Vitellibacter nionensis sp. nov., isolated from a shallow water hydrothermal vent

Description of Aequorivita aurantiaca sp. nov. Isolated from Coastal Sediment, and Comparative Genomic Analysis and Biogeographic Distribution of the Genus Aequorivita

A novel Gram-stain-negative, facultatively anaerobic, and non-motile bacterial strain, designated SDUM287046T, was isolated from the coastal sediments of Jingzi Port of Weihai, China. Cells of strain SDUM287046T were rod-shaped with widths of 0.4-0.5 μm and lengths of 0.7-1.4 μm and could produce flexirubin-type pigments. Optimum growth of strain SDUM287046T occurred at 33-35 °C, pH 7.0, and with 2% (w/v) NaCl. Oxidase activity was negative, but catalase activity was positive. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SDUM287046T was most closely related to Aequorivita aquimaris D-24T (98.3%). The main cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C17:0 3-OH, and summed feature 9 (comprised of iso-C17:1 ω9c and/or C16:0 10-methyl). The sole respiratory quinone was MK-6. The polar lipids consisted of phosphatidylethanolamine (PE), one aminolipid (AL), three unidentified glycolipids (GL), and three unidentified lipids (L). The DNA G + C content was 39.3 mol%. According to the integrated results of phylogenetic, physiological, biochemical, and chemotaxonomic characteristics, we propose that strain SDUM287046T represents a novel species of the genus Aequorivita, for which the name Aequorivita aurantiaca sp. nov. is proposed. The type strain is SDUM287046T (=KCTC 92754T = MCCC 1H01418T). Comparative genomic analysis showed that the 16 Aequorivita species shared 1453 core genes and differed mainly in amino acid metabolism, cofactor metabolism, and vitamin metabolism. Biogeographic distribution analysis indicated that the marine environments were the primary habitat of Aequorivita bacteria.

Aequorivita iocasae sp. nov., a halophilic bacterium isolated from sediment collected at a cold seep field in the South China Sea

A moderately halophilic bacterium, designated strain KX20305T, was isolated from sediment collected from a cold seep field in the South China Sea. Cells of strain KX20305T were Gram-stain-negative, rod-shaped, non-motile, facultatively anaerobic, oxidase- and catalase-positive, and grew optimally at 25–30 °C, pH 6.0–8.0 and with 3–6 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KX20305T grouped with members of the genus Aequorivita , including Aequorivita aquimaris D-24T (98.3 % sequence similarity), Aequorivita vladivostokensis KMM 3516T (98.1 %) and Aequorivita echinoideorum CC-CZW007T (97.5 %). Genome sequencing of strain KX20305T revealed a genome size of 3.35 Mb and a DNA G+C content of 38.71 mol%. Genomic average nucleotide identity (orthoANI) values of strain KX20305T with A. aquimaris D-24T, A. vladivostokensis KMM 3516T and A. echinoideorum JCM 30378T were 83.8, 81.7 and 75.4 %, respectively, while in silico DNA–DNA hybridization (GGDC) values for strain KX20305T with these strains were 27.2, 25.0 and 19.6 %, respectively. The major fatty acids of strain KX20305T were iso-C15 : 0, iso-C17 : 0 3-OH and 10-methyl C16 : 0/iso-C17 : 1  ω9c. The predominant respiratory quinone was menaquinone-6 (MK-6). The polar lipids mainly comprised phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. Based on comparative analysis of phylogenetic, phylogenomic, phenotypic and chemotaxonomic characteristics, strain KX20305T represents a novel species of the genus Aequorivita , for which the name Aequorivita iocasae sp. nov. is proposed. The type strain is KX20305T (=KCTC 82699T=MCCC 1K06238T=JCM 34635T).

Luteirhabdus pelagi gen. nov., sp. nov., a novel member of the family Flavobacteriaceae, isolated from the West Pacific Ocean

A Gram-stain-negative, aerobic, and yellow-pigmented bacterium, designated A3-108^T, was isolated from seawater of the West Pacific Ocean. Cells were non-motile and rod-shaped, with carotenoid-type pigments. Strain A3-108^T grew at pH 6.0–8.5 (optimum 6.5) and 15–40 °C (optimum 28 °C), in the presence of 0.5–10% (w/v) NaCl (optimum 1.0%). It possessed the ability to produce H₂S. Based on the 16S rRNA gene analysis, strain A3-108^T exhibited highest similarity with Aureisphaera salina A6D-50^T (90.6%). Phylogenetic analysis shown that strain A3-108^T affiliated with members of the family Flavobacteriaceae and represented an independent lineage. The principal fatty acids were iso-C_15:0, iso-C_17:0 3-OH, iso-C_15:1 G, and summed feature 3 (C_16:1ω7c and/or C_16:1ω6c). The sole isoprenoid quinone was MK-6. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified aminolipid and one unidentified lipid. The ANIb, in silico DDH and AAI values among the genomes of strain A3-108^T and three reference strains were 67.3–71.1%, 18.7–22.1%, and 58.8–71.4%, respectively. The G + C content was 41.0%. Distinctness of the phylogenetic position as well as differentiating chemotaxonomic and other phenotypic traits revealed that strain A3-108^T represented a novel genus and species of the family Flavobacteriaceae, for which the name Luteirhabdus pelagi gen. nov., sp. nov. is proposed (type strain, A3-108^T = CGMCC 1.18821^T = KCTC 82563^T).

Characterization and Diversity Analysis of the Extracellular Proteases of Thermophilic Anoxybacillus caldiproteolyticus 1A02591 From Deep-Sea Hydrothermal Vent Sediment

Protease-producing bacteria play key roles in the degradation of marine organic nitrogen. Although some deep-sea bacteria are found to produce proteases, there has been no report on protease-secreting Anoxybacillus from marine hydrothermal vent regions. Here, we analyzed the diversity and functions of the proteases, especially the extracellular proteases, of Anoxybacillus caldiproteolyticus 1A02591, a protease-secreting strain isolated from a deep-sea hydrothermal vent sediment of the East Pacific Ocean. Strain 1A02591 is a thermophilic bacterium with a strong protease-secreting ability, which displayed the maximum growth rate (0.139 h^–1) and extracellular protease production (307.99 U/mL) at 55°C. Strain 1A02591 contains 75 putative proteases, including 65 intracellular proteases and 10 extracellular proteases according to signal peptide prediction. When strain 1A02591 was cultured with casein, 12 proteases were identified in the secretome, in which metalloproteases (6/12) and serine proteases (4/12) accounted for the majority, and a thermolysin-like protease of the M4 family was the most abundant, suggesting that strain 1A02591 mainly secreted a thermophilic metalloprotease. Correspondingly, the secreted proteases of strain 1A02591 showed the highest activity at the temperature as high as 70°C, and was inhibited 70% by metalloprotease inhibitor o-phenanthroline and 50% by serine protease inhibitor phenylmethylsulfonyl fluoride. The secreted proteases could degrade different proteins, suggesting the role of strain 1A02591 in organic nitrogen degradation in deep-sea hydrothermal ecosystem. These results provide the first insight into the proteases of an Anoxybacillus strain from deep-sea hydrothermal ecosystem, which is helpful in understanding the function of Anoxybacillus in the marine biogeochemical cycle.

Aequorivita lutea sp. nov., a novel bacterium isolated from the estuarine sediment of the Pearl River in China, and transfer of Vitellibacter todarodis and Vitellibacter aquimaris to the genus Aequorivita as Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov

A Gram-negative, aerobic, rod-shaped, non-motile by gliding bacterium was isolated from the estuarine sediment of the Pearl River in PR China and designated as strain q18^T. Colonies were circular, smooth and yellow on marine agar after 48 h cultivation. Salinity, temperature and pH for optimal growth were 5 % (NaCl), 30 °C and 7, respectively. The 16S rRNA gene sequence of the strain q18^T showed the highest similarity of 97.3 % to the type strain of Aequorivita echinoideorum CC-CZW007^T. 16S rRNA gene-based phylogenetic analysis indicated that strain q18^T grouped into the genus Aequorivita in the family Flavobacteriaceae of the phylum Bacteroidetes, and was distinct from all known species in the genus. Menaquinone (MK-6) was the main respiratory quinone detected in strain q18^T. The major fatty acids were iso-C_15 : 0 and iso-C_17 : 0 3-OH. The polar lipids of strain q18^T mainly comprised phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and one unidentified polar lipid. The G+C content of the genome was ~42.8 mol%. The draft genome size of strain q18^T was 3.3 Mbp. The average nucleotide identity values were around 79.0 % between strain q18^T and reference Aequorivita strains. Based on the polyphasic analysis, strain q18^T was confirmed to represent a novel species of the genus Aequorivita, for which the name Aequorivita lutea sp. nov., is proposed. The type strain is q18^T (=CICC 24821^T=KCTC 72764 ^T). Further, based on the results of phylogenetic, chemotaxonomic and phenotypic analyses, two species previously classified into the genus Vitellibacter, Vitellibacter todarodis Kim et al. 2018 and Vitellibacter aquimaris Thevarajoo et al. 2016, are transferred to the genus Aequorivita as Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov. respectively.

Aequorivita sinensis sp. nov., isolated from sediment of the East China Sea, and reclassification of Vitellibacter todarodis as Aequorivita todarodis comb. nov. and Vitellibacter aquimaris as Aequorivita aquimaris comb. nov

The Gram-strain-negative, rod-shaped, facultatively anaerobic, non-motile bacterial strain, designated S1-10^T, was isolated from marine sediment. Strain S1-10^T grew at 4-42 °C (optimally at 30-35 °C), at pH 7.0-10 (optimally at pH 9) and in the presence of 0.5-8 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S1-10^T was related to the genus Aequorivita and had highest 16S rRNA gene sequence similarity to Aequorivita viscosa 8-1b^T (97.7%). The predominant cellular fatty acids were iso-C_15 : 0 and anteiso-C_15 : 0. The main respiratory quinone was menaquinone 6 (MK-6). The genomic DNA G+C content of strain S1-10^T was 34.6 mol%. The polar lipid profile of strain S1-10^T contained phosphatidylethanolamine, two aminolipids, two glycolipids, one phosphoglycolipid and three unidentified polar lipids. In addition, the maximum values of in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain S1-10^T and A. viscosa CGMCC 1.11023^T were 15.4 and 75.7 %, respectively. Combined data from phenotypic, phylogenetic, isDDH and ANI analyses demonstrated that strain S1-10^T is the representative of a novel species of the genus Aequorivita, for which we propose the name Aequorivita sinensis sp. nov. (type strain S1-10^T=CGMCC 1.12579^T=JCM 19789^T). We also propose that Vitellibacter todarodis and Vitellibacter aquimaris should be transferred into genus Aequorivita and be named Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov., respectively. The type strain of Aequorivita todarodis comb. nov. is MYP2-2^T (= KCTC 62141^T= NBRC 113025^T) and the type strain of Aequorivita aquimaris comb. nov. is D-24^T (=KCTC 42708^T=DSM 101732^T).

Vitellibacter todarodis sp. nov., isolated from intestinal tract of a squid (Todarodes pacificus)

A Gram-stain-negative, non-motile, aerobic and rod-shaped or ovoid bacterial strain, designated MYP2-2^T, was isolated from the intestinal tract of a squid (Todarodes pacificus) collected from the East Sea, South Korea, and subjected to a polyphasic taxonomic study. Strain MYP2-2^T grew optimally at 30-35 °C and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MYP2-2^T belonged to the genus Vitellibacter. Strain MYP2-2^T exhibited 16S rRNA gene sequence similarities of 95.4-96.6 % to the type strains of Vitellibacter species and of less than 94.5 % to the type strains of other recognized species examined. Strain MYP2-2^T contained menaquinone MK-6 as the predominant respiratory quinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain MYP2-2^T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain MYP2-2^T was 41.6 mol%. Differential phenotypic properties, together with its phylogenetic distinctiveness, revealed that strain MYP2-2^T is separated from recognized species of the genus Vitellibacter. On the basis of the data presented, strain MYP2-2^T is considered to represent a novel species of the genus Vitellibacter, for which the name Vitellibacter todarodis sp. nov. is proposed. The type strain is MYP2-2^T (=KCTC 62141^T=NBRC 113025^T).

Genome-Based Taxonomic Classification of Bacteroidetes

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

Vitellibacter echinoideorum sp. nov., isolated from a sea urchin (Tripneustes gratilla)

A Gram-stain-negative, aerobic, rod-shaped, yellow-pigment-producing bacterium (designated strain CC-CZW007(T)) was isolated from seafood samples (sea urchins) at Penghu Island in Taiwan. Strain CC-CZW007(T) grew optimally at pH 7.0 and 30 °C in the presence of 3% (w/v) NaCl. The novel strain shared highest 16S rRNA gene sequence similarity to Vitellibacter vladivostokensis JCM 11732(T) (96.8%), Vitellibacter soesokkakensis KCTC 32536(T) (96.4%), Vitellibacter nionensis KCTC 32420(T) (95.8%) and Vitellibacter aestuarii JCM 15496(T) (95.6%) and lower sequence similarity to members of other genera. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CZW007(T) with respect to other species of the genus Vitellibacter. The major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipid profile was composed of major amounts of phosphatidylethanolamine, unidentified lipids and aminolipids; a moderate amount of aminophospholipid was also detected. The DNA G + C content was 34.7 mol%. The predominant quinone system was menaquinone (MK-6). On the basis of polyphasic taxonomic evidence presented here, strain CC-CZW007(T) is proposed to represent a novel species within the genus Vitellibacter, for which the name Vitellibacter echinoideorum sp. nov. is proposed. The type strain is CC-CZW007(T) ( = BCRC 80886(T) = JCM 30378(T)).