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Thaumarchaeota from deep-sea methane seeps provide novel insights into their evolutionary history and ecological implications

文献类型：期刊论文

作者Li, Yingdong1,2,3,4; Chen, Jiawei1,2,3; Lin, Yanxun2; Zhong, Cheng1,2,3; Jing, Hongmei4; Liu, Hongbin1,2,3
刊名MICROBIOME
出版日期2024-10-09
卷号12期号:1页码:16
关键词Genomic evolution Ammonia-oxidizing archaea Methane seep Deep-sea sediment
ISSN号2049-2618
DOI10.1186/s40168-024-01912-y
英文摘要Background Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota mediate the rate-limiting step of nitrification and remove the ammonia that inhibits the aerobic metabolism of methanotrophs. However, the AOA that inhabit deep-sea methane-seep surface sediments (DMS) are rarely studied. Here, we used global DMS metagenomics and metagenome-assembled genomes (MAGs) to investigate the metabolic activity, evolutionary history, and ecological contributions of AOA. Expression of AOA-specific ammonia-oxidizing gene (amoA) was examined in the sediments collected from the South China Sea (SCS) to identify their active ammonia metabolism in the DMS. Results Our analysis indicated that AOA contribute > 75% to the composition of ammonia-utilization genes within the surface layers (above 30 cm) of global DMS. The AOA-specific ammonia-oxidizing gene was actively expressed in the DMS collected from the SCS. Phylogenomic analysis of medium-/high-quality MAGs from 18 DMS-AOA indicated that they evolved from ancestors in the barren deep-sea sediment and then expanded from the DMS to shallow water forming an amoA-NP-gamma clade-affiliated lineage. Molecular dating suggests that the DMS-AOA origination coincided with the Neoproterozoic oxidation event (NOE), which occurred similar to 800 million years ago (mya), and their expansion to shallow water coincided with the Sturtian glaciation (similar to 713 mya). Comparative genomic analysis suggests that DMS-AOA exhibit higher requirement of carbon source for protein synthesis with enhanced genomic capability for osmotic regulation, motility, chemotaxis, and utilization of exogenous organic compounds, suggesting it could be more heterotrophic compared with other lineages. Conclusion Our findings provide new insights into the evolutionary history of AOA within the Thaumarchaeota, highlighting their critical roles in nitrogen cycling in the global DMS ecosystems.
WOS关键词AMMONIA-OXIDIZING ARCHAEA ; COLD SEEPS ; NICHE DIFFERENTIATION ; OXYGEN ; ALIGNMENT ; INHIBITION ; GENOMES ; CONSUMPTION ; DIVERSITY ; OXIDATION
资助项目Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)[GML2019ZD0409] ; Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)[SMSEGL20SC01] ; Major Program of the Science and Technology Bureau of Hainan Province[ZDKJ2021036] ; National Natural Science Foundation of China[41776147] ; Hainan Provincial Natural Science Foundation of China for High-level Talents[420RC677] ; Senior User Project of RV KEXUE[KEXUE2021GH01]
WOS研究方向Microbiology
语种英语
WOS记录号WOS:001337170100002
出版者BMC
资助机构Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) ; Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) ; Major Program of the Science and Technology Bureau of Hainan Province ; National Natural Science Foundation of China ; Hainan Provincial Natural Science Foundation of China for High-level Talents ; Senior User Project of RV KEXUE
源URL[http://ir.idsse.ac.cn/handle/183446/11771]  
专题深海科学研究部_深海生物学研究室_海洋微生物分子生态学研究组
通讯作者Liu, Hongbin
作者单位1.Southern Marine Sci & Engn Guangdong Lab Guangzhou, Guangzhou, Peoples R China
2.Hong Kong Univ Sci & Technol, Dept Ocean Sci, Clear Water Bay, Hong Kong, Peoples R China
3.Hong Kong Univ Sci & Technol, Hong Kong Branch, Southern Marine Sci & Engn Guangdong Lab Guangzhou, Hong Kong, Peoples R China
4.Chinese Acad Sci, Inst Deep Sea Sci & Engn, CAS Key Lab Expt Study Under Deep Sea Extreme Cond, Sanya, Peoples R China
推荐引用方式
GB/T 7714		 Li, Yingdong,Chen, Jiawei,Lin, Yanxun,et al. Thaumarchaeota from deep-sea methane seeps provide novel insights into their evolutionary history and ecological implications[J]. MICROBIOME,2024,12(1):16.
APA Li, Yingdong,Chen, Jiawei,Lin, Yanxun,Zhong, Cheng,Jing, Hongmei,&Liu, Hongbin.(2024).Thaumarchaeota from deep-sea methane seeps provide novel insights into their evolutionary history and ecological implications.MICROBIOME,12(1),16.
MLA Li, Yingdong,et al."Thaumarchaeota from deep-sea methane seeps provide novel insights into their evolutionary history and ecological implications".MICROBIOME 12.1(2024):16.

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来源：深海科学与工程研究所

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