Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

Journal Article · Tue Apr 07 00:00:00 EDT 2015 · The ISME Journal

DOI:https://doi.org/10.1038/ismej.2015.45· OSTI ID:1415208

Zhou, Aifen; Hillesland, Kristina L.; He, Zhili; Schackwitz, Wendy; Tu, Qichao; Zane, Grant M.; Ma, Qiao; Qu, Yuanyuan; Stahl, David A.; Wall, Judy D.; Hazen, Terry C.; Fields, Matthew W.; Arkin, Adam P.; Zhou, Jizhong

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.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 1415208
• Journal Information: The ISME Journal, Vol. 9, Issue 11; ISSN 1751-7362
• Publisher: Nature Publishing Group
• Country of Publication: United States
• Language: English