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Ni J.,CAS Wuhan Institute of Hydrobiology | Ni J.,Guangdong Institute of Microbiology | Ni J.,State Key Laboratory of Applied Microbiology | Yan Q.,CAS Wuhan Institute of Hydrobiology | And 2 more authors.
FEMS Microbiology Ecology | Year: 2014

Gut microbiota have attracted extensive attention recently because of their important role in host metabolism, immunity and health maintenance. The present study focused on factors affecting the gut microbiome of grass carp (Ctenopharyngodon idella) and further explored the potential effect of the gut microbiome on metabolism. Totally, 43.39 Gb of screened metagenomic sequences obtained from 24 gut samples were fully analysed. We detected 1228 phylotypes (116 Archaea and 1112 Bacteria), most of which belonged to the phyla Firmicutes, Proteobacteria and Fusobacteria. Totally, 41 335 of the detected open reading frames (ORFs) were matched to Kyoto Encyclopedia of Genes and Genomes pathways, and carbohydrate and amino acid metabolism was the main matched pathway deduced from the annotated ORFs. Redundancy analysis based on the phylogenetic composition and gene composition of the gut microbiome indicated that gut fullness and feeding (i.e. ryegrass vs. commercial feed, and pond-cultured vs. wild) were significantly related to the gut microbiome. Moreover, many biosynthesis and metabolism pathways of carbohydrates, amino acids and lipids were significantly enhanced by the gut microbiome in ryegrass-fed grass carp. These findings suggest that the metabolic role played by the gut microbiome in grass carp can be affected by feeding. These findings contribute to the field of fish gut microbial ecology and also provide a basis for follow-up functional studies. © 2013 Federation of European Microbiological Societies. Source

Xia C.,CAS South China Botanical Garden | Xia C.,University of Chinese Academy of Sciences | Xu M.,University of Chinese Academy of Sciences | Xu M.,Guangdong Institute of Microbiology | And 5 more authors.
Bioresource Technology | Year: 2015

By operating a SMFC in heavily contaminated sediment and analyzing its global organic chemical degradation profile, this study showed a brief trend that SMFC prefers to stimulate the degradation of organic chemicals with higher polarity. As a comparison, adding nitrate as a microbial respiration-based sediment remediation strategy preferred lower polarity chemicals. Both SMFC and nitrate reactors showed high degradation capacity in benzene homologs. These results provide crucial information for the selective and proper application of SMFC in bioremediation. © 2015 Elsevier Ltd. Source

Sun W.,South China University of Technology | Sun W.,Guangdong Institute of Microbiology | Sun W.,State Key Laboratory of Applied Microbiology | Xia C.,Guangdong Institute of Microbiology | And 8 more authors.
Microbes and Environments | Year: 2013

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrification. However, limited information about the characteristics of AOA and AOB in the river ecosystem is available. The distribution and abundance of AOA and AOB in the sediments of the Dongjiang River, a drinking water source for Hong Kong, were investigated by clone library analysis and quantitative real-time PCR. Phylogenetic analysis showed that Group 1.1b-and Group 1.1b-associated sequences of AOA predominated in sediments with comparatively high carbon and nitrogen contents (e.g. total carbon (TC) >13 g kg- sediment, NH4+-N >144 mg kg- sediment), while Group 1.1a-and Group 1.1a-associated sequences were dominant in sediments with opposite conditions (e.g. TC <4 g kg- sediment, NH4+-N <93 mg kg- sediment). Although Nitrosomonas-and Nitrosospira-related sequences of AOB were detected in the sediments, nearly 70% of the sequences fell into the Nitrosomonas-like B cluster, suggesting similar sediment AOB communities along the river. Higher abundance of AOB than AOA was observed in almost all of the sediments in the Dongjiang River, while significant correlations were only detected between the distribution of AOA and the sediment pH and TC, which suggested that AOA responded more sensitively than AOB to variations of environmental factors. These results extend our knowledge about the environmental responses of ammonia oxidizers in the river ecosystem. Source

Yang Y.,South China University of Technology | Yang Y.,Guangdong Institute of Microbiology | Yang Y.,Guangdong Provincial Key Laboratory of Microbial Culture Collection | Yang Y.,State Key Laboratory of Applied Microbiology | And 9 more authors.
Bioresource Technology | Year: 2011

Biofilms formation capacities of Shewanella species in microbial fuel cells (MFCs) and their roles in current generation have been documented to be species-dependent. Understandings of the biofilms growth and metabolism are essential to optimize the current generation of MFCs. Shewanella decolorationis S12 was used in both closed-circuit and open-circuit MFCs in this study. The anodic S. decolorationis S12 biofilms could generate fivefold more current than the planktonic cells, playing a dominant role in current generation. Anodic biofilms viability was sustained at 98 ± 1.2% in closed-circuit while biofilms viability in open-circuit decreased to 72 ± 7% within 96. h. The unviable domain in open-circuit MFCs biofilms majorly located at the inner layer of biofilm. The decreased biofilms viability in open-circuit MFCs could be recovered by switching into closed-circuit, indicating that the current-generating anode in MFCs could serve as a favorable electron acceptor and provide sufficient energy to support cell growth and metabolism inside biofilms. © 2011 Elsevier Ltd. Source

Zhu C.,South China University of Technology | Zhu C.,Guangdong Institute of Microbiology | Zhu C.,State Key Laboratory of Applied Microbiology | Sun G.,Guangdong Institute of Microbiology | And 7 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2014

Six Gram-stain-positive, motile, filamentous and/or rod-shaped, spherical spore-forming bacteria (strains GY32T, L31, F01, F03, F06 and F07) showing polybrominated diphenyl ether transformation were investigated to determine their taxonomic status. After spore germination, these organisms could grow more than one hundred microns long as intact single cells and then divide into rod cells and form endospores in 33 h. The cell-wall peptidoglycan of these strains was type A4α, the predominant menaquinone was MK-7 and the major fatty acids were iso-C16 : 0, iso-C15 : 0and C16 : 1ω7C. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were detected in the polar lipid profile. Analysis of the 16S rRNA gene sequences indicated that these strains should be placed in the genus Lysinibacillus and they were most closely related to Lysinibacillus sphaericus DSM 28T(99% 16S rRNA gene sequence similarity). The gyrB sequence similarity and DNA-DNA relatedness between strain GY32Tand L. sphaericus JCM 2502Twere 81% and 52 %, respectively. The G+C content of the genomic DNA of strain GY32Twas 43.2 mol%. In addition, strain GY32Tshowed differences in nitrate reduction, starch and gelatin hydrolysis, carbon resource utilization and cell morphology. The phylogenetic distance from its closest relative measured by DNA-DNA relatedness and DNA G+C content, and its phenotypic properties demonstrated that strain GY32T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus varians sp. nov. is proposed. The type strain is GY32T(=NBRC 109424T=CGMCC 1.12212T=CCTCC M 2011307T). © 2014 IUMS. Source

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