Genomics insights into ecotype formation of ammonia‐oxidizing archaea in the deep ocean
Abstract
Summary Various lineages of ammonia‐oxidizing archaea (AOA) are present in deep waters, but the mechanisms that determine ecotype formation are obscure. We studied 18 high‐quality genomes of the marine group I AOA lineages (alpha, gamma and delta) from the Mariana and Ogasawara trenches. The genomes of alpha AOA resembled each other, while those of gamma and delta lineages were more divergent and had even undergone insertion of some phage genes. The instability of the gamma and delta AOA genomes could be partially due to the loss of DNA polymerase B ( polB) and methyladenine DNA glycosylase ( tag ) genes responsible for the repair of point mutations. The alpha AOA genomes harbour genes encoding a thrombospondin‐like outer membrane structure that probably serves as a barrier to gene flow. Moreover, the gamma and alpha AOA lineages rely on vitamin B 12 ‐independent MetE and B 12 ‐dependent MetH, respectively, for methionine synthesis. The delta AOA genome contains genes involved in uptake of sugar and peptide perhaps for heterotrophic lifestyle. Our study provides insights into co‐occurrence of cladogenesis and anagenesis in the formation of AOA ecotypes that perform differently in nitrogen and carbon cycling in dark oceans.
- Authors:
-
[1];
- Institute of Deep‐Sea Science and Engineering Chinese Academy of Sciences Sanya Hainan China
- Institute of Deep‐Sea Science and Engineering Chinese Academy of Sciences Sanya Hainan China, University of the Chinese Academy of Sciences Beijing China
- Research and Development Center for Marine Biosciences Japan Agency for Marine‐Earth Science and Technology (JAMSTEC) 2‐15 Natsushima‐cho, Yokosuka 237‐0061 Japan
- Research and Development Center for Marine Biosciences Japan Agency for Marine‐Earth Science and Technology (JAMSTEC) 2‐15 Natsushima‐cho, Yokosuka 237‐0061 Japan, Department of Subsurface Geobiological Analysis and Research Japan Agency for Marine‐Earth Science and Technology (JAMSTEC) 2‐15 Natsushima‐cho, Yokosuka 237‐0061 Japan
- Department of Subsurface Geobiological Analysis and Research Japan Agency for Marine‐Earth Science and Technology (JAMSTEC) 2‐15 Natsushima‐cho, Yokosuka 237‐0061 Japan
- Bigelow Laboratory for Ocean Sciences 60 Bigelow Drive, East Boothbay ME 04544 USA
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1493072
- Resource Type:
- Publisher's Accepted Manuscript
- Journal Name:
- Environmental Microbiology
- Additional Journal Information:
- Journal Name: Environmental Microbiology Journal Volume: 21 Journal Issue: 2; Journal ID: ISSN 1462-2912
- Publisher:
- Wiley-Blackwell
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Wang, Yong, Huang, Jiao‐Mei, Cui, Guo‐Jie, Nunoura, Takuro, Takaki, Yoshihiro, Li, Wen‐Li, Li, Jun, Gao, Zhao‐Ming, Takai, Ken, Zhang, Ai‐Qun, and Stepanauskas, Ramunas. Genomics insights into ecotype formation of ammonia‐oxidizing archaea in the deep ocean. United Kingdom: N. p., 2019.
Web. doi:10.1111/1462-2920.14518.
Wang, Yong, Huang, Jiao‐Mei, Cui, Guo‐Jie, Nunoura, Takuro, Takaki, Yoshihiro, Li, Wen‐Li, Li, Jun, Gao, Zhao‐Ming, Takai, Ken, Zhang, Ai‐Qun, & Stepanauskas, Ramunas. Genomics insights into ecotype formation of ammonia‐oxidizing archaea in the deep ocean. United Kingdom. https://doi.org/10.1111/1462-2920.14518
Wang, Yong, Huang, Jiao‐Mei, Cui, Guo‐Jie, Nunoura, Takuro, Takaki, Yoshihiro, Li, Wen‐Li, Li, Jun, Gao, Zhao‐Ming, Takai, Ken, Zhang, Ai‐Qun, and Stepanauskas, Ramunas. Thu .
"Genomics insights into ecotype formation of ammonia‐oxidizing archaea in the deep ocean". United Kingdom. https://doi.org/10.1111/1462-2920.14518.
@article{osti_1493072,
title = {Genomics insights into ecotype formation of ammonia‐oxidizing archaea in the deep ocean},
author = {Wang, Yong and Huang, Jiao‐Mei and Cui, Guo‐Jie and Nunoura, Takuro and Takaki, Yoshihiro and Li, Wen‐Li and Li, Jun and Gao, Zhao‐Ming and Takai, Ken and Zhang, Ai‐Qun and Stepanauskas, Ramunas},
abstractNote = {Summary Various lineages of ammonia‐oxidizing archaea (AOA) are present in deep waters, but the mechanisms that determine ecotype formation are obscure. We studied 18 high‐quality genomes of the marine group I AOA lineages (alpha, gamma and delta) from the Mariana and Ogasawara trenches. The genomes of alpha AOA resembled each other, while those of gamma and delta lineages were more divergent and had even undergone insertion of some phage genes. The instability of the gamma and delta AOA genomes could be partially due to the loss of DNA polymerase B ( polB) and methyladenine DNA glycosylase ( tag ) genes responsible for the repair of point mutations. The alpha AOA genomes harbour genes encoding a thrombospondin‐like outer membrane structure that probably serves as a barrier to gene flow. Moreover, the gamma and alpha AOA lineages rely on vitamin B 12 ‐independent MetE and B 12 ‐dependent MetH, respectively, for methionine synthesis. The delta AOA genome contains genes involved in uptake of sugar and peptide perhaps for heterotrophic lifestyle. Our study provides insights into co‐occurrence of cladogenesis and anagenesis in the formation of AOA ecotypes that perform differently in nitrogen and carbon cycling in dark oceans.},
doi = {10.1111/1462-2920.14518},
journal = {Environmental Microbiology},
number = 2,
volume = 21,
place = {United Kingdom},
year = {Thu Jan 31 00:00:00 EST 2019},
month = {Thu Jan 31 00:00:00 EST 2019}
}
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https://doi.org/10.1111/1462-2920.14518
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