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

IF 13.8 1区生物学 Q1 MICROBIOLOGY

Microbiome Pub Date : 2024-10-09 DOI:10.1186/s40168-024-01912-y

Yingdong Li, Jiawei Chen, Yanxun Lin, Cheng Zhong, Hongmei Jing, Hongbin Liu

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引用次数: 0

Abstract

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 ~ 800 million years ago (mya), and their expansion to shallow water coincided with the Sturtian glaciation (~ 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. Video Abstract.

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深海甲烷渗漏中的潮鲍藻为了解其进化历史和生态影响提供了新的视角。

背景：氨氧化古细菌门（AOA）介导硝化过程中的限速步骤，并清除抑制甲烷营养生物有氧代谢的氨。然而，对栖息在深海甲烷深层表层沉积物（DMS）中的厌氧动物却鲜有研究。在这里，我们利用全球 DMS 元基因组学和元基因组组装基因组（MAGs）来研究 AOA 的代谢活动、进化历史和生态贡献。在中国南海（SCS）采集的沉积物中检测了AOA特异性氨氧化基因（amoA）的表达，以确定它们在DMS中的氨代谢活动：我们的分析表明，在全球DMS表层（30厘米以上）的氨利用基因组成中，AOA所占比例大于75%。AOA特异性氨氧化基因在SCS采集的DMS中表达活跃。对来自 18 个 DMS-AOA 的中/高质量 MAG 的系统发生组分析表明，它们是从贫瘠的深海沉积物中的祖先进化而来，然后从 DMS 扩展到浅水，形成了一个与 amoA-NP-gamma 支系相关的世系。分子年代测定表明，DMS-AOA起源于距今约8亿年前的新近纪氧化事件（NOE），而它们向浅水区的扩展则与斯图尔特冰川时期（约7.13亿年前）相吻合。基因组比较分析表明，DMS-AOA对蛋白质合成的碳源要求更高，其基因组在渗透调节、运动、趋化和利用外源有机化合物方面的能力也更强，这表明与其他品系相比，DMS-AOA可能更具异养性：结论：我们的研究结果为了解陶氏古菌中AOA的进化历史提供了新的视角，凸显了它们在全球DMS生态系统氮循环中的关键作用。视频摘要

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来源期刊

Microbiome MICROBIOLOGY-

CiteScore

21.90

自引率

2.60%

发文量

198

审稿时长

4 weeks

期刊介绍： Microbiome is a journal that focuses on studies of microbiomes in humans, animals, plants, and the environment. It covers both natural and manipulated microbiomes, such as those in agriculture. The journal is interested in research that uses meta-omics approaches or novel bioinformatics tools and emphasizes the community/host interaction and structure-function relationship within the microbiome. Studies that go beyond descriptive omics surveys and include experimental or theoretical approaches will be considered for publication. The journal also encourages research that establishes cause and effect relationships and supports proposed microbiome functions. However, studies of individual microbial isolates/species without exploring their impact on the host or the complex microbiome structures and functions will not be considered for publication. Microbiome is indexed in BIOSIS, Current Contents, DOAJ, Embase, MEDLINE, PubMed, PubMed Central, and Science Citations Index Expanded.