Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan

Summary Subseafloor pelagic sediments with high concentrations of organic matter form habitats for diverse microorganisms. Here, we determined depth profiles of genes for SSU rRNA, mcrA, dsrA and amoA from just beneath the seafloor to 363.3 m below the seafloor (mbsf) using core samples obtained fro...

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Published inEnvironmental microbiology Vol. 18; no. 6; pp. 1889 - 1906
Main Authors Nunoura, Takuro, Takaki, Yoshihiro, Shimamura, Shigeru, Kakuta, Jungo, Kazama, Hiromi, Hirai, Miho, Masui, Noriaki, Tomaru, Hitoshi, Morono, Yuki, Imachi, Hiroyuki, Inagaki, Fumio, Takai, Ken
Format Journal Article
LanguageEnglish
Published England Blackwell Publishing Ltd 01.06.2016
Wiley Subscription Services, Inc
Subjects
Bacteria - classification
Bacteria - genetics
Bacteria - isolation & purification
Bacteria - metabolism
basins
Continental margins
Ecosystem
Genes
Geologic Sediments - chemistry
Geologic Sediments - microbiology
habitats
Japan
Methane - analysis
Methane - metabolism
methane production
Methanogenesis
Microbial activity
microbial communities
Microorganisms
Niches
Ocean floor
Organic matter
Phylogeny
ribosomal RNA
Sediments
Sulfate reduction
Sulfates
Sulfates - analysis
Sulfates - metabolism
Transition zone
variance
Water chemistry
Water depth
INW, Japan, Honshu, Aomori Prefect., Shimokita Peninsula
INW, Japan
Japan
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Summary:Summary Subseafloor pelagic sediments with high concentrations of organic matter form habitats for diverse microorganisms. Here, we determined depth profiles of genes for SSU rRNA, mcrA, dsrA and amoA from just beneath the seafloor to 363.3 m below the seafloor (mbsf) using core samples obtained from the forearc basin off the Shimokita Peninsula. The molecular profiles were combined with data on lithostratigraphy, depositional age, sedimentation rate and pore‐water chemistry. The SSU rRNA gene tag structure and diversity changed at around the sulfate‐methane transition zone (SMTZ), whereas the profiles varied further with depth below the SMTZ, probably in connection with the variation in pore‐water chemistry. The depth profiles of diversity and abundance of dsrA, a key gene for sulfate reduction, suggested the possible niche separations of sulfate‐reducing populations, even below the SMTZ. The diversity and abundance patterns of mcrA, a key gene for methanogenesis/anaerobic methanotrophy, suggested a stratified distribution and separation of anaerobic methanotrophy and hydrogenotrophic or methylotrophic methanogensis below the SMTZ. This study provides novel insights into the relationships between the composition and function of microbial communities and the chemical environment in the nutrient‐rich continental margin subseafloor sediments, which may result in niche separation and variability in subseafloor microbial populations.
Bibliography:Fig. S1. PCA analysis of the bacterial (A) and archaeal (B) SSU rRNA gene communities obtained from the subseafloor sediments of drilling site C9001C. Red and blue squares indicate the sediments of interglacial and glacial periods respectively. Fig. S2. Rarefaction curves of SSU rRNA gene tag communities of whole prokaryotic, bacterial, archaeal and dominant taxa/divisions at each sediment depth from drilling site C9001C. Fig. S3. Diversity, richness and evenness indices of the whole, archaeal and bacterial SSU rRNA gene tag populations in the subseafloor sediments of drilling site C9001C. Fig. S4. Jaccard dissimilarity indices of the SSU rRNA gene tag communities of dominant phyla/divisions in the subseafloor sediments of drilling site C9001C. Fig. S5. Bray dissimilarity indices of SSU rRNA gene tag communities of dominant phyla/divisions in the subseafloor sediments of drilling site C9001C. Fig. S6. Phylogenetic analysis of SSU rRNA genes in methanogenic and methanotrophic archaea based on 780 nucleotide positions including the representative SSU rRNA gene sequences obtained from the subseafloor sediments of drilling site C9001C. The bold type indicates the sequences obtained in this study. Fig. S7. Phylogenetic analysis of dsrA genes based on 150 amino-acid residues, including the representative dsrA sequences obtained from the subseafloor sediments of drilling site C9001C. The bold type indicates the sequences obtained in this study. Fig. S8. PCA of dsrA (A) and mcrA (B) communities obtained from the subseafloor sediments of drilling site C9001C. Fig. S9. The community structures of amoA genes obtained from the subseafloor sediments of drilling site C9001C. Numbers in parentheses indicate the number of clones sequenced. Fig. S10. Phylogenetic analysis of amoA genes based on 588 nucleotide positions, including the representative amoA sequences obtained from the subseafloor sediments of drilling site C9001C. The bold type indicates the sequences obtained in this study. Table S1. Distribution of representative bacterial SSU rRNA gene hylotypes along the core column in site C9001C. Table S2. Distribution of representative archaeal SSU rRNA gene phylotypes along the core column in site C9001C. Table S3. Diversity and richness indices of whole microbial (A), bacterial (B) and archaeal (C) community structures along the core column in site C9001C obtained by the SSU rRNA gene tag sequencing. Table S4. SSU rRNA gene population, and archaeal and methanogen + ANME abundance in whole prokaryotic and archaeal communities, respectively, estimated by the tag sequencing, quantitative PCR and clone analyses in the sediment samples used for tag sequencing. Table S5. Diversity and richness indices of dominant phyla/divisions along the core column in site C9001C obtained by the SSU rRNA gene tag sequencing. Table S6. Distribution of representative dsrA gene phylotypes along the core column in site C9001C. Table S7. Distribution of representative mcrA phylotypes along the core column in site C9001C. Table S8. Primers and PCR conditions used for the PCR-dependent analyses in this study.
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ISSN:1462-2912
1462-2920
1462-2920
DOI:10.1111/1462-2920.13096