Ontology highlight
ABSTRACT:
PROVIDER: PRJNA521446 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR8550983_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
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Project description:Deep-sea sediment microbial communities from Omine Ridge, Nankai Trough, Japan - KR0 metagenome
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Project description:The deep marine subsurface is one of the largest unexplored biospheres on Earth, where members of the phylum Chloroflexi are abundant and globally distributed. However, the deep-sea Chloroflexi have remained elusive to cultivation, hampering a more thorough understanding of their metabolisms. In this work, we have successfully isolated a representative of the phylum Chloroflexi, designated strain ZRK33, from deep-sea cold seep sediments. Phylogenetic analyses based on 16S rRNA genes, genomes, RpoB and EF-tu proteins indicated that strain ZRK33 represents a novel class within the phylum Chloroflexi, designated Sulfochloroflexia. We present a detailed description of the phenotypic traits, complete genome sequence and central metabolisms of the novel strain ZRK33. Notably, sulfate and thiosulfate could significantly promote the growth of the new isolate, possibly through accelerating the hydrolysis and uptake of saccharides. Thus, this result reveals that strain ZRK33 may play a crucial part in sulfur cycling in the deep-sea environments. Moreover, the putative genes associated with assimilatory and dissimilatory sulfate reduction are broadly distributed in the genomes of 27 metagenome-assembled genomes (MAGs) from deep-sea cold seep and hydrothermal vents sediments. Together, we propose that the deep marine subsurface Chloroflexi play key roles in sulfur cycling for the first time. This may concomitantly suggest an unsuspected availability of sulfur-containing compounds to allow for the high abundance of Chloroflexi in the deep sea.
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Project description:Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments
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Project description:Sulfate-reducing bacteria (SRB) are ubiquitously distributed across various biospheres and play key roles in global sulfur and carbon cycles. However, few deep-sea SRB have been cultivated and studied in situ, limiting our understanding of the true metabolism of SRB in the deep biosphere. Here, we firstly clarified the high abundance of SRB in deep-sea sediments via the operational taxonomic units (OTU) sequencing analysis. We have successfully isolated a sulfate-reducing bacterium (strain zrk46) from a cold seep sediment, by using an enriched medium supplemented with sulfate. Our genomic, physiological and phylogenetic analyses indicate that strain zrk46 is a novel species, which we propose be named: Pseudodesulfovibrio serpens. Based on the combined results from growth assays and proteomic analyses, we found that supplementation with sulfate (SO42-), thiosulfate (S2O32-), or sulfite (SO32-) promoted the growth of strain zrk46 by facilitating energy production through the dissimilatory sulfate reduction with the auxiliary functions of heterodisulfide reductases, ferredoxins, and nitrate reduction associated proteins, which were coupled to the oxidation of environmental organic matter in both laboratory and deep-sea in situ conditions. Moreover, metatranscriptomic results have also confirmed the dissimilatory sulfate reduction of deep-sea SRB in in situ environment, which might be coupled to the methane oxidation of anaerobic methanotrophic archaea (ANME-2). Overall, these findings expand our understanding of deep-sea SRB, while highlighting their importance for deep-sea sulfur and carbon cycles.
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Project description:Analysis of microbial communities in gas hydrate-bearing subseafloor sediments from the Nankai Trough
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Project description:Zero-valent sulfur (ZVS) distributes widely in the deep-sea cold seep, which is important immediate in the active sulfur cycle of cold seep. In our preview work, a novel ZVS formation pathway discovered in the deep-sea cold weep bacterium Erythrobacter flavus 21-3 was described. However, whether this pathway worked and what function roles it played in the cold seep were unknown. In this study, E. flavus 21-3 was verified to produce zero-valent sulfur in the cold seep using genes soxB and tsdA as our preview report described. Based on proteomic data, stoichiometric methods and microscopic observation, this ZVS formation pathway benefited E. flavus 21-3 in the deep-sea cold seep. Notably, 30% metagenomes contained these two genes in the shallow sediments, which present the most abundant sulfur genes and active sulfur cycle in the cold seep sediments. It suggested that this sulfur formation pathway exist across many bacteria in the cold seep. This strongly indicates that this novel pathway might be frequently used by microbes and plays an important role in the biogeochemical sulfur cycle in cold seep.
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