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Stroeva AR, Klyukina AA, Vidishcheva ON, Poludetkina EN, Solovyeva MA, Pyrkin VO, Gavirova LA, Birkeland NK, Akhmanov GG, Bonch-Osmolovskaya EA, Merkel AY. Structure of Benthic Microbial Communities in the Northeastern Part of the Barents Sea. Microorganisms 2024; 12:387. [PMID: 38399791 PMCID: PMC10892650 DOI: 10.3390/microorganisms12020387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The Barents Sea shelf is one of the most economically promising regions in the Arctic in terms of its resources and geographic location. However, benthic microbial communities of the northeastern Barents Sea are still barely studied. Here, we present a detailed systematic description of the structures of microbial communities located in the sediments and bottom water of the northeastern Barents Sea based on 16S rRNA profiling and a qPCR assessment of the total prokaryotic abundance in 177 samples. Beta- and alpha-diversity analyses revealed a clear difference between the microbial communities of diverse sediment layers and bottom-water fractions. We identified 101 microbial taxa whose representatives had statistically reliable distribution patterns between these ecotopes. Analysis of the correlation between microbial community structure and geological data yielded a number of important results-correlations were found between the abundance of individual microbial taxa and bottom relief, thickness of marine sediments, presence of hydrotrolite interlayers, and the values of pH and Eh. We also demonstrated that a relatively high abundance of prokaryotes in sediments can be caused by the proliferation of Deltaproteobacteria representatives, in particular, sulfate and iron reducers.
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Affiliation(s)
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | | | | | | | | | | | - Nils-Kåre Birkeland
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
| | | | - Elizaveta A. Bonch-Osmolovskaya
- Lomonosov Moscow State University, 119234 Moscow, Russia
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alexander Y. Merkel
- Lomonosov Moscow State University, 119234 Moscow, Russia
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
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Biogeochemical Activity of Methane-Related Microbial Communities in Bottom Sediments of Cold Seeps of the Laptev Sea. Microorganisms 2023; 11:microorganisms11020250. [PMID: 36838215 PMCID: PMC9964916 DOI: 10.3390/microorganisms11020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Bottom sediments at methane discharge sites of the Laptev Sea shelf were investigated. The rates of microbial methanogenesis and methane oxidation were measured, and the communities responsible for these processes were analyzed. Methane content in the sediments varied from 0.9 to 37 µmol CH4 dm-3. Methane carbon isotopic composition (δ13C-CH4) varied from -98.9 to -77.6‱, indicating its biogenic origin. The rates of hydrogenotrophic methanogenesis were low (0.4-5.0 nmol dm-3 day-1). Methane oxidation rates varied from 0.4 to 1.2 µmol dm-3 day-1 at the seep stations. Four lineages of anaerobic methanotrophic archaea (ANME) (1, 2a-2b, 2c, and 3) were found in the deeper sediments at the seep stations along with sulfate-reducing Desulfobacteriota. The ANME-2a-2b clade was predominant among ANME. Aerobic ammonium-oxidizing Crenarchaeota (family Nitrosopumilaceae) predominated in the upper sediments along with heterotrophic Actinobacteriota and Bacteroidota, and mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae). Members of the genera Sulfurovum and Sulfurimonas occurred in the sediments of the seep stations. Mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae) occurred in the sediments of all stations. The microbial community composition was similar to that of methane seep sediments from geographically remote areas of the global ocean.
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Shulga N, Abramov S, Klyukina A, Ryazantsev K, Gavrilov S. Fast-growing Arctic Fe-Mn deposits from the Kara Sea as the refuges for cosmopolitan marine microorganisms. Sci Rep 2022; 12:21967. [PMID: 36539439 PMCID: PMC9768204 DOI: 10.1038/s41598-022-23449-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/31/2022] [Indexed: 12/24/2022] Open
Abstract
The impact of biomineralization and redox processes on the formation and growth of ferromanganese deposits in the World Ocean remains understudied. This problem is particularly relevant for the Arctic marine environment where sharp seasonal variations of temperature, redox conditions, and organic matter inflow significantly impact the biogenic and abiotic pathways of ferromanganese deposits formation. The microbial communities of the fast-growing Arctic Fe-Mn deposits have not been reported so far. Here, we describe the microbial diversity, structure and chemical composition of nodules, crust and their underlying sediments collected from three different sites of the Kara Sea. Scanning electron microscopy revealed a high abundance of microfossils and biofilm-like structures within the nodules. Phylogenetic profiling together with redundancy and correlation analyses revealed a positive selection for putative metal-reducers (Thermodesulfobacteriota), iron oxidizers (Hyphomicrobiaceae and Scalinduaceae), and Fe-scavenging Nitrosopumilaceae or Magnetospiraceae in the microenvironments of the Fe-Mn deposits from their surrounding benthic microbial populations. We hypothesize that in the Kara Sea, the nodules provide unique redox-stable microniches for cosmopolitan benthic marine metal-cycling microorganisms in an unsteady environment, thus focusing the overall geochemical activity of nodule-associated microbial communities and accelerating processes of ferromanganese deposits formation to uniquely high rates.
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Affiliation(s)
- Natalia Shulga
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia.
| | - Sergey Abramov
- Department of Environmental Microbiology, Institute of Sanitary Engineering, Water Quality and Solid Waste Management, University of Stuttgart, Stuttgart, Germany
| | - Alexandra Klyukina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Ryazantsev
- Vernadsky Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Gavrilov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Begmatov S, Savvichev AS, Kadnikov VV, Beletsky AV, Rusanov II, Klyuvitkin AA, Novichkova EA, Mardanov AV, Pimenov NV, Ravin NV. Microbial Communities Involved in Methane, Sulfur, and Nitrogen Cycling in the Sediments of the Barents Sea. Microorganisms 2021; 9:2362. [PMID: 34835487 PMCID: PMC8625253 DOI: 10.3390/microorganisms9112362] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
A combination of physicochemical and radiotracer analysis, high-throughput sequencing of the 16S rRNA, and particulate methane monooxygenase subunit A (pmoA) genes was used to link a microbial community profile with methane, sulfur, and nitrogen cycling processes. The objects of study were surface sediments sampled at five stations in the northern part of the Barents Sea. The methane content in the upper layers (0-5 cm) ranged from 0.2 to 2.4 µM and increased with depth (16-19 cm) to 9.5 µM. The rate of methane oxidation in the oxic upper layers varied from 2 to 23 nmol CH4 L-1 day-1 and decreased to 0.3 nmol L-1 day-1 in the anoxic zone at a depth of 16-19 cm. Sulfate reduction rates were much higher, from 0.3 to 2.8 µmol L-1 day-1. In the surface sediments, ammonia-oxidizing Nitrosopumilaceae were abundant; the subsequent oxidation of nitrite to nitrate can be carried out by Nitrospira sp. Aerobic methane oxidation could be performed by uncultured deep-sea cluster 3 of gamma-proteobacterial methanotrophs. Undetectable low levels of methanogenesis were consistent with a near complete absence of methanogens. Anaerobic methane oxidation in the deeper sediments was likely performed by ANME-2a-2b and ANME-2c archaea in consortium with sulfate-reducing Desulfobacterota. Sulfide can be oxidized by nitrate-reducing Sulfurovum sp. Thus, the sulfur cycle was linked with the anaerobic oxidation of methane and the nitrogen cycle, which included the oxidation of ammonium to nitrate in the oxic zone and denitrification coupled to the oxidation of sulfide in the deeper sediments. Methane concentrations and rates of microbial biogeochemical processes in sediments in the northern part of the Barents Sea were noticeably higher than in oligotrophic areas of the Arctic Ocean, indicating that an increase in methane concentration significantly activates microbial processes.
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Affiliation(s)
- Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Alexander S. Savvichev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.S.S.); (I.I.R.); (N.V.P.)
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Igor I. Rusanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.S.S.); (I.I.R.); (N.V.P.)
| | - Alexey A. Klyuvitkin
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.K.); (E.A.N.)
| | - Ekaterina A. Novichkova
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.K.); (E.A.N.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Nikolai V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.S.S.); (I.I.R.); (N.V.P.)
- Il’ichev Pacific Institute of Oceanology, Far East Branch of the Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
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Tikhonova EN, Kadnikov VV, Rusanov II, Beletsky AV, Zakharova EE, Samylina OS, Ravin NV, Pimenov NV. Methane-Oxidizing Activity and Phylogenetic Diversity of Aerobic Methanotrophs in the Laptev Sea Upper Sediment Horizons. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721030127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Wu H, Wang X, Ganjurjav H, Hu G, Qin X, Gao Q. Effects of increased precipitation combined with nitrogen addition and increased temperature on methane fluxes in alpine meadows of the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135818. [PMID: 31841898 DOI: 10.1016/j.scitotenv.2019.135818] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/09/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Climate change and anthropogenic activities have resulted in increased atmospheric methane (CH4) concentration. Increased nitrogen deposition and precipitation accompanies climate warming and can change soil carbon and nitrogen dynamics and microbial processes and alter CH4 fluxes. To quantify the sink of the vast alpine meadows of the Tibetan Plateau and to examine how precipitation addition (P), warming (W), and nitrogen addition (N) affect CH4 fluxes in alpine meadows, we conducted continuous 3-growing season experiments in an alpine meadow using the static chamber and gas chromatograph method. Soil CH4 samples were collected during the early, peak, and late stages of the growing season from 2015 to 2017. Our results suggested that neither P, W, nor N had an interaction effect on soil CH4 uptake. P significantly increased and decreased the copies number of particulate methane monooxygenase alpha subunit (pmoA) and methyl-coenzyme M reductase alpha subunit (mcrA), respectively. However, P significantly decreased CH4 uptake, particularly under the combined treatment of P and N. Compared with the control, CH4 uptake decreased under P, N, PW, and PN by 50.64%, 6.24%, 39.37%, and 75.06%, respectively, whereas under W and WN CH4 uptake increased by 16.19% and 7.56%, respectively. Soil CH4 uptake was positively correlated with soil temperature and pmoA and negatively correlated with soil moisture and NH4+-N content. CH4 uptake was significantly affected by the sampling period. CH4 uptake was significantly lower rates during peak growing season compared with those during the early and late stages of the growing season. Our results suggest that, (1) CH4 fluxes of alpine grassland ecosystems are more sensitive to P than W or N, and (2) precipitation controls CH4 flux response to increasing nitrogen deposition in alpine meadows on the Tibetan Plateau. Therefore, future research should focus on the response and feedback of CH4 uptake to changes in precipitation.
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Affiliation(s)
- Hongbao Wu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuexia Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hasbagan Ganjurjav
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guozheng Hu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaobo Qin
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingzhu Gao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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