Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences

Qin, Wei; Wei, Stephany P.; Zheng, Yue; Choi, Eunkyung; Li, Xiangpeng; Johnston, Juliet; Wan, Xianhui; Abrahamson, Britt; Flinkstrom, Zachary; Wang, Baozhan; Li, Hanyan; Hou, Lei; Tao, Qing; Chlouber, Wyatt W.; Sun, Xin; Wells, Michael; Ngo, Long; Hunt, Kristopher A.; Urakawa, Hidetoshi; Tao, Xuanyu; Wang, Dongyu; Yan, Xiaoyuan; Wang, Dazhi; Pan, Chongle; Weber, Peter K.; Jiang, Jiandong; Zhou, Jizhong; Zhang, Yao; Stahl, David A.; Ward, Bess B.; Mayali, Xavier; Martens-Habbena, Willm; Winkler, Mari-Karoliina H.

doi:10.1038/s41564-023-01593-7

Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences

Journal Article · Wed Jan 31 00:00:00 EST 2024 · Nature Microbiology

DOI:https://doi.org/10.1038/s41564-023-01593-7· OSTI ID:2287685

^[1]; Wei, Stephany P. ^[2]; Zheng, Yue ^[3]; ^[4]; Li, Xiangpeng ^[5]; Johnston, Juliet ^[6]; ^[7]; ^[2]; ^[2]; ^[8]; Li, Hanyan ^[5]; Hou, Lei ^[9]; Tao, Qing ^[5]; Chlouber, Wyatt W. ^[5]; ^[10]; ^[5]; Ngo, Long ^[5]; ^[2]; ^[11]; Tao, Xuanyu ^[5] more »

University of Oklahoma, Norman, OK (United States); University of Washington, Seattle, WA (United States); University of Washington
University of Washington, Seattle, WA (United States)
Xiamen University, Fujian (China)
University of Florida, Davie, FL (United States)
University of Oklahoma, Norman, OK (United States)
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Princeton University, NJ (United States)
Nanjing Agricultural University, Jiangsu (China)
University of Oklahoma, Norman, OK (United States); Xiamen University, Fujian (China)
Yale University, New Haven, CT (United States)
Florida Gulf Coast University, Fort Myers, FL (United States)
Chinese Academy of Sciences, Nanjing (China)

Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. Furthermore, these results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); University of Oklahoma, Norman, OK (United States); University of Washington, Seattle, WA (United States)

Sponsoring Organization:: Defense Advanced Research Projects Agency (DARPA); National Science Foundation (NSF); USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC52-07NA27344; SC0020356

OSTI ID:: 2287685

Alternate ID(s):: OSTI ID: 2453954

Report Number(s):: LLNL--JRNL-842694

Journal Information:: Nature Microbiology, Journal Name: Nature Microbiology Journal Issue: 2 Vol. 9; ISSN 2058-5276

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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