 2001. Changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir. Appl. Environ. Microbiol. 67:2723-2733.[Abstract/Free Full Text]
26 - Simek, K., J. Vrba, J. Pernthaler, T. Posch, P. Hartman, J. Nedoma, and R. Psenner. 1997. Morphological and compositional shifts in an experimental bacterial community influenced by protists with contrasting feeding modes. Appl. Environ. Microbiol. 63:587-595.[Abstract]
27 - Simek, K., and T. H. Chrzanowski. 1992. Direct and indirect evidence of size-selective grazing on pelagic bacteria by freshwater nanoflagellates. Appl. Environ. Microbiol. 58:3715-3720.[Abstract/Free Full Text]
28 - Springer, N., R. Amann, W. Ludwig, K. H. Schleifer, and H. Schmidt. 1996. Polynucleobacter necessarius, an obligate bacterial endosymbiont of the hypotrichous ciliate Euplotes aediculatus, is a member of the beta-subclass of Proteobacteria. FEMS Microbiol. Lett. 135:333-336.[Medline]
29 - Steinle, P., G. Stucki, R. Stettler, and K. W. Hanselmann. 1998. Aerobic mineralization of 2,6-dichlorophenol by Ralstonia sp. strain RK1. Appl. Environ. Microbiol. 64:2566-2571.[Abstract/Free Full Text]
30 - Strunk, O., O. Gross, B. Reichel, M. May, S. Hermann, N. Stuckmann, B. Nonhoff, M. Lenke, A. Ginhart, A. Vilbig, T. Ludwig, A. Bode, K.-H. Schleifer, and W. Ludwig. 1998. ARB: a software environment for sequence data. Department of Microbiology, Technische Universität München, Munich, Germany.
31 - Urbach, E., K. L. Vergin, L. Young, A. Morse, G. L. Larson, and S. J. Giovannoni. 2001. Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake. Limnol. Oceanogr. 46:557-572.
32 - Zwart, G., B. C. Crump, M. P. Kamst-van Agterveld, F. Hagen, and S. K. Han. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat. Microb. Ecol. 28:141-155.[CrossRef]
Applied and Environmental Microbiology, September 2003, p. 5248-5254, Vol. 69, No. 9
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.9.5248-5254.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
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