Showing papers by "Min Wu published in 2015"

Ecological functions of uncultured microorganisms in the cobalt-rich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing

Abstract: Cobalt-rich ferromanganese is an important seafloor mineral and is abundantly present in the seamount crusts. Such crusts form potential hotspots for biogeochemical activity and microbial diversity, yet our understanding of their microbial communities is lacking. In this study, a cultivation-independent approach was used to recover genomic information and derive ecological functions of the microbes in a sediment sample collected from the cobalt-rich ferromanganese crust of a seamount region in the central Pacific. A total of 78 distinct clones were obtained by fosmid library screening with a 16S rRNA based PCR method. Proteobacteria and MGI Thaumarchaeota dominated the bacterial and archaeal 16S rRNA gene sequence results in the microbial community. Nine fosmid clones were sequenced and annotated. Numerous genes encoding proteins involved in metabolic functions and heavy metal resistance were identified, suggesting alternative metabolic pathways and stress responses that are essential for microbial survival in the cobalt-rich ferromanganese crust. In addition, genes that participate in the synthesis of organic acids and exoploymers were discovered. Reconstruction of the metabolic pathways revealed that the nitrogen cycle is an important biogeochemical process in the cobalt-rich ferromanganese crust. In addition, horizontal gene transfer (HGT) events have been observed, and most of them came from bacteria, with some occurring in archaea and plants. Clone W4-93a, belonging to MGI Thaumarchaeota, contained a region of gene synteny. Comparative analyses suggested that a high frequency of HGT events as well as genomic divergence play important roles in the microbial adaption to the deep-sea environment.

Sinimarinibacterium flocculans gen. nov., sp. nov., a gammaproteobacterium from offshore surface seawater.

Abstract: Two aerobic, rod-shaped, non-motile, non-sporulating and Gram-staining-negative bacterial strains, namely NH6-24T and Za3-11, were isolated from the surface seawater of the South China Sea and the estuary of the Yangtze River, respectively. The two isolates grew at 14–44 °C (optimum 37–40 °C) and pH 6.0–8.5 (optimum pH 7.0–7.5). The sea salt ranges for growth were 0.5–10 % (w/v) (optimum 1–2.5 %) for strain NH6-24T and 0–12 % (w/v) (optimum 0.5–4.5 %) for strain Za3-11.Both strains could grow in the absence of NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates showed closest affinity to the genera Fontimonas (96.0 %) and Solimonas (94.1–95.1 %) and formed a single lineage in the cluster of the family Solimonadaceae. The predominant isoprenoid quinone was ubiquinone-8.The major fatty acids were C18 : 1ω7c, iso-C16 : 0 and C16 : 0.The dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 65 mol%. Based on the polyphasic taxonomic characterization, strains NH6-24T and Za3-11 are considered to represent a novel species of a novel genus, for which the name Sinimarinibacterium flocculans gen. nov., sp. nov. is proposed. The type strain of the type species is NH6-24T ( = CGMCC 1.10815T = JCM 17607T) and an additional strain is Za3-11 ( = CGMCC 1.10816 = JCM 17606).

Maribacter thermophilus sp. nov., isolated from an algal bloom in an intertidal zone, and emended description of the genus Maribacter.

Abstract: A novel facultatively anaerobic, Gram-stain-negative bacterium, designated strain HT7-2T, was isolated from Ulva prolifera collected from the intertidal zone of Qingdao sea area, China, during its bloom. Cells were rod-shaped (1.9–3.5×0.4–0.6 µm), non-sporulating and motile by gliding. Strain HT7-2T was able to grow at 4–50 °C (optimum 40–42 °C), pH 5.5–8.5 (optimum pH 7.0), 0–8 % (w/v) NaCl (optimum 2–3 %) and 0.5–10 % (w/v) sea salts (optimum 2.5 %). The genomic DNA G+C content was 38.8 mol%. The phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HT7-2T belonged to the genus Maribacter with sequence similarity values of 94.5–96.6 %, and was most closely related to Maribacter aestuarii GY20T (96.6 %). Chemotaxonomic analysis showed that the main isoprenoid quinone was MK-6 and the major fatty acids were iso-C15 : 0 and unknown equivalent chain-length 13.565. The polar lipids of strain HT7-2T consisted of one phosphatidylethanolamine, four unidentified lipids and one unidentified aminolipid. On the basis of the phenotypic, phylogenetic and chemotaxonomic characteristics, strain HT7-2T ( = CGMCC 1.12207T = JCM 18466T) is concluded to represent a novel species of the genus Maribacter , for which the name Maribacter thermophilus sp. nov. is proposed. An emended description of the genus Maribacter is also proposed.

Draft Genome Sequence of Microbacterium profundi Shh49T, an Actinobacterium Isolated from Deep-Sea Sediment of a Polymetallic Nodule Environment

Abstract: Microbacterium profundi strain Shh49(T) was isolated from deep-sea sediment from a polymetallic nodule area located in the East Pacific Ocean. Strain Shh49(T) contains genes related to the reduction/oxidation of metals. It has potential application in the bioremediation of heavy metal-contaminated environments.

Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus.

Abstract: A taxonomic study was carried out on strain YN3T, which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0–10.0 and 4–32 °C in the presence of 0–9.0 % (w/v) NaCl. Strain YN3T was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3T should be assigned to the genus Gilvimarinus . ‘Gilvimarinus agarilyticus’ KCTC 23325 and Gilvimarinus chinensis QM42T had the closest phylogenetic relationship to strain YN3T, and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA–DNA hybridization studies, we propose that strain YN3T represents a novel species of the genus Gilvimarinus , for which the name Gilvimarinus polysaccharolyticus sp. nov. is proposed. The type strain is YN3T ( = KCTC 32438T = JCM 19198T). An emended description of the genus Gilvimarinus is also presented.

Roseivirga marina sp. nov., isolated from seawater

Abstract: Strain PSRT was isolated from seawater of the Pacific Ocean. Cells of the strain were Gram-stain-negative, strictly aerobic, rod-shaped and motile by gliding. Growth was observed at 4–40 °C (optimum 25–30 °C), at pH 6.0–9.5 (optimum pH 7.0–7.5) and with 0.5–8 % (w/v) NaCl (optimum 2–3 %). The major fatty acids were iso-C15 : 1 G (18.9 %), iso-C15 : 0 (26.3 %) and iso-C17 : 0 3-OH (17.9 %). The predominant isoprenoid quinone was MK-7, and the DNA G+C content was 49.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PSRT was most closely related to Roseivirga spongicola UST030701-084T (96.9 % 16S rRNA gene sequence similarity), and they formed a distinct clade in neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees with significant bootstrap supports. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain PSRT represents a novel species of the genus Roseivirga, for which the name Roseivirga marina sp. nov. is proposed. The type strain is PSRT ( = MCCC 1K00459T = KCTC 42444T).

Draft genome sequence of Halopiger salifodinae KCY07-B2 T , an extremly halophilic archaeon isolated from a salt mine

Abstract: Halopiger salifodinae strain KCY07-B2T, isolated from a salt mine in Kuche county, Xinjiang province, China, belongs to the family Halobacteriaceae. It is a strictly aerobic, pleomorphic, rod-shaped, Gram-negative and extremely halophilic archaeon. In this work, we report the features of the type strain KCY07-B2T, together with the draft genome sequence and annotation. The draft genome sequence is composed of 83 contigs for 4,350,718 bp with 65.41 % G + C content and contains 4204 protein-coding genes and 50 rRNA genes.