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Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types.
Environ Microbiol. 2016 12; 18(12):5082-5100.EM

Abstract

Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and δ13 C of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58 ± 16% to total CH4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi than the respective other sediment systems. The data showed communities of bacteria common to all sediment types, but also revealed microbial groups that were significantly different between the sediment types, which also differed in physicochemical conditions. Our study showed that function of the microbial communities may be understood on the basis of their structures, which in turn are determined by environmental heterogeneity.

Authors+Show Affiliations

Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science & Technology, Ningliu Road 219, Nanjing, 210044, China. Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany.Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria.Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany.Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany.Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil. Graduated Program in Geosciences (Geochemistry), Graduated Program in Geography, Research Center on Biomass and Water Management (NAB/UFF), Sedimentary Environmental Processes Laboratory (LAPSA/UFF), International Laboratory of Global Change (LINC-Global), Fluminense Federal University (UFF), Niterói, Brazil.Department of Chemical Oceanography, Rio de Janeiro State University, Pavilhão João Lyra Filho, sala 4008 Bloco E, Rua São Francisco Xavier, 524, Maracanã-RJ, 20550-900, Brazil.Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil. Department of Environmental Change, Linköping University, Linköping, Sweden.Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

27507000

Citation

Ji, Yang, et al. "Structure and Function of Methanogenic Microbial Communities in Sediments of Amazonian Lakes With Different Water Types." Environmental Microbiology, vol. 18, no. 12, 2016, pp. 5082-5100.
Ji Y, Angel R, Klose M, et al. Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types. Environ Microbiol. 2016;18(12):5082-5100.
Ji, Y., Angel, R., Klose, M., Claus, P., Marotta, H., Pinho, L., Enrich-Prast, A., & Conrad, R. (2016). Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types. Environmental Microbiology, 18(12), 5082-5100. https://doi.org/10.1111/1462-2920.13491
Ji Y, et al. Structure and Function of Methanogenic Microbial Communities in Sediments of Amazonian Lakes With Different Water Types. Environ Microbiol. 2016;18(12):5082-5100. PubMed PMID: 27507000.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types. AU - Ji,Yang, AU - Angel,Roey, AU - Klose,Melanie, AU - Claus,Peter, AU - Marotta,Humberto, AU - Pinho,Luana, AU - Enrich-Prast,Alex, AU - Conrad,Ralf, Y1 - 2016/08/25/ PY - 2016/03/14/received PY - 2016/08/06/accepted PY - 2016/8/11/pubmed PY - 2017/8/22/medline PY - 2016/8/11/entrez SP - 5082 EP - 5100 JF - Environmental microbiology JO - Environ Microbiol VL - 18 IS - 12 N2 - Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and δ13 C of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58 ± 16% to total CH4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi than the respective other sediment systems. The data showed communities of bacteria common to all sediment types, but also revealed microbial groups that were significantly different between the sediment types, which also differed in physicochemical conditions. Our study showed that function of the microbial communities may be understood on the basis of their structures, which in turn are determined by environmental heterogeneity. SN - 1462-2920 UR - https://www.unboundmedicine.com/medline/citation/27507000/Structure_and_function_of_methanogenic_microbial_communities_in_sediments_of_Amazonian_lakes_with_different_water_types_ L2 - https://doi.org/10.1111/1462-2920.13491 DB - PRIME DP - Unbound Medicine ER -