- Volume 74, Issue 6, 2024

A Gram-negative, aerobic, pink-pigmented, and bacteriochlorophyll a-containing bacterial strain, designated B14T, was isolated from the macroalga Fucus spiralis sampled from the southern North Sea, Germany. Based on 16S rRNA gene sequences, species of the genera Roseobacter and Sulfitobacter were most closely related to strain B14T with sequence identities ranging from 98.15 % (Roseobacter denitrificans Och 114T) to 99.11 % (Roseobacter litoralis Och 149T), whereas Sulfitobacter mediterraneus CH-B427T exhibited 98.52 % sequence identity. Digital DNA–DNA hybridization and average nucleotide identity values between the genome of the novel strain and that of closely related Roseobacter and Sulfitobacter type strains were <20 % and <77 %, respectively. The novel strain contained ubiquinone-10 as the only respiratory quinone and C18 : 1 ω7c, C16 : 0, C18 : 0, C12 : 1 ω7c, C18 : 2 ω7,13c, and C10 : 0 3-OH as the major cellular fatty acids. The predominant polar lipids of strain B14T were phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. The genome of strain B14T comprises a chromosome with a size of 4.5 Mbp, one chromid, and four plasmids. The genome contains the complete gene cluster for aerobic anoxygenic photosynthesis required for a photoheterotrophic lifestyle. The results of this study indicate that strain B14T (=DSM 116946T=LMG 33352T) represents a novel species of the genus Roseobacter for which the name Roseobacter fucihabitans sp. nov. is proposed.

In a previous study characterizing Campylobacter strains deficient in selenium metabolism, 50 strains were found to be similar to, but distinct from, the selenonegative species Campylobacter lanienae. Initial characterization based on multilocus sequence typing and the phylogeny of a set of 20 core genes determined that these strains form three putative taxa within the selenonegative cluster. A polyphasic study was undertaken here to further clarify their taxonomic position within the genus. The 50 selenonegative strains underwent phylogenetic analyses based on the sequences of the 16S rRNA gene and an expanded set of 330 core genes. Standard phenotypic testing was also performed. All strains were microaerobic and anaerobic, Gram-negative, spiral or curved cells with some displaying coccoid morphologies. Strains were motile, oxidase, catalase, and alkaline phosphatase positive, urease negative, and reduced nitrate. Strains within each clade had unique phenotypic profiles that distinguished them from other members of the genus. Core genome phylogeny clearly placed the 50 strains into three clades. Pairwise average nucleotide identity and digital DNA–DNA hybridization values were all below the recommended cut-offs for species delineation with respect to C. lanienae and other related Campylobacter species. The data presented here clearly show that these strains represent three novel species within the genus, for which the names Campylobacter devanensis sp. nov. (type strain RM3662T=LMG 33097T=NCTC 15074T), Campylobacter porcelli sp. nov. (type strain RM6137T=LMG 33098T=CCUG 77054T=NCTC 15075T) and Campylobacter vicugnae sp. nov. (type strain RM12175T=LMG 33099T=CCUG 77055T=NCTC 15076T) are proposed.

Gram-negative, aerobic, rod-shaped, non-spore-forming, motile bacteria, designated strains F2T and PGU16, were isolated from the midgut crypts of the bordered plant bug Physopelta gutta, collected in Okinawa prefecture, Japan. Although these strains were derived from different host individuals collected at different times, their 16S rRNA gene sequences were identical and showed the highest similarity to Paraburkholderia caribensis MWAP64T (99.3 %). The genome of strain F2T consisted of two chromosomes and two plasmids, and its size and G+C content were 9.28 Mb and 62.4 mol% respectively; on the other hand, that of strain PGU16 consisted of two chromosomes and three plasmids, and its size and G+C content were 9.47 Mb and 62.4 mol%, respectively. Phylogenetic analyses revealed that these two strains are members of the genus Paraburkholderia. The digital DNA–DNA hybridization value between these two strains was 92.4 %; on the other hand, the values between strain F2T and P. caribensis MWAP64T or phylogenetically closely related Paraburkholderia species were 44.3 % or below 49.1 %. The predominant fatty acids of both strains were C16 : 0, C17 : 0 cyclo, summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c), and C19 : 0 cyclo ω8c, and their respiratory quinone was ubiquinone 8. Based on the above genotypic and phenotypic characteristics, strains F2T and PGU16 represent a novel species of the genus Paraburkholderia for which the name Paraburkholderia largidicola sp. nov. is proposed. The type strain is F2T (=NBRC 115765T=LMG 32765T).

Two novel strains, designated APW6T and APW11T, were isolated from artificial pond water, and one novel strain, designated PFR6T, was isolated from a Viola mandshurica root. These strains were found to be Gram-negative, rod-shaped, motile by means of flagella, and oxidase-positive. Growth conditions of the type strains were as follows: APW6T, 15–43 °C (optimum, 28 °C), pH 6.0–12.0 (optimum, pH 7.0), with no salinity; APW11T, 4–35 °C (optimum, 25 °C), pH 6.0–11.0 (optimum, pH 9.0), with 0–1 % NaCl (w/v, optimum 0 %); PFR6T, 10–38 °C (optimum 28 °C), pH 6.0–12.0 (optimum, pH 7.0), with 0–2 % NaCl (w/v; optimum, 0 %). Strains APW6T, APW11T, and PFR6T belonged to the genus Roseateles, having the most 16S rRNA gene sequence similarity to Roseateles saccharophilus DSM 654T (98.1 %), Roseateles oligotrophus CHU3T (98.7 %), and Roseateles puraquae CCUG 52769T (98.1 %). The estimated genome sizes of APW6T, APW11T, and PFR6T were 50 50 473, 56 70 008, and 52 16 869 bp, respectively and the G+C contents were 69.5, 66, and 68.5 mol%. The digital DNA–DNA hybridization, average amino acid identity, and average nucleotide identity values among the novel strains and related taxa were all lower than 22.4, 74.7, and 78.9 %, respectively. The predominant cellular fatty acids (>10 %) of all strains were summed feature 3 (comprising C16 : 1  ω6c and/or C16 : 1  ω7c) and C16 : 0. PFR6T also had summed feature 8 (comprising C18 :  1  ω7c and/or C18 :  1  ω6c) as a major fatty acid. The polar lipid profile of all strains contained phosphatidylethanolamine, phosphoaminoglycolipid, and phosphoglycolipid. The distinct phylogenetic, physiological, and chemotaxonomic features reported in this study indicate that strains APW6T, APW11T, and PFR6T represent novel species within the genus Roseateles, for which the names Roseateles subflavus sp. nov., with the type strain APW6T (=KACC 22877T=TBRC 16606T), Roseateles aquae sp. nov., with the type strain APW11T (=KACC 22878T=TBRC 16607T), and Roseateles violae sp. nov (=KACC 23257T=TBRC 17653T) are respectively proposed.

A Gram-negative, motile, rod-shaped aerobic and alkalogenic bacterium, designated as strain YLCF04T, was isolated from chicken faeces. Its growth was optimal at 28 °C (range, 10–40 °C), pH 8 (range, pH 6–9) and in 1 % (w/v) NaCl (range, 0–10 %). It was classified to the genus Paenalcaligenes and was most closely related to Paenalcaligenes hominis CCUG 53761AT (97.5 % similarity) based on 16S rRNA gene sequence analysis. Average nucleotide identity and digital DNA–DNA hybridization values between YLCF04T and P. hominis CCUG 53761AT were 76.3 and 18.2 %, respectively. Strain YLCF04T has a genome size of 2.7 Mb with DNA G+C content of 46.3 mol%. Based on its phylogenetic, genomic, phenotypic and biochemical characteristics, strain YLCF04T represents a novel species of the genus Paenalcaligenes, for which the name Paenalcaligenes faecalis sp. nov. is proposed. The type strain is YLCF04T (=CCTCC AB 2022359T= KCTC 92789T).

A novel Gram-stain-negative strain, designated JM10B15T, was isolated from pond water for Litopenaeus vannamei collected from Jiangmen City, Guangdong province, south PR China. Cells of the strain were aerobic, rod-shaped, and motile by lateral flagella. JM10B15T could grow at 15–40 °C, pH 6.0–9.5, and in 0–3.0 % NaCl, with optimal growth at 25–35 °C, pH 7.5–8.5, and in 0 % NaCl, respectively. Furthermore, this strain grew well on Reasoner's 2A agar but not on nutrient broth agar or Luria–Bertani agar. JM10B15T was a denitrifying bacterium capable of removing nitrites and nitrates, and three key functional genes, nasA, nirS, and nosZ, were identified in its genome. The results of phylogenetic analyses based on the 16S rRNA gene and genome sequences indicated that JM10B15T belonged to the genus Gemmobacter. JM10B15T showed the highest 16S rRNA sequence similarity to Gemmobacter lutimaris YJ-T1-11T (98.8 %), followed by Gemmobacter aquatilis IFAM 1031T (98.6 %) and Gemmobacter serpentinus HB-1T (98.1 %). The average nucleotide identity and digital DNA–DNA hybridization values between JM10B15T and the other type strains of genus Gemmobacter were 78.1–82.1 % and 18.4–22.1 %, respectively. The major fatty acids of strain JM10B15T were summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) and C18 : 1  ω7c 11-methyl. In addition, the major respiratory quinone of this novel strain was Q-10, and the predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, four unidentified phospholipids, three unidentified lipids, and an unidentified aminophospholipid. Results of analyses of the phylogenetic, genomic, physiological, and biochemical characteristics indicated that JM10B15T represents a novel species of the genus Gemmobacter, for which the name Gemmobacter denitrificans sp. nov. is proposed. The type strain is JM10B15T (=GDMCC 1.4148T=KCTC 8140T).

Phylogeny of 16S rRNA gene sequences showed that Marortus luteolus ZX-21T and Zhongshania marina DSW25-10T are closely related, and form a monophyletic clade affiliated with the genus Zhongshania. Whole genome sequence comparisons showed that M. luteolus ZX-21T and Z. marina DSW25-10T shared 78.8 % digital DNA–DNA hybridization, 97.6 % average nucleotide identity and 98.1 % average amino acid identity. These values exceeded the recommended threshold values for species delineation. Thus, based on the principle of priority, we propose the reclassification of Marortus luteolus Yu et al. 2019 as a later heterotypic synonym of Zhongshania marina On et al. 2019.

A neutrophilic iron-oxidizing and -reducing bacterium, strain MIZ03T, was previously isolated from a wetland in Ibaraki, Japan. Here, we report the detailed characteristics of this strain. It was motile with a single polar flagellum, and Gram-stain-negative. It could grow not only chemolithoautotrophically but also chemoorganotrophically by aerobic respiration and fermentation. Major cellular fatty acids were C16 : 1  ω7c/C16 : 1  ω6c, and C16 : 0. Phylogenetic analyses indicated that strain MIZ03T belonged to the genus Rhodoferax. This strain was closely related to Rhodoferax ferrireducens with 98.5 % of 16S rRNA gene sequence similarity. Based on its phenotypic and genomic based characteristics, we conclude that strain MIZ03T represents a new species in the genus Rhodoferax. We propose the name Rhodoferax lithotrophicus sp. nov. to accommodate this strain. The type strain is MIZ03T (=JCM 34246T=DSM 113266T). We also propose the name Rhodoferax koreensis sp. nov., of which the type strain is DCY110T (=KCTC 52288T=JCM 31441T), for the effectively, but not yet validly, published name ‘Rhodoferax koreense’.

A genome-based polyphasic approach was used to determine the taxonomic status of two novel bacterial strains, SCSIO 12594T and SCSIO 12813T, isolated from tissues of a coral. Both strains were Gram-stain-negative and facultatively anaerobic. The genome sizes of strains SCSIO 12594T and SCSIO 12813T were 3.9 Mb and 4.1 Mb, respectively, and they possessed DNA G+C contents of 55.1 and 46.2 mol%, respectively . Both strains were found to be catalase- and oxidase-positive, while SCSIO 12594T also could hydrolyse starch. SCSIO 12594T was observed to grow at between 20 and 37 °C (optimally at 25 °C) and at a pH range from 6 to 7 and in the presence of 3–7 % (w/v) NaCl. The growth of SCSIO 12813T required seawater and occurred at 20–30 °C (optimum, 25 °C), pH 5–8 (optimum, pH 6–7) and in the presence of 3–3.7 % (w/v) NaCl. The results of 16S rRNA gene-based phylogenetic analysis indicated that SCSIO 12594T shared 92.97 % or less sequence similarity with its closest relatives Rhodobium gokarnense JA173T and other members of the order Hyphomicrobiales. The results of 16S rRNA sequences-based phylogenetic analysis of SCSIO 12813T indicated that Croceimicrobium hydrocarbonivorans A20-9T (89.34 %) was the most closely related species. SCSIO 12594T and SCSIO 12813T can be readily separated from their closest relatives, as indicated by the results of phylogenomic analysis, low average nucleotide indexes, average amino acid identity, digital DNA–DNA hybridisation (dDDH) similarities and associated phenotypic and chemical data. Consequently, the two coral isolates are considered to represent two novel genera and species for which the names Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov. are proposed, the type strains are SCSIO 12594T (= JCM 35320T = GDMCC 1.3060T) and SCSIO 12813T (= JCM 35373T = GDMCC 1.3063T), respectively. In addition, two novel families, Coralliovaceae fam. nov. and Sanyastnellaceae fam. nov are proposed to accommodate Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov., respectively.

The prokaryotic generic name Proteus Hauser 1885 (Approved Lists 1980) is a later homonym of the protozoan genus name Proteus Müller, 1786 and therefore should be considered illegitimate and in need of replacement according to Rules 51b(4) and 54 of the International Code of Nomenclature of Prokaryotes. However, it would be unwelcome for medical and veterinary community to propose by anyone any replacement name and discontinue the current usage. To prevent from any unfavourable replacement, conservation of the illegitimate prokaryotic generic name Proteus Hauser 1885 (Approved Lists 1980) according to Rules 23a Note 4 and 56b is needed, and therefore, a request for conservation by the Judicial Commission over its earlier protozoan homonym is made here by the author, with Judicial Opinions 9 and 12 serving as precedents.