ABSTRACT
The monotypic carboxydophilic genus Carbophilus has recently been transferred to the genus Aminobacter within the family Phyllobacteriaceae, and Carbophilus carboxidus was renamed Aminobacter carboxidus (comb. nov.) [Hördt et al. 2020]. Due to the poor resolution of the 16S rRNA gene-based phylogeny, an extensive phylogenomic analysis of the family Phyllobacteriaceae was conducted, with particular focus on the genus Aminobacter. Whole genome-based analyses of Phyllobacteriaceae type strains provided evidenced that the genus Aminobacter forms a monophyletic cluster, clearly demarcated from all other members of the family. Close relatedness between A. carboxidus DSM 1086T and A. lissarensis DSM 17454T was inferred from core proteome phylogeny, shared gene content, and multilocus sequence analyses. ANI and GGDC provided genetic similarity values above the species demarcating threshold for these two type strains. Metabolic profiling and cell morphology analysis corroborated the phenotypic identity between A. carboxidus DSM 1086T and A. lissarensis DSM 17454T. Search for the presence of carbon monoxide dehydrogenase (CODH) genes in Phyllobacteriaceae genomes revealed that the form II CODH is widespread in the family, whereas form I CODH was detected in few Mesorhizobium type strains, and in both A. carboxidus DSM 1086T and A. lissarensis DSM 17454T. Results of phylogenomic, chemotaxonomic, and morphological investigations, combined with the presence of similarly arranged CODH genes, indicate that A. carboxidus DSM 1086T and A. lissarensis DSM 17454T are distinct strains of the same species. Hence A. carboxidus is a later subjective heterotypic synonym of A. lissarensis.
Subject(s)
Carbon Monoxide , Phyllobacteriaceae/classification , Phylogeny , Bacterial Typing Techniques , DNA, Bacterial , Multilocus Sequence Typing , RNA, Ribosomal, 16S/genetics , Rhizobiaceae , Sequence Analysis, DNAABSTRACT
Lysobacter niastensis belongs to a group of bacterial predators that produce a number of bioactive small molecules endowed with lytic properties toward other microorganisms. Here, we report the draft genome sequence of the type strain DSM 18481 and the identification of gene clusters implicated in the biosynthesis of secondary metabolites.
ABSTRACT
Aminobacter carboxidus is a soil Gram-negative alphaproteobacterium belonging to the physiological group of carboxydobacteria which aerobically oxidize CO to CO2 Here, we report the draft genome sequence of the A. carboxidus DSM 1086 type strain and the identification of both form I and form II CO dehydrogenase systems in this strain.
ABSTRACT
Caves are extreme environments inhabited by microbial communities adapted to thrive oligotrophic conditions. Cave microbes are organised in complex ecological networks and have developed survival strategies involving the production and release of a large variety of secondary metabolites, including antibiotic-like compounds. In this study, the structure and the metabolic features of a biofilm-like microbial community lining the walls of a pristine karst cavity (the Yumugi river cave) located in a remote region of the Western New Guinea were investigated. 16S rRNA and shotgun sequence analyses highlighted the prevalence of chemoorganotrophic phyla (Proteobacteria, Actinobacteria, Firmicutes and Acidobacteria), consistent with metabolic predictions inferred from the cave metagenome analysis. Few clinically relevant antimicrobial resistance genes were detected. A culture-based approach allowed the isolation of some heterotrophic members of the bacterial community, and antimicrobial susceptibility testing revealed an overall high level of resistance to different antimicrobials classes. Isolates presumptively representing new uncharacterized members of genus Pseudomonas displayed interesting antibiotic properties against Gram-positive indicator strains. Our work supports the hypothesis that caves represent a reservoir for new bacterial species and drug discovery research.
