International Journal of Systematic and Evolutionary Microbiology

The International Code of Nomenclature of Prokaryotes (ICNP) now includes the phylum category. For the purpose of the valid publication of their names under the ICNP, we consider here four phyla. Slightly modified descriptions of ‘ Abditibacteriota ’ Tahon et al. 2018 and ‘ Desulfobacterota ’ Waite et al. 2020 are provided to meet the requirements of the ICNP for phylum names. Methanobacteriota is proposed as a substitute for ‘ Euryarchaeota ’ Garrity and Holt 2021, while Nanobdellota is proposed to replace ‘ Nanoarchaeota ’ Huber et al. 2002, based on the genus Nanobdella Kato et al. 2022.

Based on genome-wide data, Massilia species belonging to the clade including Telluria mixta LMG 11547T should be entirely transferred to the genus Telluria owing to the nomenclatural priority of the type species Telluria mixta . This results in the transfer of 35 Massilia species to the genus Telluria . The presented data also supports the creation of two new genera since peripherally branching Massilia species are distinct from Telluria and other related genera. It is proposed that 13 Massilia species are transferred to Mokoshia gen. nov. with the type species designated Mokoshia eurypsychrophila comb. nov. The species Massilia arenosa is proposed to belong to the genus Zemynaea gen. nov. as the type species Zemynaea arenosa comb. nov. The genome-wide analysis was well supported by canonical ordination analysis of Enzyme Commission (EC) codes annotated from genomes via pannzer2. This new approach was performed to assess the conclusions of the genome-based data and reduce possible ambiguity in the taxonomic decision making. Cross-validation of EC code data compared within canonical plots validated the reclassifications and correctly visualized the expected genus-level taxonomic relationships. The approach is complementary to genome-wide methodology and could be used for testing sequence alignment based data across genetically related genera. In addition to the proposed broader reclassifications, invalidly described species ‘Massilia antibiotica’, ‘Massilia aromaticivorans’, ‘Massilia cellulosiltytica’ and ‘ Massilia humi ’ are described as Telluria antibiotica sp. nov., Telluria aromaticivorans sp. nov., Telluria cellulosilytica sp. nov. and Pseudoduganella humi sp. nov., respectively. In addition, Telluria chitinolytica is reclassified as Pseudoduganella chitinolytica comb. nov. The use of combined genome-wide and annotation descriptors compared using canonical ordination clarifies the taxonomy of Telluria and its sibling genera and provides another way to evaluate complex taxonomic data.

Two strains of Gram-negative, anaerobic, rod-shaped bacteria, from an abundant but uncharacterized rumen bacterial group of the order ‘Christensenellales’, were phylogenetically and phenotypically characterized. These strains, designated R-7T and WTE2008T, shared 98.6–99.0 % sequence identity between their 16S rRNA gene sequences. R-7T and WTE2008T clustered together on a distinct branch from other Christensenellaceae strains and had <88.1 % sequence identity to the closest type-strain sequence from Luoshenia tenuis NSJ-44T. The genome sequences of R-7T and WTE2008T had 83.6 % average nucleotide identity to each other, and taxonomic assignment using the Genome Taxonomy Database indicates these are separate species within a novel family of the order ‘Christensenellales’. Cells of R-7T and WTE2008T lacked any obvious appendages and their cell wall ultra-structures were characteristic of Gram-negative bacteria. The five most abundant cellular fatty acids of both strains were C16 : 0, C16 : 0 iso, C17 : 0 anteiso, C18 : 0 and C15 : 0 anteiso. The strains used a wide range of the 23 soluble carbon sources tested, and grew best on cellobiose, but not on sugar-alcohols. Xylan and pectin were fermented by both strains, but not cellulose. Acetate, hydrogen, ethanol and lactate were the major fermentation end products. R-7T produced considerably more hydrogen than WTE2008T, which produced more lactate. Based on these analyses, Aristaeellaceae fam. nov. and Aristaeella gen. nov., with type species Aristaeella hokkaidonensis sp. nov., are proposed. Strains R-7T (=DSM 112795T=JCM 34733T) and WTE2008T (=DSM 112788T=JCM 34734T) are the proposed type strains for Aristaeella hokkaidonensis sp. nov. and Aristaeella lactis sp. nov., respectively.

A novel sulphur-reducing bacterium was isolated from a pyrite-forming enrichment culture inoculated with sewage sludge from a wastewater treatment plant. Based on phylogenetic data, strain J.5.4.2-T.3.5.2T could be affiliated with the phylum Synergistota . Among type strains of species with validly published names, the highest 16S rRNA gene sequence identity value was found with Aminiphilus circumscriptus ILE-2T (89.2 %). Cells of the new isolate were Gram-negative, non-spore-forming, straight to slightly curved rods with tapered ends. Motility was conferred by lateral flagella. True branching of cells was frequently observed. The strain had a strictly anaerobic, asaccharolytic, fermentative metabolism with peptides and amino acids as preferred substrates. Sulphur was required as an external electron acceptor during fermentative growth and was reduced to sulphide, whereas it was dispensable during syntrophic growth with a Methanospirillum species. Major fermentation products were acetate and propionate. The cellular fatty acid composition was dominated by unsaturated and branched fatty acids, especially iso-C15 : 0. Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and distinct unidentified polar lipids. Respiratory lipoquinones were not detected. Based on the obtained data we propose the novel species and genus Aminithiophilus ramosus, represented by the type strain J.5.4.2-T.3.5.2T (=DSM 107166T=NBRC 114655T) and the novel family Aminithiophilaceae fam. nov. to accommodate the genus Aminithiophilus. In addition, we suggest reclassifying certain members of the Synergistaceae into new families to comply with current standards for the classification of higher taxa. Based on phylogenomic data, the novel families Acetomicrobiaceae fam. nov., Aminiphilaceae fam. nov., Aminobacteriaceae fam. nov., Dethiosulfovibrionaceae fam. nov. and Thermovirgaceae fam. nov. are proposed.

A dark-coloured thin film of cyanobacteria growing on the bottom of a submerged stone was isolated from Basantgarh village in Udhampur district, Jammu and Kashmir, India. The isolated strain (designated 19C-PST) was characterized using a polyphasic approach. The strain exhibited typical Nostoc -like morphology with a characteristic feature of having heterocytes in series. The 16S rRNA gene phylogeny placed the strain at a well-supported and distinct node. Notably, the recently described genus, Amazonocrinis , on the addition of more 16S rRNA gene sequences, reflected a critical split, which proved to be stable and well supported in all phylogenetic analyses of the 16S rRNA gene. Interestingly, Amazonocrinis nigriterrae CENA67T (type species of the genus) clustered together with our strain 19C-PST in the 16S rRNA gene phylogenetic analysis while the rest of the members of the genus Amazonocrinis were placed at a separate and distant node. This clearly indicated that strain 19C-PST is a member of Amazonocrinis sensu stricto. However, the results of phylogenetic analysis of ITS sequences only, in strains purported to belong to Amazonocrinis did not agree with the 16S rRNA gene results and placed our strain 19C-PST in a sister clade to three strains that have not yet been speciated, UHCC 0702, NIES-4103 and SA22, with A. nigriterrae falling into a separate clade. Further, folded secondary structures of the D1–D1′, V2, BoxB and V3 helices of strain 19C-PST were found to be significantly different from those of all the phylogenetically related taxa. The study revealed an interesting case where low taxon sampling and phylogenomic interpretations came across as points of attention in cyanobacterial taxonomy. Based on the morphological, phylogenetic, 16S–23S ITS secondary structure analyses, we describe our strain as Amazonocrinis malviyae sp. nov. in accordance with the International Code of Nomenclature for algae, fungi and plants. This work also illuminates the need for further research to resolve the taxonomic discrepancies among Amazonocrinis strains.