Paracoccus onchidii sp. nov., a moderately halophilic bacterium isolated from a marine invertebrate from the South China Sea.

A novel moderately halophilic bacterial strain, designated Z330T, was isolated from the egg of a marine invertebrate of the genus Onchidium collected in the South China Sea. The 16S rRNA gene sequence of strain Z330T exhibited the highest similarity value to that of the type strain Paracoccus fistulariae KCTC 22803T (97.6%), Paracoccus seriniphilus NBRC 100798T (97.6%) and Paracoccus aestuarii DSM 19484T (97.6%). Phylogenomic and 16S rRNA phylogenetic analysis showed that strain Z330T was most closely related to P. seriniphilus NBRC 100798T and P. fistulariae KCTC 22803T. Strain Z330T grew optimally at 28-30 °C, pH 7.0-8.0 with the presence of 5.0-7.0% (w/v) NaCl. In addition, growth of strain Z330T occurred at 0.5-16% NaCl, indicated strain Z330T was a moderately halophilic and halotolerant bacterium of genus Paracoccus. The predominant respiratory quinone in strain Z330T was identified as ubiquinone-10. The major polar lipids of strain Z330T were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, glycolipid and six unidentified polar lipids. The major fatty acids of strain Z330T was summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The draft genome sequence of strain Z330T includes 4,084,570 bp in total (N50 = 174,985 bp) with a medium read coverage of 463.6 × and 83 scaffolds. The DNA G + C content of strain Z330T was 60.5%. In silico DNA-DNA hybridization with the four type strains showed 20.5, 22.3, 20.1 and 20.1% relatedness to Paracoccus fistulariae KCTC 22803T, Paracoccus seriniphilus NBRC 100798T, Paracoccus aestuarii DSM 19484T and Paracoccus denitrificans 1A10901T, respectively. And the average nucleotide identity (ANIb) values between strain Z330T and these four type strains were 76.2, 80.0, 75.8 and 73.8%, respectively, lower than the 95-96% threshold value for dividing prokaryotic species. On the basis of the phenotypic, phylogenetic, phylogenomic and chemotaxonomic properties, a novel species of the genus Paracoccus, Paracoccus onchidii sp. nov. is proposed with the type strain Z330T (= KCTC 92727T = MCCC 1K08325T).

Acremocholone, an Anti-Vibrio Steroid from the Marine Mesophotic Zone Ciocalypta Sponge-Associated Fungus Acremonium sp. NBUF150.

Mesophotic coral ecosystems (MCEs) represent an underexplored source of intriguing natural products. Efforts to discover bioactive metabolites from sponge-associated fungi in MCEs identified a new steroid, acremocholone (1) and its three known analogs (2-4), from Acremonium sp. NBUF150. The Acremonium sp. NBUF150 was isolated from a Ciocalypta sponge located 70 m deep within the South China Sea. The planar structures and absolute configuration of 1-4 were determined from NMR-derived spectroscopic data, HR-ESI-MS, and X-ray crystallography. Compound 1 exhibited antimicrobial inhibition against Vibrio scophthalmi, V. shilonii and V. brasiliensis at minimum inhibitory concentrations of 8 µg/mL; compound 2 inhibited V. shilonii and V. brasiliensis at 8 and 32 µg/mL, respectively, and compound 4 inhibited growth of V. brasiliensis at 16 µg/mL. Sponge associated fungi from MCEs represent a promising resource of anti-Vibrio drug leads for aquaculture use.

Cupidesulfovibrio liaohensis gen. nov., sp. nov., a novel sulphate-reducing bacterium isolated from an oil reservoir and reclassification of Desulfovibrio oxamicus and Desulfovibrio termitidis as Cupidesulfovibrio oxamicus comb. nov. and Cupidesulfovibrio termitidis comb. nov.

A novel sulphate-reducing, Gram-stain-negative, anaerobic strain, isolate XJ01T, recovered from production fluid at the LiaoHe oilfield, PR China, was the subject of a polyphasic study. The isolate together with Desulfovibrio oxamicus NCIMB 9442T and Desulfovibrio termitidis DSM 5308T formed a distinct, well-supported clade in the Desulfovibrionaceae 16S rRNA gene tree. The taxonomic status of the clade was underscored by complementary phenotypic data. The three isolates comprising the clade formed distinct phyletic branches and were distinguished using a combination of physiological features and by low average nucleotide identity and digital DNA-DNA hybridization values. Consequently, it is proposed that isolate XJ01T represents a novel genus and species for which the name Cupidesulfovibrio liaohensis gen. nov., sp. nov. is proposed with the type strain XJ01T (=CGMCC 1.5227T=DSM 107637T). It is also proposed that D. oxamicus and D. termitidis be reclassified as Cupidesulfovibrio oxamicus comb. nov. and Cupidesulfovibrio termitidis comb. nov., respectively.

Kandeliimicrobium roseum gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from mangrove rhizosphere soil.

A Gram-stain-negative, non-flagellated, short rod-shaped bacterium, designated XY-R6T, was isolated from the rhizosphere soil of a mangrove plant, Kandelia candel (L.) Druce, in Mai Po Nature Reserve, Hong Kong. Growth of strain XY-R6T was observed at pH 5.0-9.5 (optimum 6.5-8.0), between 8 and 42 °C (optimum 28-34 °C), and in the presence of 0-9.5 % (w/v) NaCl (optimum 1-4 %). The predominant isoprenoid quinone was ubiquinone-10. The major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) (55.61 %), C19 : 0cycloω8c (21.59 %) and C16 : 0 (11.24 %). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, aminolipid, phosphatidylcholine and diphosphatidylglycerol. The genomic DNA G+C content of strain XY-R6T was 69.3 mol%. Phylogenetic analyses, based on 16S rRNA gene sequences, revealed that strain XY-R6T belonged to the family Rhodobacteraceae of the class Alphaproteobacteria and formed a distinct lineage, showing the highest gene sequence similarities to the members of genus Wenxinia(94.5-94.3 %), followed by the genera Profundibacterium (94.3 %), Defluviimonas(93.8-92.5 %), Oceanicola (93.8 %) and Cereibacter (93.7 %). Similarities to other genera within the family Rhodobacteraceae were below 94.0 %. Based on comprehensive phenotypic, phylogenetic and chemotaxonomic characterization, it is indicated that strain XY-R6T represents a novel species of a new genus in the family Rhodobacteraceae, for which the name Kandeliimicrobium roseum gen. nov., sp. nov. is proposed, with XY-R6T (=MCCC 1K01498T=KCTC 52266T=DSM 104294T) as the type strain.

Pseudooceanicola lipolyticus sp. nov., a marine alphaproteobacterium, reclassification of Oceanicola flagellatus as Pseudooceanicola flagellatus comb. nov. and emended description of the genus Pseudooceanicola.

A Gram-stain-negative, rod-shaped bacterium, designated 157T, was isolated from seawater collected from the Philippine Sea. Cells of strain 157T grew in medium containing 0.5-10.0 % NaCl (w/v, optimum 3 %), at pH 6.0-8.5 (optimum 7.0) and at 15-40 °C (optimum 30 °C). Tweens 20, 40 and 80 as well as urea were hydrolysed. The 16S rRNA gene sequence of strain 157T had a high sequence similarity with respect to Pseudooceanicola marinus AZO-CT (97.2 %), and exhibited less than 97.0 % sequence similarity to other type strains of the species with validly published names. Phylogenetic analyses revealed that strain 157T fell within a cluster comprising the Pseudooceanicola species and formed a coherent clade with P. marinus AZO-CT and Pseudooceanicola antarcticus Ar-45T. Strain 157T exhibited average nucleotide identity values of 74.5 and 74.9 % to P. marinus LMG 23705T and P. antarcticus Ar-45T, respectively. In silico DNA-DNA hybridization analysis revealed that strain 157T shared 20.2 % DNA relatedness with P. marinus LMG 23705T and 20.6 % with P. antarcticus Ar-45T, respectively. The sole isoprenoid quinone was ubiquinone 10. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C19 : 0 cyclo ω8c, C16 : 0 2-OH and C16 : 0. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid and one unidentified glycolipid. The DNA G+C content was 64.6 mol%. According to the phylogenetic, chemotaxonomic and phenotypic data, it represents a novel species of the genus Pseudooceanicola, for which the name Pseudooceanicolalipolyticus is proposed. The type strain is 157T (=KCTC 52654T=MCCC 1K03317T). In addition, the description of the genus Pseudooceanicola is emended and Oceanicola flagellatus is reclassified as Pseudooceanicola flagellatus comb. nov., with the type strain DY470T (=CGMCC 1.12664T=LMG 27871T) proposed.

Rhizobium marinum sp. nov., a malachite-green-tolerant bacterium isolated from seawater.

A motile, Gram-stain-negative, non-pigmented bacterial strain, designated MGL06T, was isolated from seawater of the South China Sea on selection medium containing 0.1 % (w/v) malachite green. Strain MGL06T showed highest 16S rRNA gene sequence similarity to Rhizobium vignae CCBAU 05176T (97.2 %), and shared 93.2-96.9 % with the type strains of other recognized Rhizobium species. Phylogenetic analyses based on 16S rRNA and housekeeping gene sequences showed that strain MGL06T belonged to the genus Rhizobium. Mean levels of DNA-DNA relatedness between strain MGL06T and R. vignae CCBAU 05176T, Rhizobium huautlense S02T and Rhizobium alkalisoli CCBAU 01393T were 20 ± 3, 18 ± 2 and 14 ± 3 %, respectively, indicating that strain MGL06T was distinct from them genetically. Strain MGL06T did not form nodules on three different legumes, and the nodD and nifH genes were also not detected by PCR or based on the draft genome sequence. Strain MGL06T contained Q-10 as the predominant ubiquinone. The major fatty acid was C18 : 1ω7c/C18 : 1ω6c with minor amounts of C19 : 0 cyclo ω8c, C16 : 0 and C18 : 1ω7c 11-methyl. Polar lipids of strain MGL06T included unknown glycolipids, phosphatidylcholine, aminolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unknown polar lipid and aminophospholipid. Based on its phenotypic and genotypic data, strain MGL06T represents a novel species of the genus Rhizobium, for which the name Rhizobium marinum sp. nov. is proposed. The type strain is MGL06T ( = MCCC 1A00836T = JCM 30155T).

Burkholderia jiangsuensis sp. nov., a methyl parathion degrading bacterium, isolated from methyl parathion contaminated soil.

A methyl parathion (MP) degrading bacterial strain, designated MP-1(T), was isolated from a waste land where pesticides were formerly manufactured in Jiangsu province, China. Polyphasic taxonomic studies showed that MP-1(T) is a Gram-stain-negative, non-spore-forming, rod-shaped and motile bacterium. The bacterium could grow at salinities of 0-1 % (w/v) and temperatures of 15-40 °C. Strain MP-1(T) could reduce nitrate to nitrite, utilize d-glucose and l-arabinose, but not produce indole, or hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that MP-1(T) belongs to the genus Burkholderia, showing highest sequence similarity to Burkholderia grimmiae DSM 25160(T) (98.5 %), and similar strains including Burkholderia zhejiangensis OP-1(T) (98.2 %), Burkholderia choica LMG 22940(T) (97.5 %), Burkholderia glathei DSM 50014(T) (97.4 %), Burkholderia terrestris LMG 22937(T) (97.2 %) and Burkholderia telluris LMG 22936(T) (97.0 %). In addition, the gyrB and recA gene segments of strain MP-1(T) exhibited less than 89.0 % and 95.1 % similarities with the most highly-related type strains indicated above. The G+C content of strain MP-1(T) was 62.6 mol%. The major isoprenoid quinone was ubiquinone Q-8. The predominant polar lipids comprised phosphatidyl ethanolamine, phosphatidyl glycerol, aminolipid and phospholipid. The principal fatty acids in strain MP-1(T) were C18 : 1ω7c/C18 : 1ω6c (23.3 %), C16 : 0 (16.8 %), cyclo-C17 : 0 (15.0 %), C16 : 1ω7c/C16 : 1ω6 (8.5 %), cyclo-C19 : 0ω8c (8.1 %), C16 : 1 iso I/C14 : 0 3-OH (5.7 %), C16 : 0 3-OH (5.6 %) and C16 : 02-OH (5.1 %). The DNA-DNA relatedness values between strain MP-1(T) and the three type strains (B. grimmiae DSM 25160(T), B. zhejiangensis OP-1(T) and B. glathei DSM 50014(T)) ranged from 24.6 % to 37.4 %. In accordance with phenotypic and genotypic characteristics, strain MP-1(T) represents a novel species of the genus Burkholderia, for which the name Burkholderia jiangsuensis sp. nov. is proposed, the type strain is MP-1(T) (LMG 27927(T) = MCCC 1K00250(T)).

Draft Genome Sequence of Burkholderia sp. Strain MP-1, a Methyl Parathion (MP)-Degrading Bacterium from MP-Contaminated Soil.

Burkholderia sp. strain MP-1 was isolated from pesticide-contaminated soil. Herein, we report the draft genome sequence of strain MP-1, which contains 168 contigs of 8,611,053 bp, with a G+C content of 62.55% and 7,631 protein-coding genes.