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Bryanskaya AV, Shipova AA, Rozanov AS, Kolpakova OA, Lazareva EV, Uvarova YE, Efimov VM, Zhmodik SM, Taran OP, Goryachkovskaya TN, Peltek SE. Diversity and Metabolism of Microbial Communities in a Hypersaline Lake along a Geochemical Gradient. Biology 2022; 11:biology11040605. [PMID: 35453804 PMCID: PMC9031644 DOI: 10.3390/biology11040605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022]
Abstract
In the south of western Siberia (Russia), there are many unique and unexplored soda, saline, and freshwater lakes. In this study, the results are presented on microbial diversity, its metabolic potential, and their relation with a set of geochemical parameters for a hypersaline lake ecosystem in the Novosibirsk region (Oblast). The metagenomic approach used in this work allowed us to determine the composition and structure of a floating microbial community, the upper layer of silt, and the strata of bottom sediments in a natural saline lake via two bioinformatic approaches, whose results are in good agreement with each other. In the floating microbial community and in the upper layers of the bottom sediment, bacteria of the Proteobacteria (Gammaproteobacteria), Cyanobacteria, and Bacteroidetes phyla were found to predominate. The lower layers were dominated by Proteobacteria (mainly Deltaproteobacteria), Gemmatimonadetes, Firmicutes, and Archaea. Metabolic pathways were reconstructed to investigate the metabolic potential of the microbial communities and other hypothetical roles of the microbial communities in the biogeochemical cycle. Relations between different taxa of microorganisms were identified, as was their potential role in biogeochemical transformations of C, N, and S in a comparative structural analysis that included various ecological niches.
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Affiliation(s)
- Alla V. Bryanskaya
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Correspondence: or ; Tel.: +7-383-363-4963 (ext. 4120)
| | - Aleksandra A. Shipova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Alexei S. Rozanov
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Oxana A. Kolpakova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Elena V. Lazareva
- V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia; (E.V.L.); (S.M.Z.)
| | - Yulia E. Uvarova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Vadim M. Efimov
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Sergey M. Zhmodik
- V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia; (E.V.L.); (S.M.Z.)
| | - Oxana P. Taran
- FRC Krasnoyarsk Science Center SB RAS, Institute of Chemistry and Chemical Technology SB RAS, 660036 Krasnoyarsk, Russia;
| | - Tatyana N. Goryachkovskaya
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Sergey E. Peltek
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
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Korzhuk AV, Myagkaya IN, Rozanov AS, Ershov NI, Saryg-Ool BOY, Malov VI, Gustaytis MA, Shipova AA, Lazareva EV, Peltek SE. Metagenomics data of microbial communities of natural organic matter from the dispersion train of sulfide tailings. Data Brief 2021; 35:106720. [PMID: 33537377 PMCID: PMC7838707 DOI: 10.1016/j.dib.2021.106720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/16/2020] [Accepted: 01/05/2021] [Indexed: 12/02/2022] Open
Abstract
Below is data on the microbial diversity of natural organic matter from the Dispersion Train of Sulfide Tailings (northern Salaire Ridge, southwestern Siberia, Russia, Ursk Village). Data was obtained using 16s rRNA amplicon directed metagenomic sequencing on Illumina MiSeq. The raw sequence data used for analysis is available in NCBI under the Sequence Read Archive (SRA) with BioProject No. PRJNA670045 and SRA accession number SRX9314152, SRX9314376. The data sequences of the 16s rRNA gene are presented at the links MW142408-MW142413, MW142414-MW142447.
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Affiliation(s)
- Anton V Korzhuk
- Laboratory of molecular biotechnology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 10 Lavrentjeva Ave., Novosibirsk 630090, Russia.,Kurchatov Genomics Center, Institute of Cytology and Genetics, SB RAS, 10 Lavrentjeva Ave., Novosibirsk 630090, Russia
| | - Irina N Myagkaya
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences (IGM SB RAS), Novosibirsk 630090, Russia
| | - Alexei S Rozanov
- Laboratory of molecular biotechnology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 10 Lavrentjeva Ave., Novosibirsk 630090, Russia.,Kurchatov Genomics Center, Institute of Cytology and Genetics, SB RAS, 10 Lavrentjeva Ave., Novosibirsk 630090, Russia.,V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences (IGM SB RAS), Novosibirsk 630090, Russia
| | - Nikita I Ershov
- Laboratory of molecular biotechnology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 10 Lavrentjeva Ave., Novosibirsk 630090, Russia
| | - Bagai-Ool Yu Saryg-Ool
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences (IGM SB RAS), Novosibirsk 630090, Russia
| | - Victor I Malov
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences (IGM SB RAS), Novosibirsk 630090, Russia
| | - Maria A Gustaytis
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences (IGM SB RAS), Novosibirsk 630090, Russia
| | - Aleksandra A Shipova
- Laboratory of molecular biotechnology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 10 Lavrentjeva Ave., Novosibirsk 630090, Russia.,Kurchatov Genomics Center, Institute of Cytology and Genetics, SB RAS, 10 Lavrentjeva Ave., Novosibirsk 630090, Russia
| | - Elena V Lazareva
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences (IGM SB RAS), Novosibirsk 630090, Russia
| | - Sergey E Peltek
- Laboratory of molecular biotechnology, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 10 Lavrentjeva Ave., Novosibirsk 630090, Russia
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Bryanskaya AV, Shipova AA, Rozanov AS, Volkova OA, Lazareva EV, Uvarova YE, Goryachkovskaya TN, Peltek SE. Metagenomics dataset used to characterize microbiome in water and sediments of the lake Solenoe (Novosibirsk region, Russia). Data Brief 2020; 34:106709. [PMID: 33490329 PMCID: PMC7807203 DOI: 10.1016/j.dib.2020.106709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/14/2020] [Accepted: 12/28/2020] [Indexed: 11/24/2022] Open
Abstract
This is data on the microbial diversity in the floating cyanobacterial community and sediment samples from the lake Solenoe (Novosibirsk region, Russia) obtained by metagenomic methods. Such a detailed data of the microbial diversity of the Novosibirsk oblast lake ecosystem was carried out for the first time. The purpose of our work was to reveal microbial taxonomic diversity and abundance, metabolic pathways and new enzyme findings the studied lake ecosystem using the next-generation sequencing (NGS) technology and metagenomic analysis. The data was obtained using metagenomics DNA whole genome sequencing (WGS) on Illumina NextSeq and NovaSeq. The raw sequence data used for analysis is available in NCBI under the Sequence Read Archive (SRA) with the BioProjects and SRA accession numbers: PRJNA493912 (SRR7943696), PRJNA493952 (SRR7943839) and PRJNA661775 (SRR12601635, SRR12601634, SRR12601633) corresponding to floating cyanobacterial community and sediment layers samples, respectively.
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Affiliation(s)
- Alla V Bryanskaya
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Aleksandra A Shipova
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Alexei S Rozanov
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Oxana A Volkova
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Elena V Lazareva
- The V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 3 Koptyuga Aven., Novosibirsk 630090, Russia
| | - Yulia E Uvarova
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Tatyana N Goryachkovskaya
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
| | - Sergey E Peltek
- Laboratory of Molecular Biotechnologies of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia.,Kurchatov Genomics Center of Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk 630090, Russia
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Shekhovtsov SV, Shipova AA, Poluboyarova TV, Vasiliev GV, Golovanova EV, Geraskina AP, Bulakhova NA, Szederjesi T, Peltek SE. Species Delimitation of the Eisenia nordenskioldi Complex (Oligochaeta, Lumbricidae) Using Transcriptomic Data. Front Genet 2020; 11:598196. [PMID: 33365049 PMCID: PMC7750196 DOI: 10.3389/fgene.2020.598196] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/09/2020] [Indexed: 01/22/2023] Open
Abstract
Eisenia nordenskioldi (Eisen, 1879) is the only autochthonous Siberian earthworm with a large distribution that ranges from tundra to steppe and broadleaved forests. This species has a very high morphological, ecological, karyological, and genetic diversity, so it was proposed that E. nordenskioldi should be split into several species. However, the phylogeny of the complex was unclear due to the low resolution of the methods used and the high diversity that should have been taken into account. We investigated this question by (1) studying the diversity of the COI gene of E. nordenskioldi throughout its range and (2) sequencing transcriptomes of different genetic lineages to infer its phylogeny. We found that E. nordenskioldi is monophyletic and is split into two clades. The first one includes the pigmented genetic lineages widespread in the northern and western parts of the distribution, and the second one originating from the southern and southeastern part of the species' range and representing both pigmented and non-pigmented forms. We propose to split the E. nordenskioldi complex into two species, E. nordenskioldi and Eisenia sp. 1 (aff. E. nordenskioldi), corresponding to these two clades. The currently recognized non-pigmented subspecies E. n. pallida will be abolished as a polyphyletic and thus a non-natural taxon, while Eisenia sp. 1 will be expanded to include several lineages earlier recognized as E. n. nordenskioldi and E. n. pallida.
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Affiliation(s)
- Sergei V Shekhovtsov
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomic Center, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Laboratory of Biocenology, Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - Aleksandra A Shipova
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomic Center, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatiana V Poluboyarova
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomic Center, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Laboratory of Biocenology, Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - Gennady V Vasiliev
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena V Golovanova
- Laboratory of Systematics and Ecology of Invertebrates, Omsk State Pedagogical University, Omsk, Russia
| | - Anna P Geraskina
- Center for Forest Ecology and Productivity of the Russian Academy of Sciences, Moscow, Russia
| | - Nina A Bulakhova
- Laboratory of Biocenology, Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia.,Laboratory of Biodiversity and Ecology, Tomsk State University, Tomsk, Russia
| | - Tímea Szederjesi
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Sergei E Peltek
- Department of Molecular Biotechnology, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomic Center, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Brekhov EI, Mizin SP, Repin IG, Shipova AA. [The substantiation of the method of gastrointestinal reconstruction after the gastric resection]. Khirurgiia (Mosk) 2013:8-13. [PMID: 23887255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Functional results of 289 major gastric resections and gastrectomies were analyzed. New methods of the gastrointestinal reconstruction after these procedures. The comparative analysis of immediate and long-term results allowed to work out criteria of choice for the reconstructive procedure. Benefits of the suggested reconstructive techniques demonstrated with the use of modern diagnostic means.
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