Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts.

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
Applied and Environmental Microbiology (Impact Factor: 3.95). 03/2006; 72(2):1680-3. DOI: 10.1128/AEM.72.2.1680-1683.2006
Source: PubMed

ABSTRACT Although microbes associated with shallow-water corals have been reported, deepwater coral microbes are poorly characterized. A cultivation-independent analysis of Alaskan seamount octocoral microflora showed that Proteobacteria (classes Alphaproteobacteria and Gammaproteobacteria), Firmicutes, Bacteroidetes, and Acidobacteria dominate and vary in abundance. More sampling is needed to understand the basis and significance of this variation.

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Available from: Jonathan A Eisen, Jul 28, 2015
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    • "), which matched clone ctg_NISA008 from seawater surrounding Alaskan octocorals (Penn et al., 2006) and a SAR324 fragment (GBSar324) from the Guyamas Basin hydrocarbon-dominated vent plume (Sheik et al., 2013). "
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    ABSTRACT: Deep-sea coral reefs do not receive sunlight and depend on plankton. Little is known about the plankton composition at such reefs, even though they constitute habitats for many invertebrates and fish. We investigated plankton communities from three reefs at 260-350 m depth at hydrocarbon fields off the mid-Norwegian coast using a combination of cultivation and small subunit (SSU) rRNA gene and transcript sequencing. Eight-month incubations of a reef water sample with minimal medium, supplemented with carbon dioxide and gaseous alkanes at in situ-like conditions, enabled isolation of mostly Alphaproteobacteria (Sulfitobacter, Loktanella), Gammaproteobacteria (Colwellia) and Flavobacteria (Polaribacter). The relative abundance of isolates in the original sample ranged from ∼0.01-0.80 %. Comparisons of bacterial SSU sequences from filtered plankton of reef and non-reef control samples indicated high abundance and metabolic activity of primarily Alphaproteobacteria (SAR11 Ia), Gammaproteobacteria (ARCTIC96BD-19), but also of Deltaproteobacteria (Nitrospina, SAR324). Eukaryote SSU sequences indicated metabolically active microalgae and animals, including codfish, at the reef sites. The plankton community composition varied between reefs and differed between DNA- and RNA assessments. Over 5,000 operational taxonomic units (OTUs) were detected, some indicators of reef sites (e.g., Flavobacteria, Cercozoa, Demospongiae) and some more active at reef sites (e.g., Gammaproteobacteria, Ciliophora, Copepoda).
    Environmental Microbiology 06/2014; DOI:10.1111/1462-2920.12531 · 6.24 Impact Factor
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    • "The second subcluster grouped 62% of our Nitrospina-like bacterial sequences that were closely related to sequences obtained from MI_LOCO survey from deepwater samples (890 m) of San Pedro Ocean time-series station (Brown et al., 2005) and from the ETNP OMZ (Beman et al., 2013). This subcluster also grouped sequences derived from contrasting environments, such as microflora from deep-sea corals on Gulf of Alaska seamounts (Penn et al., 2006) and microbial fuel cells reactors inoculated with marine sediment (Wrighton et al., 2008; Fig. 2). The microdiversity of Nitrospina-like bacteria found in the study area as in other marine environments , like the ETNP, indicates the presence of different dominant ecotypes during both winter and summertime. "
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    ABSTRACT: Aerobic nitrite oxidation in marine environments plays a key role in the nitrification process. Marine bacteria involved in this nitrate-producing process have however been seldom studied compared with the ammonia-oxidizing community. Here, we report for the first time the community structure of aerobic nitrite-oxidizing bacteria (NOB) in the seasonal upwelling and oxygen-deficient area off Central Chile. Analysis of 16S rRNA by tag pyrosequencing was combined with specific quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR in summer and wintertime. Nitrospina-like bacteria were the only known NOB detected by means of pyrosequencing between 30 and 80 m depth, accounting for up to 5% of total bacteria. This guild was represented by 11 and 7 operational taxonomic units (97% cut-off) in winter and summertime respectively. Nitrospina-like bacteria were phylogenetically related to sequences retrieved from coastal upwelling, oxygen minimum zones and deep-sea environments. This group was also detected by qPCR with abundances that increased with depth throughout the water column. Importantly, Nitrospina from surface layers showed low abundances but high 16S rRNA : rDNA ratios and mainly in summertime. Overall, our results highlight the seasonal variability between the structure and physiological state of this community and suggest a significant role of Nitrospina in the nitrogen cycle of seasonal upwelling areas.
    Environmental Microbiology Reports 03/2014; 6(6):565-573. DOI:10.1111/1758-2229.12158 · 3.26 Impact Factor
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    • "Phylogenetic analysis showed that the GB-SAR324 16S rRNA gene is affiliated with the ctg_NISA008 clade and shares 98–100% sequence identity with others in this group (Fig. 1) (Penn et al., 2006; Pham et al., 2008). This clade contains other pelagic SAR324 including two sequenced fosmids (ALOHA and Monterey Bay) and the two dark ocean single amplified genomes (Swan et al., 2011) (Fig. 1; see Table 1 for % similarities of 16S rRNA genes). "
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    ABSTRACT: Chemolithotrophy is a pervasive metabolic lifestyle for microorganisms in the dark ocean. The SAR324 group of Deltaproteobacteria is ubiquitous in the ocean and has been implicated in sulfur oxidation and carbon fixation, but also contains genomic signatures of C1 utilization and heterotrophy. Here, we reconstructed the metagenome and metatranscriptome of a population of SAR324 from a hydrothermal plume and surrounding waters in the deep Gulf of California to gain insight into the genetic capability and transcriptional dynamics of this enigmatic group. SAR324's metabolism is signified by genes that encode a novel particulate hydrocarbon monooxygenase (pHMO), degradation pathways for corresponding alcohols and short-chain fatty acids, dissimilatory sulfur oxidation, formate dehydrogenase (FDH) and a nitrite reductase (NirK). Transcripts of the pHMO, NirK, FDH and transporters for exogenous carbon and amino acid uptake were highly abundant in plume waters. Sulfur oxidation genes were also abundant in the plume metatranscriptome, indicating SAR324 may also utilize reduced sulfur species in hydrothermal fluids. These results suggest that aspects of SAR324's versatile metabolism (lithotrophy, heterotrophy and alkane oxidation) operate simultaneously, and may explain SAR324's ubiquity in the deep Gulf of California and in the global marine biosphere.
    Environmental Microbiology 06/2013; 16(1). DOI:10.1111/1462-2920.12165 · 6.24 Impact Factor
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