Polyphasic analysis in the description of Sulfitobacter salinus sp. nov., a marine alphaproteobacterium isolated from seawater

Purpose

A polyphasic analysis was performed on a novel bacterium, designated strain KMU-143^T, which was isolated from seawater collected in the Republic of Korea.

Methods

A novel marine bacterium KMU-143^T was analyzed and described using a polyphasic taxonomic method including 16S rRNA gene sequence analysis, DNA–DNA hybridization, and physiological, biochemical, and chemotaxonomic analyses.

Results

Strain KMU-143^T was Gram-stain-negative, strictly aerobic, oval-shaped, non-motile, and chemoorganoheterotrophic. Phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that the novel marine bacterium belongs to the family Rhodobacteraceae, of the class Alphaproteobacteria, and that it possessed the highest (97.1%) sequence similarity with Sulfitobacter pontiacus ChLG 10^T and Sulfitobacter undariae W-BA2^T. DNA–DNA relatedness values between strains KMU-143^T, S. pontiacus JCM 21789^T, and S. undariae KCTC 42200^T were less than 70%. The major isoprenoid quinone of the novel isolate was ubiquinone-10 (Q-10) and the major (> 10%) cellular fatty acids were C16:0 and C18:1 ω7c. The genomic DNA G+C content of strain KMU-143^T was 56.1 mol%. The polar lipid profile of the strain KMU-143^T was found to consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, and two unidentified lipids.

Conclusion

Based on the discriminative phylogenetic position and combination of genotypic and phenotypic properties, the strain is considered to represent a new species of the genus Sulfitobacter for which the name Sulfitobacter salinus sp. nov. is proposed. The type strain of S. salinus sp. nov. is KMU-143^T (= KCCM 90322^T = NBRC 113459^T).

     

Alexandriicola marinus gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from marine phycosphere

Two yellow-pigmented bacterial strains, LZ-14 ^T and ABI-LZ29, were isolated from the cultivable phycosphere microbiota of the highly toxic marine dinoflagellate Alexandrium catenella LZT09 and demonstrated obvious microalgae growth-promoting potentials toward the algal host. To elucidate the taxonomic status of the two bioactive bacterial strains, they were subjected to a polyphasic taxonomic characterization. Both strains were found to be Gram-negative, aerobic, rod-shaped and motile; to contain Q-10 as the predominant ubiquinone; summed feature 8, C_16:0, C_18:1 ω7c 11-methyl and summed feature 3 as the major fatty acids; and diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and two unidentified phospholipids as the predominant polar lipids. Based on the phylogenetic analysis, phylogenomic inferences and phenotypic characteristics, the strains could be clearly distinguished from phylogenetically closely related species and formed a distinct monophyletic lineage in the family Rhodobacteraceae. The size of the draft genome of strain LZ-14 ^T is 4.615 Mb, with a DNA G?+?C content of 63.3 mol%. It contains ten predicted secondary metabolite biosynthetic gene clusters and core genes for bacterial exopolysaccharide biosynthesis. Therefore, strain LZ-14 ^T (= CCTCC AB 2017230 ^T?=?KCTC 62342 ^T) represents a novel species of a new genus, for which the name Alexandriicola marinus gen. nov., sp. nov., is proposed.

     

Taxonomic description of Pseudomonas rhizovicinus sp. nov., isolated from the rhizosphere of a desert shrub Haloxylon ammodendron

A Gram-negative aerobic bacterium, strain M30-35 ^T, was isolated from the rhizosphere of Haloxylon ammodendron in Tengger desert, Gansu province, northwest China. Our previous research indicated that strain M30-35 ^T can promote the growth of ryegrass (Lolium perenne L.). In this study, strain M30-35 ^T was subjected to a polyphasic taxonomic study. Phylogenetic analysis of the 16S rRNA gene and two other housekeeping genes (gyrB, rpoD) showed that strain M30-35 ^T is a member of Pseudomonas anguilliseptica group. The average nucleotide identity (ANI) scores for strains KMM 3042 ^T and FR1439^T were 76.5% and 83.7%, respectively, and DNA-DNA hybridization (DDH) were 21.6% and 26.6%, respectively, and the rates were less than the threshold range for species determination. The dominant cellular fatty acids of strain M30-35 ^T were C_16:0 (22.7%), summed feature 3 (C_16:1ω7c and/or C_16:1ω6c; 18.5%), summed feature 8 (C_18:1ω7c and/or C_18:1ω6c; 23.1%). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipid and aminophospholipid and the predominant respiratory quinone was ubiquinone (Q9). On the basis of above data, it can be concluded that strain M30-35 ^T represents a novel species in the genus Pseudomonas, for which the name Pseudomonas rhizovicinus sp. nov. is proposed. The type strain is M30-35 ^T (=?MCCC 1K03247^T?=?KCTC 52664 ^T).

     

Nisaea sediminum sp. nov., a heavy metal resistant bacterium isolated from marine sediment in the East China Sea

A Gram-negative, rod-shaped, motile and strictly aerobic bacterium, designated NBU1469^T, was isolated from marine sediment sampled on Meishan Island located in the East China Sea. Strain NBU1469^T grew optimally at temperature of 40 °C, NaCl concentration of 2.0% (w/v) and pH 7.5. Catalase and oxidase activities, H₂S production, nitrate reduction and hydrolysis of Tween 20 were positive. Indole, methyl red reaction, urease, hydrolysis of gelatin, starch, casein, Tweens 40, 60 and 80 were negative. The major cellular fatty acids were C_16:0, C_19:0 cyclo ω8c and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). The only respiratory quinone was ubiquinone-10 (Q-10). The major polar lipids were phosphatidylglycerol, two unidentified amino-phospholipids and two unidentified phospholipids. Comparative analysis of the 16S rRNA gene sequence showed highest similarities to the species with validated name Nisaea nitritireducens DR41_18^T (98.1%) and Nisaea denitrificans DR41_21^T (97.6%). Phylogenetic analyses indicated that strain NBU1469^T formed a distinct lineage with strains Nisaea nitritireducens DR41_18^T and Nisaea denitrificans DR41_21^T within the genus Nisaea. The average nucleotide identity and digital DNA-DNA hybridization values between strain NBU1469^T and related species of genus Nisaea were well below the threshold limit for prokaryotic species delineation. The DNA G?+?C content was 63.6%. Based on its phenotypic, chemotaxonomic and genotypic data, strain NBU1469^T is considered to be a representative of a novel species in the genus Nisaea, for which the name Nisaea sediminum sp. nov. is proposed. The type strain is NBU1469^T (=KCTC 82224 ^T?=MCCC 1K04763^T).

     

<Emphasis Type="Italic">Hoeflea prorocentri</Emphasis> sp. nov., isolated from a culture of the marine dinoflagellate <Emphasis Type="Italic">Prorocentrum mexicanum</Emphasis> PM01

A Gram-stain negative, aerobic, rod-shaped, non-motile, yellow-pigmented and non-spore-forming bacterial strain, designated PM5-8^T, was isolated from a culture of a marine toxigenic dinoflagellate Prorocentrum mexicanum PM01. Strain PM5-8^T grew at 15–35 °C (optimum, 25–30 °C) and pH 6–11 (optimum, 7.5–8). Cells required at least 1.5% (w/v) NaCl for growth, and can tolerate up to 7.0% with the optimum of 4%. Phylogenetic analysis based on 16S rRNA gene sequence revealed that the strain PM5-8^T is closely related to members of the genus Hoeflea, with high sequence similarities with Hoeflea halophila JG120-1^T (97.06%) and Hoeflea alexandrii AM1V30^T (97.01%). DNA–DNA hybridization values between the isolate and other type strains of recognized species of the genus Hoeflea were between 11.8 and 25.2%, which is far below the value of 70% threshold for species delineation. The DNA G?+?C content was 50.3 mol%. The predominant cellular fatty acids of the strain were identified as summed feature 8 (C_16:1 ω7c and/or C_16:1 ω6c; 51.5%), C_18:1 ω7c 11-methyl (20.7%), C_16:0 (17.2%) and C_18:0 (5.7%). The major respiratory quinone was Q-10. Polar lipids profiles contained phosphatidylcholine, phosphatidylglycerol, sulfoquinovosyl diacylglycerol, phosphatidylmono- methylethanolamine, phosphatidylethanolamine and four unidentified lipids. On the basis of the polyphasic taxonomic data presented, strain PM5-8^T (=?CCTCC AB 2016294^T?=?KCTC 62490^T) represents a novel species of the genus Hoeflea, for which the name Hoeflea prorocentri sp. nov. is proposed.     

A genomic overview including polyphasic taxonomy of Thalassoroseus pseudoceratinae gen. nov., sp. nov. isolated from a marine sponge,Pseudoceratina sp.

A pink-coloured, salt- and alkali-tolerant planctomycetal strain (JC658^T) with oval to pear-shaped, motile, aerobic, Gram-negative stained cells was isolated from a marine sponge, Pseudoceratina sp. Strain JC658^T shares the highest 16S rRNA gene sequence identity with Maioricimonas rarisocia Mal4^T (<?89.2%) in the family Planctomycetaceae. The genomic analysis of the new strain indicates its biotechnological potential for the production of various industrially important enzymes, notably sulfatases and carbohydrate-active enzymes (CAZymes), and also potential antimicrobial compounds. Several genes encoding restriction-modification (RM) and CRISPR-CAS systems are also present. NaCl is obligate for growth, of which strain JC658^T can tolerate a concentration up to 6% (w/v). Optimum pH and temperature for growth are 8.0 (range 7.0–9.0) and 25 ºC (range 10–40 °C), respectively. The major respiratory quinone of strain JC658^T is MK6. Major fatty acids are C_16:1ω7c/C_16:1ω6c, C_18:0 and C_16:0. Major polar lipids are phosphatidylcholine, phosphatidyl-dimethylethanolamine and phosphatidyl-monomethylethanolamine. The genomic size of strain JC658^T is 7.36 Mb with a DNA G?+?C?content of 54.6 mol%. Based on phylogenetic, genomic (ANI, AAI, POCP, dDDH), chemotaxonomic, physiological and biochemical characteristics, we conclude that strain JC658^T belongs to a novel genus and constitutes a novel species within the family Planctomycetaceae, for which we propose the name Thalassoroseus pseudoceratinae gen. nov., sp. nov. The novel species is represented by the type strain JC658^T (=?KCTC 72881 ^T?=?NBRC 114371 ^T).

     

Nonhongiella spirulinensis gen. nov., sp. nov., a bacterium isolated from a cultivation pond of Spirulina platensis in Sanya, China

A Gram-negative, aerobic, motile rod strain, designated Ma-20^T, was isolated from a pool of marine Spirulina platensis cultivation, Sanya, China, and was subjected to a polyphasic taxonomy study. Strain Ma-20^T can grow in the presence of 0.5–11 % (w/v) NaCl, 10–43 °C and pH 6–10, and grew optimally at 30 °C, pH 7.5–9.0 in natural seawater medium. The polar lipids were composed of phosphatidylethanolamine, three unidentified phospholipids and three unidentified polar lipids. The respiratory quinone was ubiquinone 8 (Q-8) and the major fatty acids were C_18:1ω6c/C_18:1ω7c (summed feature 8, 32.84 %), C_16:1ω6c/C_16:1ω7c (summed feature 3, 30.76 %), C_16:0 (13.54 %), C_12:03-OH (4.63 %), and C_12:0 (4.09 %). The DNA G+C content of strain Ma-20^T was 58 mol %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Ma-20^T belonging to Gammaproteobacteria, it shared 88.46–91.55 and 89.21–91.26 % 16S rRNA gene sequence similarity to the type strains in genus Hahella and Marinobacter, respectively. In addition to the large 16S rRNA gene sequence difference, Ma-20^T can also be distinguished from the reference type strains Hahella ganghwensis FR1050^T and Marinobacter hydrocarbonoclasticus sp. 17^T by several phenotypic characteristics and chemotaxonomic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic properties, strain Ma-20^T is suggested to represent a novel species of a new genus in Gammaproteobacteria, for which the name Nonhongiella spirulinensis gen. nov., sp. nov. is proposed. The type strain is Ma-20^T (=KCTC 32221^T=LMG 27470^T).     

Shinella oryzae sp. nov., a novel zearalenone-resistant bacterium isolated from rice paddy soil

A novel bacterium, designated Z-25 ^T, was isolated from a rice paddy rhizosphere soil sample from Wuchang County, China. The Z-25 ^T strain is gram-negative, rod-shaped, non-spore-forming, aerobic, motile by unipolar flagella and straw white in color. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain Z-25 belongs to the genus Shinella, and the closest members are Shinella zoogloeoides ATCC 19623 ^T with 98.58% similarity, S. kummerowiae CCBAU 25,048 T (98.03%) and S. granuli Ch06 ^T (97.37%). The average nucleotide identity and in silico DNA-DNA hybridization values between strain Z-25 ^T and the closest members were less than 85.29% and 28.70%, respectively. The predominant fatty acids were the sums of features comprising C_18:1 ω7c and/or C_18:1 ω6c (34.62%), C_18:1 ω7c -11-methyl (20.48%), and C_19:0 cyclo ω8c (18.19%). The only respiratory quinone was ubiquinone-10, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Additionally, a genome analysis showed that Z-25 ^T presented potential functional genes related to the degradation of zearalenone (ZEN). An HPLC analysis indicated that Z-25 ^T could remove 74.13% of 10 mg/L ZEN after 144 h at 30 °C. Therefore, based on phenotypic, chemotaxonomic, phylogenetic and genotypic analyses, strain Z-25 ^T represents a novel species in the genus Shinella, for which the name Shinella oryzae sp. nov. is proposed. The type strain is Z-25 ^T (=?GDMCC 1.2424 ^T?=?KCTC 82660 ^T).

     

Altererythrobacter flava sp. nov., a new member of the family Erythrobacteraceae,isolated from a surface seawater sample

A Gram-stain-negative, light yellow pigmented, non-motile and aerobic bacterial strain, designated HHU E2-1 ^T, was isolated from a surface seawater sample. The 16S rRNA gene sequence analysis indicated that HHU E2-1 ^T shared the highest sequence similarity to the type strain Qipengyuania gaetbuli DSM 16225 ^T (96.90%), which belongs to the family Erythrobacteraceae. Combined phylogeny of 288 single-copy orthologous gene clusters, analysis of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), average amino acid identity (AAI) and evolutionary distances suggested that HHU E2-1 ^T can be considered as a member of the genus Altererythrobacter based on the recently proposed standard for defining genera of Erythrobacteraceae. Strain HHU E2-1 ^T grew at 15–35 °C and pH 5.0–8.0, with optimum growth at 28 °C and pH 7.0. Tolerance to NaCl was up to 4% (w/v) with optimum growth in 2–3% NaCl. The major fatty acids (>?10%) were C_18:1ω7c11-methyl, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). The predominant isoprenoid quinone was ubiquinone-10. The genomic G?+?C content was 57.40%. On the basis of the phenotypic, phylogenetic and chemotaxonomic characterizations, HHU E2-1 ^T represents a novel species of the genus Altererythrobacter, for which the name Altererythrobacter flava sp. nov. is proposed. The type strain is HHU E2-1 ^T (=?CGMCC 1.17394 ^T?=?KCTC 72835 ^T?=?MCCC 1K04226^T).

     

Microvirga splendida sp. nov., bacteria isolated from soil

Two bacterial strains, BT325^T and BT690, were isolated from soil samples collected in Korea. Both strains were Gram stain-negative, short rod-shaped, and formed light-pink colored colonies. The 16S rRNA sequence similarity of strains BT325^T and BT690 shared a sequence similarity of 99.7%. Both strains shared the highest 16S rRNA gene similarity of 98.6% with Microvirga arabica SV2184P^T, followed by Microvirga ossetica V5/3 M T (98.5% and 98.2%, respectively), Microvirga soli R491^T (98.3% and 98.2%, respectively), Microvirga aerilata (98.2% and 98.08%, respectively), Microvirga makkahensis (98.08% and 97.8%, respectively). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BT325^T and BT690 were positioned in a distinct lineage within the family Methylobacteriaceae (order Rhizobiales, class Alphaproteobacteria). The genome size of strain BT325^T was 5,200,315 bp and the genomic DNA G?+?C content was 64.3 mol%. The sole respiratory quinone of strain BT325^T was Q-10 and the predominant cellular fatty acids were summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) and summed feature 8 (C_18:1 ω7c/C_18:1 ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. Polyphasic taxonomic analysis of biochemical, chemotaxonomic, and phylogenetic analyses suggested that strains BT325^T represents a novel bacterial species within the genus Microvirga, for which the name Microvirga splendida is proposed. The type strain of Microvirga splendida is BT325^T (=?KCTC 72406 ^T?=?NBRC 114847 ^T).

     

Genome mining revealed polyhydroxybutyrate biosynthesis by Ramlibacter agri sp. nov., isolated from agriculture soil in Korea

A white-colony-forming, facultative anaerobic, motile and Gram-stain-negative bacterium, designated G-1-2-2 ^T was isolated from soil of agriculture field near Kyonggi University, Republic of Korea. Strain G-1-2-2 ^T synthesized the polyhydroxybutyrate and could grow at 10–35 °C. The phylogenetic analysis based on 16S rRNA gene sequence showed that, strain G-1-2-2 ^T formed a lineage within the family Comamonadaceae and clustered as a member of the genus Ramlibacter. The 16S rRNA gene sequence of strain G-1-2-2 ^T showed high sequence similarities with Ramlibacter ginsenosidimutans BXN5-27 ^T (97.9%), Ramlibacter monticola G-3-2 ^T (97.9%) and Ramlibacter alkalitolerans CJ661^T (97.5%). The sole respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and an unidentified phospholipid. The principal cellular fatty acids were C_16:0, cyclo-C_17:0, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). The genome of strain G-1-2-2 ^T was 7,200,642 bp long with 13 contigs, 6,647 protein-coding genes, and DNA G?+?C content of 68.9%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain G-1-2-2 ^T and close members were?≤?81.2 and 24.1%, respectively. The genome of strain G-1-2-2 ^T showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Genome mining revealed the presence of atoB, atoB2, phaS, phbB, phbC, and bhbD genes in the genome which are responsible for polyhydroxybutyrate biosynthesis. Based on these data, strain G-1-2-2 ^T represents a novel species in the genus Ramlibacter, for which the name Ramlibacter agri sp. nov. is proposed. The type strain is G-1-2-2 ^T (=?KACC 21616 ^T?=?NBRC 114389 ^T).

     

Hymenobacter taeanensis sp. nov., radiation resistant bacterium isolated from coastal sand dune

An aerobic, Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, and light pink-colored bacterial strain, designated TS19^T, was isolated from a sand sample obtained from a coastal sand dune after exposure to 3 kGy of gamma radiation. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the isolate was a member of the genus Hymenobacter and was most closely related to H. wooponensis WM78^T (98.3% similarity). Strain TS19^T and H. wooponensis showed resistance to gamma radiation with D₁₀ values (i.e., the dose required to reduce the bacterial population by tenfold) of 7.3 kGy and 3.5 kGy, respectively. The genome of strain TS19^T consists of one contig with 4,879,662 bp and has a G?+?C content of 56.2%. The genome contains 3,955 protein coding sequences, 44 tRNAs, and 12 rRNAs. The predominant fatty acids of strain TS19^T were iso-C_15:0, summed feature 4 (iso-C_17:1 I and/or anteiso-C_17:1 B), summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c), and C_16:1 ω5c. The major polar lipids were phosphatidylethanolamine, and one unidentified aminophospholipid. The main respiratory quinone was menaquinone-7. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain TS19^T represents a novel species, for which the name Hymenobacter taeanensis sp. nov. is proposed. The type strain is TS19^T (=?KCTC 72897^T?=?JCM 34023^T).

     

Oryzicola mucosus gen. nov., sp. nov., a novel slime producing bacterium belonging to the family Phyllobacteriaceae isolated from the rhizosphere of rice plants

A novel Gram-stain negative, asporogenous, slimy, rod-shaped, non-motile bacterium ROOL2^T was isolated from the root samples collected from a rice field located in Ilsan, South Korea. Phylogenetic analysis of the 16S rRNA sequence showed 96.5% similarity to Tianweitania sediminis Z8^T followed by species of genera Mesorhizobium (96.4–95.6%), Aquabacterium (95.9–95.7%), Rhizobium (95.8%) and Ochrobactrum (95.6%). Strain ROOL2^T grew optimally at 30 °C in the presence of 1–6% (w/v) NaCl and at pH 7.5. The major respiratory quinone was ubiquinone-10 and the major cellular fatty acids were C_18:1ω7c, summed feature 4 (comprising iso-C_17:1 I and/or anteiso-C_17:1 B) and summed feature 8 (comprising C_18:1ω6c and/or C_18:1ω7c). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylglycerol, one unidentified aminolipid and two unidentified lipids. The assembled draft genome of strain ROOL2^T had 28 contigs with N50 value of 656,326 nt, total length of 4,894,583 bp and a DNA G?+?C content of 61.5%. The average amino acid identity (AAI) values of strain ROOL2^T against the genomes of related members belonging to the same family were below 68% and the ANI and dDDH values between the strain ROOL2^T and the type strains of phylogenetically related species were 61.8–76.3% and 19.4–21.1%, respectively. Strain ROOL2^T only produces carotenoid-type pigment when grown on LB agar and slime on R2A agar. In the presence of tryptophan, strain ROOL2^T produced indole acetic acid (IAA), a phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphatase and tryptophan synthase were found in the genome of strain ROOL2^T. The genotypic and phenotypic characteristics indicated that strain ROOL2^T represents a novel genus belonging the family Phyllobacteriaceae, for which the name Oryzicola mucosus gen. nov., sp. nov. is proposed. The type strain is ROOL2^T (KCTC 82711 ^T?=?NBRC 114717 ^T).

     

Hyphomonas sediminis sp. nov., isolated from marine sediment

A Gram-staining-negative, aerobic and pear-shaped bacterial strain, designated WL0036^T, was isolated from coastal sediment sample collected in Nantong city, Jiangsu province of China (120° 51′ 13″ E, 32° 6′ 26″ N) in October 2020. Strain WL0036^T was found to grow at 20–37 °C (optimum, 28 °C) with 0–9.0% NaCl (optimum, 2.5–4.0%) and displayed alkaliphilic growth with the pH range of pH 6.0–10.0 (optimum, pH 7.0–8.0). The polar lipids profile of strain WL0036^T included phosphatidylcholine, phosphatidylethanolamine, glycolipid and an unidentified lipid. The major isoprenoid quinone was determined to be Q-11 and the major fatty acids were C_16:0, 11-methyl-C_18:1ω7c, and summed features 8 (C_18:1ω6c and/or C_18:1ω7c). The G?+?C content of genomic DNA was 61.8%. Phylogenetic trees constructed based on 16S rRNA gene sequence and bac120 gene set (a collection of 120 single-copy protein sequences prevalent in bacteria) indicted that strain WL0036^T clustered with strains Hyphomonas neptunium ATCC 15444^T and H. polymorpha PS728^T. The average nucleotide identities between strain WL0036^T and strains H. neptunium ATCC 15444^T and H. polymorpha PS728^T were 80.7% and 81.2%, respectively. Strain WL0036^T showed 22.8% and 23.2% of digital DNA-DNA hybridization identities with H. neptunium ATCC 15444^T and H. polymorpha PS728^T, respectively. As inferred from the phenotypic and genotypic characteristics and the phylogenetic trees, strain WL0036^T ought to be recognized as a novel species in genus Hyphomonas, for which the name Hyphomonas sediminis sp. nov. is proposed. The type strain is WL0036^T (=?MCCC 1K05843^T?=?JCM 34658^T?=?GDMCC 1.2413^T).

     

Spongiibacter pelagi sp. nov., a marine gammaproteobacterium isolated from coastal seawater

A novel gammaproteobacterium, designated as KMU-158^T, was isolated from seawater collected on the coastline of Dadaepo in the Republic of Korea, and characterized using a polyphasic taxonomic approach. Strain KMU-158^T was Gram-staining-negative, pale beige-colored, strictly aerobic, rod-shaped, motile, and chemoorganoheterotrophic. The novel isolate was able to grow at 0–3% NaCl concentrations (w/v), pH 6.5–9.5, and 15–40 °C. The analysis based on 16S rRNA gene sequences indicated that strain KMU-158^T belongs to the family Spongiibacteraceae and shared the highest similarity with Spongiibacter tropicus CL-CB221^T (96.1%). The major cellular fatty acids were summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and C_17:1 ω8c. The only respiratory quinone was identified as ubiquinone-8. The polar lipids of strain KMU-158^T contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and two unidentified lipids. The assembled draft genome size of strain KMU-158^T was 3.29 Mbp with a DNA G?+?C content of 51.3%. The average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity values of KMU-158^T and the representatives of the genus Spongiibacter were found to be 78.5–79.1%, 13.8–14.1%, and 66.6–66.8%, respectively. From the distinct phenotypic, phylogenetic, genomic, and chemotaxonomic properties, the strain KMU-158^T is considered to represent a novel species of the genus Spongiibacter, for which the name Spongiibacter pelagi sp. nov. is proposed. The type strain of the species S. pelagi sp. nov. is KMU-158^T (=?KCCM 90448^T?=?NBRC 114307^T).

     

Vibrio nitrifigilis sp. nov., a marine nitrogen-fixing bacterium isolated from the lagoon sediment of an islet inside an atoll

A nitrogen-fixing isolate of facultatively anaerobic, marine bacterium, designated strain NFV-1^T, was recovered from the lagoon sediment of Dongsha Island, Taiwan. It was a Gram-negative rod which exhibited motility with monotrichous flagellation in broth cultures. The strain required NaCl for growth and grew optimally at about 25–35 °C, 3% NaCl and pH 7–8. It grew aerobically and could achieve anaerobic growth by fermenting d-glucose or other carbohydrates as substrates. NH₄Cl could serve as a sole nitrogen source for growth aerobically and anaerobically, whereas growth with N₂ as the sole nitrogen source was observed only under anaerobic conditions. Cellular fatty acids were predominated by C_16:1 ω7c, C_16:0, and C_18:1 ω7c. The major polar lipids consisted of phosphatidylethanolamine and phosphatidylserine. Strain NFV-1^T had a DNA G?+?C content of 42.5 mol%, as evaluated according to the chromosomal DNA sequencing data. Analyses of sequence similarities and phylogeny based on the 16S rRNA genes, together with the housekeeping genes, gyrB, ftsZ, mreB, topA and gapA, indicated that the strain formed a distinct species-level lineage in the genus Vibrio of the family Vibrionaceae. These phylogenetic data and those from genomic and phenotypic characterisations support the establishment of a novel Vibrio species, for which the name Vibrio nitrifigilis sp. nov. (type strain NFV-1^T?=?BCRC 81211^T?=?JCM 33628^T) is proposed.

     

Methylobacterium bullatum sp. nov., a methylotrophic bacterium isolated from Funaria hygrometrica

A novel, pink-pigmented aerobic, facultatively methylotrophic bacterial strain (F3.2^T) isolated from the phyllosphere of Funaria hygrometrica, was analyzed using a polyphasic approach. Cells were Gram-negative, motile rods, strictly aerobic and non-spore-forming and exhibited surface structures varying in quantity, distribution and morphology. The isolate grew at 10–33 °C over a pH range of 5.5–8.0 and in the presence of less than 1.0% NaCl. Strain F3.2^T shared less than 70% DNA–DNA binding to the next type strain of the genus Methylobacterium (M. adhaesivum DSM 17169^T). In addition to the major cellular fatty acid C_18:1ω7c (81.7%), present in all Methylobacterium species (and also members of the genus Alphaproteobacteria), a high value (11.7%) of the fatty acids (summed feature) C_16:1ω7c and/or iso-C_15:02OH was determined. Phylogenetic analyses based on 16S rDNA and methanol dehydrogenase gene sequences, DNA–DNA hybridization values, chemotaxonomic and phenotypic characteristics indicate that the strain F3.2^T represents a novel species within the genus Methylobacterium. We propose the name Methylobacterium bullatum sp. nov. for this species. The type strain is the strain F3.2^T (DSM 21893^T = LMG 24788^T).     

Maricoccus atlantica gen. nov. sp. nov., isolated from deep sea sediment of the Atlantic Ocean

A taxonomic study was carried out on strain 22II-S10r2^T, which was isolated from the deep sea sediment of the Atlantic Ocean using oil-degrading enrichment. The bacterium was Gram-negative, oxidase positive and catalase negative, spherical in shape, and motile by polar flagella. Growth was observed at salinities of 0.5–7 % and at temperatures of 10–41 °C. The isolate was capable of aesculin hydrolysis, but unable to reduce nitrate to nitrite or degrade Tween 80 or gelatine. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II-S10r2^T belonged to the family Ectothiorhodospiraceae, with highest sequence similarity to Thioalkalivibrio sulfidiphilus HL-EbGR7^T (90.9 % similarity). The principal fatty acids were Sum In Feature 8 (C_18:1 ω7c/ω6c (29.9 %), C_18:1 ω9c (13.5 %), C_16:1 ω5c (12.3 %), C_12:03OH (6.8 %), C_18:1 ω5c (5.7 %) and C_16:0 (5.3 %). The G+C content of the chromosomal DNA was 60.7 mol%. The respiratory quinone was determined to be Q-7 (25 %) and Q-8 (75 %). Phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid, glycolipid, three phospholipids and lipid were present. The strain was aerobic, non-phototrophic and non-chemolithoautotrophic. The combined genotypic and phenotypic data show that strain 22II-S10r2^T represents a novel species within a novel genus, for which the name Maricoccus atlantica gen. nov. sp. nov. is proposed, with the type strain 22II-S10r2^T (=CGMCC NO.1.12317^T = LMG 27155^T = MCCC 1A09384^T).     

Ottowia shaoguanensis sp. nov., Isolated From Coking Wastewater

A Gram-negative, short rod-shaped, floc-forming bacterial strain J5-66^T without any flagellum was isolated from coking wastewater collected from Shaoguan, Guangdong, China. It was capable of optimal growth at pH 7, 30 °C, and 1–2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belonged to the genus Ottowia in Comamonadaceae, and the highest 16S rRNA gene sequence similarity was 96.2 % with Ottowia pentelensis DSM 21699^T. The major cellular fatty acids of strain J5-66^T were C_16:1 ω7c/C_16:1 ω6c (45.0 %), C_16:0 (21.1 %), C_18:1 ω7c or/and C_18:1 ω6c (19.2 %). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, glycolipid and two unidentified phospholipids (PL1 and PL2). The predominant ubiquinone was Q-8, and the G+C content of the genome DNA was 64.4 mol%. On the basis of genetic, phenotypic and chemotaxonomic analyses, strain J5-66^T represents a novel species of the genus Ottowia for which the name Ottowia shaoguanensis sp. nov. is proposed. The type strain is J5-66^T (=CGMCC 1.12431^T =LMG 27408^T).     

Devosia lucknowensis sp. nov., a bacterium isolated from hexachlorocyclohexane (HCH) contaminated pond soil

Strain L15^T, a Gram-negative, motile, orange colored bacterium was isolated from pond soil in the surrounding area of a hexachlorocyclohexane (HCH) dump site at Ummari village in Lucknow, India. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain L15^T belongs to the family Hyphomicrobiaceae in the order Rhizobiales. Strain L15^T showed highest 16S rRNA gene sequence similarity to Devosia chinhatensis IPL18^T (98.0%). Chemotaxonomic data revealed that the major fatty acids were summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c), C_18:1 ω7c 11-methyl, C_16:0 and C_18:0. The major polar lipids of strain L15^T were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content of strain L15^T was 59.8%. Polyamine profile showed the presence of sym-homospermidine with traces of putrescine. Ubiquinone Q-10 was the major respiratory quinone present. Based on these data, strain L15^T (=CCM 7977^T =DSM 25398^T) was classified as a type strain of a novel species, for which the name Devosia lucknowensis sp. nov. is proposed.