Eleven acid mine drainage (AMD) samples were obtained from southeast of China for the analysis of the microbial communities diversity, and the relationship with geochemical variables and spatial distance by using a ...Eleven acid mine drainage (AMD) samples were obtained from southeast of China for the analysis of the microbial communities diversity, and the relationship with geochemical variables and spatial distance by using a culture-independent 16S rDNA gene phylogenetic analysis approach and multivariate analysis respectively. The principle component analysis (PCA) of geochemical variables shows that eleven AMDs can be clustered into two groups, relative high and low metal rich (RHMR and RLMR) AMDs. Total 1691 clone sequences are obtained and the detrended correspondence analysis (DCA) of operational taxonomic units (OTUs) shows that, ~,-Proteobacteria, Acidobacteria, Actinobacteria, Cyanobacteria, Firmicutes and Nitrospirae are dominant species in RHMR AMDs. In contrast, a-Proteobacteria, fl-Proteobacteria, Planctomycetes and Bacteriodetes are dominant species in RLMR AMD. Results also show that high-abundance putative iron-oxidizing and only putative sulfur-oxidizing microorganisms are found in RHMR AMD. Multivariate analysis shows that both geochemical variables (r=0.429 3, P=-0.037 7) and spatial distance (r=0.321 3, P=-0.018 1) are significantly positively correlated with microbial community and pH, Mg, Fe, S, Cu and Ca are key geochemistry factors in shaping microbial community. Variance partitioning analysis shows that geochemical variables and spatial distance can explain most (92%) of the variation.展开更多
Soil bacteria Sinorhizobium meliloti had enormous agricultural value, due to their ability in fixing nitrogen symbiotically with an important forage crop legume--alfalfa. The aims of the present study were (1) to is...Soil bacteria Sinorhizobium meliloti had enormous agricultural value, due to their ability in fixing nitrogen symbiotically with an important forage crop legume--alfalfa. The aims of the present study were (1) to isolate indigenous S. meliloti from different field sites in lraq; (2) to evaluate the isolates tolerance to induced drought using polyethylene glycol-6000; (3) assessing genetic diversity and genetic relationships among isolates of natural population with drought tolerant abilities. Drought tolerance study revealed vast variations between Sinorhizobium isolates, the highest tolerant isolates to drought were 12 from total thirty (40%), tolerated from -3 up to -4 MPa, while the drought sensitive isolates tolerated up to -1.5 MPa, except isolate Bs 58 which tolerated up to -1 Mpa water potential. The growth declined with the increase of drought stress. Cluster analysis based on Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) of the 16S rDNA showed two divergent groups with 41% similarity, the first group included three drought sensitive isolates (Bs 44, Bs 54 and Bs 58), the second group comprised the rest nine isolates (moderate and high drought tolerant), except for Bs 55 which was drought sensitive isolate, all isolates in the two groups showed no differences between them. The PCR-RFLP of 16S rDNA method revealed a genetic variance between the drought sensitive and tolerant isolates.展开更多
Bacterial diversity of 14 sites of the East China Sea was investigated by culture-dependent methods. The impact of human activities on marine bacteria was primarily studied and characteristics of bacteria communities ...Bacterial diversity of 14 sites of the East China Sea was investigated by culture-dependent methods. The impact of human activities on marine bacteria was primarily studied and characteristics of bacteria communities in different areas were analyzed. A total of 396 strains were obtained. These strains belong to 4 phyla, 9 classes and 146 species according to 16S rDNA sequences alignment. For 32 strains, the 16S rDNA sequences similarities between isolated strains and their most closely related species were lower than 98%. The result indicated that there are abundant microbial diversity and a large number of unknown microbial resources in the East China Sea. Isolated strains were dominated byy-proteobacteria (64%), ct-proteobacteria (18%) and Firmicutes (15%). Actinobacteria and Bacteroidetes were less than 3%. Microbial community composition, diversity and abundance among areas with varies distances from land were different. The far the regions from the land, the lower the Shannon index (H') and the Margalef index (DMg) values were.展开更多
A number of basic and applied questions in ecology and environmental management require the characterization of soil and leaf litter faunal diversity. Recent advances in high-throughput sequencing of barcode-gene ampl...A number of basic and applied questions in ecology and environmental management require the characterization of soil and leaf litter faunal diversity. Recent advances in high-throughput sequencing of barcode-gene amplicons ('metabarcoding') have made it possible to survey biodiversity in a robust and efficient way. However, one obstacle to the widespread adoption of this technique is the need to choose amongst many candidates for bioinformatic processing of the raw sequencing data. We compare three candidate pipelines for the processing of 18S small subunit rDNA metabarcode data from solid substrates: (i) USEARCH/CROP, (ii) Denoiser/UCLUST, and (iii) OCTUPUS. The three pipelines produced reassuringly similar and highly correlated assessments of community composition that are dominated by taxa known to characterize the sampled environments. However, OCTUPUS appears to inflate phylogenetic diversity, because of higher sequence noise. We therefore recommend either the USEARCH/CROP or Denoiser/UCLUST pipelines, both of which can be run within the QIIME (Quantitative Insights Into Microbial Ecology) environment.展开更多
基金Project(2010CB630901) supported by the National Basic Research Program of ChinaProject(50621063) supported by Creative Research Group of China+2 种基金Projects(51104189, 50321402, 50774102) supported by the National Natural Science Foundation of ChinaProject (1343-77341) supported by the Graduate Education Innovative Program of Central South University, ChinaProject(DOE-ER64125) supported by the Department of Energy, Office of Science under the Environmental Remediation Science Program of USA
文摘Eleven acid mine drainage (AMD) samples were obtained from southeast of China for the analysis of the microbial communities diversity, and the relationship with geochemical variables and spatial distance by using a culture-independent 16S rDNA gene phylogenetic analysis approach and multivariate analysis respectively. The principle component analysis (PCA) of geochemical variables shows that eleven AMDs can be clustered into two groups, relative high and low metal rich (RHMR and RLMR) AMDs. Total 1691 clone sequences are obtained and the detrended correspondence analysis (DCA) of operational taxonomic units (OTUs) shows that, ~,-Proteobacteria, Acidobacteria, Actinobacteria, Cyanobacteria, Firmicutes and Nitrospirae are dominant species in RHMR AMDs. In contrast, a-Proteobacteria, fl-Proteobacteria, Planctomycetes and Bacteriodetes are dominant species in RLMR AMD. Results also show that high-abundance putative iron-oxidizing and only putative sulfur-oxidizing microorganisms are found in RHMR AMD. Multivariate analysis shows that both geochemical variables (r=0.429 3, P=-0.037 7) and spatial distance (r=0.321 3, P=-0.018 1) are significantly positively correlated with microbial community and pH, Mg, Fe, S, Cu and Ca are key geochemistry factors in shaping microbial community. Variance partitioning analysis shows that geochemical variables and spatial distance can explain most (92%) of the variation.
文摘Soil bacteria Sinorhizobium meliloti had enormous agricultural value, due to their ability in fixing nitrogen symbiotically with an important forage crop legume--alfalfa. The aims of the present study were (1) to isolate indigenous S. meliloti from different field sites in lraq; (2) to evaluate the isolates tolerance to induced drought using polyethylene glycol-6000; (3) assessing genetic diversity and genetic relationships among isolates of natural population with drought tolerant abilities. Drought tolerance study revealed vast variations between Sinorhizobium isolates, the highest tolerant isolates to drought were 12 from total thirty (40%), tolerated from -3 up to -4 MPa, while the drought sensitive isolates tolerated up to -1.5 MPa, except isolate Bs 58 which tolerated up to -1 Mpa water potential. The growth declined with the increase of drought stress. Cluster analysis based on Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) of the 16S rDNA showed two divergent groups with 41% similarity, the first group included three drought sensitive isolates (Bs 44, Bs 54 and Bs 58), the second group comprised the rest nine isolates (moderate and high drought tolerant), except for Bs 55 which was drought sensitive isolate, all isolates in the two groups showed no differences between them. The PCR-RFLP of 16S rDNA method revealed a genetic variance between the drought sensitive and tolerant isolates.
文摘Bacterial diversity of 14 sites of the East China Sea was investigated by culture-dependent methods. The impact of human activities on marine bacteria was primarily studied and characteristics of bacteria communities in different areas were analyzed. A total of 396 strains were obtained. These strains belong to 4 phyla, 9 classes and 146 species according to 16S rDNA sequences alignment. For 32 strains, the 16S rDNA sequences similarities between isolated strains and their most closely related species were lower than 98%. The result indicated that there are abundant microbial diversity and a large number of unknown microbial resources in the East China Sea. Isolated strains were dominated byy-proteobacteria (64%), ct-proteobacteria (18%) and Firmicutes (15%). Actinobacteria and Bacteroidetes were less than 3%. Microbial community composition, diversity and abundance among areas with varies distances from land were different. The far the regions from the land, the lower the Shannon index (H') and the Margalef index (DMg) values were.
基金supported by Yunnan Province (20080A001)Chinese Academy of Sciences (0902281081,KSCX2-YW-Z-1027)+2 种基金the National Natural Science Foundation of China (31170498)Ministry of Science and Technology of China (2012FY110800)Kunming Institute of Zoology,and the University of East Anglia
文摘A number of basic and applied questions in ecology and environmental management require the characterization of soil and leaf litter faunal diversity. Recent advances in high-throughput sequencing of barcode-gene amplicons ('metabarcoding') have made it possible to survey biodiversity in a robust and efficient way. However, one obstacle to the widespread adoption of this technique is the need to choose amongst many candidates for bioinformatic processing of the raw sequencing data. We compare three candidate pipelines for the processing of 18S small subunit rDNA metabarcode data from solid substrates: (i) USEARCH/CROP, (ii) Denoiser/UCLUST, and (iii) OCTUPUS. The three pipelines produced reassuringly similar and highly correlated assessments of community composition that are dominated by taxa known to characterize the sampled environments. However, OCTUPUS appears to inflate phylogenetic diversity, because of higher sequence noise. We therefore recommend either the USEARCH/CROP or Denoiser/UCLUST pipelines, both of which can be run within the QIIME (Quantitative Insights Into Microbial Ecology) environment.