Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris.

Autor: Wu B; Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA., Liu F; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.; Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, 510070, China., Zhou A; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA., Li J; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China., Shu L; Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China., Kempher ML; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA., Yang X; Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China., Ning D; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA., Pan F; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA., Zane GM; Departments of Biochemistry and Molecular Microbiology & Immunology, University of Missouri-Columbia, Columbia, MO, 65211, USA., Wall JD; Departments of Biochemistry and Molecular Microbiology & Immunology, University of Missouri-Columbia, Columbia, MO, 65211, USA., Van Nostrand JD; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA., Juneau P; Départment des Sciences Biologiques, TOXEN, Ecotoxicology of Aquatic Microorganisms Laboratory, Université du Québec à Montréal, Montréal, Canada., Chen S; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. chenshouwen@mail.hzau.edu.cn.; State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, China. chenshouwen@mail.hzau.edu.cn., Yan Q; Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China. yanqy6@mail.sysu.edu.cn.; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA. yanqy6@mail.sysu.edu.cn., Zhou J; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA. jzhou@ou.edu.; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. jzhou@ou.edu.; School of Environment, Tsinghua University, Beijing, 100084, China. jzhou@ou.edu., He Z; Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China. hezhili@mail.sysu.edu.cn.; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA. hezhili@mail.sysu.edu.cn.; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China. hezhili@mail.sysu.edu.cn.
Jazyk: angličtina
Zdroj: The ISME journal [ISME J] 2020 Nov; Vol. 14 (11), pp. 2862-2876. Date of Electronic Publication: 2020 Sep 15.
DOI: 10.1038/s41396-020-00753-5
Abstrakt: Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO 3 for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. We observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.
Databáze: MEDLINE
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