title: Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss.
abstract: Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated withSulfobacillusthermosulfidooxidansHere, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of theSulfobacillusgenomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. TheSulfobacillusstrains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history ofSulfobacillusstrains.IMPORTANCEHorizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT. Furthermore, genome streamlining may be a critical force in driving the evolution of microbial genomes. Taken together, this study provides insights into the importance of both HGT and gene loss in the evolution and diversification of bacterial genomes.
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China.|Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
authors.forename: Xian
authors.initials: X
authors.lastname: Zhang
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China.|Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
authors.forename: Xueduan
authors.initials: X
authors.lastname: Liu
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China.|Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
authors.forename: Yili
authors.initials: Y
authors.lastname: Liang
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Guo
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China.
authors.forename: Yunhua
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China.
authors.forename: Liyuan
authors.initials: L
authors.lastname: Ma
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China.|Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Miao
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China.|Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Liu
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Deliang
authors.initials: D
authors.lastname: Peng
authors.affiliation: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Wenkun
authors.initials: W
authors.lastname: Huang
authors.affiliation: Institute of Forestry Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing, China.
authors.forename: Yuguang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China yinhuaqun@gmail.com.|Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
authors.forename: Huaqun
authors.initials: H
authors.lastname: Yin
mesh_terms: D000068016:Eubacteriales / Q000235:genetics*; D019295:Computational Biology; D019143:Evolution, Molecular; D017353:Gene Deletion; D022761:Gene Transfer, Horizontal; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D053858:Metabolic Networks and Pathways; D008957:Models, Genetic; D010802:Phylogeny; D013312:Stress, Physiological
keywords: Sulfobacillus thermosulfidooxidans; adaptive evolution; genomic streamlining; horizontal gene transfer