Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia)
We analyzed the amplicons of the 16S rRNA genes and assembled metagenome-assembled genomes (MAGs) of the enrichment culture from the Fe-Mn layer to have an insight into the diversity and metabolic potential of microbial communities from sediments of two sites in the northern basin of Lake Baikal. Or...
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MDPI AG
2023-07-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/7/1865 |
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| author | Anna Lomakina Sergei Bukin Olga Shubenkova Tatyana Pogodaeva Vyacheslav Ivanov Yuri Bukin Tamara Zemskaya |
| author_facet | Anna Lomakina Sergei Bukin Olga Shubenkova Tatyana Pogodaeva Vyacheslav Ivanov Yuri Bukin Tamara Zemskaya |
| author_sort | Anna Lomakina |
| collection | DOAJ |
| description | We analyzed the amplicons of the 16S rRNA genes and assembled metagenome-assembled genomes (MAGs) of the enrichment culture from the Fe-Mn layer to have an insight into the diversity and metabolic potential of microbial communities from sediments of two sites in the northern basin of Lake Baikal. Organotrophic <i>Chloroflexota</i>, <i>Actionobacteriota</i>, and <i>Acidobacteriota</i>, as well as aerobic and anaerobic participants of the methane cycle (<i>Methylococcales</i> and <i>Methylomirabilota</i>, respectively), dominated the communities of the surface layers. With depth, one of the cores showed a decrease in the proportion of the <i>Chloroflexota</i> and <i>Acidobacteriota</i> members and a substantial increase in the sequences of the phylum Firmicutes. The proportion of the <i>Desulfobacteriota</i> and <i>Thermodesulfovibronia</i> (<i>Nitrospirota</i>) increased in another core. The composition of archaeal communities was similar between the investigated sites and differed in depth. Members of ammonia-oxidizing archaea (<i>Nitrososphaeria</i>) predominated in the surface sediments, with an increase in anaerobic methanotrophs (<i>Methanoperedenaceae</i>) and organoheterotrophs (<i>Bathyarchaeia</i>) in deep sediments. Among the 37 MAGs, <i>Gammaproteobacteria</i>, <i>Desulfobacteriota</i>, and <i>Methylomirabilota</i> were the most common in the microbial community. Metagenome sequencing revealed the assembled genomes genes for N, S, and CH<sub>4</sub> metabolism for carbon fixation, and genes encoding Fe and Mn pathways, indicating the likely coexistence of the biogeochemical cycle of various elements and creating certain conditions for the development of taxonomically and functionally diverse microbial communities. |
| first_indexed | 2024-03-11T00:48:04Z |
| format | Article |
| id | doaj.art-97871d40b0564f17ac1cb71bb6798c74 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-11T00:48:04Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-97871d40b0564f17ac1cb71bb6798c742023-11-18T20:37:33ZengMDPI AGMicroorganisms2076-26072023-07-01117186510.3390/microorganisms11071865Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia)Anna Lomakina0Sergei Bukin1Olga Shubenkova2Tatyana Pogodaeva3Vyacheslav Ivanov4Yuri Bukin5Tamara Zemskaya6Limnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, RussiaLimnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, RussiaLimnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, RussiaLimnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, RussiaLimnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, RussiaLimnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, RussiaLimnological Institute, Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 664033 Irkutsk, RussiaWe analyzed the amplicons of the 16S rRNA genes and assembled metagenome-assembled genomes (MAGs) of the enrichment culture from the Fe-Mn layer to have an insight into the diversity and metabolic potential of microbial communities from sediments of two sites in the northern basin of Lake Baikal. Organotrophic <i>Chloroflexota</i>, <i>Actionobacteriota</i>, and <i>Acidobacteriota</i>, as well as aerobic and anaerobic participants of the methane cycle (<i>Methylococcales</i> and <i>Methylomirabilota</i>, respectively), dominated the communities of the surface layers. With depth, one of the cores showed a decrease in the proportion of the <i>Chloroflexota</i> and <i>Acidobacteriota</i> members and a substantial increase in the sequences of the phylum Firmicutes. The proportion of the <i>Desulfobacteriota</i> and <i>Thermodesulfovibronia</i> (<i>Nitrospirota</i>) increased in another core. The composition of archaeal communities was similar between the investigated sites and differed in depth. Members of ammonia-oxidizing archaea (<i>Nitrososphaeria</i>) predominated in the surface sediments, with an increase in anaerobic methanotrophs (<i>Methanoperedenaceae</i>) and organoheterotrophs (<i>Bathyarchaeia</i>) in deep sediments. Among the 37 MAGs, <i>Gammaproteobacteria</i>, <i>Desulfobacteriota</i>, and <i>Methylomirabilota</i> were the most common in the microbial community. Metagenome sequencing revealed the assembled genomes genes for N, S, and CH<sub>4</sub> metabolism for carbon fixation, and genes encoding Fe and Mn pathways, indicating the likely coexistence of the biogeochemical cycle of various elements and creating certain conditions for the development of taxonomically and functionally diverse microbial communities.https://www.mdpi.com/2076-2607/11/7/1865microbial communitiesLake BaikalFe-Mn layersdiversity of 16S rRNA sequencesmetagenome-assembled genomes (MAGs) |
| spellingShingle | Anna Lomakina Sergei Bukin Olga Shubenkova Tatyana Pogodaeva Vyacheslav Ivanov Yuri Bukin Tamara Zemskaya Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia) Microorganisms microbial communities Lake Baikal Fe-Mn layers diversity of 16S rRNA sequences metagenome-assembled genomes (MAGs) |
| title | Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia) |
| title_full | Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia) |
| title_fullStr | Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia) |
| title_full_unstemmed | Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia) |
| title_short | Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia) |
| title_sort | microbial communities in ferromanganese sediments from the northern basin of lake baikal russia |
| topic | microbial communities Lake Baikal Fe-Mn layers diversity of 16S rRNA sequences metagenome-assembled genomes (MAGs) |
| url | https://www.mdpi.com/2076-2607/11/7/1865 |
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