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S V, T J, E AP, A MHA. Antibiotic resistance of heterotrophic bacteria from the sediments of adjoining high Arctic fjords, Svalbard. Braz J Microbiol 2024; 55:2371-2383. [PMID: 38767750 PMCID: PMC11405572 DOI: 10.1007/s42770-024-01368-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/08/2024] [Indexed: 05/22/2024] Open
Abstract
Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are now considered major global threats. The Kongsfjorden and Krossfjorden are the interlinked fjords in the Arctic that are currently experiencing the effects of climate change and receiving input of pollutants from distant and regional sources. The present study focused on understanding the prevalence of antibiotic resistance of retrievable heterotrophic bacteria from the sediments of adjacent Arctic fjords Kongsfjorden and Krossfjorden. A total of 237 bacterial isolates were tested against 16 different antibiotics. The higher resistance observed towards Extended Spectrum β-lactam antibiotic (ESBL) includes ceftazidime (45.56%) followed by trimethoprim (27%) and sulphamethizole (24.05%). The extent of resistance was meagre against tetracycline (2.53%) and gentamycin (2.95%). The 16S rRNA sequencing analysis identified that Proteobacteria (56%) were the dominant antibiotic resistant phyla, followed by Firmicutes (35%), Actinobacteria (8%) and Bacteroidetes. The dominant resistant bacterial isolates are Bacillus cereus (10%), followed by Alcaligenes faecalis (6.47%), Cytobacillus firmus (5.75%) Salinibacterium sp. (5%) and Marinobacter antarcticus (5%). Our study reveals the prevalence of antibiotic resistance showed significant differences in both the inner and outer fjords of Kongsfjorden and Krossfjorden (p < 0.05). This may be the input of antibiotic resistance bacteria released into the fjords from the preserved permafrost due to the melting of glaciers, horizontal gene transfer, and human influence in the Arctic region act as a selection pressure for the development and dissemination of more antibiotic resistant bacteria in Arctic fjords.
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Affiliation(s)
- Vishnupriya S
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India.
| | - Jabir T
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, 403 804, Vasco- da-Gama, Goa, India
| | - Akhil Prakash E
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India
| | - Mohamed Hatha A A
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India
- CUSAT NCPOR Centre for Polar Sciences, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, India
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2
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Trejos-Espeleta JC, Marin-Jaramillo JP, Schmidt SK, Sommers P, Bradley JA, Orsi WD. Principal role of fungi in soil carbon stabilization during early pedogenesis in the high Arctic. Proc Natl Acad Sci U S A 2024; 121:e2402689121. [PMID: 38954550 PMCID: PMC11252988 DOI: 10.1073/pnas.2402689121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 06/04/2024] [Indexed: 07/04/2024] Open
Abstract
Climate warming is causing widespread deglaciation and pioneer soil formation over glacial deposits. Melting glaciers expose rocky terrain and glacial till sediment that is relatively low in biomass, oligotrophic, and depleted in nutrients. Following initial colonization by microorganisms, glacial till sediments accumulate organic carbon and nutrients over time. However, the mechanisms driving soil nutrient stabilization during early pedogenesis after glacial retreat remain unclear. Here, we traced amino acid uptake by microorganisms in recently deglaciated high-Arctic soils and show that fungi play a critical role in the initial stabilization of the assimilated carbon. Pioneer basidiomycete yeasts were among the predominant taxa responsible for carbon assimilation, which were associated with overall high amino acid use efficiency and reduced respiration. In intermediate- and late-stage soils, lichenized ascomycete fungi were prevalent, but bacteria increasingly dominated amino acid assimilation, with substantially decreased fungal:bacterial amino acid assimilation ratios and increased respiration. Together, these findings demonstrate that fungi are important drivers of pedogenesis in high-Arctic ecosystems that are currently subject to widespread deglaciation from global warming.
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Affiliation(s)
- Juan Carlos Trejos-Espeleta
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany, 80333
| | - Juan P. Marin-Jaramillo
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany, 80333
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO80309
| | - Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO80309
| | - James A. Bradley
- Aix Marseille University, University of Toulon, Centre national de la recherche scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Mediterranean Institute of Oceanography (MIO), Marseille, France13009
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom, E1 4NS
| | - William D. Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany, 80333
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany, 80333
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3
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Yadav P, Das J, Sundharam SS, Krishnamurthi S. Analysis of Culturable Bacterial Diversity of Pangong Tso Lake via a 16S rRNA Tag Sequencing Approach. Microorganisms 2024; 12:397. [PMID: 38399801 PMCID: PMC10892101 DOI: 10.3390/microorganisms12020397] [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: 11/29/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 02/25/2024] Open
Abstract
The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing approach based on long read technology to determine the spectrum of bacterial diversity supported by axenic media. The phyla Pseudomonadota, Bacteriodetes, and Actinomycetota were retrieved as the predominant taxa in both water and sediment samples. The genera Hydrogenophaga and Rheinheimera, Pseudomonas, Loktanella, Marinomonas, and Flavobacterium were abundantly present in the sediment and water samples, respectively. Low nutrient conditions supported the growth of taxa within the phyla Bacteriodetes, Actinomycetota, and Cyanobacteria and were biased towards the selection of Pseudomonas, Hydrogenophaga, Bacillus, and Enterococcus spp. Our study recommends that media formulations can be finalized after analyzing culturable diversity through a high-throughput sequencing effort to retrieve maximum species diversity targeting novel/relevant taxa.
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Affiliation(s)
- Pooja Yadav
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
| | - Joyasree Das
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
| | - Shiva S. Sundharam
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
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Handler ER, Andersen SDJ, Gradinger R, McGovern M, Vader A, Poste AE. Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat. FEMS Microbiol Ecol 2024; 100:fiad162. [PMID: 38111220 PMCID: PMC10799726 DOI: 10.1093/femsec/fiad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 10/26/2023] [Accepted: 12/14/2023] [Indexed: 12/20/2023] Open
Abstract
Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a river-intertidal-subtidal-fjord gradient. We paired metabarcoding of in situ communities with in vitro carbon-source utilization assays. Bacterial communities differed in space and time, alongside varying environmental conditions driven by local seasonal processes and riverine inputs, with salinity emerging as the dominant structuring factor. Terrestrial and riverine taxa were found throughout the system, likely transported with runoff. In vitro assays revealed sediment bacteria utilized a broader range of organic matter substrates when incubated in fresh and brackish water compared to marine water. These results highlight the importance of salinity for ecosystem processes in these dynamic tidal flats, with the highest potential for utilization of terrestrially derived organic matter likely limited to tidal flat areas (and times) where sediments are permeated by freshwater. Our results demonstrate that intertidal flats must be included in future studies on impacts of increased riverine discharge and transport of terrestrial organic matter on coastal carbon cycling in a warming Arctic.
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Affiliation(s)
- Eleanor R Handler
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Sebastian D J Andersen
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Rolf Gradinger
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Maeve McGovern
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
| | - Amanda E Poste
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
- Norwegian Institute for Nature Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
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Hwang K, Choe H, Kim KM. Complete genome of Polaribacter huanghezhanensis KCTC 32516 T isolated from glaciomarine fjord sediment of Svalbard. Mar Genomics 2023; 72:101068. [PMID: 38008528 DOI: 10.1016/j.margen.2023.101068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 11/28/2023]
Abstract
Polaribacter huanghezhanensis KCTC 32516T is an aerobic, non-flagellated, Gram-negative, orange-colony-forming bacterium that was isolated from the surficial glaciomarine sediment of inner basin of Kongsfjorden, Svalbard. The sampling site is characterized by a sedimentation of organic depleted lithogenous particles from the nearby glaciers, resulting in reduction of organic matter concentration. In order to understand microbial adaptation to the oligotrophic environment, we here sequenced the complete genome of the P. huanghezhanensis KCTC 32516T. The genome consists of 2,587,874 bp (G + C content of 31.5%) with a single chromosome, 2391 protein-coding genes, 39 tRNAs, and 2 rRNA operons. Our comparative analysis revealed that the P. huanghezhanensis possess the smallest genome in fifteen Polaribacter species with genome. The streamlined genome of this species, required less resource in replication, could evolved by the nutrient deficiency in surrounding environment. Simultaneously, the 15 KOs involved in amino acid biosynthesis and anaplerotic carbon fixation is uniquely absent in the P. huanghezhanensis. In addition, although the advantage of small genome, other 15 KOs involved in resource recycling and stress resistance is uniquely present in sequenced genome. This result demonstrates that the sequenced genome serves as a valuable model for further studies aimed at elucidating the molecular mechanisms associated with adaptation to oligotrophic habitat.
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Affiliation(s)
- Kyuin Hwang
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea.
| | - Hanna Choe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup 56212, Republic of Korea
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
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Kumar Chaudhary D, Bajagain R, Seo D, Hong Y, Han S. Depth-dependent microbial communities potentially mediating mercury methylation and various geochemical processes in anthropogenically affected sediments. ENVIRONMENTAL RESEARCH 2023; 237:116888. [PMID: 37586452 DOI: 10.1016/j.envres.2023.116888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
Metal contamination and other geochemical alterations affect microbial composition and functional activities, disturbing natural biogeochemical cycles. Therefore, it is essential to understand the influences of multi-metal and geochemical interactions on microbial communities. This work investigated the distributions of total mercury (THg), methylmercury (MeHg), and trace metals in the anthropogenically affected sediment. The microbial communities and functional genes profiles were further determined to explore their association with Hg-methylation and geochemical features. The levels of THg and MeHg in sediment cores ranged between 10 and 40 mg/kg and 0.01-0.16 mg/kg, respectively, with an increasing trend toward bottom horizons. The major metals present at all depths were Al, Fe, Mn, and Zn. The enrichment and contamination indices confirmed that the trace metals were highly enriched in the anthropogenically affected sediment. Various functional genes were detected in all strata, indicating the presence of active microbial metabolic processes. The microbial community profiles revealed that the phyla Proteobacteria, Bacteroidetes, Bathyarchaeota, and Euryarchaeota, and the genera Thauera, Woeseia, Methanomethylovorans, and Methanosarcina were the dominant microbes. Correlating major taxa with geochemical variables inferred that sediment geochemistry substantially affects microbial community and biogeochemical cycles. Furthermore, archaeal methanogens and the bacterial phyla Chloroflexi and Firmicutes may play crucial roles in enhancing MeHg levels. Overall, these findings shed new light on the microbial communities potentially involved in Hg-methylation process and other biogeochemical cycles.
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea
| | - Rishikesh Bajagain
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea
| | - DongGyun Seo
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea
| | - Yongseok Hong
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea.
| | - Seunghee Han
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
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7
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Touchette D, Maggiori C, Altshuler I, Tettenborn A, Bourdages LJ, Magnuson E, Blenner-Hassett O, Raymond-Bouchard I, Ellery A, Whyte LG. Microbial Characterization of Arctic Glacial Ice Cores with a Semiautomated Life Detection System. ASTROBIOLOGY 2023; 23:756-768. [PMID: 37126945 DOI: 10.1089/ast.2022.0130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The search for extant microbial life will be a major focus of future astrobiology missions; however, no direct extant life detection instrumentation is included in current missions to Mars. In this study, we developed the semiautomated MicroLife detection platform that collects and processes environmental samples, detects biosignatures, and characterizes microbial activity. This platform is composed of a drill for sample collection, a redox dye colorimetric system for microbial metabolic activity detection and assessment (μMAMA [microfluidics Microbial Activity MicroAssay]), and a MinION sequencer for biosignature detection and characterization of microbial communities. The MicroLife platform was field-tested on White Glacier on Axel Heiberg Island in the Canadian high Arctic, with two extracted ice cores. The μMAMA successfully detected microbial metabolism from the ice cores within 1 day of incubation. The MinION sequencing of the ice cores and the positive μMAMA card identified a microbial community consistent with cold and oligotrophic environments. Furthermore, isolation and identification of microbial isolates from the μMAMA card corroborated the MinION sequencing. Together, these analyses support the MicroLife platform's efficacy in identifying microbes natively present in cryoenvironments and detecting their metabolic activity. Given our MicroLife platform's size and low energy requirements, it could be incorporated into a future landed platform or rovers for life detection.
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Affiliation(s)
- David Touchette
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
- Environmental Engineering Institute, River Ecosystems Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Catherine Maggiori
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
| | - Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- Environmental Engineering Institute, MACE Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alex Tettenborn
- Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, Canada
| | - Louis-Jacques Bourdages
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- Department of Mechanical Engineering, Faculty of Engineering, McGill University, Montréal, Canada
| | - Elisse Magnuson
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
| | - Olivia Blenner-Hassett
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
| | - Alex Ellery
- Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
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Venkatachalam S, Gopinath A, Krishnan KP. Fjords of the western and northern regions of Svalbard harbour distinct bacterioplankton community structures. World J Microbiol Biotechnol 2022; 39:57. [PMID: 36572813 DOI: 10.1007/s11274-022-03493-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022]
Abstract
Fjords are highly dynamic ecosystems that are known to be sentinels to climate change due to increased glaciomarine interactions. The convergence and mixing of warm Atlantic water (AtW) and cold Arctic water (ArW) is known to influence the hydrodynamics and ecology of the Arctic fjords. However, most past studies were limited to single-fjord ecosystems, determining the baseline knowledge of inter-fjord comparison on bacterioplankton diversity and distribution patterns. In the present study, we investigated the bacterial diversity and community composition across three Arctic fjords located in the western and northern regions of Svalbard. Our observations show that the bacterial community structure varied significantly among the fjords, while abundant Operational Taxonomic Units (OTUs) were widespread (n = 100) between all the samples and rare OTUs (n = 2221) mainly contributed to these differences. Phylogenetic classification revealed that Alpha (27.3-55%) and Gamma-proteobacteria (16-51.3%), followed by Bacteroidota (17-35.7%) were dominant in the St.Jonsfjorden and Magdalenefjorden, while Verrucomicrobiota (up to 84.19%) and Actinobacteriota (up to 76.5%) were predominant in the Raudfjorden. Temperature, dissolved inorganic phosphate (DIP) and depth were found to significantly influence the community composition of abundant bacterial groups, whereas the rare bacterial groups were affected by temperature, DIP, dissolved inorganic nitrate (DIN), ammonium and depth. A comparative meta-analysis along with Kongsfjorden and Krossfjorden also showed that each fjord had a significantly different bacterioplankton community structure.
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Affiliation(s)
- Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Anu Gopinath
- Department of Aquatic Environment Management, Kerala University of Fisheries and Ocean Studies (KUFOS), Madavana, Kerala, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India.
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Chaudhary DK, Karki HP, Bajagain R, Kim H, Rhee TS, Hong JK, Han S, Choi YG, Hong Y. Mercury and other trace elements distribution and profiling of microbial community in the surface sediments of East Siberian Sea. MARINE POLLUTION BULLETIN 2022; 185:114319. [PMID: 36343547 DOI: 10.1016/j.marpolbul.2022.114319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
In this study, total mercury (THg), methylmercury (MeHg), various trace elements, and microbial communities were measured in surface sediments of the East Siberian Sea (ESS). The results showed that the average values of THg and MeHg were 58.8 ± 15.21 μg/kg and 0.50 ± 0.22 μg/kg, respectively. The notable levels of trace elements present in both surface sediment and porewater were Al, Fe, and Mn. The enrichment factor and geoaccumulation index analyses found that both natural phenomena and anthropogenic activities contributed to elevated concentrations of metals in the ESS. The redox proxy metals, pH, and SO42- were the major factors influencing the THg and MeHg distributions. Microbial profiles were substantially affected by metals and other abiotic factors. Proteobacteria and Thaumarchaeota were the most abundant phyla. Overall, the findings presented here facilitate the understanding of the current status of metal contamination, its influencing factors, and metal-microbiota-interactions in ESS.
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - Hem Prakash Karki
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - Rishikesh Bajagain
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - Hwansuk Kim
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - Tae Siek Rhee
- Korea Polar Research Institute, 26 Songdomirae-ro, Incheon 21990, Republic of Korea
| | - Jong Kuk Hong
- Korea Polar Research Institute, 26 Songdomirae-ro, Incheon 21990, Republic of Korea
| | - Seunghee Han
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Young-Gyun Choi
- Department of Environmental Engineering, Chungnam National University, Daejeon City, Republic of Korea
| | - Yongseok Hong
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea.
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Total nitrogen influence bacterial community structure of active layer permafrost across summer and winter seasons in Ny-Ålesund, Svalbard. World J Microbiol Biotechnol 2022; 38:28. [PMID: 34989908 DOI: 10.1007/s11274-021-03210-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/13/2021] [Indexed: 10/19/2022]
Abstract
The permafrost in the polar regions is vital for maintaining the status quo of the earth's climate by limiting greenhouse gas emissions. The present study aims to investigate the seasonal variations and the influence of physicochemical parameters on the bacterial diversity and community structure of active layer permafrost (AL) around Ny-Ålesund, Svalbard. The AL soil samples were collected from four different geographical locations around Ny-Ålesund during the winter and summer seasons. The 16S rDNA amplicon sequencing was carried out to investigate the diversity and distribution profiles of bacterial communities among the collected AL samples. Physico-chemical parameters including soil pH, moisture content, total carbon (TC), total nitrogen (TN), and trace metals concentrations were measured. Bacterial phyla, Proteobacteria (15.4%-26%) and Chloroflexi (9.6%-22.5%) were predominantly distributed across both seasons. In the winter samples, Verrucomicrobiota (14.12%-23.39%) phylum, consisting of genera Chthoniobacter and Opitutus were highly abundant (Lefse, p < 0.05), whereas in summer bacterial genera belonging to Gemmatimonadota (3.3%-13.74%) and Acidobacteriota (18.02%-28.52%) phyla were highly abundant. The bacterial richness and diversity index were not significantly different between the winter and summer seasons. Principal coordinate analysis (PCoA) has revealed a distinct grouping between two seasons (PERMANOVA, p < 0.05). Bacterial community structure was significantly varied between winter and summer seasons, whereas the physico-chemical variable, TN, influenced the community structure. About 37.8% of the total operational taxonomic units (OTUs) were shared between seasons, whereas 25.4% and 36.8% of OTUs were unique to the summer and winter seasons. The present study revealed that the conditions prevailing during winter and summer has shaped bacterial community structure in AL samples albeit the stable diversity and most of the variation was explained by TN, indicating its critical role in oligotrophic permafrost.
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Zhang Y, Xu H, Wang L, Liu R, Fu L, Lin K. Unique bacterial communities and potential function along the vertical gradient in the deepest marine blue hole. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:911-927. [PMID: 34490729 DOI: 10.1111/1758-2229.13001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/18/2021] [Accepted: 08/10/2021] [Indexed: 05/27/2023]
Abstract
The Sansha Yongle Blue Hole is the deepest blue hole in the world discovered so far, while its great potential and values have not been fully exploited regarding microbial communities. A large-scale sampling was performed at different depths (0-270 m) inside the blue hole. Based on high-throughput sequencing, the diversity and richness of bacterial communities were relatively higher in oxic and euphotic layer, and at depths of 180-230 m in anoxic layer. Proteobacteria was dominant with mean relative abundance of 64.7%. As the representative genera, Thiomicrospira and Arcobacter were detected with higher abundances up to 96.1% and 31.5% in the anaerobic environment. Principal co-ordinates analysis, one-way ANOVA and network analysis highlighted the distinctive species at different depths. Correlation analysis illustrated the significant correlations between the bacteria and environmental elements of dissolved oxygen, temperature, salinity, pH, sulphur and nutrient. Phylogenetic analysis indicated that the microbial ecosystem was characterized with infrequent and unidentified microorganisms in the deep layer. This research revealed the unique microbial ecosystem and potential functions in regulating ecosystem productivity and cycling of carbon, sulphur and nitrogen. Comprehensive and long-term investigations in the Sansha Blue Hole should be taken to conserve the peculiar ecosystem.
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Affiliation(s)
- Yuxuan Zhang
- State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Huitao Xu
- State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Liping Wang
- State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Ruizhi Liu
- State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Liang Fu
- Sansha Trackline Institute of Coral Reef Environment Protection, Sansha, 571400, China
| | - Kuixuan Lin
- State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
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12
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Jain A, Balmonte JP, Singh R, Bhaskar PV, Krishnan KP. Spatially resolved assembly, connectivity and structure of particle-associated and free-living bacterial communities in a high Arctic fjord. FEMS Microbiol Ecol 2021; 97:fiab139. [PMID: 34626180 PMCID: PMC8536490 DOI: 10.1093/femsec/fiab139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/07/2021] [Indexed: 01/08/2023] Open
Abstract
The assembly processes that underlie the composition and connectivity of free-living (FL) and particle-associated (PA) bacterial communities from surface to deep waters remain little understood. Here, using phylogenetic null modeling, we quantify the relative influence of selective and stochastic mechanisms that assemble FL and PA bacterial communities throughout the water column in a high Arctic fjord. We demonstrate that assembly processes acting on FL and PA bacterial communities are similar in surface waters, but become increasingly distinct in deep waters. As depth increases, the relative influence of homogeneous selection increases for FL but decreases for PA communities. In addition, dispersal limitation and variable selection increase with depth for PA, but not for FL communities, indicating increased residence time of taxa on particles and less frequent decolonization. As a consequence, beta diversity of PA communities is greater in bottom than in surface waters. The limited connectivity between these communities with increasing depth leads to highly distinct FL and PA bacterial communities in bottom waters. Finally, depth-related trends for FL and PA beta diversity and connectivity in this study are consistent with previous observations in the open ocean, suggesting that assembly processes for FL and PA bacterial communities may also be distinct in other aquatic environments.
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Affiliation(s)
- Anand Jain
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama 403 804, Goa, India
| | - John Paul Balmonte
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
- HADAL and NordCEE, Department of Biology, University of Southern Denmark, Odense, 5230, Denmark
| | - Richa Singh
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi 221 005, Uttar Pradesh, India
| | - Parli Venkateswaran Bhaskar
- Ocean Science Group, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama 403 804, Goa, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama 403 804, Goa, India
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13
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Thomas FA, Mohan M, Krishnan KP. Bacterial diversity and their metabolic profiles in the sedimentary environments of Ny-Ålesund, Arctic. Antonie van Leeuwenhoek 2021; 114:1339-1360. [PMID: 34148162 DOI: 10.1007/s10482-021-01604-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/01/2021] [Indexed: 11/26/2022]
Abstract
Sedimentary environments in the Arctic are known to harbor diverse microbial communities playing a crucial role in the remineralization of organic matter and associated biogeochemical cycles. In this study, we used a combination of culture-dependent and culture-independent approaches to understanding the bacterial community composition associated with the sediments of a terrestrial versus fjord system in the Svalbard Arctic. Community-level metabolic profiling and growth response of retrieved bacterial isolates towards different carbon substrates at varying temperatures were also studied to assess the metabolic response of communities and isolates in the system. Bacterial species belonging to Cryobacterium and Psychrobacter dominated the terrestrial and fjord sediment retrievable fraction. Amplicon sequencing analysis revealed higher bacterial diversity in the terrestrial sediments (Shannon index; 8.135 and 7.935) as compared to the fjord sediments (4.5-5.37). Phylum Proteobacteria and Bacteroidetes dominated both terrestrial and fjord sediments. Phylum Verrucomicrobia and Cyanobacteria were abundant in terrestrial sediments while Epsilonbacteraeota and Fusobacteriia dominated the fjord sediments. Significant differences were observed in the carbon substrate utilization profiles between the terrestrial and fjord sediments at both 4 °C and 20 °C incubations (p < 0.005). Utilization of N-acetyl-D-glucosamine, D-mannitol and Tween-80 by the sediment communities and bacterial isolates from both systems, irrespective of their temperature incubations implies the affinity of bacteria for such substrates as energy sources and for their survival in cold environments. Our results suggest the ability of sediment bacterial communities to adjust their substrate utilization profiles according to condition changes in the ecosystems and are found to be less influenced by their phylogenetic relatedness.
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Affiliation(s)
- Femi Anna Thomas
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco da Gama, Goa, 403804, India
- School of Earth, Ocean and Atmospheric Sciences, Goa University, Taleigao Plateau Goa, 403206, India
| | - Mahesh Mohan
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam, Kerala, 686560, India
| | - K P Krishnan
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco da Gama, Goa, 403804, India.
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14
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Delpech LM, Vonnahme TR, McGovern M, Gradinger R, Præbel K, Poste AE. Terrestrial Inputs Shape Coastal Bacterial and Archaeal Communities in a High Arctic Fjord (Isfjorden, Svalbard). Front Microbiol 2021; 12:614634. [PMID: 33717004 PMCID: PMC7952621 DOI: 10.3389/fmicb.2021.614634] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/29/2021] [Indexed: 11/13/2022] Open
Abstract
The Arctic is experiencing dramatic changes including increases in precipitation, glacial melt, and permafrost thaw, resulting in increasing freshwater runoff to coastal waters. During the melt season, terrestrial runoff delivers carbon- and nutrient-rich freshwater to Arctic coastal waters, with unknown consequences for the microbial communities that play a key role in determining the cycling and fate of terrestrial matter at the land-ocean interface. To determine the impacts of runoff on coastal microbial (bacteria and archaea) communities, we investigated changes in pelagic microbial community structure between the early (June) and late (August) melt season in 2018 in the Isfjorden system (Svalbard). Amplicon sequences of the 16S rRNA gene were generated from water column, river and sediment samples collected in Isfjorden along fjord transects from shallow river estuaries and glacier fronts to the outer fjord. Community shifts were investigated in relation to environmental gradients, and compared to river and marine sediment microbial communities. We identified strong temporal and spatial reorganizations in the structure and composition of microbial communities during the summer months in relation to environmental conditions. Microbial diversity patterns highlighted a reorganization from rich communities in June toward more even and less rich communities in August. In June, waters enriched in dissolved organic carbon (DOC) provided a niche for copiotrophic taxa including Sulfitobacter and Octadecabacter. In August, lower DOC concentrations and Atlantic water inflow coincided with a shift toward more cosmopolitan taxa usually associated with summer stratified periods (e.g., SAR11 Clade Ia), and prevalent oligotrophic marine clades (OM60, SAR92). Higher riverine inputs of dissolved inorganic nutrients and suspended particulate matter also contributed to spatial reorganizations of communities in August. Sentinel taxa of this late summer fjord environment included taxa from the class Verrucomicrobiae (Roseibacillus, Luteolibacter), potentially indicative of a higher fraction of particle-attached bacteria. This study highlights the ecological relevance of terrestrial runoff for Arctic coastal microbial communities and how its impacts on biogeochemical conditions may make these communities susceptible to climate change.
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Affiliation(s)
- Lisa-Marie Delpech
- Department of Biology, École Normale Supérieure de Lyon, Université de Lyon, Lyon, France.,Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway.,Norwegian Institute for Water Research (NIVA), Tromsø, Norway
| | - Tobias R Vonnahme
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maeve McGovern
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway.,Norwegian Institute for Water Research (NIVA), Tromsø, Norway
| | - Rolf Gradinger
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kim Præbel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Amanda E Poste
- Norwegian Institute for Water Research (NIVA), Tromsø, Norway
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15
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Bacterial Communities Associated with the Biofilms Formed in High-Altitude Brackish Water Pangong Tso Located in the Himalayan Plateau. Curr Microbiol 2020; 77:4072-4084. [PMID: 33079205 DOI: 10.1007/s00284-020-02244-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
Pangong Tso is a long and narrow lake situated at an altitude of ~ 4266 m amsl in the Himalayan Plateau on the side of the India/China border. Biofilm has been observed in a small area near the shore of Pangong Tso. Bacterial communities of the lake sediment, water and biofilms were studied using amplicon sequencing of V3-V4 region of the 16S rRNA gene. The standard QIIME pipeline was used for analysis. The metabolic potential of the community was predicted using functional prediction tool Tax4Fun. Bacterial phyla Proteobacteria, followed by Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria, and Firmicutes, were found to be dominant across these samples. Shannon's and Simpson's alpha diversity analysis revealed that sediment communities are the most diverse, and water communities are the least diverse. Principal Coordinates based beta diversity analysis showed significant variation in the bacterial communities of the water, sediment and biofilm samples. Bacterial phyla Verrucomicrobia, Deinococcus-Thermus and Cyanobacteria were explicitly enriched in the biofilm samples. Predictive functional profiling of these bacterial communities showed a higher abundance of genes involved in photosynthesis, biosynthesis of secondary metabolites, carbon fixation in photosynthetic organisms and glyoxylate and dicarboxylate metabolism in the biofilm sample. In conclusion, the Pangong Tso bacterial communities are quite similar to other saline and low-temperature lakes in the Tibetan Plateau. Bacterial community structure of the biofilm samples was significantly different from that of the water and sediment samples and enrichment of saprophytic communities was observed in the biofilm samples, indicating an important succession event in this high-altitude lake.
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Cameron KA, Müller O, Stibal M, Edwards A, Jacobsen CS. Glacial microbiota are hydrologically connected and temporally variable. Environ Microbiol 2020; 22:3172-3187. [PMID: 32383292 DOI: 10.1111/1462-2920.15059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/15/2020] [Accepted: 05/02/2020] [Indexed: 11/29/2022]
Abstract
Glaciers are melting rapidly. The concurrent export of microbial assemblages alongside glacial meltwater is expected to impact the ecology of adjoining ecosystems. Currently, the source of exported assemblages is poorly understood, yet this information may be critical for understanding how current and future glacial melt seasons may influence downstream environments. We report on the connectivity and temporal variability of microbiota sampled from supraglacial, subglacial and periglacial habitats and water bodies within a glacial catchment. Sampled assemblages showed evidence of being biologically connected through hydrological flowpaths, leading to a meltwater system that accumulates prokaryotic biota as it travels downstream. Temporal changes in the connected assemblages were similarly observed. Snow assemblages changed markedly throughout the sample period, likely reflecting changes in the surrounding environment. Changes in supraglacial meltwater assemblages reflected the transition of the glacial surface from snow-covered to bare-ice. Marked snowmelt across the surrounding periglacial environment resulted in the flushing of soil assemblages into the riverine system. In contrast, surface ice within the ablation zone and subglacial meltwaters remained relatively stable throughout the sample period. Our results are indicative that changes in snow and ice melt across glacial environments will influence the abundance and diversity of microbial assemblages transported downstream.
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Affiliation(s)
- Karen A Cameron
- Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DD, UK.,Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, 1350, Denmark.,Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen, 1350, Denmark.,School of Geographical and Earth Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Oliver Müller
- Department of Biological Sciences, University of Bergen, Bergen, 5006, Norway
| | - Marek Stibal
- Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, 1350, Denmark.,Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen, 1350, Denmark.,Department of Ecology, Faculty of Science, Charles University, Prague, 128 44, Czech Republic
| | - Arwyn Edwards
- Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DD, UK
| | - Carsten Suhr Jacobsen
- Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, 1350, Denmark.,Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen, 1350, Denmark.,Department of Environmental Science, Aarhus University, Roskilde, 4000, Denmark
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