Abstract: Acid mine drainage (AMD) represents a uniquely acidic ecosystem, marked by oligotrophic conditions, a low pH environment, and elevated concentrations of heavy metals. Within this milieu, a diverse array of acidophilic and acid-tolerant microorganisms thrives, playing pivotal roles in the biogeochemical cycling of carbon, nitrogen, sulfur, and various other elements. The complex interplay between heterotrophic and autotrophic microorganisms underscores a significant ecological niche, with theAcidiphiliumgenus, a group of facultative heterotrophic microorganisms constituting a minor proportion (<1%) of the AMD microbial community. Notably, these organisms often engage in symbiotic interactions with prevalent species likeAcidibacillus, suggesting thatAcidiphiliumspecies fulfill unique and crucial ecological functions within the AMD ecosystem. In order to investigate the ecological function ofAcidiphilium, a strain ofAcidiphiliumwas isolated from an extremely acidic environment. It was identified asAcidiphilium cryptumAcc2 after being compared with ANI by 16S rDNA. TheAcidiphilium cryptumAcc2 genome contained 1066 protein-coding genes with a total sequence length of 4917178 bp, all of which were larger than the gene size of other strains in the genus. It was an open genome, containing 47242 protein-coding genes, 699 protein-coding genes (1.48%) were identified as core genes, 33457 protein-coding genes were variable genes (70.82%), and 2705 protein-coding genes were unique genes (5.73%). The Ka/Ks values of heavy metal resistance genes of 95.5% were all lower than 1, which showed strong purification selection. The flow and exchange frequency between genes in the genome of the genusAcidiphiliumwas higher than that of other species, and it had a greater positive impact on the evolution and environmental adaptability of strains. This research shed light on their evolutionary trajectories and gene transfer mechanisms, offering insights into their environmental adaptation mechanism and ecological significance in AMD environments.

Key words: AMD;Acidiphilium, environmental adaptation mechanism, comparative genomics, horizontal gene transfer