Microbial diversity and stratification of South Pacific abyssal marine sediments

Durbin, Alan M.; Teske, Andreas

doi:10.1111/j.1462-2920.2011.02544.x

Cited by 135 publications

(139 citation statements)

References 98 publications

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“…Proteobacteria, Acidobacteria, and Bacteroidetes were present in all stations and all seasons in our study. These phyla have been always identified as dominant groups in sediment environments and were generally important contributors to biogeochemical processes (Durbin and Teske 2011;Wang et al 2012). Proteobacteria were dominant in most surface marine sediments, comprising >50 % of the microbial biomass (Bowman and McCuaig 2003), and it seems that γ-Proteobacteria was the most significant clade in marine sediments (Feng et al 2009;Wang et al 2012).…”

Section: Bacterial Communities In Comparable Habitsmentioning

confidence: 99%

Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

Liu

et al. 2014

J Soils Sediments

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Purpose Although coastal marine sediments harbor diverse bacteria with important ecological and environmental functions, a comprehensive view of their community characteristics is still lacking in typical environments along the China coast. We studied the diversity and composition of bacterial community in the sediment of Jiaozhou Bay and characterized their spatiotemporal patterns, aiming to analyze the effects of geographic heterogeneity, seasonal difference, anthropogenic activity, and eutrophication gradient on the bacterial ecology. Materials and methods Sixteen full-length bacterial 16S rRNA gene clone libraries were constructed from the sediment bacteria at four stations (A5, B2, D1, and D7) of Jiaozhou Bay over four seasons (February, May, August, and November). The bacterial diversity and community structure variation were analyzed. Results and discussion A total of 1088 16S rRNA gene sequences and 746 distinct operational taxonomic units (OTUs) (at 97 % sequence similarity level) were retrieved from the 16 clone libraries. Libraries of each sample revealed a high diversity, and a total of 17 bacterial phyla were identified.Bacteria lineages Proteobacteria (mostly γ-Proteobacteria and δ-Proteobacteria), Actinobacteria, Bacteroidetes, and Planctomycetes, which are commonly found in marine sediments, were the dominant divisions in our samples. Meanwhile, some uncommon phyla, such as Deinococcus-Thermus and Lentisphaerae, were also detected. Distinct spatial patterns and noticeable seasonal variations of bacteria community were observed, indicating that environmental heterogeneity in spatial variation other than in temporal variation may be more important in determining the bacterial communities. Most of the abundant OTUs were related to sequences retrieved from the heavy-metal-polluted environments, indicating that the Jiaozhou Bay might be influenced by pollution. Conclusions The bacterial communities in Jiaozhou Bay sediments are highly diverse. The four typical stations that we chose might experience different anthropogenic effects and eutrophication gradients, which shaped their bacterial community composition. The environment of Jiaozhou Bay may be under pressure exerted by multi-dimension anthropogenic activities. This study provided a novel insight into the bacterial community variations in Jiaozhou Bay, enriching knowledge about ecological bioindicators and mechanisms that maintain bacterial diversity and shape bacterial community composition.

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Section: Bacterial Communities In Comparable Habitsmentioning

confidence: 99%

Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

Liu

et al. 2014

J Soils Sediments

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“…Further, genes for reductive dehalogenases were not detected with PCR using primers targeting these genes using MDA-derived DNA as template. Considering there is speculation that some marine subsurface DEH-affiliated bacteria could perform reductive dehalogenation (Adrian, 2009;Futagami et al, 2009;Valentine, 2010;Durbin and Teske, 2011;Wagner et al, 2012), the apparent absence of genes encoding reductive dehalogenases is worthy to note because this is the first genomic data from relatives of known organohalide-respiring DEH. Even if genes for reductive dehalogenases were in the missing genomic content, the DEH-J10 bacterium is considerably different to cultivated DEH because it does not appear to harbour a high proportion of genetic material dedicated to organohalide respiration.…”

Section: Electron Donating and Processing Reactionsmentioning

confidence: 99%

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

et al. 2013

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Bacteria of the class Dehalococcoidia (DEH), phylum Chloroflexi, are widely distributed in the marine subsurface, yet metabolic properties of the many uncultivated lineages are completely unknown. This study therefore analysed genomic content from a single DEH cell designated 'DEH-J10' obtained from the sediments of Aarhus Bay, Denmark. Real-time PCR showed the DEH-J10 phylotype was abundant in upper sediments but was absent below 160 cm below sea floor. A 1.44 Mbp assembly was obtained and was estimated to represent up to 60.8% of the full genome. The predicted genome is much larger than genomes of cultivated DEH and appears to confer metabolic versatility. Numerous genes encoding enzymes of core and auxiliary beta-oxidation pathways were identified, suggesting that this organism is capable of oxidising various fatty acids and/or structurally related substrates. Additional substrate versatility was indicated by genes, which may enable the bacterium to oxidise aromatic compounds. Genes encoding enzymes of the reductive acetyl-CoA pathway were identified, which may also enable the fixation of CO 2 or oxidation of organics completely to CO 2 . Genes encoding a putative dimethylsulphoxide reductase were the only evidence for a respiratory terminal reductase. No evidence for reductive dehalogenase genes was found. Genetic evidence also suggests that the organism could synthesise ATP by converting acetyl-CoA to acetate by substrate-level phosphorylation. Other encoded enzymes putatively conferring marine adaptations such as salt tolerance and organo-sulphate sulfohydrolysis were identified. Together, these analyses provide the first insights into the potential metabolic traits that may enable members of the DEH to occupy an ecological niche in marine sediments.

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“…Furthermore, geochemical characteristics of deeper sediments indicate microbial activity as several chemical transformations are linked to microbial processes (Parkes et al, 2000;D'Hondt et al, 2004). During the last decades we got insights into microbial community composition and diversity within the deep subsurface (Inagaki et al, 2006;Sørensen and Teske, 2006;Webster et al, 2006;Fry et al, 2008;Lipp et al, 2008;Teske and Sørensen, 2008;Durbin and Teske, 2011).…”

Section: Introductionmentioning

confidence: 99%

Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments

et al. 2012

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Bacteriophages might be the main 'predators' in the marine deep subsurface and probably have a major impact on indigenous microbial communities. To identify their function within this habitat, we have determined their abundance and distribution along the sediment columns of two continental margin and two open ocean sites that were recovered during Leg 201 of the Ocean Drilling Program. For all investigated sites, viral abundance followed the total cell numbers with a virus-to-cell ratio between 1 and 10 in the upper 100 mbsf (meters below seafloor). An increasing ratio of about 20 in deeper layers indicated an ongoing viral production in up to 11 Ma old sediments. We have used Rhizobium radiobacter as the most frequently isolated organism from the deep subsurface with a high in situ abundance to identify the frequency of associated rhizobiophages. In this study, 16S rRNA gene copies of R. radiobacter accounted for up to 5.6% of total bacterial 16S rRNA genes (average: 0.75%) as detected by quantitative PCR. A distinctive distribution was identified for R. radiobacter as indicated by a site-specific arrangement of genetically similar populations. Whole genome information of rhizobiophage RR1-A was used to generate a primer system for quantitative PCR specifically targeting the prophage antirepressor gene, indicative for temperate phages. The quantification of this gene within various sediment horizons showed a contribution of temperate phages of up to 14.3% to the total viral abundance. Thus, the high amount of temperate phages within the sediments and among all investigated isolates indicates that lysogeny is the main viral proliferation mode in deep subsurface populations.

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Microbial diversity and stratification of South Pacific abyssal marine sediments

Cited by 135 publications

References 98 publications

Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments

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