Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands.
Netherlands Earth System Science Centre, Utrecht University, Utrecht, The Netherlands.
Antonie Van Leeuwenhoek. 2022 Oct;115(10):1229-1244. doi: 10.1007/s10482-022-01767-z. Epub 2022 Aug 10.
Archaea belonging to the phylum Bathyarchaeota are the predominant archaeal species in cold, anoxic marine sediments and additionally occur in a variety of habitats, both natural and man-made. Metagenomic and single-cell sequencing studies suggest that Bathyarchaeota may have a significant impact on the emissions of greenhouse gases into the atmosphere, either through direct production of methane or through the degradation of complex organic matter that can subsequently be converted into methane. This is especially relevant in permafrost regions where climate change leads to thawing of permafrost, making high amounts of stored carbon bioavailable. Here we present the analysis of nineteen draft genomes recovered from a sediment core metagenome of the Polar Fox Lagoon, a thermokarst lake located on the Bykovsky Peninsula in Siberia, Russia, which is connected to the brackish Tiksi Bay. We show that the Bathyarchaeota in this lake are predominantly peptide degraders, producing reduced ferredoxin from the fermentation of peptides, while degradation pathways for plant-derived polymers were found to be incomplete. Several genomes encoded the potential for acetogenesis through the Wood-Ljungdahl pathway, but methanogenesis was determined to be unlikely due to the lack of genes encoding the key enzyme in methanogenesis, methyl-CoM reductase. Many genomes lacked a clear pathway for recycling reduced ferredoxin. Hydrogen metabolism was also hardly found: one type 4e [NiFe] hydrogenase was annotated in a single MAG and no [FeFe] hydrogenases were detected. Little evidence was found for syntrophy through formate or direct interspecies electron transfer, leaving a significant gap in our understanding of the metabolism of these organisms.
古菌门广古菌门中的古菌是寒冷、缺氧海洋沉积物中的主要古菌物种，此外还存在于各种自然和人为的栖息地中。宏基因组和单细胞测序研究表明，广古菌门可能通过直接产生甲烷或通过降解复杂有机物而对温室气体向大气中的排放产生重大影响，随后这些有机物可被转化为甲烷。这在永久冻土地区尤为相关，因为气候变化导致永久冻土融化，使大量储存的碳变得生物可利用。在这里，我们介绍了从西伯利亚别科夫半岛的极地狐狸泻湖沉积物宏基因组中恢复的 19 个草案基因组的分析结果，该湖与半咸水的提克西湾相连。我们表明，该湖中广古菌门主要是肽降解菌，通过肽的发酵产生还原型铁氧还蛋白，而植物衍生聚合物的降解途径被发现是不完整的。几个基因组通过伍德-吕根达尔途径编码了产乙酸的潜力，但由于缺乏产甲烷过程中的关键酶甲基辅酶 M 还原酶，产甲烷被认为不太可能。许多基因组缺乏回收还原型铁氧还蛋白的明确途径。氢代谢也几乎没有发现：一个类型 4e [NiFe]氢化酶在单个 MAG 中被注释，并且没有检测到 [FeFe]氢化酶。通过甲酸盐或直接种间电子转移发现很少有证据表明共生作用，这使得我们对这些生物代谢的理解存在重大差距。
