Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments
Candidate phylum Atribacteria JS1 lineage is one of the predominant bacterial groups in anoxic subseafloor sediments, especially in organic-rich or gas hydrate-containing sediments. However, due to the lack of axenic culture representatives, metabolic potential and biogeochemical roles of this phylu...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-11-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2018.02909/full |
| _version_ | 1819040315894398976 |
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| author | Yung Mi Lee Kyuin Hwang Kyuin Hwang Jae Il Lee Mincheol Kim Chung Yeon Hwang Hyun-Ju Noh Hakkyum Choi Hong Kum Lee Jongsik Chun Soon Gyu Hong Seung Chul Shin |
| author_facet | Yung Mi Lee Kyuin Hwang Kyuin Hwang Jae Il Lee Mincheol Kim Chung Yeon Hwang Hyun-Ju Noh Hakkyum Choi Hong Kum Lee Jongsik Chun Soon Gyu Hong Seung Chul Shin |
| author_sort | Yung Mi Lee |
| collection | DOAJ |
| description | Candidate phylum Atribacteria JS1 lineage is one of the predominant bacterial groups in anoxic subseafloor sediments, especially in organic-rich or gas hydrate-containing sediments. However, due to the lack of axenic culture representatives, metabolic potential and biogeochemical roles of this phylum have remained elusive. Here, we examined the microbial communities of marine sediments of the Ross Sea, Antarctica, and found candidate phylum Atribacteria JS1 lineage was the most abundant candidate phylum accounting for 9.8–40.8% of the bacterial communities with a single dominant operational taxonomic unit (OTU). To elucidate the metabolic potential and ecological function of this species, we applied a single-cell genomic approach and obtained 18 single-cell amplified genomes presumably from a single species that was consistent with the dominant OTU throughout the sediments. The composite genome constructed by co-assembly showed the highest genome completeness among available Atribacteria JS1 genomes. Metabolic reconstruction suggested fermentative potential using various substrates and syntrophic acetate oxidation coupled with hydrogen or formate scavenging methanogens. This metabolic potential supports the predominance of Atribacteria JS1 in anoxic environments expanding our knowledge of the ecological function of this uncultivated group. |
| first_indexed | 2024-12-21T09:07:09Z |
| format | Article |
| id | doaj.art-61fd13518ff94b4faf47642440e5a38d |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-21T09:07:09Z |
| publishDate | 2018-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-61fd13518ff94b4faf47642440e5a38d2022-12-21T19:09:18ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-11-01910.3389/fmicb.2018.02909412865Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine SedimentsYung Mi Lee0Kyuin Hwang1Kyuin Hwang2Jae Il Lee3Mincheol Kim4Chung Yeon Hwang5Hyun-Ju Noh6Hakkyum Choi7Hong Kum Lee8Jongsik Chun9Soon Gyu Hong10Seung Chul Shin11Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South KoreaDivision of Polar Life Sciences, Korea Polar Research Institute, Incheon, South KoreaDepartment of Polar Science, University of Science and Technology, Daejeon, South KoreaDivision of Polar Paleoenvironment, Korea Polar Research Institute, Incheon, South KoreaDivision of Polar Life Sciences, Korea Polar Research Institute, Incheon, South KoreaDivision of Polar Life Sciences, Korea Polar Research Institute, Incheon, South KoreaDivision of Polar Life Sciences, Korea Polar Research Institute, Incheon, South KoreaDivision of Polar Earth-System Sciences, Korea Polar Research Institute, Incheon, South KoreaDivision of Polar Life Sciences, Korea Polar Research Institute, Incheon, South KoreaSchool of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, South KoreaDivision of Polar Life Sciences, Korea Polar Research Institute, Incheon, South KoreaUnit of Polar Genomics, Korea Polar Research Institute, Incheon, South KoreaCandidate phylum Atribacteria JS1 lineage is one of the predominant bacterial groups in anoxic subseafloor sediments, especially in organic-rich or gas hydrate-containing sediments. However, due to the lack of axenic culture representatives, metabolic potential and biogeochemical roles of this phylum have remained elusive. Here, we examined the microbial communities of marine sediments of the Ross Sea, Antarctica, and found candidate phylum Atribacteria JS1 lineage was the most abundant candidate phylum accounting for 9.8–40.8% of the bacterial communities with a single dominant operational taxonomic unit (OTU). To elucidate the metabolic potential and ecological function of this species, we applied a single-cell genomic approach and obtained 18 single-cell amplified genomes presumably from a single species that was consistent with the dominant OTU throughout the sediments. The composite genome constructed by co-assembly showed the highest genome completeness among available Atribacteria JS1 genomes. Metabolic reconstruction suggested fermentative potential using various substrates and syntrophic acetate oxidation coupled with hydrogen or formate scavenging methanogens. This metabolic potential supports the predominance of Atribacteria JS1 in anoxic environments expanding our knowledge of the ecological function of this uncultivated group.https://www.frontiersin.org/article/10.3389/fmicb.2018.02909/fullcandidate divisionAtribacteriaJS1single-cell genomicsAntarcticaRoss Sea |
| spellingShingle | Yung Mi Lee Kyuin Hwang Kyuin Hwang Jae Il Lee Mincheol Kim Chung Yeon Hwang Hyun-Ju Noh Hakkyum Choi Hong Kum Lee Jongsik Chun Soon Gyu Hong Seung Chul Shin Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments Frontiers in Microbiology candidate division Atribacteria JS1 single-cell genomics Antarctica Ross Sea |
| title | Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments |
| title_full | Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments |
| title_fullStr | Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments |
| title_full_unstemmed | Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments |
| title_short | Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments |
| title_sort | genomic insight into the predominance of candidate phylum atribacteria js1 lineage in marine sediments |
| topic | candidate division Atribacteria JS1 single-cell genomics Antarctica Ross Sea |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2018.02909/full |
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