- Volume 71, Issue 8, 2021

A strictly anaerobic, resistant starch-degrading, bile-tolerant, autolytic strain, IPLA60002T, belonging to the family Ruminococcaceae , was isolated from a human bile sample of a liver donor without hepatobiliary disease. Cells were Gram-stain-positive cocci, and 16S rRNA gene and whole genome analyses showed that Ruminococcus bromii was the phylogenetically closest related species to the novel strain IPLA60002T, though with average nucleotide identity values below 90 %. Biochemically, the new isolate has metabolic features similar to those described previously for gut R. bromii strains, including the ability to degrade a range of different starches. The new isolate, however, produces lactate and shows distinct resistance to the presence of bile salts. Additionally, the novel bile isolate displays an autolytic phenotype after growing in different media. Strain IPLA60002T is phylogenetically distinct from other species within the genus Ruminococcus . Therefore, we propose on the basis of phylogenetic, genomic and metabolic data that the novel IPLA60002T strain isolated from human bile be given the name Ruminococcoides bili gen. nov., sp. nov., within the new proposed genus Ruminococcoides and the family Ruminococcaceae . Strain IPLA60002T (=DSM 110008T=LMG 31505T) is proposed as the type strain of Ruminococcoides bili.

A strict aerobic bacterium, strain JW14T was isolated from soil in the Republic of Korea. Cells were Gram-stain-positive, non-endospore-forming and motile rods showing catalase-positive and oxidase-negative activities. Growth of strain JW14T was observed at 20–37 °C (optimum, 30 °C), pH 6.0–10.0 (optimum, pH 7.0) and in the presence of 0–2.0% NaCl (optimum, 0%). Strain JW14T contained menaquinone-7 as the sole isoprenoid quinone, anteiso-C15:0, C16:0 and iso-C16 : 0 as the major fatty acids (>10.0%), and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and an unidentified lipid as the major polar lipids. The cell-wall peptidoglycan of strain JW14T contained meso-diaminopimelic acid. The DNA G+C content of strain JW14T calculated from the whole genome sequence was 48.1 mol%. Strain JW14T was most closely related to Paenibacillus graminis DSM 15220T with 97.4% 16S rRNA gene sequence similarity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JW14T formed a distinct phyletic lineage from closely related type strains within the genus Paenibacillus . Based on the results of phenotypic, chemotaxonomic and molecular analyses, strain JW14T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus agri sp. nov. is proposed. The type strain is JW14T (=KACC 21840T=JCM 34279T).

A Gram-stain-positive, moderately halophilic, aerobic, endospore-forming, rod-shaped bacterium, designated strain DP4-553-ST, was isolated from hypersaline sediment collected from the Dalangtan Playa in the Qaidam Basin, Northwest PR China. Growth occurred within 0–21.6% (w/v) NaCl (optimum 7.2%) at pH 5.5–9.0 (optimum pH 7.0) and at 4–45 °C (optimum 37 °C). Phylogeny based on 16S rRNA gene sequences indicated that strain DP4-553-ST belonged to the genus Sediminibacillus , with high 16S rRNA gene sequence similarity to Sediminibacillus halophilus EN8dT (99.5 %), Sediminibacillus terrae JSM 102062T (99.4 %), Virgibacillus senegalensis SK-1T (99.3 %) and Sediminibacillus albus NHBX5T (98.3 %). The G+C content of the chromosomal DNA was 43.6 mol %. The average amino acid identity, average nucleotide identity and digital DNA–DNA hybridization values between strain DP4-553-ST and the four close type strains were 71.2–93.3, 74.0–90.5 and 20.0–41.4 %, respectively. The whole genomic analysis showed that strain DP4-553-ST constituted a different taxon separated from the recognized Sediminibacillus species. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, C16 : 0 and iso-C15 : 0. The type strain contained cell-wall peptidoglycan based on diaminopimelic acid and possessed menaquinone-7 as the major respiratory isoprenoid quinone. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, four unidentified glycolipids, phosphatidylcholine, aminophospholipid, aminolipid and seven unidentified phospholipids. The combined data from phenotypic and genotypic studies demonstrated that strain DP4-553-ST represents a novel species of the genus Sediminibacillus , for which the name Sediminibacillus dalangtanensis sp. nov. is proposed, the type strain is DP4-553-ST (=MCCC 1K03838T= KCTC 43250T).

A Gram-negative bacterium, designated S1-65T, was isolated from soil samples collected from a cotton field located in the Xinjiang region of PR China. Results of 16S rRNA gene sequence analysis revealed that strain S1-65T was affiliated to the genus Steroidobacter with its closest phylogenetic relatives being ‘Steroidobacter cummioxidans’ 35Y (98.4 %), ‘ Steroidobacter agaridevorans ’ SA29-B (98.3 %) and Steroidobacter agariperforans KA5-BT (98.3 %). 16S rRNA-directed phylogenetic analysis showed that strain S1-65T formed a unique phylogenetic subclade next to ‘ S. agaridevorans ’ SA29-B and S. agariperforans KA5-BT, suggesting that strain S1-65T should be identified as a member of the genus Steroidobacter . Further, substantial differences between the genotypic properties of strain S1-65T and the members of the genus Steroidobacter , including average nucleotide identity and digital DNA–DNA hybridization, resolved the taxonomic position of strain S1-65T and suggested its positioning as representing a novel species of the genus Steroidobacter . The DNA G+C content of strain S1-65T was 62.5 mol%, based on its draft genome sequence. The predominant respiratory quinone was ubiquinone-8. The main fatty acids were identified as summed feature 3 (C16:1ω6c/C16:1ω7c), C16 : 0 and iso-C15 : 0. In addition, its polar lipid profile was composed of aminophospholipid, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Here, we propose a novel species of the genus Steroidobacter : Steroidobacter gossypii sp. nov. with the type strain S1-65T (=JCM 34287T=CGMCC 1.18736T).

Taxonomic positions of four Gram-negative bacterial strains, which were isolated from larvae of two insects in Jeju, Republic of Korea, were determined by a polyphasic approach. Strains CWB-B4, CWB-B41 and CWB-B43 were recovered from larvae of Protaetia brevitarsis seulensis, whereas strain BWR-B9T was from larvae of Allomyrina dichotoma. All the isolates grew at 10–37 °C, at pH 5.0–9.0 and in the presence of 4 % (w/v) NaCl. The 16S rRNA gene phylogeny showed that the four isolates formed two distinct sublines within the order Enterobacteriales and closely associated with members of the genus Jinshanibacter . The first group represented by strain CWB-B4 formed a tight cluster with Jinshanibacter xujianqingii CF-1111T (99.3 % sequence similarity), whereas strain BWR-B9T was most closely related to Jinshanibacter zhutongyuii CF-458T (99.5 % sequence similarity). The 92 core gene analysis showed that the isolates belonged to the family Budviciaceae and supported the clustering shown in 16S rRNA gene phylogeny. The genomic DNA G+C content of the isolates was 45.2 mol%. A combination of overall genomic relatedness and phenotypic distinctness supported that three isolates from Protaetia brevitarsis seulensis are different strains of Jinshanibacter xujianqingii , whereas one isolate from Allomyrina dichotoma represents a new species of the genus Jinshanibacter . On the basis of results obtained here, Jinshanibacter allomyrinae sp. nov. (type strain BWR-B9T=KACC 22153T=NBRC 114879T) and Insectihabitans xujianqingii gen. nov., comb. nov. are proposed, with the emended descriptions of the genera Jinshanibacter , Limnobaculum and Pragia .

Two Gram-stain-negative, motile, facultatively anaerobic, rod-shaped strains, FJAT-53720T and FJAT-53726, were isolated from rhizosphere sediment of plant Cyperus malaccensis. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that strains FJAT-53720T and FJAT-53726 were affiliated to the genus Shewanella (forming an independent cluster) with the highest sequence similarity to the type strain of Shewanella algae . Optimum growth of both strains was observed at 30 °C and pH 7. The respiratory quinones were Q-7, Q-8 and MK-7. The polar lipid profile included phosphatidylmethyl ethanolamine, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified aminophospholipid and four unknown phospholipids. The major fatty acids of strains FJAT-53720T and FJAT-53726 were iso-C15:0, C17 : 1 ω8c and summed feature 3. The genomic DNA G+C content of strain FJAT-53720T was 55.6 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between FJAT-53720T and FJAT-53726 were 97.4 and 77.9 %, confirming that they were similar species and hence FJAT-53720T was selected for further analysis. The ANI and dDDH values between FJAT-53720T and other members of the genus Shewanella were below the cut-off level (95–96 %; 70 %) for species delineation. Based on the above results, FJAT-53720T represents a novel species of the genus Shewanella , for which the name Shewanella cyperi sp. nov. is proposed. The type strain is FJAT-53720T (=KCTC 82444T=GDMCC 1.2207T).

Four Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (Y26, Y57T, ZJ14WT and RP18W) were isolated from mariculture fishponds in PR China. Comparisons based on 16S rRNA gene sequences showed that strains Y26 and Y57T share 16S rRNA gene sequence similarities in the range of 95.1−98.5 % with species of the genus Bowmanella , and strains ZJ14WT and RP18W share 16S rRNA gene sequence similarities in the range of 96.7 −98.8 % with species of the genus Amphritea , respectively. The genome sizes of strains Y26, Y57T, ZJ14WT and RP18W were about 4.85, 5.40, 4.70 and 4.70 Mbp with 49.5, 51.7, 51.2 and 51.3 mol% G+C content, respectively. The calculated pairwise OrthoANIu values among strains Y26, Y57T and species of the genus Bowmanella were in the range of 72.6−83.1 %, but the value between strains Y26 and Y57T was 96.2 %. The pairwise OrthoANIu values among strains ZJ14WT, RP18W and other species of the genus Amphritea were all less than 93.9 %, but the value between strains ZJ14WT and RP18W was 99.3 %. Q-8 was the major respiratory quinone of strains Y26, Y57T, ZJ14WT and RP18W, and the major fatty acids of these strains were all C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c. The predominant polar lipids of strains Y26 and Y57T included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol, but strains ZJ14WT and RP18W only contained phosphatidylethanolamine and phosphatidylglycerol. Combining phenotypic, biochemical and genotypic characteristics, strains Y26 and Y57T should belong to the same species and represent a novel member of the genus Bowmanella , and strains ZJ14WT and RP18W should belong to the same species and represent a novel member of the genus Amphritea , for which the names Bowmanella yangjiangensis sp. nov. (type strain Y57T=GDMCC 1.2180T=KCTC 82439T) and Amphritea pacifica sp. nov. (type strain ZJ14WT=GDMCC 1.2203T=KCTC 82438T) are proposed.

A novel facultatively anaerobic, non-motile, Gram-stain-negative, non-endospore-forming alphaproteobacterium, strain 1011MAR3C25T, was isolated from a white biofilm colonizing the walls of the Andalusian show cave Gruta de las Maravillas (Huelva, Spain). Strain 1011MAR3C25T grew at 8–42 °C (optimum, 20–30 °C), at pH 5.0–9.0 (optimum, pH 5.0–6.0) and in the presence of 0–12 % (w/v) NaCl (optimum 3–5 %). Cells were catalase- and oxidase-positive. The strain grew heterotrophically with various carbon sources and chemoautotrophically with thiosulfate under aerobic conditions. Results of phylogenetic analysis showed that strain 1011MAR3C25T was related to Paracoccus saliphilus DSM 18447T and Paracoccus alkanivorans LMG 30882T (97.90 % and 97.32 % 16S rRNA sequence identity values, respectively). The major respiratory quinone was ubiquinone Q-10 and the predominant fatty acid was C18 : 1 ω7c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid, an unidentified glycolipid and an unidentified polar lipid. The DNA G+C content was 60.3 mol%. Based on a polyphasic taxonomic study it is proposed that strain 1011MAR3C25T (=CECT 9092T=LMG 29414T) represents a novel species of the genus Paracoccus , for which the name Paracoccus onubensis sp. nov. is proposed.

A novel bacterial strain, designated SW136T, was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW136T represented a novel member of the genus Aurantimonas , forming a distinct cluster with ‘ Aurantimonas litoralis ’, Aurantimonas coralicida and Aurantimonas manganoxydans (98.2, 98.1 and 97.9% sequence similarity, respectively). The predominant cellular fatty acid of strain SW136T was C18 : 1  ω7c. Strain SW136T contained ubiquinone-10 as the dominant respiratory quinone, and diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G+C content was 64.3 mol%. The average nucleotide identity and digital DNA–DNA hybridization values of strain SW136T with A. coralicida CGMCC 1.12222T and A. manganoxydans CGMCC 1.12225T were 78.8 and 78.6 % and 21.5 and 25.5 %, respectively. On the basis of phylogenetic inference and phenotypic characteristics, we propose that strain SW136T represents a novel species of the genus Aurantimonas , with the name Aurantimonas marina sp. nov. The type strain is SW136T (=CGMCC 1.17725T=KCTC 82366T).

Three highly alkaliphilic bacterial strains designated as A1T, H1T and B1T were isolated from two highly alkaline springs at The Cedars, a terrestrial serpentinizing site. Cells from all strains were motile, Gram-negative and rod-shaped. Strains A1T, H1T and B1T were mesophilic (optimum, 30 °C), highly alkaliphilic (optimum, pH 11) and facultatively autotrophic. Major cellular fatty acids were saturated and monounsaturated hexadecenoic and octadecanoic acids. The genome size of strains A1T, H1T and B1T was 2 574 013, 2 475 906 and 2 623 236 bp, and the G+C content was 66.0, 66.2 and 66.1 mol%, respectively. Analysis of the 16S rRNA genes showed the highest similarity to the genera Malikia (95.1–96.4 %), Macromonas (93.0–93.6 %) and Hydrogenophaga (93.0–96.6 %) in the family Comamonadaceae . Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis based on core gene sequences revealed that the isolated strains diverged from the related species, forming a distinct branch. Average amino acid identity values of strains A1T, H1T and B1T against the genomes of related members in this family were below 67 %, which is below the suggested threshold for genera boundaries. Average nucleotide identity by blast values and digital DNA–DNA hybridization among the three strains were below 92.0 and 46.6 % respectively, which are below the suggested thresholds for species boundaries. Based on phylogenetic, genomic and phenotypic characterization, we propose Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov. (type strain A1T=NBRC 111848T=DSM 103917T), Serpentinimonas barnesii sp. nov. (type strain H1T= NBRC 111849T=DSM 103920T) and Serpentinimonas maccroryi sp. nov. (type strain B1T=NBRC 111850T=DSM 103919T) belonging to the family Comamonadaceae . We have designated Serpentinimonas raichei the type species for the genus because it is the dominant species in The Cedars springs.

Denitrification is a vital link in the global bio-nitrogen cycle. Here, we isolated a strain (M9-3-2T) that is a novel benzo[a]pyrene (BaP)-tolerant, anaerobic and aerobic denitrifying bacterium from a continuous BaP-enrichment cultured mangrove sediment. In silico comparative genomics and taxonomic analysis clearly revealed that strain M9-3-2T (=MCCC 1K03313T=JCM 32045T) represents a novel species of a novel genus named as Nitrogeniibacter mangrovi gen. nov., sp. nov., belonging to family Zoogloeaceae , order Rhodocyclales . In addition, the species Azoarcus pumilus is transferred into genus Aromatoleum and named Aromatoleum pumilum comb. nov. The predominant respiratory quinone of strain M9-3-2T was ubiquinone-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and three unidentified aminophospholipids. In this study, the capacity of strain M9-3-2T to eliminate nitrate was detected under anaerobic and aerobic conditions, and the removal rates of nitrate were 6.1×10−6 µg N/l/h/cell and 3×10−7 µg N/l/h/cell, respectively. Our results suggested that strain M9-3-2T could play an important role in the nitrogen removal regardless of the presence of oxygen in natural or/and man-made ecosystems.

Nine strains of a Rodentibacter -related bacterium were isolated over a period of 38 years from a laboratory mouse (Mus musculus), seven laboratory rats (Rattus norvegicus) and a Syrian hamster (Mesocricetus auratus) in Düsseldorf and Heidelberg, Germany. The isolates are genotypically and phenotypically distinct from all previously described Rodentibacter species. Sequence analysis of 16S rRNA and rpoB gene sequences placed the isolates as a novel lineage within the genus Rodentibacter . In addition to the single-gene analysis, the whole genome sequence of the strain 1625/19T revealed distinct genome-to-genome distance values to the other Rodentibacter species. The genomic DNA G+C content of strain 1625/19T was 40.8 mol% within the range of Rodentibacter . At least six phenotypic characteristics separate the new isolates from the other Rodentibacter species, with Rodentibacter heylii being the most closely related. In contrast to the latter, the new strains display β-haemolysis and are β-glucuronidase, d-mannitol and sorbitol positive, but fail to produce lysine decarboxylase and trehalose. The genotypic and phenotypic differences between the novel strains and the other closely related strains of the genus Rodentibacter indicate that they represent a novel species within the genus Rodentibacter , family Pasteurellaceae , for which the name Rodentibacter haemolyticus sp. nov. is proposed. The type strain 1625/19T, (=DSM 111151T=CCM 9081T), was isolated in 2019 from the nose of a laboratory mouse (Mus musculus) in Düsseldorf, Germany.

In the present study, in an attempt to explore the diversity of bacteria in the roots of rice plants, a Gram-stain-negative, motile, facultatively anaerobic, non-pigmented, catalase-positive, oxidase-negative and rod-shaped bacterium with polar flagella was isolated. Phylogenetic analysis based on 16S rRNA gene sequences revealed highest sequence similarity to Limnohabitans parvus KCTC 42859T (98.2%) followed by Limnohabitans curvus KCTC 42562T (98%), Limnohabitans planktonicicus II-D5T (97.9%) and Limnohabitans australis MWH-BRAZ-DAM2DT (97.4%). Growth of strain JUR4T occurred at 10–37 °C (optimum, 30 °C), at pH 5.5–8.0 (optimum, 6.5–7) and in the presence of 0–0.2% NaCl (optimum, 0%, w/v). The genome size of strain JUR4T was found to be 3.34 Mb containing 3139 predicted protein-coding genes with a DNA G+C content of 61.5 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between the genome sequence of strain JUR4T and closely related reference strains were 21.0–24.8% and 74.7–81.4%, respectively. Strain JUR4T contained diphosphatidylglycerol, phoshatidylethanolamine, one unidentified phosphoglycolipid, one unidentified aminophosphoglycolipid, one unidentified phospholipid and seven unidentified glycolipids. The major fatty acids were C16:0 and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c), and ubiquinone Q-8 was the sole isoprenoid quinone. So far, all species belonging to the genus Limnohabitans have been described as non-motile and devoid of flagella. All species were isolated from freshwater and are therefore denoted as planktonic bacteria. This present study introduces a novel motile member of Limnohabitans isolated from the root of rice plant, and introduces the genes associated with motility and methyl-accepting chemotaxis proteins. Phylogenetic, phenotypic, chemotaxonomic and genotypic data clearly indicates that strain JUR4T represents a novel species of the genus Limnohabitans for which the name Limnohabitans radicicola sp. nov. is proposed. The type strain is JUR4T (=KACC 21745T=NBRC 114484T).

A Gram-stain-negative, rod-shaped and facultatively aerobic bacterial strain, designated F7430T, was isolated from coastal sediment collected at Jingzi Wharf in Weihai, PR China. Cells of strain F7430T were 0.3–0.4 µm wide, 2.0–2.6 µm long, non-flagellated, non-motile and formed pale-beige colonies. Growth was observed at 4–40 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.5–8.0) and at NaCl concentrations of 1.0–10.0 % (w/v; optimum, 1.0 %). The sole respiratory quinone of strain F7430T was ubiquinone 8 and the predominant cellular fatty acids were summed feature 8 (C18 : 1  ω7c / C18 : 1  ω6c; 60.7 %), summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c; 30.2 %) and C15 : 0 iso (13.9 %). The polar lipids of strain F7430T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid and three unidentified lipids. Results of 16S rRNA gene sequences analyses indicated that this strain belonged to the family Halieaceae and had high sequence similarities to Parahaliea aestuarii JCM 51547T (95.3 %) and Halioglobus pacificus DSM 27932T (95.2 %) followed by 92.9–95.0 % sequence similarities to other type species within the aforementioned family. The rpoB gene sequences analyses indicated that the novel strain had the highest sequence similarities to Parahaliea aestuarii JCM 51547T (82.2 %) and Parahaliea mediterranea DSM 21924T (82.2 %) followed by 75.2–80.5 % sequence similarities to other type species within this family. Phylogenetic analyses showed that strain F7430T constituted a monophyletic branch clearly separated from the other genera of family Halieaceae . Whole-genome sequencing of strain F7430T revealed a 3.3 Mbp genome size with a DNA G+C content of 52.6 mol%. The genome encoded diverse metabolic pathways including the Entner–Doudoroff pathway, assimilatory sulphate reduction and biosynthesis of dTDP-l-rhamnose. Based on results from the current polyphasic study, strain F7430T is proposed to represent a novel species of a new genus within the family Halieaceae , for which the name Sediminihaliea albiluteola gen. nov., sp. nov. is proposed. The type strain of the type species is F7430T (=KCTC 72873T=MCCC 1H00420T).

Three phytopathogenic bacterial strains (Pc19-1T, Pc19-2 and Pc19-3) were isolated from seedlings displaying water-soaked, dark brown-to-black, necrotic lesions on pepper (Capsicum annuum) leaves in Georgia, USA. Upon isolation on King’s medium B, light cream-coloured colonies were observed and a diffusible fluorescent pigment was visible under ultraviolet light. Analysis of their 16S rRNA gene sequences showed that they belonged to the genus Pseudomonas , with the highest similarity to Pseudomonas cichorii ATCC 10857T (99.7 %). The fatty acid analysis revealed that the majority of the fatty acids were summed feature 3 (C16  :  1 ω7c/C16  :  1 ω6c), C16  :  0 and summed feature 8 (C18  :  1 ω7c/C18  :  1 ω6c). Phylogenomic analyses based on whole genome sequences demonstrated that the pepper strains belonged to the Pseudomonas syringae complex with P. cichorii as their closest neighbour, and formed a separate monophyletic clade from other species. Between the pepper strains and P. cichorii , the average nucleotide identity values were 91.3 %. Furthermore, the digital DNA–DNA hybridization values of the pepper strains when compared to their closest relatives, including P. cichorii , were 45.2 % or less. In addition, biochemical and physiological features were examined in this study and the results indicate that the pepper strains represent a novel Pseudomonas species. Therefore, we propose a new species Pseudomonas capsici sp. nov., with Pc19-1T (=CFBP 8884T=LMG 32209T) as the type strain. The DNA G+C content of the strain Pc19-1T is 58.4 mol%.

A novel, aerobic nitrogen-fixing methylotrophic bacterium, strain 29kT, was enriched and isolated from sludge generated during wastewater treatment at a paper mill in Baikal, Russian Federation. Cells were Gram-stain-variable. The cell wall was of the negative Gram-type. Cells were curved oval rod-shaped, 0.5–0.7×1.7–3.4 µm and formed yellow-coloured colonies. Cells tended to be pleomorphic if grown on media containing succinate or coccoid if grown in the presence of methyl alcohol as the sole carbon source. Cells were non-motile, non-spore-forming and contained retractile (polyphosphate) and lipid (poly-β-hydroxybutyrate) bodies. The major respiratory quinone was ubiquinone Q-10 and the predominant cellular fatty acids were C18:1 ω7, C19:0 cyclo and C16:0. The genomic DNA G+C content was 67.95 mol%. Strain 29kT was able to grow at 4–37 °C (optimum, 30 °C), at pH 6.0–8.5 (optimum, pH 6.5–7.0) and at salinities of 0–0.5% (w/v) NaCl (optimum, 0% NaCl). Catalase and oxidase were positive. Strain 29kT could grow chemolithoautotrophically in mineral media under an atmosphere of H2, O2 and CO2 as well as chemoorganoheterotrophically on methanol, ethanol, n-propanol, n-butanol and various organic acids. The carbohydrate utilization spectrum is limited by glucose and raffinose. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the newly isolated strain was a member of the genus Xanthobacter with Xanthobacter autotrophicus 7cT (99.9% similarity) and Xanthobacter viscosus 7dT (99.4 % similarity) as closest relatives among species with validly published names. The average nucleotide identity and digital DNA–DNA hybridization values of 92.7 and 44.9%, respectively, of the 29kT to the genome of the most closely related species, X. autotrophicus 7cT, were below the species cutoffs. Based on genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Xanthobacter oligotrophicus sp. nov. The type strain is 29kT (=KCTC 72777T=VKM B-3453T).

Species belonging to the genus Sphingomonas have been isolated from environments such as soil, water and plant tissues. Many strains are known for their capability of degrading aromatic molecules and producing extracellular polymers. A Gram-stain-negative, strictly aerobic, motile, red-pigmented, oxidase-negative, catalase-positive, rod-shaped strain, designated DH-S5T, has been isolated from pork steak packed under CO2-enriched modified atmosphere. Cell diameters were 1.5×0.9 µm. Growth optima were at 30 °C and at pH 6.0. Phylogenetic analyses based on both complete 16S rRNA gene sequence and whole-genome sequence data revealed that strain DH-S5T belongs to the genus Sphingomonas , being closely related to Sphingomonas alpina DSM 22537T (97.4 % gene sequence similarity), followed by Sphingomonas qilianensis X1T (97.4 %) and Sphingomonas hylomeconis GZJT-2T (97.3 %). The DNA G+C content was 64.4 mol%. The digital DNA–DNA hybridization value between the isolate strain and S. alpina DSM 22537T was 21.0 % with an average nucleotide identity value of 77.03 %. Strain DH-S5T contained Q-10 as the ubiquinone and major fatty acids were C18 : 1 cis 11 (39.3 %) and C16 : 1 cis 9 (12.5 %), as well as C16 : 0 (12.1 %) and C14 : 0 2-OH (11.4 %). As for polar lipids, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, dimethylphosphatidylethanolamine and sphingoglycolipid could be detected, alongside traces of monomethylphosphatidylethanolamine. Based on its phenotypic, chemotaxonomic and phylogenetic characteristics, strain DH-S5T (=DSM 110829T=LMG 31606T) is classified as a representative of the genus Sphingomonas , for which the name Sphingomonas aliaeris sp. nov. is proposed.

In this study, we report a Gram-stain-negative, rod-shaped, non-pigmented, motile and aerobic bacterium named strain MTZ26T, which was isolated from deep-sea sediment sampled at a cold seep in the South China Sea. Growth of strain MTZ26T occurred at 4–40 °C (optimum, 25–30 °C), pH 6.0–10.0 (optimum, 7.0–8.0) and with 1.0–11.0 % (w/v) NaCl (optimum, 6.0–8.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MTZ26T belonged to the genus Psychrosphaera and was closely related to Psychrosphaera aestuarii PSC101T (97.5 % sequence similarity) and Psychrosphaera haliotis KDW4T (97.5 %). Genomic analysis indicated that strain MTZ26T contains a circular chromosome of 3 331 814 bp with G+C content of 42.2 mol%. The predominant respiratory quinone of MTZ26T was ubiquinone-8. The polar lipids of MTZ26T contained phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid and one unidentified phospholipid. The major fatty acids of strain MTZ26T contained C15:0, C16:0, C17:0, C17 : 1 ω8c, C10 : 0 3-OH, C11 : 0 3-OH, C15 : 1 ω8c and summed feature 8 (C18 : 1 ω7c or/and C18 : 1 ω6c). Results of phylogenetic, physiological, biochemical and morphological analyses suggested that strain MTZ26T represents a novel species of the genus Psychrosphaera , and the name Psychrosphaera ytuae sp. nov. is proposed with the type strain MTZ26T (=MCCC 1K05568T=JCM 34321T).

Strain S02T was isolated from a surface sediment sample collected from the Bering Sea (64.3361° N, 170.9541° W). The cells were Gram-stain-negative, motile and rod-shaped. The temperature range for growth was 4–25 °C and the pH for growth was 5.5–9.0, with optimum growth occurring at 20–25 °C and pH 7.0–8.0. Growth occurred in the presence of 0–7 % (w/v) NaCl (optimum, 2–5 %). Strain S02T had menaquinone-8 as the major respiratory quinone and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C16:0, C17 : 0 cyclo, summed feature 3 (C16 : 1  ω7c /C16 : 1  ω7c), C17 : 0 and C18 : 0 as major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two glycolipids. The genomic DNA G+C content was approximately 63.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S02T belonged to the genus Devosia . Strain S02T showed the highest sequence similarities to Devosia psychrophila Cr7-05T (97.5 %), Devosia naphthalenivorans CM5-1T (97.7 %), Devosia submarina KMM 9415T (97.4 %), Devosia epidermidihirudinis E84T (97.44 %), Devosia euplotis LIV5T (97.1 %) and Devosia limi DSM 17137T (96.7 %). On the basis of phylogenetic analyses and phenotypic characteristics, a novel species of the genus Devosia , Devosia beringensis sp. nov., is proposed, with the type strain S02T (=JCM 33772=CCTCC AB 2019343).