title: Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris.
abstract: To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Aifen
authors.initials: A
authors.lastname: Zhou
authors.affiliation: Biological Sciences, University of Washington Bothell, Bothell, WA, USA.
authors.forename: Kristina L
authors.initials: KL
authors.lastname: Hillesland
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Wendy
authors.initials: W
authors.lastname: Schackwitz
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Qichao
authors.initials: Q
authors.lastname: Tu
authors.affiliation: Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA.
authors.forename: Grant M
authors.initials: GM
authors.lastname: Zane
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.|Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China.
authors.forename: Qiao
authors.initials: Q
authors.lastname: Ma
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.|Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Qu
authors.affiliation: Civil and Environmental Engineering, University of Washington, Seattle, WA, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Stahl
authors.affiliation: Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA.
authors.forename: Judy D
authors.initials: JD
authors.lastname: Wall
authors.affiliation: Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, USA.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
authors.forename: Terry C
authors.initials: TC
authors.lastname: Hazen
authors.affiliation: Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Fields
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.|Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.|State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D001673:Biodegradation, Environmental; D018533:Biomass; D004252:DNA Mutational Analysis; D016969:Desulfovibrio vulgaris / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D005787:Gene Frequency; D005838:Genotype; D019216:Metals, Heavy / Q000737:chemistry; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D010641:Phenotype; D011110:Polymorphism, Genetic; D054712:Salinity; D055049:Salt Tolerance / Q000235:genetics; D012965:Sodium Chloride / Q000737:chemistry; D013455:Sulfur / Q000737:chemistry
chemical_list: D019216:Metals, Heavy; D012965:Sodium Chloride; D013455:Sulfur
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