Roseococcus microcysteis sp. nov., isolated from a Microcystis aeruginosa culture sample

Strain NIBR12T (=KACC 22094T=HAMBI 3739T), a novel Gram-stain-negative, obligate aerobic, non-spore-forming, non-motile and coccobacillus-shaped bacterium, was isolated from a cyanobacterial sample culture (Microcysitis aeruginosa NIBRCYC000000452). The newly identified bacterial strain grew optimally in modified Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5 and 35 °C. Phylogenetic analysis using the 16S rRNA gene sequence confirmed that strain NIBR12T belongs to the genus Roseococcus , with its closest neighbours being Roseococcus suduntuyensis SHETT (98.8%), Roseococcus thiosulfatophilus RB-3T (97.7%), “Sediminicoccus rosea” R-30T (95.7 %) and Rubritepida flocculans H-8T (95.0 %). Genomic comparison of strain NIBR12T with type species in the genus Roseococcus was conducted using digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity analyses, resulting in values of ≤53.7, ≤93.7 and ≤96.1 %, respectively. The genomic DNA G+C content of strain NIBR12T was 70.9 mol%. The major fatty acids of strain NIBR12T were summed feature 8 (C18 : 1 ω7c and/or C18:1 ω6c) and summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c). Q-9 was its major respiratory quinone. Moreover, the major polar lipids of strain NIBR12T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Based on our chemotaxonomic, genotypic and phenotype analyses, strain NIBR12T is identified as represeting a novel species of the genus Roseococcus , for which the name Roseococcus microcysteis sp. nov. is proposed.

Pseudomonas guryensis sp. nov. and Pseudomonas ullengensis sp. nov., isolated from soil

Two Gram-staining-negative, aerobic, rod-shaped bacteria designated strains SR9T and UL070T, were isolated from soil and subjected to taxonomic characterization. Strain SR9T grew at 10–37 °C (optimum 30 °C), at pH 4.0–10.0 (optimum pH 8.0) and in the presence of 0–1 % NaCl (optimum 0 %), and UL070T at 4–33 °C (optimum 30 °C), at pH 4.0–10.0 (optimum pH 7.0) and in the presence of 0–2 % NaCl (optimum 0 %), respectively. Strain UL070T was motile with flagella. Analysis of 16S rRNA gene sequences indicated that the two strains fell into phylogenetic clusters belonging to the genus Pseudomonas . Both strains SR9T and UL070T were mostly related to Pseudomonas campi S1-A32-2T with 99.70 and 99.01% sequence similarities, and the similarity between the two isolates was 98.90 %. The genome-based in silico analyses indicated that each of the strains SR9T and UL070T was clearly separated from other species of Pseudomonas , as the orthologous average nucleotide identity (OrthoANI) and the digital DNA–DNA hybridization (dDDH) values were no higher than 93.09 and 50.03% respectively with any related species, which were clearly below the cutoff for species distinction. The fatty acid profiles of the two strains mainly consisting of unsaturated components, the presence of ubiquinone 9 (Q-9) as the major respiratory quinone, and phosphatidylethanolamine (PE) and diphosphatidylglycerol (DPG) as the diagnostic polar lipids were consistent with their classification into Pseudomonas . The DNA G+C contents of strains SR9T and UL070T were 63.2 mol% and 63.6 mol% respectively. On the basis of both phenotypic and phylogenetic evidences, each of the isolated strains should be classified as a novel species, for which the names Pseudomonas guryensis sp. nov. (type strain=SR9T=KCTC 82228T=JCM 34509T) and Pseudomonas ullengensis sp. nov. (type strain=UL070T=KCTC 82229T=JCM 34510T) are proposed.

Halomonas Salinarum sp. nov., a Moderately Halophilic Bacterium, Isolated from Saline Soil in Yingkou, China

Strains of Halomonas, thought to play vital roles in the environment for their versatility, are ubiquitous in hypersaline environments. A Gram-staining-negative, moderately halotolerant, facultatively aerobic, motile bacterium, designated G5-11T, was isolated from saline soil in Yingkou of Liaoning, China. The cells of strain G5-11T grew at 4-35 ℃ (optimum 30 ℃), at pH 6.0-9.0 (optimum 8.0) and in the presense of 3-15 % (w/v) NaCl (optimum 5 %). The strain could be clearly distinguished from the related species of the genus Halomonas by its phylogenetic position and biochemical characteristics. It presented Q-9 as the major respiratory quinone and the dominant cellular fatty acids were summed feature 8 (C18:1 ω7c/ C18:1 ω6c), C16:0 and summed feature 3 (C16:1 ω7c/ C16:1 ω6c). The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol as the major components. The G+C content of strain G5-11T genome was 61.0 mol%. 16S rRNA analysis showed that strain G5-11T had the highest similarity to Halomonas niordiana LMG 31227T and Halomonas taeanensis DSM 16463T, both reaching 98.3 %, followed by Halomonas pacifica NBRC 102220T with a value of 95.8 %. Based on phenotypic, chemotaxonomic and phylogenetic inferences, strain G5-11T represents a novel species of the genus Halomonas, for which the name Halomonas salinarum sp. nov. is proposed. The type strain of Halomonas salinarum is G5-11T (=CGMCC 1.12051T=LMG 31677T).

Halorubrum Salipaludis Sp. Nov., Isolated From the Saline–Alkaline Soil

Strain WN019T, an aerobic, motile, and pleomorphic rods bacterium, was isolated from the natural saline-alkali wetland soil of Binhai new district, Tianjin, China. Cells of strain WN019T were 0.5-0.8 µm in width and 2.0-2.5 µm in length, and the growth occurred optimally at 33-37 ℃, pH 7.5-8.0, and in the presence of 15.0-20.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolate belonged to the genus Halorubrum and exhibited high sequence similarity of 97.8 % to Halorubrum saccharovorum JCM 8865T. The major respiratory quinone of strain WN019T were MK-8 and MK-8 (H2), and the major polar lipids were Glycolipid (GL), Phospholipid (PL), Phosphatidylglycerol-Sulfate (PGS), Phosphatidylglycerol (PG) and Phosphatidylglycerol-Phosphate-Methyl Ester (Me-PGP). The DNA G+C content of the strain was 67.3 mol%. The average nucleotide identity (ANI) based on whole genome sequences of strain WN019T and Halorubrum saccharovorum JCM 8865T was 87.5 %, and the digital DNA-DNA hybridization (dDDH) value between them was determined to be 35.4 %. Phenotypic, chemotaxonomic, phylogenetic, and genomic analyses suggested that strain WN019T represent a novel species of the genus Halorubrum, for which the name Halorubrum salipaludis sp. nov. is proposed. The type strain is WN019T (= KCTC 4269T = ACCC 19977T).

Massilia puerhi sp. nov., isolated from soil of Pu-erh tea cellar

A Gram-reaction-negative, yellow-pigmented, non-spore-forming rod, aerobic, motile bacterium, designated SJY3T, was isolated from soil samples collected from a Pu-erh tea cellar in Bolian Pu-erh tea estate Co. Ltd. in Pu'er city, Yunnan, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Massilia . The closest phylogenetic relative was Massilia arenae CICC 24458T (99.5 %), followed by M. timonae CCUG45783T (97.9 %), M. oculi CCUG43427AT (97.8 %), and M. aurea DSM 18055T (97.8 %). The major fatty acids were C16 : 0 and C16 : 1 ω7c and/or C16 : 1 ω6c. The major respiratory quinone was ubiquinone Q-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Genome sequencing revealed a genome size of 5.97 M bp and a G+C content of 65.4 mol%. Pairwise determined whole genome average nucleotide identity (gANI) values and digital DNA–DNA hybridization (dDDH) values were all below the threshold. Although the 16S rRNA gene similarity of stain SJY3T and Massilia arenae CICC 24458T was more than 99 %, the gANI, dDDH values and genomic tree clearly indicated that they were not of the same species. In summary, strain SJY3T represents a new species, for which we propose the name Massilia puerhi sp. nov. with the type strain SJY3T (=CGMCC 1.17158T=KCTC 82193T).

Fibrivirga Algicola Gen. Nov., Sp. Nov., An Algicidal Bacterium Isolated from a Freshwater River

An aerobic, gram-negative, pink-colored, non-motile, rod-shaped algicidal bacterium, designated JA-25T was isolated from the freshwater of the Geumgang River, Republic of Korea. It grew at 15–30°C, 6.0–9.0 pH, and in the presence of 0–1% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JA-25T belongs to the Family ‘Spirosomaceae’ and is most closely related to Fibrella aestuarina BUZ 2T (93.6%). The strain JA-25T showed < 90% sequence similarity to other members of the Family ‘Spirosomaceae’. The average nucleotide identity(ANI), in silico DNA-DNA hybridization and the average amino acid identity(AAI) values based on the genomic sequences of JA-25T and F. aestuarina BUZ 2T were 74.4, 20.5 and 73.6 %, respectively. The genomic DNA G + C content was 52.5mol %. The major cellular fatty acids were Summed feature 3 (C16:1 ω6c/C16:1 ω7c), C16:1 ω5c, C16:0 (> 10%). The genomic DNA G + C content was 52.5 mol %. The major respiratory quinone was MK-7 and the polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two phospholipids and five unidentified lipids. Considering the phylogenetic inference, phenotypic and chemotaxonomic data, strain JA-25T should be classified as a novel species of the novel genus Fibrivirga, with the proposed name Fibrivirga algicola sp. nov. The type strain is JA-25T (= KCCM 43334T = NBRC 114259T).

Devosia beringensis sp. nov., isolated from surface sediment of the Bering Sea

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).

Xanthobacter oligotrophicus sp.nov., isolated from paper mill sewage

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).

Paracoccus onubensis sp. nov., a novel alphaproteobacterium isolated from the wall of a show cave

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.

Chitinophaga oryzae sp. nov., an epiphytic bacterium isolated from rice root surfaces

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16–37 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga . Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729T, Chitinophaga qingshengii JN246T, Chitinophaga varians 10-7 W-9003T and Chitinophaga fulva G-6-1-13T. When the genomic sequences of strains 1303T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA–DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C15 : 0, C16 : 1 ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303T and 1310 represent members of a novel species of the genus Chitinophaga , for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303T (=KACC 22075T=TBRC 12926T).