AUTHOR=Singh Nitin K. , Lavire Céline , Nesme Joseph , Vial Ludovic , Nesme Xavier , Mason Christopher E. , Lassalle Florent , Venkateswaran Kasthuri 

TITLE=Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.765943

DOI=10.3389/fmicb.2021.765943

ISSN=1664-302X

ABSTRACT=<p>Strains of <italic>Agrobacterium</italic> genomospecies 3 (i.e., genomovar G3 of the <italic>Agrobacterium tumefaciens</italic> species complex) have been previously isolated from diverse environments, including in association with plant roots, with algae, as part of a lignocellulose degrading community, from a hospital environment, as a human opportunistic pathogen, or as reported in this study, from a surface within the International Space Station. Polyphasic taxonomic methods revealed the relationship of <italic>Agrobacterium</italic> G3 strains to other <italic>Agrobacterium</italic> spp., which supports the description of a novel species. The G3 strains tested (<italic>n</italic> = 9) were phenotypically distinguishable among the strains from other genomospecies of the genus <italic>Agrobacterium.</italic> Phylogenetic analyses of the 16S rRNA gene, <italic>gyr</italic>B gene, multi-locus sequence analysis, and 1,089-gene core-genome gene concatenate concur that tested G3 strains belong to the <italic>Agrobacterium</italic> genus and they form a clade distinct from other validly described <italic>Agrobacterium</italic> species. The distinctiveness of this clade was confirmed by average nucleotide identity (ANI) and <italic>in silico</italic> digital DNA–DNA hybridization (dDDH) comparisons between the G3 tested strains and all known <italic>Agrobacterium</italic> species type strains, since obtained values were considerably below the 95% (ANI) and 70% (dDDH) thresholds used for the species delineation. According to the core-genome phylogeny and ANI comparisons, the closest relatives of G3 strains were <italic>Agrobacterium</italic> sp. strains UGM030330-04 and K599, members of a novel genomospecies we propose to call genomovar G21. Using this polyphasic approach, we characterized the phenotypic and genotypic synapomorphies of <italic>Agrobacterium</italic> G3, showing it is a <italic>bona fide</italic> bacterial species, well separated from previously named <italic>Agrobacterium</italic> species or other recognized genomic species. We thus propose the name <italic>Agrobacterium tomkonis</italic> for this species previously referred to as <italic>Agrobacterium</italic> genomospecies 3. The type strain of <italic>A. tomkonis</italic> is IIF1SW-B1<sup>T</sup> (= LMG 32164 = NRRL B-65602). Comparative genomic analysis show <italic>A. tomkonis</italic> strains have species-specific genes associated with secretion of secondary metabolites, including an exopolysaccharide and putative adhesins and resistance to copper. <italic>A. tomkonis</italic> specific gene functions notably relate to surface adhesion and could be involved to colonize nutrient-poor and harsh habitats. The <italic>A. tomkonis</italic> strains from the ISS showed presence of a 40-kbp plasmid and several other potential mobile genetic elements detected that could also be part of conjugative elements or integrated prophages.</p>