Xiaochong Shi

Spatial Variations in Microbial Community Composition in Surface Seawater from the Ultra-Oligotrophic Center to Rim of the South Pacific Gyre

Surface seawater in the South Pacific Gyre (SPG) is one of the cleanest oceanic environments on earth, and the photosynthetic primary production is extremely low. Despite the ecological significance of the largest aquatic desert on our planet, microbial community composition in the ultra-oligotrophic seawater remain largely unknown. In this study, we collected surface seawater along a southern transect of the SPG during the Integrated Ocean Drilling Program (IODP) Expedition 329. Samples from four distinct sites (Sites U1368, U1369, U1370 and U1371) were examined, representing ∼5400 kilometers of transect line from the gyre heart to the edge area. Real-time PCR analysis showed 16S rRNA gene abundance in the gyre seawater, ranging from 5.96×105 to 2.55×106 copies ml−1 for Bacteria and 1.17×103 to 1.90×104 copies ml−1 for Archaea. The results obtained by statistic analyses of 16S rRNA gene clone libraries revealed the community composition in the southern SPG area: diversity richness estimators in the gyre center (Sites U1368 & U1369) are generally lower than those at sites in the gyre edge (Sites U1370 & U1371) and their community structures are clearly distinguishable. Phylogenetic analysis showed the predominance of Proteobacteria (especially Alphaproteobacteria) and Cyanobacteria in bacterial 16S rRNA gene clone libraries, whereas phylotypes of Betaproteobacteria were only detected in the central gyre. Archaeal 16S rRNA genes in the clone libraries were predominated by the sequences of Marine Group II within the Euryarchaeota, and the Crenarchaeota sequences were rarely detected, which is consistent with the real-time PCR data (only 9.9 to 22.1 copies ml−1). We also performed cultivation of heterotrophic microbes onboard, resulting in 18.9% of phylogenetically distinct bacterial isolates at least at the species level. Our results suggest that the distribution and diversity of microbial communities in the SPG surface seawater are closely related to the ultra-oligotrophic oceanographic features in the Pacific Ocean.

Evaluation of a new high-throughput method for identifying quorum quenching bacteria

Quorum sensing (QS) is a population-dependent mechanism for bacteria to synchronize social behaviors such as secretion of virulence factors. The enzymatic interruption of QS, termed quorum quenching (QQ), has been suggested as a promising alternative anti-virulence approach. In order to efficiently identify QQ bacteria, we developed a simple, sensitive and high-throughput method based on the biosensor Agrobacterium tumefaciens A136. This method effectively eliminates false positives caused by inhibition of growth of biosensor A136 and alkaline hydrolysis of N-acylhomoserine lactones (AHLs), through normalization of β-galactosidase activities and addition of PIPES buffer, respectively. Our novel approach was successfully applied in identifying QQ bacteria among 366 strains and 25 QQ strains belonging to 14 species were obtained. Further experiments revealed that the QQ strains differed widely in terms of the type of QQ enzyme, substrate specificity and heat resistance. The QQ bacteria identified could possibly be used to control disease in aquaculture.

Description of Thalassotalea piscium gen. nov., sp. nov., isolated from flounder (Paralichthys olivaceus), reclassification of four species of the genus Thalassomonas as members of the genus Thalassotalea gen. nov. and emended description of the genus Thalassomonas.

A Gram-staining-negative, aerobic, rod-shaped bacterium, designated strain T202(T), was isolated from the gill of a cultured flounder (Paralichthys olivaceus). Based on 16S rRNA gene sequence similarity, strain T202(T) was a member of the family Colwelliaceae and shared 93.32-96.58 % similarity with type strains of all members of the most closely related genus Thalassomonas. Phylogenetically, the isolate shared a root with the type strains of four marine species, Thalassomonas agariperforans M-M1(T), Thalassomonas agarivorans TMA1(T), Thalassomonas loyana CBMAI 722(T) and Thalassomonas ganghwensis JC2041(T). Optimal growth occurred in the presence of 2-4 % (w/v) NaCl, at pH 7.0-8.0 and at 28 °C. Ubiquinone 8 (Q-8) was the predominant respiratory quinone. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω9c and C17 : 1ω8c. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain T202(T) was 37 mol%. On the basis of polyphasic analysis, especially the phylogenetic relationships and the lower DNA G+C content, strain T202(T) is considered to represent a novel species in a new genus, for which the name Thalassotalea piscium gen. nov., sp. nov. is proposed. The type strain of Thalassotalea piscium is T202(T) ( = JCM 18590(T) = DSM 26287(T) = KCTC 32144(T)). Because Thalassomonas agariperforans M-M1(T), Thalassomonas agarivorans TMA1(T), Thalassomonas loyana CBMAI 722(T) and Thalassomonas ganghwensis JC2041(T) formed a phylogenetic group together with strain T202(T) that was clearly separated from other known strains of Thalassomonas, these four species are reclassified as members of the genus Thalassotalea as Thalassotalea agariperforans comb. nov. (type strain M-M1(T) = KCTC 23343(T) = CCUG 60020(T)), Thalassotalea agarivorans comb. nov. (type strain TMA1(T) = BCRC 17492(T) = JCM 13379(T) = DSM 19706(T)), Thalassotalea loyana comb. nov. (type strain CBMAI 722(T) = LMG 22536(T)) and Thalassotalea ganghwensis comb. nov. (type strain JC2041(T) = IMSNU 14005(T) = KCTC 12041(T) = DSM 15355(T)). The type species of the genus Thalassotalea is Thalassotalea ganghwensis gen. nov., comb. nov. An emended description of the genus Thalassomonas is also proposed.

Flaviramulus ichthyoenteri sp. nov., an N-acylhomoserine lactone-degrading bacterium isolated from the intestine of a flounder (Paralichthys olivaceus), and emended descriptions of the genus Flaviramulus and Flaviramulus basaltis.

A Gram-stain-negative, strictly aerobic, yellow-pigmented, rod-shaped and N-acylhomoserine lactone-degrading bacterium, designated strain Th78(T), was isolated from the intestine of a cultured flounder (Paralichthys olivaceus). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Th78(T) belonged to the genus Flaviramulus (family Flavobacteriaceae) and showed the highest 16S rRNA gene sequence similarity to Flaviramulus basaltis H35(T) (96.70 %). Optimal growth occurred in the presence of 2-3 % (w/v) NaCl, at pH 7.0-8.0 and at 28 °C. The major fatty acids were iso-C15 : 0 3-OH, iso-C15 : 1 G and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and three unidentified polar lipids. Menaquinone 6 (MK-6) was the only respiratory quinone. The DNA G+C content of strain Th78(T) was 31.5 mol%. On the basis of polyphasic analysis, strain Th78(T) is considered to represent a novel species of the genus Flaviramulus, for which the name Flaviramulus ichthyoenteri sp. nov. is proposed. The type strain is Th78(T) ( = JCM 18634(T) = KCTC 32142(T) = DSM 26285(T)). Emended descriptions of the genus Flaviramulus and Flaviramulus basaltis are also proposed.

Phenotypic diversity of Edwardsiella tarda isolated from different origins

Aims:  To evaluate the diversity of phenotypic characteristics among isolates of Edwardsiella tarda from various origins.

Xuhuaishuia manganoxidans gen. nov., sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediments from the Pacific Polymetallic Nodule Province.

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped, manganese-oxidizing bacterial strain, designated DY6-4T, was isolated from the surface sediment of the Pacific Clarion-Clipperton Fracture Zone. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain DY6-4T formed a lineage within the family Rhodobacteraceae and was distinct from the most closely related genera Sulfitobacter, Aliiroseovarius and Loktanella (94.0-96.0 %, 93.4-96.0 % and 91.9-95.9 % 16S rRNA gene sequence similarity, repectively). Optimal growth occurred in the presence of 1 % (w/v) NaCl, at pH 7.0 and at 28 °C. Strain DY6-4T contained ubiquinone-10 (Q-10) as the major ubiquinone, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and one unidentified aminolipid as the predominant polar lipids, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the main fatty acids (>10 % of the total). The DNA G+C content of strain DY6-4T was 66.6 mol%. On the basis of the polyphasic analyses, strain DY6-4T is considered to represent a novel species of a novel genus in the Roseobacter clade of the family Rhodobacteraceae, for which the name Xuhuaishuia manganoxidans gen. nov., sp. nov. is proposed. The type strain is DY6-4T ( = KCTC 42421T = MCCC 1K00502T).

Roseivivax marinus sp. nov., isolated from deep water.

A Gram-stain-negative, strictly aerobic, non-motile, cream, long rod-shaped bacterium, designated strain ZL136(T), was isolated from deep water of the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain belonged to the genus Roseivivax with highest sequence similarity to Roseivivax halodurans OCh 239(T) (97.0%), followed by Roseivivax isoporae sw-2(T) (96.9%). Growth occurred at 4-37 °C (optimum 32 °C), pH 6.0-10.0 (optimum 8.0) and in the presence of 0-12% (w/v) NaCl (optimum 3-4%) in marine broth 2216. Strain ZL136(T) did not produce bacteriochlorophyll a. The predominant fatty acids were C(18 : 1)ω7c and/or C(18 : 1)ω6c, C(18 : 0), C(16 : 0) and 11-methyl C(18 : 1)ω7c. The major polar lipids of ZL136(T) were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified lipid. The major respiratory quinone was ubiquinone Q-10. The genomic DNA G+C content of strain ZL136(T) was 67.0 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain ZL136(T) was classified as a representative of a novel species in the genus of Roseivivax, for which the name Roseivivax marinus sp. nov. is proposed. The type strain is ZL136(T) ( = JCM 19386(T) = KCTC 32470(T)).

Salipiger nanhaiensis sp. nov., a bacterium isolated from deep sea water

A Gram-stain-negative, facultatively anaerobic, chemoheterotrophic, moderately halophilic, exopolysaccharide (EPS)-producing, cream, non-motile and rod-shaped bacterium, designated strain ZH114(T), was isolated from deep water of the South China Sea, and was subjected to a polyphasic taxonomic study. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that this strain belongs to the genus Salipiger with the highest sequence similarity to Salipiger mucescens LMG 22090(T) (96.83%), followed by Pseudodonghicola xiamenensis LMG 24574(T) (96.12%). Growth occurred at 4-37 °C (optimum 32 °C), pH 6.0-10.0 (optimum pH 9.0-10.0) and in the presence of 0-19% NaCl (w/v) (optimum 6%, w/v). It did not produce poly-β-hydroxyalkanoate granules or bacteriochlorophyll a. Acid was produced from glycerol, erythrose, ribose, D-xylose, galactose, glucose, fructose, mannitol, cellobiose, maltose, lactose, melibiose, turanose, D-lyxose, D-tagatose, D-fucose, D-arabitol and L-arabitol after inoculating for 24 h and weakly positive results were also detected after 48 h in API 50CH strips with D-arabinose, L-arabinose, L-xylose, adonitol, mannose, aesculin, salicin, sucrose, mycose and L-fucose. The predominant fatty acids were C(18 : 1)ω7c and/or C(18 : 1)ω6c, C(16 : 0), C(18 : 0) and 11-methyl C(18 : 1)ω7c. The major polar lipids of ZH114(T) were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The major respiratory quinone was ubiquinone Q-10. The genomic DNA G+C content of strain ZH114(T) was 63.8 mol%. Based on this phenotypic, chemotaxonomic and phylogenetic analysis, strain ZH114(T) should be classified as a representative of a novel species of the genus Salipiger , for which the name Salipiger nanhaiensis sp. nov. is proposed. The type strain is ZH114(T) ( = JCM 19383(T) = KCTC 32468(T)).

Ferrimonas sediminum sp. nov., isolated from coastal sediment of an amphioxus breeding zone

A Gram-stain-negative, facultatively anaerobic rod with a polar flagellum, designated strain JYr13(T), was isolated from coastal sediment of an amphioxus breeding zone located in Qingdao, China. The isolate utilized Fe(III) oxyhydroxide, Fe(III) citrate, SeO3(2-) and SeO4(2-) as electron acceptors. Strain JYr13(T) grew optimally at 25-28 °C, pH 7.0-8.0 and in presence of 3 % (w/v) NaCl. Strain JYr13(T) contained menaquinone-7 and ubiquinones Q-7 and Q-8 as the predominant isoprenoid quinones, and C18 : 1ω9c, iso-C15 : 0, C17 : 1ω8c and C16 : 0 as the major fatty acids. The DNA G+C content of strain JYr13(T) was 59 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the closest phylogenetic neighbour of strain JYr13(T) was Ferrimonas kyonanensis DSM 18153(T) (96.0 % 16S rRNA gene sequence similarity). Based on the phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain JYr13(T) is considered to represent a novel species of the genus Ferrimonas, for which the name Ferrimonas sediminum sp. nov. is proposed. The type strain is JYr13(T) ( = DSM 23317(T) = LMG 25564(T)).

Flavobacterium ovatum sp. nov., a marine bacterium isolated from an Antarctic intertidal sandy beach

A rod-shaped, Gram-staining-negative, strictly aerobic, non-motile bacterium with no flexirubin-type pigment, designated as W201ET, was isolated from an intertidal sandy beach in Antarctica. The organism formed faintly yellow, round colonies on marine agar 2216E. The strain required sea salts for growth and grew optimally in the presence of 2 % (w/v) NaCl at pH 7.0, 20 °C. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain W201ET belonged to the genus Flavobacterium and showed the highest sequence similarity to Flavobacterium algicola NBRC 102673T (96.5 %). The major respiratory quinone was menaquinone 6, and the predominant fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH and summed feature 3 (which comprises C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids of strain W201ET comprised one phosphatidylethanolamine, two unidentified aminolipids and three unidentified polar lipids. The DNA G+C content of strain W201ET was 34.1 mol%. On the basis of the polyphasic analyses, this isolate was considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium ovatum sp. nov. is proposed. The type strain is W201ET (=KCTC 52693T=MCCC 1K03251T=CGMCC 1.16053T).