Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers
Abstract
Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth’s largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to Nitrosospira dominated over ammonia-oxidizing archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival under conditions where ammonia oxidation is inhibited or substrate limited. Nitrite-oxidizing bacteria (NOB) “Candidatus Nitrotoga” and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less-productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resourcemore »
- Authors:
-
[1]
- University of Chicago, IL (United States)
- University of Wisconsin, Madison, WI (United States)
- Publication Date:
- Research Org.:
- USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); Illinois-Indiana Sea Grant; UChicago Women’s Board; National Science Foundation (NSF)
- OSTI Identifier:
- 1904118
- Grant/Contract Number:
- AC02-05CH11231; NA14OAR170095; OCE-1830011
- Resource Type:
- Accepted Manuscript
- Journal Name:
- mBio (Online)
- Additional Journal Information:
- Journal Name: mBio (Online); Journal Volume: 13; Journal Issue: 3; Journal ID: ISSN 2150-7511
- Publisher:
- American Society for Microbiology (ASM)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; biogeochemistry; ecological genomics; freshwater; metagenomics; nitrification
Citation Formats
Podowski, Justin C., Paver, Sara F., Newton, Ryan J., and Coleman, Maureen L. Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers. United States: N. p., 2022.
Web. doi:10.1128/mbio.02379-21.
Podowski, Justin C., Paver, Sara F., Newton, Ryan J., & Coleman, Maureen L. Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers. United States. https://doi.org/10.1128/mbio.02379-21
Podowski, Justin C., Paver, Sara F., Newton, Ryan J., and Coleman, Maureen L. Mon .
"Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers". United States. https://doi.org/10.1128/mbio.02379-21. https://www.osti.gov/servlets/purl/1904118.
@article{osti_1904118,
title = {Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers},
author = {Podowski, Justin C. and Paver, Sara F. and Newton, Ryan J. and Coleman, Maureen L.},
abstractNote = {Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth’s largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to Nitrosospira dominated over ammonia-oxidizing archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival under conditions where ammonia oxidation is inhibited or substrate limited. Nitrite-oxidizing bacteria (NOB) “Candidatus Nitrotoga” and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less-productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change.},
doi = {10.1128/mbio.02379-21},
journal = {mBio (Online)},
number = 3,
volume = 13,
place = {United States},
year = {Mon Apr 18 00:00:00 EDT 2022},
month = {Mon Apr 18 00:00:00 EDT 2022}
}
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