- Volume 69, Issue 6, 2019

Biological nitrogen fixation performed by diazotrophic bacteria is a vital process for agricultural and environmental sustainability. In recent years, bacterial classification has been based on genomic data, accelerating our understanding about the diversity, and resulting in the description of several new species. In this study, four strains (CNPSo 3140T, CNPSo 3235, CNPSo 3236 and CNPSo 3237) trapped by Phaseolus vulgaris and Mimosa pudica from soil samples of the Brazilian Atlantic Forest biome (Mata Atlântica) were submitted to polyphasic analysis to investigate their proper classification within the genus Mesorhizobium . The 16S rRNA gene phylogram showed that the strains present sequences identical to those of Mesorhizobium acaciae and Mesorhizobium plurifarium , not allowing a clear taxonomic classification; however, when using multilocus sequence analysis methodology, the strains were grouped into a well-supported distinct clade, with <94.5 % nucleotide identity with the other species of the genus. The average nucleotide identity of CNPSo 3140T genome showed values below the threshold in relation to the closest species, of 89.75 % with Mesorhizobium plurifarium and of 88.83 % with Mesorhizobium hawassense ; the digital DNA–DNA hybridization values were 39 and 37.70 % with the same species, respectively. Nodulation gene (nodC) phylogeny positioned the strains in an isolated cluster, showing greater similarity to Mesorhizobium shonense. All data obtained in this study support the description of the novel species Mesorhizobium atlanticum sp. nov. The type strain is CNPSo 3140T (=ABIP 206T=LMG 30305T=U1602T), isolated from a nodule of Phaseolus vulgaris.

A Gram-stain-negative, strictly aerobic, oxidase- and catalase-positive, non-gliding, motile with a single polar flagellum, and short rod-shaped bacterial strain, designated XYN52T, was isolated from a freshwater lake in the west of China. Phylogenetic analysis of the 16S rRNA gene determined that strain XYN52T was a member of the genus Pelagibacterium within the family Hyphomicrobiaceae . Strain XYN52T was able to grow at 4–37 °C (optimum, 30 °C), pH 6.0–9.0 (pH 7.5) and in the presence of up to 7.0 % w/v NaCl (0.5 %).The major quinone was ubiquinone 10. The major cellular fatty acids were C_18 : 1ω6c/C_18 : 1ω7c, C_19 : 0ω8c cyclo and 11-methyl C_18 : 1ω7c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and three kinds of glycolipids. The genomic DNA G+C content was 64.5 mol%. On the basis of these data, strain XYN52T represents a novel species in the genus Pelagibacterium , for which the name Pelagibacterium lacus sp. nov. is proposed. The type strain is XYN52T (=KCTC 62845T=MCCC 1H00348T).

A Gram-stain-negative, rod-shaped, facultatively anaerobic bacterium, designated as strain HYN0051T, was isolated from lake water. 16S rRNA gene sequence analyses indicated that the isolate shares the highest sequence similarity with the genus Pragia (97.1 %) of the family Enterobacteriaceae . Strain HYN0051T did not form a rigid clade with the genus Pragia in any of the phylogenetic trees, demonstrating the novel generic status of the isolate. The genome of strain HYN0051T (CP029185) is a single circular chromosome of 3.84 Mb. The major fatty acids detected were C_14 : 0, C_16 : 0, summed feature 2 (C_12 : 0 aldehyde and/or unknown 10.928), summed feature 3 (C_16 : 1ω6c and/or C_16 : 1ω7c) and summed feature 8 (C_18 : 1 ω6c and/or C_18 : 1 ω7c). The isoprenoid quinones were Q-8, MK-8 and DMK-8. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid. The genome size, G+C content and fatty acid profile were very similar to that of the genus Pragia , but the composition of isoprenoid quinones and polar lipids, and numerous phenotypic properties also supported the distinctiveness of the new isolate from the genus Pragia . Thus, based on phylogenetic and phenotypic data, a novel species of a new genus, Limnobaculum parvum gen. nov., sp. nov., is proposed. The type strain of Limnobaculum parvum is HYN0051T (=KACC 19186T=NBRC 112742T).

The extent of the diversity of yeasts in tropical rain forest and different environments from French Guiana was investigated. A total of 365 samples were collected from various substrates, such as plants, fruits and insects, at 13 locations, yielding 276 pure yeast isolates. Sequence analysis of the D1/D2 domains of the large subunit rRNA gene indicated that 210 isolates out of 276 belonged to 82 described species (67 Saccharomycotina, 14 Basidiomycota and 1 Pezizomycotina). In addition to these, a total of 54 Saccharomycotina isolates could not be assigned to a known species. These belonged to 14 genera and should be studied further from a taxonomic point of view. In addition, among the 43 Basidiomycotina isolates found, 12 could not be assigned to a known species. This report shows an unexpected biodiversity and indicates that oversea territories, such as French Guiana, constitute a largely unexplored reservoir for yeast diversity. Two Saccharomycotina strains, CLIB 1706 and CLIB 1725, isolated from an insect and from a fern respectively, were characterized further and were shown to belong to the Suhomyces clade on the basis of the rDNA sequence comparison. CLIB 1706TrDNA sequences showed nine substitutions and three indels out of 556 bp (D1/D2 domains) and 32 substitutions and 12 indels out of 380 bp [internal transcribed spacer (ITS)] with that of the most closely related species Suhomyces guaymorum CBS 9823T. CLIB 1725T rDNA sequences presented 18 substitutions and one indel out of 549 bp (D1/D2 domains) and 48 substitutions and 11 indels out of 398 bp (ITS) with that of its closest relative Suhomyces vadensis CBS 9454T. Two novel species of the genus Suhomyces were described to accommodate these two strains: Suhomyces coccinellae f.a. sp. nov. (CLIB 1706T=CBS 14298T) and Suhomyces faveliae f.a. sp. nov. (CLIB 1725T=CBS 14299T).

The International Code of Nomenclature of Prokaryotes currently caters for the names of ranks from class to subspecies. The form of names and their typification is dealt with under Rules 7–22. The nature of names at different ranks has a direct influence on the structure of the Code. However, with minor changes it is possible to simplify the structure and the links between names and their nomenclatural types, even if the proposed solution may cause some changes that create a degree of upheaval in the short term.

Minutes of the meeting of the Subcommittee on the Taxonomy of Rhizobia and Agrobacteria (ICSP), video conference on 11 July 2018.