Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibriovulgaris

Wu, Bo; Liu, Feifei; Zhou, Aifen; Li, Juan; Shu, Longfei; Kempher, Megan L.; Yang, Xueqin; Ning, Daliang; Pan, Feiyan; Zane, Grant M.; Wall, Judy D.; Van Nostrand, Joy D.; Juneau, Philippe; Chen, Shouwen; Yan, Qingyun; Zhou, Jizhong; He, Zhili

doi:10.1038/s41396-020-00753-5

Title: Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibriovulgaris

Journal Article · Tue Sep 15 00:00:00 UTC 2020 · The ISME Journal

DOI: https://doi.org/10.1038/s41396-020-00753-5 · OSTI ID:1778206

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Sun Yat-Sen Univ., Guangzhou (China); Univ. of Oklahoma, Norman, OK (United States)
Univ. of Oklahoma, Norman, OK (United States); Guangdong Institute of Microbiology, Guangzhou (China)
Univ. of Oklahoma, Norman, OK (United States)
Hunan Agricultural University, Changsha (China)
Sun Yat-Sen Univ., Guangzhou (China)
Univ. of Missouri, Columbia, MO (United States)
Université du Québec à Montréal (Canada)
Huazhong Agricultural University, Wuhan (China); Hubei University, Wuhan (China)
Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Tsinghua Univ., Beijing (China)
Sun Yat-Sen Univ., Guangzhou (China); Univ. of Oklahoma, Norman, OK (United States); Hunan Agricultural University, Changsha (China)

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 NaNO₃ 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. In this work, 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. Additionally, 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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: National Natural Science Foundation of China (NSFC); National Program on Key Basic Research; Special Funds for Scientific and Technological Innovation in Guangdong Province; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1778206

Journal Information:: The ISME Journal, Journal Name: The ISME Journal Journal Issue: 11 Vol. 14; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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