候选嗜酸菌门,具有耐酸适应能力的代谢和系统发育多样化的陆地门。

Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations.

机构信息

School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Randwick, NSW, Australia.

Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, China.

出版信息

ISME J. 2021 Sep;15(9):2692-2707. doi: 10.1038/s41396-021-00944-8. Epub 2021 Mar 22.

Abstract

Candidatus phylum Eremiobacterota (formerly WPS-2) is an as-yet-uncultured bacterial clade that takes its name from Ca. Eremiobacter, an Antarctic soil aerobe proposed to be capable of a novel form of chemolithoautotrophy termed atmospheric chemosynthesis, that uses the energy derived from atmospheric H-oxidation to fix CO through the Calvin-Benson-Bassham (CBB) cycle via type 1E RuBisCO. To elucidate the phylogenetic affiliation and metabolic capacities of Ca. Eremiobacterota, we analysed 63 public metagenome-assembled genomes (MAGs) and nine new MAGs generated from Antarctic soil metagenomes. These MAGs represent both recognized classes within Ca. Eremiobacterota, namely Ca. Eremiobacteria and UBP9. Ca. Eremiobacteria are inferred to be facultatively acidophilic with a preference for peptides and amino acids as nutrient sources. Epifluorescence microscopy revealed Ca. Eremiobacteria cells from Antarctica desert soil to be coccoid in shape. Two orders are recognized within class Ca. Eremiobacteria: Ca. Eremiobacterales and Ca. Baltobacterales. The latter are metabolically versatile, with individual members having genes required for trace gas driven autotrophy, anoxygenic photosynthesis, CO oxidation, and anaerobic respiration. UBP9, here renamed Ca. Xenobia class. nov., are inferred to be obligate heterotrophs with acidophilic adaptations, but individual members having highly divergent metabolic capacities compared to Ca. Eremiobacteria, especially with regard to respiration and central carbon metabolism. We conclude Ca. Eremiobacterota to be an ecologically versatile phylum with the potential to thrive under an array of "extreme" environmental conditions.

摘要

未培养细菌门坎地栖菌门(原 WPS-2)是一个尚未培养的细菌类群,其名称来自 Ca. Eremiobacter,一种拟南芥土壤需氧菌,被认为能够进行一种新型的化能自养形式,称为大气化学合成,它利用大气 H-氧化产生的能量通过 1E 型 RuBisCO 通过卡尔文-本森-巴斯汉姆(CBB)循环固定 CO。为了阐明 Ca. Eremiobacterota 的系统发育关系和代谢能力,我们分析了 63 个公共宏基因组组装基因组(MAG)和从南极土壤宏基因组中生成的 9 个新的 MAG。这些 MAG 代表了 Ca. Eremiobacterota 内的两个公认的类群,即 Ca. Eremiobacteria 和 UBP9。Ca. Eremiobacteria 被推断为兼性嗜酸菌,偏爱肽和氨基酸作为营养源。荧光显微镜显示来自南极洲沙漠土壤的 Ca. Eremiobacteria 细胞呈球形。在 Ca. Eremiobacterota 类中,共识别出两个目:Ca. Eremiobacterales 和 Ca. Baltobacterales。后者代谢功能多样,其成员具有与痕量气体驱动自养、厌氧光合作用、CO 氧化和无氧呼吸相关的基因。UBP9,现更名为 Ca. Xenobia 类。nov.,被推断为专性异养生物,具有嗜酸适应,但与 Ca. Eremiobacteria 相比,个体成员具有高度分化的代谢能力,尤其是在呼吸和中心碳代谢方面。我们得出结论,Ca. Eremiobacterota 是一个生态多功能的门,有可能在一系列“极端”环境条件下茁壮成长。

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