Cong Sun

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).

The functional characterization and comparison of two single CRD containing C-type lectins with novel and typical key motifs from Portunus trituberculatus

ABSTRACT C‐type lectins are a superfamily of Ca2+‐dependent carbohydrate‐recognition proteins, which play crucial roles in innate immunity including nonself‐recognition and pathogen elimination. In the present study, two single‐CRD containing C‐type lectins were identified from swimming crab Portunus trituberculatus (designated as PtCTL‐2 and PtCTL‐3). The open reading frame (ORF) of PtCTL‐2 encoded polypeptides of 485 amino acids with a signal peptide and a single carbohydrate‐recognition domain (CRD), while PtCTL‐3s ORF encoded polypeptides of 241 amino acids with a coiled‐coil region and a single‐CRD. The key motifs determining carbohydrate binding specificity in PtCTL‐2 and PtCTL‐3 were EPR (Glu‐Pro‐Arg) and QPD (Gln‐Pro‐Asp). EPR is a motif being identified for the first time, whereas QPD is a typical motif in C‐type lectins. Different PAMPs binding features of the two recombinant proteins ‐ PtCTL‐2 (rPtCTL‐2) and PtCTL‐3 (rPtCTL‐3) have been observed in our experiments. rPtCTL‐2 could bind three pathogen‐associated molecular patterns (PAMPs) with relatively high affinity, including glucan, lipopolysaccharide (LPS) and peptidoglycan (PGN), while rPtCTL‐3 could barely bind any of them. However, rPtCTL‐2 could bind seven kinds of microbes and rPtCTL‐3 could bind six kinds in microbe binding assay. Moreover, rPtCTL‐2 and rPtCTL‐3 exhibited similar agglutination activity against Gram‐positive bacteria, Gram‐negative bacteria and fungi in agglutination assay. All these results illustrated that PtCTL‐2 and PtCTL‐3 could function as important pattern‐recognition receptors (PRR) with broad nonself‐recognition spectrum involved in immune defense against invaders. In addition, the results of carbohydrate binding specificity showed that PtCTL‐2 with novel key motif had broad carbohydrate binding specificity, while PtCTL‐3 with typical key motif possessed different carbohydrate binding specificity from the classical binding rule. Furthermore, PtCTL‐2 and PtCTL‐3 could also function as opsonin to enhance encapsulation of hemocytes against Ni‐NTA beads. HighlightsTwo novel C‐type lectins could function as PRR with broad nonself‐recognition ability.PtCTL‐2 with EPR motif had broad carbohydrate binding specificity.PtCTL‐3 with QPD motif had different carbohydrate binding specificity from the classical carbohydrate binding rule.PtCTL‐2 and PtCTL‐3 could enhance encapsulation of hemocytes against nonself particles.

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).

Chryseobacterium lineare sp. nov., isolated from a limpid stream

A Gram-stain-negative, aerobic, non-motile, rod-shaped, yellow-pigmented bacterial strain, XC0022T, isolated from freshwater of a limpid stream in Zhejiang, China, was studied using a polyphasic approach. The phylogenetic analysis based on 16S rRNA gene sequences clearly showed an allocation to the genus Chryseobacterium with the highest sequence similarities of 98.0 % to Chryseobacterium taeanense PHA3-4T, 97.2 % to Chryseobacterium taihuense THMBM1T, 97.1 % to Chryseobacterium rigui CJ16T and 97.1 % to Chryseobacteriumprofundimaris DY46T. 16S rRNA gene sequence similarities to all other species of the genus Chryseobacterium were below 97.0 % (92.3-96.8 %). DNA-DNA hybridization results showed that strain XC0022T was 55.3 %, 49.8 % and 31.1 % related to C. taeanense DSM 17071T, Chryseobacteriumtaichungense DSM 17453T and Chryseobacteriumgleum JCM 2410T, respectively. The quinone system was composed only of MK-6. Strain XC0022T possessed iso-C15 : 0, iso-C17 : 0 3-OH, C18 : 1ω9c and summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c) as the major fatty acids. The polar lipids profile consisted of one phosphatidylethanolamine, one unidentified glycolipid, four unidentified aminolipids and two unidentified lipids. The G+C content of the genomic DNA was 29.7 mol%. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain XC0022T (=KCTC 52364T=MCCC 1K02723T) represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium lineare sp. nov. is proposed.

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).

Kordiimonas pumila sp. nov., isolated from coastal sediment

A novel Gram-stain-negative, translucent-white, aerobic, motile and rod-shaped strain, designated N18T, was isolated from a coastal sediment sample collected in Zhoushan, Zhejiang Province, China. 16S rRNA gene similarity analysis revealed that strain N18T demonstrated highest similarity to the genus Kordiimonas(95.3-97.2 %). Phylogenetic analysis of 16S rRNA gene sequence showed that strain N18T represented a distinct lineage in the clade consisting of the genus Kordiimonas. Strain N18T was found to grow at 10-37 °C (optimum 28 °C), pH 6.0-8.0 (optimum 7.0) and with 1.0-4.0 % (w/v) NaCl (optimum 2.5 %). The G+C content of the genomic DNA was 55.3 mol%. The major cellular fatty acids were identified as summed feature 3 (comprising iso-C15 : 0 2-OH/C16 : 1ω7c), iso-C17 : 1ω9c and iso-C15 : 0. The polar lipid profile of N18T consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified glycolipid, an unidentified aminoglycolipid, an unidentified aminophospholipid and five unidentified lipids. The respiratory quinone was Q-10. Based on chemotaxonomic, morphological and physiological properties, strain N18T could be distinguished from its closest phylogenetic neighbours. Thus, we propose Kordiimonas pumila sp. nov., the type strain is N18T (=MCCC 1K03436T=KCTC 62164T).

Rhodohalobacter barkolensis sp. nov., isolated from a saline lake and emended description of the genus Rhodohalobacter

A Gram-stain-negative, non-motile, aerobic, rod-shaped bacterium, designated 15182T, was isolated from a saline lake in China. The novel strain 15182T was able to grow at 10-40 °C (optimum, 37 °C), pH 7.0-8.0 (optimum, 7.5) and with 0.5-4 % NaCl (optimum, 2-3 %, w/v). The phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 15182T was most closely related to the genus Rhodohalobacter by sharing the highest sequence similarity of 97.0 % with Rhodohalobacter halophilus JZ3C29T. Chemotaxonomic analysis showed that the sole respiratory quinone was menaquinone 7, the major fatty acids included C16 : 0 N alcohol and C16 : 1ω11c. The major polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four uncharacterized glycolipids, one uncharacterized phospholipid and two uncharacterized lipids. The genomic DNA G+C content of the strain 15182T was 42.4 mol%. The average nucleotide identity value between 15182T and R. halophilus JZ3C29T was 75.4 %, and the in silico DNA-DNA hybridization value of the two strains was 19.1 %. On the basis of its phenotypic, chemotaxonomic, genotypic and genomic characteristics presented in this study, strain 15182T is suggested to represent a novel species in the genus Rhodohalobacter, for which the name Rhodohalobacter barkolensis sp. nov. is proposed. The type strain is 15182T (=KCTC 62172T=MCCC 1K03442T). An emended description of the genus Rhodohalobacter is also presented.

Roseovarius nitratireducens sp. nov., a halotolerant bacterium isolated from a saline lake

A Gram-stain-negative, aerobic, non-motile and ovoid- to rod-shaped bacterial strain, designated TFZT, was isolated from a water sample of a saline lake in Xinjiang, China and subjected to polyphasic taxonomic investigation. Strain TFZT grew at 4-42 °C and pH 6.5-10.0 (optimum, 30 °C and pH 7.0) and with 0.5-18.0 % (w/v) NaCl (optimum, 1.5 %). According to phylogenetic analysis based on 16S rRNA gene sequences, strain TFZT was assigned to the genus Roseovarius with highest 16S rRNA gene sequence similarity of 97.5 % to Roseovarius tolerans EL-172T, followed by Roseovarius azorensis SSW084T (96.6 %) and Roseovarius mucosus DSM 17069T (95.5 %). Digital DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) were determined to evaluate the genomic relationship between strain TFZT and R. tolerans EL-172T. Digital DDH estimation (22.80±2.35 %) as well as ANI (80.1 %) proved the dissimilarity of strain TFZT. Chemotaxonomic analysis showed that strain TFZT contained ubiquinone-10 as the predominant respiratory quinone and possessed summed feature 8 (comprising C18 : 1ω7c and/or ω6c) and C16 : 0 as the predominant form of fatty acid. The polar lipids of strain TFZT consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and five unidentified lipids. The DNA G+C content was 65.4 mol% (by genome sequencing). Based on the polyphasic taxonomic characterization, strain TFZT is considered to represent a novel species of the genus Roseovarius, for which the name Roseovariusnitratireducens sp. nov. is proposed (type strain TFZT=MCCC 1K03339T=KCTC 52967T).