Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota
Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota
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小古菌 Micrarchaeota 和 Parvarchaeota 的代谢多样性
DOI：
10.1038/s41396-017-0002-z
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发表时间：
2018-03-01
期刊：
影响因子：
11
通讯作者：
Shu, Wen-Sheng
中科院分区：
文献类型：
--
作者：
Chen, Lin-Xing;Mendez-Garcia, Celia;Shu, Wen-Sheng
属于微古菌门和小古菌门的小型嗜酸古菌已知在自然界中与一些热原体成员发生物理相互作用。然而，由于缺乏培养和手头有限的基因组，它们的生物多样性、代谢和生理学在很大程度上仍未得到解决。在这里，我们从世界各地的酸性矿井排水（AMD）和温泉环境中获得了39个基因组。基于16S rRNA基因的分析显示，细小古细菌只在AMD和温泉生境中检测到，而微古细菌也在土壤、泥炭、高盐垫和淡水中检测到，表明该门的多样性比预期的要高得多，栖息地分布也比预期的要广泛。尽管它们的基因组很小（0.64-1.08 Mb），但这些古细菌可能通过降解多种糖类和蛋白质来促进碳和氮循环，并通过有氧呼吸和发酵产生ATP。此外，我们在6个细小古菌基因组中发现了几个与铁氧化相关的同源基因，表明它们在铁循环中可能起作用。然而，这两个门缺乏氨基酸和核苷酸的生物合成途径，这表明它们可能从环境和/或其他群落成员中清除这些生物分子。此外，实验室的低氧富集证实了我们的猜测，即这两个门都是微氧/厌氧的，这是基于在它们身上发现的几个特定基因。此外，系统发育分析提供了深入了解两个门与热原体之间能量相关功能的密切进化史。这些结果通过揭示这些难以捉摸的古细菌参与碳、氮和铁循环，扩大了我们对这些古细菌的理解，并表明它们在基因组尺度上与热原体的潜在相互作用。
Small acidophilic archaea belonging to Micrarchaeota and Parvarchaeota phyla are known to physically interact with some Thermoplasmatales members in nature. However, due to a lack of cultivation and limited genomes on hand, their biodiversity, metabolisms, and physiologies remain largely unresolved. Here, we obtained 39 genomes from acid mine drainage (AMD) and hot spring environments around the world. 16S rRNA gene based analyses revealed that Parvarchaeota were only detected in AMD and hot spring habitats, while Micrarchaeota were also detected in others including soil, peat, hypersaline mat, and freshwater, suggesting a considerable higher diversity and broader than expected habitat distribution for this phylum. Despite their small genomes (0.64–1.08 Mb), these archaea may contribute to carbon and nitrogen cycling by degrading multiple saccharides and proteins, and produce ATP via aerobic respiration and fermentation. Additionally, we identified several syntenic genes with homology to those involved in iron oxidation in six Parvarchaeota genomes, suggesting their potential role in iron cycling. However, both phyla lack biosynthetic pathways for amino acids and nucleotides, suggesting that they likely scavenge these biomolecules from the environment and/or other community members. Moreover, low-oxygen enrichments in laboratory confirmed our speculation that both phyla are microaerobic/anaerobic, based on several specific genes identified in them. Furthermore, phylogenetic analyses provide insights into the close evolutionary history of energy related functionalities between both phyla with Thermoplasmatales. These results expand our understanding of these elusive archaea by revealing their involvement in carbon, nitrogen, and iron cycling, and suggest their potential interactions with Thermoplasmatales on genomic scale.