Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA.
University of Guelph, School of Environmental Sciences, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
ISME J. 2023 Jun;17(6):891-902. doi: 10.1038/s41396-023-01397-x. Epub 2023 Apr 3.
The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. Here, we use phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree-species-tree reconciliation methods to investigate the life histories of these two phyla. We find that basal clades of both phyla primarily inhabit marine and terrestrial subsurface environments. The genomes of basal clades in both phyla appear smaller and more densely coded than the later-branching clades. The extant basal clades of both phyla share many traits inferred to be present in their respective common ancestors, including hydrogen, one-carbon, and sulfur-based metabolisms. Later-branching groups, namely the more frequently studied classes Nitrospiria and Nitrospinia, are both characterized by genome expansions driven by either de novo origination or laterally transferred genes that encode functions expanding their metabolic repertoire. These expansions include gene clusters that perform the unique nitrogen metabolisms that both phyla are most well known for. Our analyses support replicated evolutionary histories of these two bacterial phyla, with modern subsurface environments representing a genomic repository for the coding potential of ancestral metabolic traits.
由于其对生物地球化学和工业过程至关重要的独特氮代谢，Nitrospirota 和 Nitrospinota 门受到了广泛关注。这两个门是海洋和陆地地下环境中的常见居民，除了亚硝酸盐氧化和氨完全氧化外，还包含具有多种生理特性的成员。在这里，我们使用系统发生基因组学和基于基因的分析，结合祖先状态重建和基因树-物种树协调方法，研究了这两个门的生活史。我们发现，这两个门的基础分支主要栖息在海洋和陆地地下环境中。这两个门的基础分支的基因组比后来的分支更小，编码密度更高。这两个门现存的基础分支共享许多被推断为其各自祖先存在的特征，包括氢、一碳和硫代谢。后来的分支，即研究较多的 Nitrospiria 和 Nitrospinia 类群，都具有由从头起源或侧向转移基因驱动的基因组扩张，这些基因编码的功能扩展了它们的代谢范围。这些扩张包括执行这两个门最著名的独特氮代谢的基因簇。我们的分析支持这两个细菌门的复制进化历史，现代地下环境代表了祖先代谢特征编码潜力的基因组库。
