International Journal of Systematic and Evolutionary Microbiology

A novel member of class Alphaproteobacteria was isolated from marine sediment of the South China Sea. Cells of strain LMO-2T were Gram-stain negative, greyish in colour, motile, with a single lateral flagellum and short rod in shape with a slight curve. Strain LMO-2T was positive for oxidase and negative for catalase. The bacterium grew aerobically at 10–40 °C (optimum, 25–30 °C), pH 5.5–10.0 (optimum, pH 7.0) and 0–9 % NaCl (w/v; optimum, 2–3 %). Phylogenetic analysis of the 16S rRNA gene sequence and phylogenomic analysis of the whole genome sequence indicated that strain LMO-2T represents a new genus and a new species within the family Devosiaceae , class Alphaproteobacteria , phylum Pseudomonadota . Comparisons of the 16S rRNA gene sequences of strain LMO-2T showed 94.8 % similarity to its closest relative. The genome size is ~3.45 Mbp with a DNA G+C content of 58.17 mol%. The strain possesses potential capability for the degradation of complex organic matter, i.e. fatty acid and benzoate. The predominant cellular fatty acids (>10 %) were C16 : 0 and C18 : 1 ω7c 11-methyl. The sole respiratory quinone was ubiquinone-10. The major identified polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phospholipid. Based on the polyphasic taxonomic data, strain LMO-2T represents a novel genus and a novel species for which the name Mariluticola halotolerans gen. nov., sp. nov., was proposed in the family Devosiaceae . The type strain is LMO-2T (=CGMCC 1.19273T=JCM 34934T).

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.

Appendix 9, Section E of the International Code of Nomenclature of Prokaryotes provides guidelines on how to form adjectival specific and subspecific epithets that reflect the geographical location where the organism was found or studied. It does not mention ways of naming genera after geographical locations. We here propose emendation of Appendix 9 with the recommendations on how to form such names. Comments on the implementation of the current wording of Appendix 9, Section E are also made.

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.

The International Code of Nomenclature of Prokaryotes (ICNP) recently underwent some major modifications regarding the higher taxonomic ranks. On the one hand, the phylum category was introduced into the ICNP, which rapidly led to the valid publication of more than forty names of phyla. On the other hand, a decision on the retroactivity of Rule 8 regarding the names of classes was made, which removed most of the nomenclatural uncertainty that had affected those names during the last decade. However, it turned out that a number of names at the ranks of class, order and family are either not validly published or are validly published but illegitimate, although these names occur in the literature and are based on the type genus of a phylum with a validly published name. A closer examination of the literature for these and similar cases indicates that the names are unavailable under the ICNP either because of minor formal errors in the original descriptions, because another name should have been adopted for the taxon when the name was proposed, because of taxonomic uncertainties that were settled in the meantime, or because the names were placed on the list of rejected names. The purpose of this article is to fill the gaps by providing the missing formal descriptions and to ensure that the resulting taxon names are attributed to the original authors who did the taxonomic work.