Phylogenomic analysis and characterization of carbon monoxide utilization genes in the family Phyllobacteriaceae with reclassification of Aminobacter carboxidus (Meyer et al. 1993, Hördt et al. 2020) as Aminobacter lissarensis comb. nov. (McDonald et al. 2005)

Irene Artuso; Paolo Turrini; Mattia Pirolo; Massimiliano Lucidi; Marco Tescari; Daniela Visaggio; Antonella Mansi; Gabriele Andrea Lugli; Marco Ventura; Paolo Visca

doi:10.1016/j.syapm.2021.126199

Phylogenomic analysis and characterization of carbon monoxide utilization genes in the family Phyllobacteriaceae with reclassification of Aminobacter carboxidus (Meyer et al. 1993, Hördt et al. 2020) as Aminobacter lissarensis comb. nov. (McDonald et al. 2005)

Syst Appl Microbiol. 2021 May;44(3):126199. doi: 10.1016/j.syapm.2021.126199. Epub 2021 Mar 26.

Affiliations

¹ Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy.
² Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, Italian Workers' Compensation Authority (INAIL), Monte Porzio Catone, Rome, Italy.
³ Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy.
⁴ Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy. Electronic address: paolo.visca@uniroma3.it.

PMID: 33848814
DOI: 10.1016/j.syapm.2021.126199

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 1086^T and A. lissarensis DSM 17454^T 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 1086^T and A. lissarensis DSM 17454^T. 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 1086^T and A. lissarensis DSM 17454^T. Results of phylogenomic, chemotaxonomic, and morphological investigations, combined with the presence of similarly arranged CODH genes, indicate that A. carboxidus DSM 1086^T and A. lissarensis DSM 17454^T are distinct strains of the same species. Hence A. carboxidus is a later subjective heterotypic synonym of A. lissarensis.

Keywords: Aminobacter carboxidus; Aminobacter lissarensis; Reclassification.

MeSH terms

Bacterial Typing Techniques
Carbon Monoxide*
DNA, Bacterial
Multilocus Sequence Typing
Phyllobacteriaceae / classification*
Phylogeny*
RNA, Ribosomal, 16S / genetics
Rhizobiaceae
Sequence Analysis, DNA

Substances

DNA, Bacterial
RNA, Ribosomal, 16S
Carbon Monoxide

Supplementary concepts

Aminobacter lissarensis
Carbophilus carboxidus