Duganella vulcania sp. nov., Rugamonas fusca sp. nov., Rugamonas brunnea sp. nov. and Rugamonas apoptosis sp. nov., isolated from subtropical streams, and phylogenomic analyses of the genera Janthinobacterium, Duganella, Rugamonas, Pseudoduganella and Massilia

Abstract

Six Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT81WT, FT82W, FT107W, FT3ST, LX20WT and LX47WT) sharing high 16S rRNA gene sequence similarities with species of the genera Janthinobacterium (97.0–98.3 %), Duganella (96.3–98.8 %), Rugamonas (97.8–98.6 %), Pseudoduganella (96.8–97.5 %) and Massilia (94.5–98.6 %) were isolated from subtropical streams in PR China. The phylogenetic trees reconstructed using the 16S rRNA gene sequences indicated that the species of above five genera often mix together, indicating that the taxonomic statuses of some species were questionable. Phylogenomic reconstruction based on 369 single-copy orthologous clusters indicated that the species of the genus Janthinobacterium form a distinct cluster, strains FT81WT, FT82W and FT107W form a tight cluster with the species of the genus Duganella , and strains FT3ST, LX20WT and LX47WT form a tight cluster with the species of genus Rugamonas , and the species of genus Pseudoduganella form a tight cluster with Massilia guangdongensis , Massilia ginsengisoli , Massilia rivuli , Massilia namucuonensis , Massilia aquatica sensu Lu et al., Massilia buxea , Massilia armeniaca , Massilia plicata , Massilia flava , Massilia lurida , Massilia dura , Massilia lutea , Massilia umbonata , Massilia albidiflava and Massilia violacea . It should be noted that Massilia aquatica Lu et al. 2020 non Massilia aquatica Holochová et al. 2020 is a later homonym and an illegitimate name. The GTDB Release 202 also supported the proposal that M. guangdongensis , M. ginsengisoli , M. rivuli , M. namucuonensis , M. aquatica sensu Lu et al., M. buxea , M. armeniaca , M. plicata , M. flava , M. lurida , M. dura , M. lutea , M. umbonata , M. albidiflava and M. violacea should be transferred into the genus Pseudoduganella . The calculated pairwise orthologous average nucleotide identity by usearch (OrthoANIu) values were between 95.0 % and 95.6 % among strains FT81WT, FT82W and FT107W, but were less than 91.5 % among strains FT3ST, LX20WT, LX47WT and other related strains. Combining the results of phylogenomic analyses, phenotypic, biochemical and genotypic characteristics, strains FT81WT, FT82W and FT107W should represent a novel species of the genus Duganella , and strains FT3ST, LX20WT and LX47WT should represent three novel species of the genus Rugamonas , for which the names Duganella vulcania sp. nov. (type strain FT81WT=GDMCC 1.1679T =KACC 21471T), Rugamonas fusca sp. nov. (type strain FT3ST=GDMCC 1.1907T =KACC 21952T), Rugamonas brunnea sp. nov. (type strain LX20WT=GDMCC 1.1911T =KACC 21956T) and Rugamonas apoptosis sp. nov. (type strain LX47WT=GDMCC 1.1914T =KACC 21959T) are proposed.

Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov.

“…mixta is 67 %). As mentioned above genome wide analyses indicate species of the genus Massilia belong to new genera besides those already transferred to genus Pseudoduganella [2]. To examine the species content more deeply, genomes of what is currently Massilia were obtained for eight Massilia species type strains.…”

“…Genome data, including data from metagenomes, clearly indicates Massilia timonae and other related species found in clinical samples are environmental and not host associated (Table S1). Since all the remaining Massilia species are transferred to new genera (as mentioned above) or to Pseudoduganella [2] the name Massilia should be retired from use entirely. Phenotypic information for the genus Telluria compiled from accumulated description papers is shown in Table S3.…”

“…For example, species of Telluria do not form a separate lineage but instead are closely related to Massilia and Pseudoduganella species. The use of phylogenomic approaches have been rapidly adopted and, on the basis of conserved protein family distributions, Lu and colleagues [2] transferred 15 species of the genus Massilia to Pseudoduganella . In this study, the goal was to use a range of genome-wide (phylogenomic) methods as well as ordination methods to resolve the genus-level taxonomy, mainly of the genera Massilia and Telluria .…”

Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat

“…Our work provides the first molecular characterization of prodiginines produced by a member of the Massilia genus. Holochová et al (2020) noted the pigmentation and BGC for prodigiosin in four Antarctic Massilia species, and Woodhams et al (2018) examined a mesophilic Massilia (now Pseudoduganella; Lu et al, 2022) for the production of prodigiosins, however none were detected. In our study, mass defect analysis (Figure 8) identified several metabolites congruent with prodiginines detected within similar retention times (5-8 min), including analogs formed from either the addition of oxygen, reduction, or cyclization.…”