Cevallos Miguel Angel, Degli Esposti Mauro
Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico.
Microorganisms. 2022 Feb 16;10(2):455. doi: 10.3390/microorganisms10020455.
We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MAGs) that remain poorly defined in their taxonomic position within Alphaproteobacteria. The traditional classification of NCBI taxonomy is increasingly complemented by the Genome Taxonomy Database (GTDB), but the two taxonomies differ considerably in the classification of several Alphaproteobacteria, especially from ocean metagenomes. We analyzed the classification of Alphaproteobacteria lineages that are most common in marine environments, using integrated approaches of phylogenomics and functional profiling of metabolic features that define their aerobic metabolism. Using protein markers such as NuoL, the largest membrane subunit of complex I, we have identified new clades of Alphaproteobacteria that are specific to marine niches with steep oxygen gradients (oxycline). These bacteria have relatives among MAGs found in anoxic strata of Lake Tanganyika and together define a lineage that is distinct from either Rhodospirillales or Sneathiellales. We characterized in particular the new 'oxycline' clade. Our analysis of Alphaproteobacteria also reveals new clues regarding the ancestry of mitochondria, which likely evolved in oxycline marine environments.
我们在此概述α-变形菌纲，这是一大类生理特性多样的细菌，自2007年以来被划分为几个目。目前，越来越多的海洋宏基因组组装基因组（MAG）在α-变形菌纲中的分类地位仍不明确，其分类存在相当大的不确定性。美国国立医学图书馆分类法的传统分类越来越多地得到基因组分类数据库（GTDB）的补充，但这两种分类法在几种α-变形菌纲的分类上存在很大差异，尤其是来自海洋宏基因组的分类。我们使用系统发育基因组学和定义其有氧代谢的代谢特征功能分析的综合方法，分析了海洋环境中最常见的α-变形菌纲谱系的分类。使用诸如NuoL（复合体I最大的膜亚基）等蛋白质标记，我们鉴定出了α-变形菌纲的新分支，这些分支特定于具有陡峭氧梯度（氧cline）的海洋生态位。这些细菌在坦噶尼喀湖缺氧地层中发现的MAG中有亲缘关系，共同定义了一个与红螺菌目或斯内氏菌目都不同的谱系。我们特别对新的“氧cline”分支进行了表征。我们对α-变形菌纲的分析还揭示了有关线粒体起源的新线索，线粒体可能是在氧cline海洋环境中进化而来的。
