Qi Yan-Ling, Evans Paul N, Li Yu-Xian, Rao Yang-Zhi, Qu Yan-Ni, Tan Sha, Jiao Jian-Yu, Chen Ya-Ting, Hedlund Brian P, Shu Wen-Sheng, Hua Zheng-Shuang, Li Wen-Jun
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queenslandgrid.1003.2, St Lucia, Queensland, Australia.
mSystems. 2021 Aug 31;6(4):e0025221. doi: 10.1128/mSystems.00252-21. Epub 2021 Jul 20.
" Bathyarchaeia" is a phylogenetically diverse and widely distributed lineage often in high abundance in anoxic submarine sediments; however, their evolution and ecological roles in terrestrial geothermal habitats are poorly understood. In the present study, 35 . Bathyarchaeia metagenome-assembled genomes (MAGs) were recovered from hot spring sediments in Tibet and Yunnan, China. Phylogenetic analysis revealed all MAGs of . Bathyarchaeia can be classified into 7 orders and 15 families. Among them, 4 families have been first discovered in the present study, significantly expanding the known diversity of . Bathyarchaeia. Comparative genomics demonstrated . Bathyarchaeia MAGs from thermal habitats to encode a large variety of genes related to carbohydrate degradation, which are likely a metabolic adaptation of these organisms to a lifestyle at high temperatures. At least two families are potential methanogens/alkanotrophs, indicating a potential for the catalysis of short-chain hydrocarbons. Three MAGs from Family-7.3 are identified as alkanotrophs due to the detection of an Mcr complex. Family-2 contains the largest number of genes relevant to alkyl-CoM transformation, indicating the potential for methylotrophic methanogenesis, although their evolutionary history suggests the ancestor of . Bathyarchaeia was unable to metabolize alkanes. Subsequent lineages have acquired the ability via horizontal gene transfer. Overall, our study significantly expands our knowledge and understanding of the metabolic capabilities, habitat adaptations, and evolution of . Bathyarchaeia in thermal environments. . Bathyarchaeia MAGs from terrestrial hot spring habitats are poorly revealed, though they have been studied extensively in marine ecosystems. In this study, we uncovered the metabolic capabilities and ecological role of . Bathyarchaeia in hot springs and give a comprehensive comparative analysis between thermal and nonthermal habitats to reveal the thermal adaptability of . Bathyarchaeia. Also, we attempt to determine the evolutionary history of methane/alkane metabolism in . Bathyarchaeia, since it appears to be the first archaea beyond which contains the genes. The reclassification of . Bathyarchaeia and significant genomic differences among different lineages largely expand our knowledge on these cosmopolitan archaea, which will be beneficial in guiding the future studies.
“深古菌纲（Bathyarchaeia）”是一个系统发育多样且分布广泛的谱系，在缺氧海底沉积物中通常丰度较高；然而，它们在陆地地热生境中的进化和生态作用却知之甚少。在本研究中，从中国西藏和云南的温泉沉积物中获得了35个深古菌纲的宏基因组组装基因组（MAG）。系统发育分析表明，所有深古菌纲的MAG可分为7个目和15个科。其中，有4个科是在本研究中首次发现的，显著扩展了深古菌纲已知的多样性。比较基因组学表明，来自热生境的深古菌纲MAG编码大量与碳水化合物降解相关的基因，这可能是这些生物体对高温生活方式的一种代谢适应。至少有两个科是潜在的产甲烷菌/烷烃营养菌，表明它们具有催化短链烃的潜力。由于检测到Mcr复合物，来自7.3科的3个MAG被鉴定为烷烃营养菌。2科包含与烷基辅酶M转化相关的基因数量最多，表明其具有甲基营养型产甲烷的潜力，尽管它们的进化历史表明深古菌纲的祖先无法代谢烷烃。随后的谱系通过水平基因转移获得了这种能力。总体而言，我们的研究显著扩展了我们对深古菌纲在热环境中的代谢能力、生境适应性和进化的认识。尽管深古菌纲MAG在海洋生态系统中已得到广泛研究，但来自陆地温泉生境的深古菌纲MAG却鲜有揭示。在本研究中，我们揭示了深古菌纲在温泉中的代谢能力和生态作用，并对热生境和非热生境进行了全面的比较分析，以揭示深古菌纲的热适应性。此外，我们试图确定深古菌纲中甲烷/烷烃代谢的进化历史，因为它似乎是第一个含有相关基因的古菌。深古菌纲的重新分类以及不同谱系之间显著的基因组差异极大地扩展了我们对这些世界性古菌的认识，这将有助于指导未来的研究。
