Phylogenetic diversity, ecological function, and evolutionary history of three novel phyla: Yinglongibacterota, Xuanmingibacterota, and Gonggongibacterota

Abstract

Geothermal systems harbor abundant novel microorganisms, representing substantial phylogenetic and functional diversity among yet‐to‐be‐cultivated bacteria with significant ecological roles. Nevertheless, research on the diversity, metabolic potential, and evolutionary history of these uncultured taxa remains limited. In this study, 19 metagenome‐assembled genomes (MAGs) were recovered from hot springs in Tengchong, Yunnan Province. Phylogenetic analyses indicate that these MAGs form sister lineages to an existing clade, leading to their proposed classification within three novel phyla: Yinglongibacterota, Xuanmingibacterota, and Gonggongibacterota, named after figures from the traditional Chinese legend, Classics of Mountains and Seas. Sequence analysis of both hot spring‐derived and published MAGs reveals that all three phyla exhibit similar facultative anaerobic lifestyles. Multiple substrates, including cellulose, glucan, pectin, and xylan, can be degraded by these phyla, especially Gonggongibacterota, suggesting their critical role in converting complex plant matter into more readily degradable substrates and contributing to sugar fermentation. Furthermore, the ability of these phyla to reduce selenite facilitates environmental detoxification. Notably, gene loss events have resulted in widespread auxotrophy for heme and biotin in these lineages, which may indicate microbial cross‐feeding in the community as an adaptation strategy. These pioneering results provide a comprehensive overview of the taxonomic and metabolic characteristics of the three novel phyla, offering insights into their ecological significance and guiding future cultivation efforts.