Ge-yi Fu

Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci

ABSTRACT The members of the phylum Bacteroidetes are recognized as some of the most important specialists for the degradation of polysaccharides. However, in contrast to research on Bacteroidetes in the human gut, research on polysaccharide degradation by marine Bacteroidetes is still rare. The genus Algibacter belongs to the Flavobacteriaceae family of the Bacteroidetes, and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides of algae. In this work, a novel brown-seaweed-degrading strain designated HZ22 was isolated from the surface of a brown seaweed (Laminaria japonica). On the basis of its physiological, chemotaxonomic, and genotypic characteristics, it is proposed that strain HZ22 represents a novel species in the genus Algibacter with the proposed name Algibacter alginolytica sp. nov. The genome of strain HZ22, the type strain of this species, harbors 3,371 coding sequences (CDSs) and 255 carbohydrate-active enzymes (CAZymes), including 104 glycoside hydrolases (GHs) and 18 polysaccharide lyases (PLs); this appears to be the highest proportion of CAZymes (∼7.5%) among the reported strains in the class Flavobacteria. Seventeen polysaccharide utilization loci (PUL) are predicted to be specific for marine polysaccharides, especially algal polysaccharides from red, green, and brown seaweeds. In particular, PUL N is predicted to be specific for alginate. Taking these findings together with the results of assays of crude alginate lyases, we prove that strain HZ22T can completely degrade alginate. This work reveals that strain HZ22T has good potential for the degradation of algal polysaccharides and that the structure and related mechanism of PUL in strain HZ22T are worth further research.

Hyphobacterium vulgare gen. nov., sp. nov., a novel alpha-proteobacterium isolated from seawater in the South China Sea.

A Gram-stain-negative, aerobic, non-spore-forming, non-motile, oval to rod-shaped, prosthecate bacterium, designated strain WM6T, was isolated from a seawater sample collected from the South China Sea at a depth of 150 m and subjected to a polyphasic taxonomic investigation. Cells of strain WM6T were approximately 0.5-0.6 µm in width and 0.8-1.2 µm in length, and colonies were smooth, circular, convex and whitish yellow. Strain WM6T was found to grow at 10-45 °C (optimum, 30 °C), at pH 6.5-9.0 (optimum, pH 7.5-8.5) and with 1-6 % (w/v) NaCl (optimum, 1-2 %). Chemotaxonomic analysis showed the predominant respiratory quinone and the major fatty acid of strains WM6T were ubiquinone-10 and C18 : 1ω7c, respectively. The polar lipids of strain WM6T were phosphatidylglycerol, glucuronopyranosyldiglyceride, monoglycosyldiglyceride, sulfo-quinovosyl diacylglycerol, seven unknown glycolipids and two unknown lipids. The DNA G+C content of strain WM6T was determined to be 59.8 mol% by HPLC. 16S rRNA gene sequence similarities showed that strain WM6T was related most closely to the genus Maricaulis with a similarity range from 92.3 to 93.8 %. Phylogenetic trees reconstructed with the neighbour-joining and maximum-likelihood methods using mega and maximum-likelihood methods using arb showed that strain WM6T constituted a separated branch in the family Hyphomonadaceae. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain WM6T is clearly distinct from any validly published genus. On the basis of these features, strain WM6T represents a novel species of a new genus with the name Hyphobacterium vulgare gen. nov., sp. nov. The type strain of Hyphobacterium vulgare is WM6T (=MCCC 1K03222T=KCTC 52487T).

Maripseudobacter aurantiacus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a sedimentation basin

A Gram-stain negative, orange-pigmented, aerobic, non-motile and ovoid- to rod-shaped bacterial strain, designated CDA4T, was isolated from a sediment sample collected from the sedimentation basin of a mariculture farm in Zhejiang province, China. The temperature range for growth of strain CDA4T was 15-40 °C, wirrth an optimum at 35 °C. The pH range for growth was 6.0-8.5, with an optimum around pH 7.5. NaCl was required for growth at the concentration range 0.5-5.0 % (w/v), with an optimum at 2.0 % (w/v). Chemotaxonomic analysis indicated that the main respiratory quinone was menaquinone 6 (MK-6), the predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, unknown ECL 13.565 and iso-C17 : 0 3-OH, and the major polar lipids were phosphatidylethanolamine, two unidentified lipids, two unidentified phospholipids and four unidentified aminolipids. The genomic DNA G+C content of strain CDA4T was 38.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CDA4T formed a distinct lineage in the clade of the family Flavobacteriaceae. Based on the polyphasic taxonomic characterization, strain CDA4T is considered to represent a novel species of a new genus, for which the name Maripseudobacter aurantiacus gen. nov., sp. nov. is proposed. The type strain of the type species is CDA4T (=KCTC 52409T=MCCC 1K03210T).

Mesorhizobium oceanicum sp. nov., isolated from deep seawater

A novel Gram-staining-negative, oval-shaped (0.4-0.6×0.8-1.0 µm), non-motile strain without flagella, designated B7T, was isolated from deep seawater in the South China Sea. Strain B7T was able to grow at 25-40 °C (optimum 35 °C), at pH 5.5-9.0 (optimum pH 7.0) and with 0-8 % (w/v) NaCl (optimum 3 %). Chemotaxonomic analysis showed that the predominant isoprenoid quinone was Q-10 and the dominant fatty acids were C19 : 0 cyclo 8c and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c). The polar lipids of strain B7T were diphosphatidyglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unknown aminophospholipid, one unknown glycolipid and three unknown lipids. The DNA G+C content of the genomic DNA was 65.1 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed that strain B7T belongs to the genus Mesorhizobium with similarities ranging from 96.2 to 97.5 %. Phylogenetic analyses of housekeeping genes recA, atpD and glnII indicated that strain B7T represented a distinct evolutionary lineage with the genus Mesorhizobium. OrthoANI values between strain B7T and related strains of the genus Mesorhizobium (<80 %) were lower than the threshold value of 95 % ANI relatedness for species demarcation. Therefore, strain B7T is concluded to represent a novel species of the genus Mesorhizobium, for which the name Mesorhizobium oceanicumsp. nov. is proposed. The type strain is B7T (=KCTC 42783T=MCCC 1K02305T).

Marinibaculum pumilum gen. nov., sp. nov., isolated from seawater

A Gram-stain-negative, facultatively anaerobic, motile and rod-shaped strain, designed H2T, was isolated from the Western Pacific Ocean, and subjected to a taxonomic investigation using a polyphasic approach. Strain H2T grew at 15-40 °C and pH 6.0-9.0 (optimum 37 °C and pH 6.5), and with 1-10 % (w/v) NaCl (optimum 2 %). The predominant respiratory quinone was ubiquinone-10 (Q-10) and the major fatty acids identified were C19 : 0 cyclo ω8c, C18 : 1ω7c, C18 : 0 and 11-methyl-C18 : 1ω7c. The polar lipids of strain H2T consisted of phosphatidylglycerol, one unknown phospholipid, one unknown glycolipid and three unidentified aminolipids. The DNA G+C content was 75.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H2T formed a distinct clade belong to the family Rhodospirillaceae within the Alphaproteobacteria. On the basis of morphological, physiological and chemotaxonomic characteristics, together with the results of phylogenetic analysis, strain H2T represents a novel species in a new genus in the family Rhodospirillaceae, for which the name Marinibaculumpumilum gen. nov., sp. nov. is proposed. The type strain of the type species is H2T(=MCCC 1K02279T=KCTC 42964T).

Marinicaulis flavus gen. nov., sp. nov., a novel stalked bacterium of the family Parvularculaceae

A Gram-stain-negative, aerobic, ovoid or short rod-shaped bacterium with prosthecates and flagella, designated SY-3-19T, was isolated from the surface seawater of the South China Sea, and subjected to a polyphasic taxonomic study. The isolate grew at 4-40 °C and pH 5.0-9.0 (optimum 28 °C and pH 6.5-7.5), and with 0.5-16.0 % (w/v) NaCl (optimum 4 %). It was positive for oxidase and catalase activity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SY-3-19T constituted a separate branch in the family Parvularculaceae, sharing the highest sequence similarities to the genera Aquisalinus (91.9 %), Amphiplicatus (91.1 %) and Parvularcula(91.0-89.4 %). The sole respiratory quinone was ubiquinone-10 and the principal fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), 11 methyl C18 : 1ω7c and C16 : 0. The polar lipids of strain SY-3-19T consisted of phosphatidylglycerol, nine unidentified glycolipids and four unidentified lipids. The DNA G+C content was 60.9 mol%. On the basis of morphological, physiological and chemotaxonomic characteristics, together with the results of phylogenetic analysis, strain SY-3-19T is described as a novel species in a novel genus, for which the name Marinicaulis flavus gen. nov., sp. nov. (type strain SY-3-19T=MCCC 1K03432T=KCTC 62156T) is proposed.

Luteolibacter flavescens sp. nov., isolated from deep seawater

A novel Gram-stain-negative, rod-shaped, non-motile strain, designated GKXT, was isolated from deep seawater. Strain GKXT was able to grow at 20-35 °C (optimum, 25 °C), pH 5.5-9.5 (optimum, 7.5) and 0-4.0 % (w/v) NaCl (optimum, 1.0 %). The major fatty acids were C16 : 1ω9c (15.4 %), C16 : 0 (18.4 %), C14 : 0 (12.0 %), iso-C14 : 0 (30.1 %) and anteiso-C15 : 0 (5.7 %). Strain GKXT contained phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid as the main polar lipids. The only isoprenoid quinone was menaquinone-9. The diagnostic amino acids of the cell-wall peptidoglycan contained meso-diaminopimelic acid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GKXT belonged to the genus Luteolibacter in the family Verrucomicrobiaceae. The 16S rRNA gene sequence of this strain showed 98.0, 93.5 and 93.3 % sequence similarity, respectively, with those of Luteolibacter arcticus MC 3726T, L.uteolibacter pohnpeiensisA4T-83T and L.uteolibacter cuticulihirudinis E100T. DNA-DNA hybridization value of strain GKXT with L. arcticus MC 3726T was 33.1 %. The G+C content of the genomic DNA was 59.5 mol%. On the basis of the genotypic, phenotypic, phylogenetic and chemotaxonomic characteristics, strain GKXT was proposed to represent a novel species of the genus Luteolibacter, named Luteolibacter flavescens sp. nov. (type strain GKXT=MCCC 1K03193T=KCTC 52361T).

Marinobacterium zhoushanense sp. nov., isolated from surface seawater.

A Gram-stain-negative, facultatively anaerobic bacterium, designated WM3T, was isolated from surface seawater collected from the East China Sea. Cells were catalase- and oxidase-positive, short rods and motile by means of a single polar flagellum. Growth occurred at 15-43 °C (optimum 37-40 C), pH 5.5-9.5 (optimum pH 6.5-7.5) and with 0.25-9.0 % (w/v) NaCl (optimum 1.0-1.5 %). Chemotaxonomic analysis showed that the respiratory quinone was ubiquinone-8, the major fatty acids included C16 : 0 (23.6 %), C18 : 1ω7c (26.2 %) and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH, 22.1 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain WM3T was most closely related to the genus Marinobacterium, sharing the highest 16S rRNA gene sequence similarity of 95.5 % with both Marinobacterium litorale KCTC 12756T and Marinobacterium mangrovicola DSM 27697T. The genomic DNA G+C content of the strain WM3T was 55.8 mol%. On the basis of phenotypic, chemotaxonomic and genotypic characteristics presented in this study, strain WM3T is suggested to represent a novel species of the genus Marinobacterium, for which the name Marinobacterium zhoushanense sp. nov. is proposed. The type strain is WM3T (=KCTC 42782T=CGMCC 1.15341T).

Halomonas endophytica sp. nov., isolated from liquid in the stems of Populus euphratica

A Gram-stain-negative, aerobic, motile and rod-shaped bacterium, designated MC28T, was isolated from storage liquid collected from the stems of Populus euphratica in the Xinjiang province of China. The growth range of NaCl concentration was 0.5-6.0 % (w/v), with an optimum at 3.0 % (w/v), the temperature range for growth was 10-45 °C, with an optimum at 40 °C, and the pH range for growth was 6.0-9.0, with an optimum around pH 8.5. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MC28T formed a distinct lineage in the clade of genus Halomonas and is closely related to Halomonas desiderata DSM 9502T (96.4 %), Halomonas heilongjiangensis DSM 26881T (96.2 %) and Halomonas urumqiensis JCM 30202T (95.2 %). The average nucleotide identity, average amino acid identity and in silico DNA-DNA hybridization values between strain MC28T and the references strains were 77.2-80.3, 65.8-76.8 and 21.6-25.6 %, respectively. Chemotaxonomic analysis indicated that the main respiratory quinones were Q-9 and Q-8, the predominant cellular fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω9c, C16 : 0 and C17 : 1ω9c, the major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannoside, an aminophospholipid, an unidentified phospholipid, an unidentified aminolipid and two unidentified lipids. Based on its phenotypic, chemotaxonomic and phylogenetic characteristics, strain MC28T is considered to represent a novel species, for which the name Halomonas endophytica sp. nov. is proposed. The type strain is MC28T (=KCTC 52999T=MCCC 1K03343T).

Emcibacter congregatus sp. nov., isolated from sediment cultured in situ

A Gram-negative, aerobic, motile, rod-shaped, pale-yellow bacterial strain, designated as ZYLT, isolated from a cultured in situ sediment sample collected from the East China Sea coast, was studied using a polyphasic taxonomic approach. Strain ZYLT grew at 4-30 °C (optimum, 25 °C), at pH 6.0-8.5 (pH 7.0) and with 0-7.0 % (w/v) NaCl (2.0 %). Results of phylogenetic analysis based on 16S rRNA gene sequences clearly showed that strain ZYLT and Emcibacter nanhaiensis HTCJW17T, which was most closely related to strain ZYLT with 93.6 % sequence similarity, clustered together. The genomic DNA G+C content was 51.5 % (genome sequence). The quinone system was composed only of ubiquinone-10. Strain ZYLT possessed C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8), iso-C15 : 0 2-OH and/or C16 : 1ω7c (summed feature 3), C14 : 0 2-OH and C14 : 0 as the major fatty acids. The content of summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) in strain ZYLT was far greater than that in E. nanhaiensis. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, three unidentified phospholipids, one unidentified aminolipid and four unidentified lipids. One unidentified aminophospholipid and two unidentified lipids present in strain ZYLT were not found in E. nanhaiensis in this research. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain ZYLT (=KCTC 62328T=JCM 32378T=MCCC 1K03526T) represents a novel species of the genus Emcibacter for which the name Emcibacter congregatus sp. nov. is proposed.