Genomic analysis of family UBA6911 (Group 18 Acidobacteria) expands the metabolic capacities of the phylum and highlights adaptations to terrestrial habitats.
Genomic analysis of family UBA6911 (Group 18 Acidobacteria) expands the metabolic capacities of the phylum and highlights adaptations to terrestrial habitats.
复制标题
UBA6911 家族（酸杆菌第 18 组）的基因组分析扩大了该门的代谢能力，并强调了对陆地栖息地的适应。
DOI：
10.1101/2021.04.09.439258
复制
发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Archana Yadav, Jenna Borrelli
中科院分区：
文献类型：
--
作者：
Archana Yadav, Jenna Borrelli
恢复和分析属于新颖的、迄今为止尚未探索的细菌谱系的基因组的方法为了解尚未培养的类群的代谢能力和生态作用提供了宝贵的见解。酸杆菌门是地球上最普遍、生态上最成功的谱系之一，但目前，该门内的多个谱系仍未被探索。在这里，我们利用从俄克拉荷马州西南部的 Zodletone Spring（一种厌氧硫化物和富含硫的泉水）以及多个不同的土壤和非土壤生境中回收的基因组，来检查 UBA6911（第 18 组）酸杆菌家族成员的代谢能力和生态作用。分析的基因组分为五个不同的属，其中 Gp18_AA60 和 QHZH01 属从土壤中回收，Ga0209509 属从厌氧消化器中回收，Ga0212092 和 UBA6911 属从淡水栖息地回收。所有基因组分析表明，酸杆菌第 18 组的成员是代谢多功能的异养生物，能够利用多种蛋白质、氨基酸和糖作为碳源，具有呼吸和发酵能力，并且几乎没有营养缺陷。土壤栖息属的特点是基因组规模更大、CRISPR位点数量更多、扩展的碳水化合物活性酶（CAZyme）机器能够使特定糖从聚合物中脱支、拥有C1（甲醇和甲胺）降解机器以及完全依赖有氧呼吸。相比之下，非土壤基因组编码了更通用的氧气、亚硝酸盐、硫酸盐和三甲胺N-氧化物（TMAO）呼吸的呼吸能力，以及在异养生长期间利用Wood-Ljungdahl（WL）途径作为电子汇的潜力。我们的研究结果不仅扩展了我们对尚未培养的细菌谱系代谢的认识，而且还提供了关于陆地化和生态位适应如何驱动酸细菌内代谢专业化的有趣线索。重要性酸细菌的成员是全球生物地球化学循环中的重要参与者，特别是在土壤中。目前仍有大量酸杆菌谱系尚未被探索。我们提出了酸杆菌门 UBA6911 家族（也称为第 18 组）基因组的详细基因组特征。基因组属于不同属，并从土壤（Gp18_AA60 属和 QHZH01 属）、淡水栖息地（Ga0212092 和 UBA6911 属）和厌氧消化器（Ga0209509 属）中获得。虽然该科的所有成员都有共同的代谢特征，例如异养呼吸能力、广泛的底物利用能力和很少的营养缺陷型，但观察到土壤属和非土属之间的明显差异。土壤属的特点是基因组扩大、CRISPR位点数量增多、碳水化合物活性酶（CAZyme）库更大，能够从聚合物侧链中提取单体，以及甲基营养（甲醇和甲胺）降解能力。相比之下，非土壤属编码了更通用的呼吸能力，除了利用氧气作为电子受体外，还利用亚硝酸盐、硫酸盐、TMAO 和 WL 途径。我们的结果不仅拓宽了我们对酸性细菌代谢能力的理解，而且还为陆地化如何塑造酸性细菌进化和生态位适应提供了有趣的线索。
Approaches for recovering and analyzing genomes belonging to novel, hitherto-unexplored bacterial lineages have provided invaluable insights into the metabolic capabilities and ecological roles of yet-uncultured taxa. The phylumAcidobacteriais one of the most prevalent and ecologically successful lineages on Earth, yet currently, multiple lineages within this phylum remain unexplored. Here, we utilize genomes recovered from Zodletone Spring, an anaerobic sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil and nonsoil habitats, to examine the metabolic capabilities and ecological role of members of family UBA6911 (group 18)Acidobacteria. The analyzed genomes clustered into five distinct genera, with genera Gp18_AA60 and QHZH01 recovered from soils, genus Ga0209509 from anaerobic digestors, and genera Ga0212092 and UBA6911 from freshwater habitats. All genomes analyzed suggested that members ofAcidobacteriagroup 18 are metabolically versatile heterotrophs capable of utilizing a wide range of proteins, amino acids, and sugars as carbon sources, possess respiratory and fermentative capacities, and display few auxotrophies. Soil-dwelling genera were characterized by larger genome sizes, higher numbers of CRISPR loci, an expanded carbohydrate active enzyme (CAZyme) machinery enabling debranching of specific sugars from polymers, possession of a C1(methanol and methylamine) degradation machinery, and a sole dependence on aerobic respiration. In contrast, nonsoil genomes encoded a more versatile respiratory capacity for oxygen, nitrite, sulfate, and trimethylamineN-oxide (TMAO) respiration, as well as the potential for utilizing the Wood-Ljungdahl (WL) pathway as an electron sink during heterotrophic growth. Our results not only expand our knowledge of the metabolism of a yet-uncultured bacterial lineage but also provide interesting clues on how terrestrialization and niche adaptation drive metabolic specialization within theAcidobacteria.IMPORTANCEMembers of theAcidobacteriaare important players in global biogeochemical cycles, especially in soils. A wide range of acidobacterial lineages remain currently unexplored. We present a detailed genomic characterization of genomes belonging to family UBA6911 (also known as group 18) within the phylumAcidobacteria. The genomes belong to different genera and were obtained from soil (genera Gp18_AA60 and QHZH01), freshwater habitats (genera Ga0212092 and UBA6911), and an anaerobic digestor (genus Ga0209509). While all members of the family shared common metabolic features, e.g., heterotrophic respiratory abilities, broad substrate utilization capacities, and few auxotrophies, distinct differences between soil and nonsoil genera were observed. Soil genera were characterized by expanded genomes, higher numbers of CRISPR loci, a larger carbohydrate active enzyme (CAZyme) repertoire enabling monomer extractions from polymer side chains, and methylotrophic (methanol and methylamine) degradation capacities. In contrast, nonsoil genera encoded more versatile respiratory capacities for utilizing nitrite, sulfate, TMAO, and the WL pathway, in addition to oxygen as electron acceptors. Our results not only broaden our understanding of the metabolic capacities within theAcidobacteriabut also provide interesting clues on how terrestrialization shapedAcidobacteriaevolution and niche adaptation.