Author:
Park Mi-Jeong,Kim Yun Jae,Park Myeongkyu,Yu Jihyun,Namirimu Teddy,Roh Yoo-Rim,Kwon Kae Kyoung
Abstract
Bacteria in the Desulfovibrionaceae family, which contribute to S element turnover as sulfate-reducing bacteria (SRB) and disproportionation of partially oxidized sulfoxy anions, have been extensively investigated since the importance of the sulfur cycle emerged. Novel species belonging to this taxon are frequently reported, because they exist in various environments and are easy to culture using established methods. Due to the rapid expansion of the taxon, correction and reclassification have been conducted. The development of high-throughput sequencing facilitated rapid expansion of genome sequence database. Genome-based criteria, based on these databases, proved to be potential classification standard by overcoming the limitations of 16S rRNA-based phylogeny. Although standards methods for taxogenomics are being established, the addition of a novel genus requires extensive calculations with taxa, including many species, such as Desulfovibrionaceae. Thus, the genome-based criteria for classification of Desulfovibrionaceae were established and validated in this study. The average amino-acid identity (AAI) cut-off value, 63.43 ± 0.01, was calculated to be an appropriate criterion for genus delineation of the family Desulfovibrionaceae. By applying the AAI cut-off value, 88 genomes of the Desulfovibrionaceae were divided into 27 genera, which follows the core gene phylogeny results. In this process, two novel genera (Alkalidesulfovibrio and Salidesulfovibrio) and one former invalid genus (“Psychrodesulfovibrio”) were officially proposed. Further, by applying the 95–96% average nucleotide identity (ANI) standard and the 70% digital DNA–DNA hybridization standard values for species delineation of strains that were classified as the same species, five strains have the potential to be newly classified. After verifying that the classification was appropriately performed through relative synonymous codon usage analysis, common characteristics were listed by group. In addition, by detecting metal resistance related genes via in silico analysis, it was confirmed that most strains display metal tolerance.
Funder
Korea Institute of Ocean Science and Technology
Ministry of Oceans and Fisheries
Subject
Microbiology (medical),Microbiology
Reference156 articles.
1. Desulfovibrio alkalitolerans sp. nov., a novel alkalitolerant, sulphate-reducing bacterium isolated from district heating water.;Abildgaard;Int. J. Syst. Evol. Microbiol.,2006
2. Purification and properties of thiosulfate reductase from Desulfovibrio vulgaris, Miyazaki F.;Aketagawa;J. Biochem.,1985
3. Desulfovibrio hydrothermalis sp. nov., a novel sulfate-reducing bacterium isolated from hydrothermal vents.;Alazard;Int. J. Syst. Evol. Microbiol.,2003
4. Phylogenomic re-assessment of the thermophilic genus Geobacillus.;Aliyu;Syst. Appl. Microbiol.,2016
5. Desulfovibrio carbinoliphilus sp. nov., a benzyl alcohol-oxidizing, sulfate-reducing bacterium isolated from a gas condensate-contaminated aquifer.;Allen;Int. J. Syst. Evol. Microbiol.,2008
Cited by
20 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献