Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, <italic toggle="yes">Desulfovibrio vulgaris</italic>
Aifen Zhou,
Rebecca Lau,
Richard Baran,
Jincai Ma,
Frederick von Netzer,
Weiling Shi,
Drew Gorman-Lewis,
Megan L. Kempher,
Zhili He,
Yujia Qin,
Zhou Shi,
Grant M. Zane,
Liyou Wu,
Benjamin P. Bowen,
Trent R. Northen,
Kristina L. Hillesland,
David A. Stahl,
Judy D. Wall,
Adam P. Arkin,
Jizhong Zhou
Affiliations
Aifen Zhou
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
Rebecca Lau
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Richard Baran
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Jincai Ma
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
Frederick von Netzer
Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
Weiling Shi
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
Drew Gorman-Lewis
Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
Megan L. Kempher
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
Zhili He
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
Yujia Qin
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
Zhou Shi
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
Grant M. Zane
Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri—Columbia, Columbia, Missouri, USA
Liyou Wu
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
Benjamin P. Bowen
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Trent R. Northen
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Kristina L. Hillesland
School of Science, Technology, Engineering and Mathematics, University of Washington Bothell, Bothell, Washington, USA
David A. Stahl
Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
Judy D. Wall
Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri—Columbia, Columbia, Missouri, USA
Adam P. Arkin
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Jizhong Zhou
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
ABSTRACT Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, in addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance in D. vulgaris. The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection. IMPORTANCE High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies. Desulfovibrio vulgaris Hildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation of D. vulgaris Hildenborough with experimental evolution. Here, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ω9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution.
