Comparative Genomic Analysis Reveals Preserved Features in Organohalide-Respiring Sulfurospirillum Strains

• Published in: mSphere 2022-02, Vol.7 (1), p.e0093121-e0093121
• Main Authors: Yang, Yi, Schubert, Torsten, Lv, Yan, Li, Xiuying, Yan, Jun
• Format: Article
• Language: English
• Subjects: Anthropogenic factors; Bacteria - genetics; Bioremediation; comparative genomics; Dechlorination; Detoxification; Ecophysiology; Energy conservation; Environmental Microbiology; Environmental Pollutants - metabolism; Evolution; Fermentation; Gene expression; Genetic engineering; Genome editing; Genomes; Genomic analysis; Genomics; Geology; Groundwater; Humans; Metabolism; Metabolites; Microorganisms; organohalide respiration; pH effects; Phylogenetics; Phylogeny; Physiology; Plasmids; Pollutants; Pyruvic acid; Quinones; Research Article; Respiration; RNA, Ribosomal, 16S - genetics; rRNA 16S; Species; Strains (organisms); Sulfur; Sulfurospirillum; Tetrachloroethylene - metabolism; Trichloroethylene; Urease
• ISSN: 2379-5042; 2379-5042
• DOI: 10.1128/msphere.00931-21

species strains are frequently detected in various pristine and contaminated environments and participate in carbon, sulfur, nitrogen, and halogen elements cycling. Recently we obtained the complete genome sequences of two newly isolated strains, ACS and ACS , capable of dechlorinating tetrachloroethene to -1,2-dichloroethene and trichloroethene under low-pH conditions, but a detailed analysis of these two genomes in reference to other genomes for an improved understanding of evolution and ecophysiology has not been accomplished. Here, we performed phylogenetic and pangenome analyses with 12 completed genomes, including those of strain ACS and strain ACS , to unravel the evolutionary and metabolic potentials in the genus . Based on 16S rRNA gene and whole-genome phylogenies, strains ACS , ACS , and JPD-1 could be clustered into a single species, proposed as " Sulfurospirillum acididehalogenans." TimeTree analysis suggested that the organohalide-respiring (OHR) might acquire the ability to use chlorinated electron acceptors later than other energy conservation processes. Nevertheless, the ambiguity of the phylogenetic relations among strains complicated the interpretation of acquisition and loss of metabolic traits. Interestingly, all OHR genomes except the ones of Sulfurospirillum multivorans strains harbor a well-aligned and conserved region comprising the genetic components required for the organohalide respiration chain. Pangenome results further revealed that a total of 34,620 gene products, annotated from the 12 genomes, can be classified into 4,118 homolog families and 2,075 singleton families. Various species strains have conserved metabolisms as well as individual enzymes and biosynthesis capabilities. For instance, only the OHR species strains possess the quinone-dependent pyruvate dehydrogenase (PoxB) gene, and only " Sulfurospirillum acididehalogenans" strains harbor urea transporter and urease genes. The plasmids found in strain ACS and strain ACS feature genes coding for type II toxin-antitoxin systems and transposases and are promising tools for the development of robust gene editing tools for . Organohalide-respiring bacteria (OHRB) play critical roles in the detoxification of chlorinated pollutants and bioremediation of subsurface environments (e.g., groundwater and sediment) impacted by anthropogenic chlorinated solvents. The majority of known OHRB cannot perform reductive dechlorination below neutral pH, hampering the applications of OHRB