Phylogenetic analysis of the succession of bacterial communities in the Great South Bay (Long Island)

Kelly, Karen; Chistoserdov, Andrei Y.

doi:10.1111/j.1574-6941.2001.tb00791.x

Cited by 57 publications

(44 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In 16S rDNA studies, this group is rarely found in pelagic samples, having been reported only during enrichments, e.g. during a brown tide bloom of Aureococcus anophagefferens (Kelly & Chistoserdov 2001) and in a mesocosm diatom bloom (Riemann et al 2000). However, we did not determine if this phylotype would have been missed in a multi-liter sample.…”

contrasting

confidence: 39%

Microscale patchiness of bacterioplankton assemblage richness in seawater

Long

Azam²

2001

Aquat. Microb. Ecol.

164

110

View full text Add to dashboard Cite

We sought to test the hypothesis that bacterial species richness and composition vary at the millimeter scale in the marine pelagic environment, in response to the heterogeneous distribution of organic matter. To test this hypothesis, it was necessary to design and test a protocol to sample, lyse and analyze (by polymerase chain reaction/denaturing gradient gel electrophoresis [PCR-DGGE]) bacterioplankton species richness in a single microliter of seawater. Significant variation in bacterial species richness was found amongst 1 µl samples. Greater species richness was seen when seawater was enriched with diatom detritus. Examination of species richness at 2 mm intervals over a 20 mm transect showed greater variability during the peak abundance of Lingulodinium polyedrum when compared to the late stage of the bloom. Overall species richness was highest in samples enriched with organic particles. These results suggest that particulate organic matter may, in part, regulate the level of bacterial species richness as well as cause patchiness in the small-scale distribution of species. Microscale patchiness of bacterial species may have important implications in carbon cycling and biogeochemistry, not only at the microscale but also at the ocean basin scale.KEY WORDS: Species richness · Diversity · Lyse-N-Go™ · DGGE · Community structure Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 26: [103][104][105][106][107][108][109][110][111][112][113] 2001 clude clustering (Azam & Ammerman 1984, Blackburn et al. 1998), attachment to algae or detritus (Biddanda & Pomeroy 1988, Smith et al. 1995 and interactions with the gel particle matrix , Long & Azam 1996. Indeed, one might even envision the formation of monospecific microcolonies of bacteria at specific organic matter loci in seawater (J. W. Ammerman et al. unpubl.).There are potentially profound biogeochemical implications of microscale variations in bacterial abundance or bacterial composition, diversity and richness.While a few studies have tested for microscale variation in bacterial abundance, there has been no direct examination of bacterial community richness at the microscale level in the ocean. Bacterial counts in microliter samples have been used to test for variations in abundance. Duarte & Vaque (1992) found a 2.5-fold variation, while Mitchell & Fuhrman (1989) found 3.5-fold variation over a centimeter scale. However, MullerNiklas et al. (1996) detected no significant variation amongst 100 nl samples. Seymour et al. (2000) took 50 µl seawater samples 4.5 mm apart from each other. They found unstirred samples to have low variation but a 16-fold variation was observed if seawater was stirred prior to sampling. They attribute this difference to turbulent flows that spatially structure bacteria populations as well as to the interaction of bacteria with the gel particle matrix. No previous study has tested the hypothesis that microscale variations in species richness and patchiness exist in seawater. The...

show abstract

contrasting

confidence: 39%

Microscale patchiness of bacterioplankton assemblage richness in seawater

Long

Azam²

2001

Aquat. Microb. Ecol.

164

110

View full text Add to dashboard Cite

show abstract

“…1 (see SI Tables 3-7 for details) or in the complex medium SYPG containing the following compounds per liter of distilled water: 35.0 g of sea salts, 0.5 g of yeast extract, 0.25 g of Trypticase peptone, and 0.1 g of sodium L-glutamate. Utilization of substrates was tested in a mineral medium containing (per liter) 35.0 g of sea salts, 0.1 g of NH 4 Cl, 0.05 g of K 2 HPO 4 , and 10 ml of a vitamin solution (see DSMZ medium 141, www.dsmz.de). Standard tests for the detection of enzymes like catalase, oxidase, lipase/esterase, and proteases were done according to the protocols given in ref.…”

Section: Methodsmentioning

confidence: 99%

“…In the following years, many sequences have been retrieved that were related to the clone OM60 (e.g., refs. [3][4][5][6][7][8]. By the end of 2005, Ͼ180 partial and full length 16S rRNA sequences available within the public databases were related to KT71 and OM60.…”

Section: N 1999 Eilers Et Al (1) Isolated a Bacterial Strain Desimentioning

confidence: 99%

Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis

Fuchs

Spring

Teeling

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

125

119

View full text Add to dashboard Cite

Members of the gammaproteobacterial clade NOR5/OM60 regularly form an abundant part, up to 11%, of the bacterioplankton community in coastal systems during the summer months. Here, we report the nearly complete genome sequence of one cultured representative, Congregibacter litoralis strain KT71, isolated from North Sea surface water. Unexpectedly, a complete photosynthesis superoperon, including genes for accessory pigments, was discov- from a surface water sample taken near the North Sea island Helgoland, by direct plating on complex low-nutrient media. Phylogenetic analysis showed that KT71 was the first cultured representative of a cosmopolitan gammaproteobacterial lineage, which we in the following refer to as the NOR5/OM60 clade (Fig. 1). The first indication for this clade dates back to 1997, when Rappe et al. retrieved two 16S rRNA clones, OM60 and OM241, from the continental shelf off Cape Hatteras, NC (2). In the following years, many sequences have been retrieved that were related to the clone OM60 (e.g.,. By the end of 2005, Ͼ180 partial and full length 16S rRNA sequences available within the public databases were related to KT71 and OM60.KT71 is a Gram-negative, pleomorphic, strictly aerobic, and motile bacterium. It is of an average size of 2 ϫ 0.5 m, has a generation time of 4.5 h, and often grows in flocs. Based on this conspicuous trait and the site of isolation, the name Congregibacter litoralis has been proposed. A full taxonomic description of strain KT71 is currently ongoing (B.M.F., S.S., and R.A., unpublished work). Several more strains belonging to the NOR5/ OM60 clade were isolated off the coast of Oregon, in sterilized seawater, using a high-throughput dilution-to-extinction technique (9, 10). Meanwhile, representatives of the NOR5/OM60 clade were also isolated from Arctic sea ice (11) and coastal sediments (12,13).FISH with rRNA-targeted oligonucleotide probes for NOR5/ OM60 confirmed this clade as an abundant component of the bacterioplankton community in the North Sea around the island Helgoland (1). By the end of July 1998, up to 8% of the total bacterioplankton community comprised members of the NOR5/ OM60 clade (1). A second peak of NOR5/OM60 cells was visible in mid-June (6%). However, NOR5/OM60 was not detected by FISH during the winter months, October to March, suggesting a marked seasonality. The fraction of DNA-synthesizing NOR5/ OM60 cells seems to be quite variable. Active DNA synthesis could be detected in August but not in May 2002, even though NOR5/OM60 was present in high numbers in both samples (6% and 11% of total bacterioplankton cell, respectively) (14).In 2004, KT71 was selected for whole-genome sequencing as part of the Gordon and Betty Moore Foundation (GBMF) Marine Microbiology Initiative. Here, we present data derived from the analysis of the genome of strain KT71 and from ecophysiological experiments addressing some of the predictions derived from genome annotation. Results and Discussion Structure and Phylogenetic Analysis of the Photosynthesis (PS)Operon. The...

show abstract

“…Natural clean water of station IV was fetched every two or three days during the experiment for nearly 40 days. During this time, the species of station IV also had a seasonal succession, because it has reported that community composition can change drastically within weeks (Kelly and Chistoserdov, 2001). This is why the average similarity coefficient of within-sample was just 0.33 but not higher.…”

Section: Discussionmentioning

confidence: 92%

“…Many works have been reported to study the structural and functional variables of aquatic communities in relation to the ecological succession (Kowalchuk et al, 2000;Kelly and Chistoserdov, 2001;Merila et al, 2002;Noll et al, 2005;Michail et al, 2005). Since the last decade of last century, nature management has embodied a lot of projects to restore damaged ecosystems (Hemerik and Brussaard, 2002;Clewell and Aronson, 2006).…”

Section: Introductionmentioning

confidence: 99%