Acinetobacter nematophilus sp. nov., Alcaligenes nematophilus sp. nov., Enterobacter nematophilus sp. nov., and Kaistia nematophila sp. nov., Isolated from Soil-Borne Nematodes and Proposal for the Elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the Species Level

Abstract

Four bacterial strains, A-IN1T, A-TC2T, E-TC7T, and K-TC2T, isolated from soil-borne nematodes of the species Oscheius tipulae and Acrobeloides bodenheimeri, were found to represent new species of the genera Acinetobacter, Alcaligenes, Enterobacter, and Kaistia, respectively. In this study, we described these new species using a polyphasic taxonomic approach that included whole-genome and whole-proteome phylogenomic reconstructions, core genome sequence comparisons, and phenotypic characterization. Phylogenomic reconstructions using whole-genome and whole-proteome sequences show that A-IN1T is closely related to Acinetobacter guillouiae DSM 590T and to Acinetobacter bereziniae LMG 1003T. The dDDH values between A-IN1T and these latest strains are 25.1 and 39.6%, respectively, which are below the 70% divergence threshold for prokaryotic species delineation. A-TC2T is closely related to Alcaligenes faecalis subsp. faecalis DSM 30030T and to Alcaligenes faecalis subsp. phenolicus DSM 16503T. The dDDH values between A-TC2T and these latest strains are 47.0 and 66.3%, respectively. In addition, the dDDH values between Alcaligenes faecalis subsp. faecalis DSM 30030T, Alcaligenes faecalis subsp. phenolicus DSM 16503T, and Alcaligenes faecalis subsp. parafaecalis are always lower than 70%, demonstrating that the three strains represent species within the genus Alcaligenes rather than subspecies within Alcaligenes faecalis. E-TC7T is closely related to Enterobacter kobei DSM 13645T, Enterobacter chuandaensis 090028T, and to Enterobacter bugandensis STN0717-56T. The dDDH values between E-TC7T and these strains are 43.5, 42.9, and 63.7%, respectively. K-TC2T is closely related to Kaistia terrae DSM 21341T and to Kaistia defluvii JCM 18034T. The dDDH values between these strains are 29.2 and 30.7%, respectively. Several biochemical tests allow to differentiate the type strains of the newly described species from the type strains of their more closely related species. Based on the results of this polyphasic taxonomic approach, the following new species are proposed: Acinetobacter nematophilus sp. nov. with A-IN1T (=CCM 9231T =CCOS 2018T) as the type strain, Alcaligenes nematophilus sp. nov. with A-TC2T (=CCM 9230T =CCOS 2017T) as the type strain, Enterobacter nematophilus sp. nov. with E-TC7T (=CCM 9232T =CCOS 2020T) as the type strain, and Kaistia nematophila sp. nov. with K-TC2T (=CCM 9239T =CCOS 2022T) as the type strain. In addition, we propose the elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the species level. Therefore, we propose the creation of Alcaligenes parafaecalis sp. nov. with DSM 13975T as the type strain, and Alcaligenes phenolicus sp. nov. with DSM 16503T as the type strain. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of bacteria associated with soil-borne nematodes.

Taxonomic and molecular characterization of a new entomopathogenic nematode species, Heterorhabditis casmirica n. sp., and whole genome sequencing of its associated bacterial symbiont

“…The Photorhabdus entomopathogenic bacteria associated with the different H. casmirica n. sp. nematode populations were isolated as described previously [ 55 , 56 ]. Briefly, larvae of G. mellonella (Lepidoptera: Pyralidae) were exposed to 100 nematode IJs.…”

“…An initial molecular characterization, using 16S rRNA gene sequences, was carried out to determine the taxonomic affiliation of the obtained bacterial cultures as described previously [ 3 , 4 , 17 , 56 ]. Phylogenetic reconstruction and sequence comparisons based on whole genome sequences were carried out to confirm the taxonomic affiliation of the obtained bacterial cultures as described previously [ 3 , 55 , 56 ]. Briefly, genomic DNA was extracted and purified using the GenElute Bacterial Genomic DNA Kit (Sigma-Aldrich, Switzerland) following the manufacturer’s instructions.…”

“…The final assemblies were polished using Pilon 1.22 [ 59 ]. Phylogenetic relationships were reconstructed based on the assembled genomes and the genome sequences of all valid published species of the genus [ 3 , 55 , 56 ]. For this, core genome alignments were created using Roary 3.6.2 [ 60 ].…”

Comparative Genomics Reveals Novel Species and Insights into the Biotechnological Potential, Virulence, and Resistance of Alcaligenes

“…parafaecalis DSM 13975 and A. faecalis subsp. phenolicus DSM 16503 [ 35 ], and also supported by ANI analysis, we propose to designate these groups as Alcaligenes parafaecalis and Alcaligenes phenolicus , respectively, and reclassify all genomes accordingly. Further, clinical isolates were identified in all groups, except for A4 and A5.…”

Looking Back on 2023—A Fruitful Year for Taxonomy

“…Thirtythree new species of bacteria, plants, and animals have been described in Taxonomy in 2023, documenting the need for reliable and serious journals devoted to taxonomy. Of course, papers on taxonomy and systematics-morphology-based [1][2][3] or with a focus on molecular data [4][5][6]-prevailed by far, but we also published papers with a focus on methodology [7,8].…”