Bacteria in the phylum Gemmatimonadota are globally distributed and abundant in microbial communities of various environments, playing an important role in driving biogeochemical cycling on Earth. Although high diversities in taxonomic composition and metabolic capabilities have been reported, little is known about the environmental preferences and associated functional features that facilitate adaptation among different Gemmatimonadota lineages. This study systematically analyzed the relationships between the environments, taxonomy, and functions of Gemmatimonadota lineages, by using a comparative genomics approach based on 1356 Gemmatimonadota genomes (213 high-quality and non-redundant genomes) available in a public database (NCBI). The taxonomic analysis showed that the 99.5% of the genomes belong to the class Gemmatimonadetes, and the rest of the genomes belong to the class Glassbacteria. Functional profiling revealed clear environmental preference among different lineages of Gemmatimonadota, and a marine group and two non-marine groups were identified and tested to be significantly different in functional composition. Further annotation and statistical comparison revealed a large number of functional genes (e.g., amiE, coxS, yfbK) that were significantly enriched in genomes from the marine group, supporting enhanced capabilities in energy acquisition, genetic information regulation (e.g., DNA repair), electrolyte homeostasis, and growth rate control. These genomic features are important for their survival in the marine environment, which is oligotrophic, variable, and with high salinity. The findings enhanced our understanding of the metabolic processes and environmental adaptation of Gemmatimonadota, and further advanced the understanding of the interactions of microorganisms and their habitats.

The discharge of pollutants into rivers has been increasing with the rapid industrial development and extensive agricultural use of pesticides and herbicides. Halogenated organic compounds (HOCs) represent a significant class of environmental pollutants. It has been found that microorganisms have the ability not only to degrade HOCs but also to synthesize them. Little is known about the halogenation and dehalogenation potential of microorganisms in river waters. In this study, we investigated the halogenation and dehalogenation potentials of microorganisms in the Yangtze River, which originates from the Tibetan Plateau, flows through southwestern, central and eastern China, and finally joins the East China Sea. A systematic metagenomic and bioinformatics analysis identified and quantified genes encoding four dehalogenases and two halogenases, providing fundamental data for the halogen cycle in the Yangtze River water body. The study showed that the microbial community in the Yangtze water body was mainly associated with dehalogenation potential, and the relative abundance of dehalogenase genes was higher than that of halogenase genes. Among the microorganisms with halogenation and dehalogenation potentials, Pseudomonadota and Actinomycetota dominated. Some microorganisms possessed both halogenation and dehalogenation functions, suggesting a potential adaptive strategy to environmental fluctuations. The presence of diverse and complete dehalogenation metabolic pathways highlights the microbial potential for bioremediation. These microorganisms not only contribute to the degradation of halogenated organic matter but also play crucial roles in carbon, nitrogen, and sulfur cycling. This study provides essential data for understanding microbial halogenation and dehalogenation potential in the Yangtze River, offering insights into the microbial-driven biogeochemical cycling mechanisms in its waters.