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Cheung S, Zehr JP, Xia X, Tsurumoto C, Endo H, Nakaoka SI, Mak W, Suzuki K, Liu H. Gamma4: a genetically versatile Gammaproteobacterial nifH phylotype that is widely distributed in the North Pacific Ocean. Environ Microbiol 2021; 23:4246-4259. [PMID: 34046993 DOI: 10.1111/1462-2920.15604] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 05/15/2021] [Accepted: 05/16/2021] [Indexed: 11/30/2022]
Abstract
Despite the increasing reports of non-cyanobacterial diazotrophs (NCDs) in pelagic waters, only one NCD (GammaA) has been relatively well described, whose genome and physiology are still unclear. Here we present a comprehensive analysis of the biogeography and ecophysiology of a widely distributed NCD, Gamma4. Gamma4 was the most abundant Gammaproteobacterial NCD along transects across the subtropical North Pacific. Using quantitative PCR, Gamma4 was detectable throughout the surface waters of North Pacific (7°N-55°N, 138°E-80°W), whereas GammaA was detected at <2/3 of the stations. Gamma4 was abundant during autumn-winter and positively correlated with chlorophyll a, while GammaA thrived during spring-summer and was positively correlated with temperature. Environmental clones affiliated with Gamma4 were widely detected in pelagic waters, oxygen minimum zones and even dinoflagellate microbiomes. By analysing the metabolic potential of a genome of Gamma4 reconstructed from the Tara Oceans dataset, we suggest that Gamma4 is a versatile heterotrophic NCD equipped with multiple strategies in scavenging phosphate (and iron) and for respiratory protection of nitrogenase. The transcription of nitrogenase genes is putatively regulated by Fnr-NifL-NifA and GlnD-GlnK systems that respond to intracellular oxygen and glutamate concentration. These results provide important implications for the potential life strategies of pelagic NCDs.
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Affiliation(s)
- Shunyan Cheung
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.,Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Chihiro Tsurumoto
- Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan
| | - Shin-Ichiro Nakaoka
- Center for Global Environmental Research, National Institute for Environmental Studies, Tsukuba, Japan
| | - Wingkwan Mak
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Koji Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan.,Faculty of Environmental Earth Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.,Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
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