Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean
Wang, Yong1; Huang, Jiao-Mei1,2; Cui, Guo-Jie1,2; Nunoura, Takuro3; Takaki, Yoshihiro3,4; Li, Wen-Li1,2; Li, Jun1; Gao, Zhao-Ming1; Takai, Ken4; Zhang, Ai-Qun1; Stepanauskas, Ramunas5
2019-02-01
Source PublicationENVIRONMENTAL MICROBIOLOGY
ISSN1462-2912
Volume21Issue:2Pages:716-729
Abstract

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.

DOI10.1111/1462-2920.14518
Indexed BySCI
Funding OrganizationNational Science Foundation of China ; Strategic Priority Research Program B of the Chinese Academy of Sciences ; National Key Research and Development Program of China ; Japan Society for the Promotion of Science (JSPS) ; NSF
Language英语
Funding ProjectNational Science Foundation of China[41476104] ; National Science Foundation of China[31460001] ; Strategic Priority Research Program B of the Chinese Academy of Sciences[XDB06010201] ; Strategic Priority Research Program B of the Chinese Academy of Sciences[XDB06040101] ; National Key Research and Development Program of China[2016YFC0302500] ; Japan Society for the Promotion of Science (JSPS)[30070015] ; NSF[OCE-1232982] ; NSF[OCE-1335810] ; NSF[EF-0826924]
WOS KeywordUniversal Stress-protein ; Ribosomal-rna ; Single Cells ; Gene ; Dna ; Diversity ; Sequence ; Bacteria ; Adaptations ; Physiology
WOS Research AreaMicrobiology
WOS SubjectMicrobiology
WOS IDWOS:000459172700015
PublisherWILEY
Citation statistics
Cited Times:4[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Version出版稿
Identifierhttp://ir.idsse.ac.cn/handle/183446/6677
Collection深海科学研究部_深海生物学研究室_海洋微生物宏基因组与分子进化研究组
Corresponding AuthorWang, Yong
Affiliation1.Chinese Acad Sci, Inst Deep Sea Sci & Engn, Sanya, Hainan, Peoples R China
2.Univ Chinese Acad Sci, Beijing, Peoples R China
3.Japan Agcy Marine Earth Sci & Technol JAMSTEC, Res & Dev Ctr Marine Biosci, 2-15 Natsushima Cho, Yokosuka, Kanagawa 2370061, Japan
4.Japan Agcy Marine Earth Sci & Technol JAMSTEC, Dept Subsurface Geobiol Anal & Res, 2-15 Natsushima Cho, Yokosuka, Kanagawa 2370061, Japan
5.Bigelow Lab Ocean Sci, 60 Bigelow Dr, East Boothbay, ME 04544 USA
Recommended Citation
GB/T 7714
Wang, Yong,Huang, Jiao-Mei,Cui, Guo-Jie,et al. Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean[J]. ENVIRONMENTAL MICROBIOLOGY,2019,21(2):716-729.
APA Wang, Yong.,Huang, Jiao-Mei.,Cui, Guo-Jie.,Nunoura, Takuro.,Takaki, Yoshihiro.,...&Stepanauskas, Ramunas.(2019).Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean.ENVIRONMENTAL MICROBIOLOGY,21(2),716-729.
MLA Wang, Yong,et al."Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean".ENVIRONMENTAL MICROBIOLOGY 21.2(2019):716-729.
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