Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin

Department of Biology, Portland State University, Portland, OR, USA.
Geobiology (Impact Factor: 3.83). 03/2012; 10(4):333-46. DOI: 10.1111/j.1472-4669.2012.00325.x
Source: PubMed


Diverse microbial communities thrive on and in deep-sea hydrothermal vent mineral deposits. However, our understanding of the inter-field variability in these communities is poor, as limited sampling and sequencing efforts have hampered most previous studies. To explore the inter-field variability in these communities, we used barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA gene to characterize the archaeal and bacterial communities of over 30 hydrothermal deposit samples from six vent fields located along the Eastern Lau Spreading Center. Overall, the bacterial and archaeal communities of the Eastern Lau Spreading Center are similar to other active vent deposits, with a high diversity of Epsilonproteobacteria and thermophilic Archaea. However, the archaeal and bacterial communities from the southernmost vent field, Mariner, were significantly different from the other vent fields. At Mariner, the epsilonproteobacterial genus Nautilia and the archaeal family Thermococcaceae were prevalent in most samples, while Lebetimonas and Thermofilaceae were more abundant at the other vent fields. These differences appear to be influenced in part by the unique geochemistry of the Mariner fluids resulting from active degassing of a subsurface magma chamber. These results show that microbial communities associated with hydrothermal vent deposits in back-arc basins are taxonomically similar to those from mid-ocean ridge systems, but differences in geologic processes between vent fields in a back-arc basin can influence microbial community structure.

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    • "We expanded on existing microbiological observations from similar geologic settings (e.g. Kato et al., 2010; Flores et al., 2012; Sylvan et al., 2013) to illustrate the dominance of the rTCA pathway in vent primary productivity on active structures that emit H 2S-rich and H2 and CH4-poor fluids. Our data also further offer new detail through a more refined subsampling strategy, suggesting hitherto unobserved variations in δ "
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    ABSTRACT: Sulfide 'chimneys' characteristic of seafloor hydrothermal venting are diverse microbial habitats. (13) C/(12) C ratios of microbial lipids have rarely been used to assess carbon assimilation pathways on these structures, despite complementing gene- and culture-based approaches. Here, we integrate analyses of the diversity of intact polar lipids (IPL) and their side-chain δ(13) C values (δ(13) Clipid ) with 16S rRNA gene-based phylogeny to examine microbial carbon flow on active and inactive sulfide structures from the Manus Basin. Surficial crusts of active structures, dominated by Epsilonproteobacteria, yield bacterial δ(13) Clipid values higher than biomass δ(13) C (total organic carbon), implicating autotrophy via the reverse tricarboxylic acid cycle. Our data also suggest δ(13) Clipid values vary on individual active structures without accompanying microbial diversity changes. Temperature and/or dissolved substrate effects - likely due to variable advective-diffusive fluxes to chimney exteriors - may be responsible for differing (13) C fractionation during assimilation. In an inactive structure, δ(13) Clipid values lower than biomass δ(13) C and a distinctive IPL and 16S rRNA gene diversity suggest a shift to a more diverse community and an alternate carbon assimilation pathway after venting ceases. We discuss here the potential of IPL and δ(13) Clipid analyses to elucidate carbon flow in hydrothermal structures when combined with other molecular tools.
    Full-text · Article · Jun 2014 · Environmental Microbiology
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    • "Our study on the distribution of the Aquificales along the ELSC/VFR shows that the communities differ between distinct geographical locations and are influenced by the host-rock of the vent field and deposit type where they were detected. These trends are similar to those reported by other authors [4] [11] [37] who showed a north–south shift in microbial diversity patterns in different vent communities concomitant with the north–south geochemical gradient along the ELSC/VFR. Furthermore, our comprehensive survey revealed that the ELSC/VFR contains the largest diversity of Aquificales ever reported in a single geographical area and that this geochemical diverse system may harbor new members of the Aquificales, in particular, some Hydrogenothermaceae that might be 'endemic' to this hydrothermal system. "
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    ABSTRACT: The microbial diversity associated with actively venting deep-sea hydrothermal deposits is tightly connected to the geochemistry of the hydrothermal fluids. Although the dominant members of these deposits drive the structure of the microbial communities, it is less well understood whether the lower abundance groups are as closely connected to the geochemical milieu, or driven perhaps by biotic factors such as microbial community interactions. We used the natural geochemical gradients that exist in the back-arc basin, Eastern Lau Spreading Center and Valu-Fa Ridge (ELSC/VFR) in the Southwestern Pacific, to explore whether the chemolithotrophic Aquificales are influenced by geographical location, host-rock of the vent field or deposit type. Using a combination of cloning, DNA fingerprinting (DGGE) and enrichment culturing approaches, all genera of this order previously described at marine vents were detected, i.e., Desulfurobacterium, Thermovibrio, Aquifex, Hydrogenivirga, Persephonella and Hydrogenothermus. The comparison between clone libraries and DGGE showed similar patterns of distribution of different Aquificales whereas results differed for the enrichment cultures that were retrieved. However, the use of cultivation-based and -independent methods did provide complementary phylogenetic diversity overview of the Aquificales in these systems. Together, this survey revealed that the ELSC/VFR contains some of the largest diversity of Aquificales ever reported at a deep-sea vent area, that the diversity patterns are tied to the geography and geochemistry of the system, and that this geochemical diverse back-arc basin may harbor new members of the Aquificales.
    Full-text · Article · May 2014 · Systematic and Applied Microbiology
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    • "Deep sequencing of hydrothermal vent fluid samples has shown that Lebetimonas is among the dominant Epsilonproteobacteria from Mariana Arc seamounts and that geographical isolation may have a role in structuring these populations (Huber et al., 2010). Lebetimonas has also been identified as dominant in hydrothermal vent deposits from the Eastern Lau Spreading Center, constituting more than half of all reads in some samples (Flores et al., 2012). Finally, Lebetimonas was detected as the only phylotype in the 16S rRNA gene clone library of white microbial mat at the Iceberg vent at NW Rota-1 seamount in one sample year and showed a decrease in abundance during a subsequent sample year, when diffuse fluid temperatures decreased and representatives of the mesophilic genera Sulfurovum and Sulfurimonas were detected (Davis and Moyer, 2008). "
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    ABSTRACT: Chemolithoautotrophic Epsilonproteobacteria are ubiquitous in sulfidic, oxygen-poor habitats, including hydrothermal vents, marine oxygen minimum zones, marine sediments and sulfidic caves and have a significant role in cycling carbon, hydrogen, nitrogen and sulfur in these environments. The isolation of diverse strains of Epsilonproteobacteria and the sequencing of their genomes have revealed that this group has the metabolic potential to occupy a wide range of niches, particularly at dynamic deep-sea hydrothermal vents. We expand on this body of work by examining the population genomics of six strains of Lebetimonas, a vent-endemic, thermophilic, hydrogen-oxidizing Epsilonproteobacterium, from a single seamount in the Mariana Arc. Using Lebetimonas as a model for anaerobic, moderately thermophilic organisms in the warm, anoxic subseafloor environment, we show that genomic content is highly conserved and that recombination is limited between closely related strains. The Lebetimonas genomes are shaped by mobile genetic elements and gene loss as well as the acquisition of novel functional genes by horizontal gene transfer, which provide the potential for adaptation and microbial speciation in the deep sea. In addition, these Lebetimonas genomes contain two operons of nitrogenase genes with different evolutionary origins. Lebetimonas expressed nifH during growth with nitrogen gas as the sole nitrogen source, thus providing the first evidence of nitrogen fixation in any Epsilonproteobacteria from deep-sea hydrothermal vents. In this study, we provide a comparative overview of the genomic potential within the Nautiliaceae as well as among more distantly related hydrothermal vent Epsilonproteobacteria to broaden our understanding of microbial adaptation and diversity in the deep sea.The ISME Journal advance online publication, 21 November 2013; doi:10.1038/ismej.2013.206.
    Full-text · Article · Nov 2013 · The ISME Journal
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