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 cu...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 1 691 clone sequences are obtained and the detrended correspondence analysis (DCA) of operational taxonomic units (OTUs) shows that, γ-Proteobacteria, Acidobacteria, Actinobacteria, Cyanobacteria, Firmicutes and Nitrospirae are dominant species in RHMR AMDs. In contrast, α-Proteobacteria, β-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
Our previously described environmental DNA extraction method has been widely used in environmental microbial community analysis.However,residual humic substances may remain with obtained environmental DNA,which interf...Our previously described environmental DNA extraction method has been widely used in environmental microbial community analysis.However,residual humic substances may remain with obtained environmental DNA,which interferes downstream molecular analyses.To remedy this situation,two DNA extraction buffers (PIPES and Tris-HCl) and four purification strategies including our new modified low melting point gel purification method and three commercial kits from QIAEX,Omega and Promega were evaluated with diverse soil samples.The PIPES buffer (pH 6.5) is found to be more effective for removing the humic substances,but it leads to lower DNA yield and causes more severe DNA shearing than using the Tris-HCl buffer (pH 8.0).Gel purification and the Promega purification kit achieve much higher DNA recoveries than QIAEX or Omega kit,and higher purity of DNA is obtained by gel purification than by the Promega kit with both DNA extraction buffers mentioned above.Considering all results together,two alternative methods for DNA extraction and purification are proposed:one uses Tris-HCl buffer extraction and gel purification as the primary approach when the amount of soil or biomass is not a major concern,and the other uses PIPES buffer extraction and the Promega kit purification when severe DNA shearing and/or limited biomass occurs.Purified DNA samples by both methods are amenable for use as templates for whole community genome amplifications and PCR amplifications of bacterial 16S rRNA genes.It is demonstrated that these two alternative methods could be applied to a wide variety of environmental samples.展开更多
Biofilm systems are effective for biosorption of metal ions. Shewanella oneidensis MR-1, a Gram-negative facultative anaerobe, is a natural pellicle-like biofilm former. The mechanisms of pellicle formation by S. onei...Biofilm systems are effective for biosorption of metal ions. Shewanella oneidensis MR-1, a Gram-negative facultative anaerobe, is a natural pellicle-like biofilm former. The mechanisms of pellicle formation by S. oneidensis MR-1 have not yet been understood. 17 S. oneidensis MR-1 deletion mutants, including 12 c-type cytochromes were generated and tested if they were involved in pellicle formation. The results show that △SO4666, △SO1777, △SO1782, △SO2361 and △SO2363 have varying deficiency in pellicle formation. The deletion mutant △SO4666 cannot form a pellicle under non-shake conditions, suggesting that it may play an important role in pellicle formation by S. oneidensis MR-1. Overall, these data suggest a very complex picture of aerobic respiration by S. oneidensis MR-1.展开更多
尽管微生物-气候的相互作用已得到越来越多的研究者和决策者的认可,但微生物的高多样性和对气候环境变化多变量的响应导致预测微生物在未来气候背景下的分布格局非常困难.本研究依托于中国土壤微生物组计划,基于采集自中国东部森林的160...尽管微生物-气候的相互作用已得到越来越多的研究者和决策者的认可,但微生物的高多样性和对气候环境变化多变量的响应导致预测微生物在未来气候背景下的分布格局非常困难.本研究依托于中国土壤微生物组计划,基于采集自中国东部森林的1600多个样品的16S r RNA基因测序数据,首先证实了微生物群落组成和多样性的纬度分布规律且温度对微生物群落组成有显著的直接作用.其次,利用核心微生物代替整体群落来进行多样性的缩减,并将这些核心微生物根据其对环境的偏好性划分为不同的生态集群,这些生态集群在空间上的热点区域,即高丰度区域相互不重叠.此外,通过Cubist模型预测未来不同气候变化情景下(RCP2.6和RCP8.5)各生态集群的丰度变化并将其投影到中国森林生态系统分布区域,通过与现在的分布格局做对比得到增温驱动的生态集群空间分布格局的变化.这些变化一方面可以指示集群内微生物对未来气候变化的适应性,另一方面考虑到每一类生态集群所代表的环境偏好性,这些变化也可进一步用来指示未来气候变化背景下土壤属性的变化.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 1 691 clone sequences are obtained and the detrended correspondence analysis (DCA) of operational taxonomic units (OTUs) shows that, γ-Proteobacteria, Acidobacteria, Actinobacteria, Cyanobacteria, Firmicutes and Nitrospirae are dominant species in RHMR AMDs. In contrast, α-Proteobacteria, β-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.
基金Project(51104189)supported by the National Natural Science Foundation of ChinaProject(2010CB630901)supported by the National Basic Research Program of China+1 种基金Project(1343-77341)supported by the Graduate Education Innovative Program of Central South University,ChinaProject(DOE-ER64125)supported by Department of Energy,Office of Science under the Environmental Remediation Science Program of the United States
文摘Our previously described environmental DNA extraction method has been widely used in environmental microbial community analysis.However,residual humic substances may remain with obtained environmental DNA,which interferes downstream molecular analyses.To remedy this situation,two DNA extraction buffers (PIPES and Tris-HCl) and four purification strategies including our new modified low melting point gel purification method and three commercial kits from QIAEX,Omega and Promega were evaluated with diverse soil samples.The PIPES buffer (pH 6.5) is found to be more effective for removing the humic substances,but it leads to lower DNA yield and causes more severe DNA shearing than using the Tris-HCl buffer (pH 8.0).Gel purification and the Promega purification kit achieve much higher DNA recoveries than QIAEX or Omega kit,and higher purity of DNA is obtained by gel purification than by the Promega kit with both DNA extraction buffers mentioned above.Considering all results together,two alternative methods for DNA extraction and purification are proposed:one uses Tris-HCl buffer extraction and gel purification as the primary approach when the amount of soil or biomass is not a major concern,and the other uses PIPES buffer extraction and the Promega kit purification when severe DNA shearing and/or limited biomass occurs.Purified DNA samples by both methods are amenable for use as templates for whole community genome amplifications and PCR amplifications of bacterial 16S rRNA genes.It is demonstrated that these two alternative methods could be applied to a wide variety of environmental samples.
基金Project(50321402) supported by Chinese Science Foundation for Distinguished GroupProject(30428014) supported by National Science Fund for Distinguished Young Scholars in Hong Kong and Abroad
文摘Biofilm systems are effective for biosorption of metal ions. Shewanella oneidensis MR-1, a Gram-negative facultative anaerobe, is a natural pellicle-like biofilm former. The mechanisms of pellicle formation by S. oneidensis MR-1 have not yet been understood. 17 S. oneidensis MR-1 deletion mutants, including 12 c-type cytochromes were generated and tested if they were involved in pellicle formation. The results show that △SO4666, △SO1777, △SO1782, △SO2361 and △SO2363 have varying deficiency in pellicle formation. The deletion mutant △SO4666 cannot form a pellicle under non-shake conditions, suggesting that it may play an important role in pellicle formation by S. oneidensis MR-1. Overall, these data suggest a very complex picture of aerobic respiration by S. oneidensis MR-1.
基金National Key Basic Research Program of China(No.2013CB956601,2013CB956000)National High Technology Research and Development Program of China(863 Program,No.2012AA061401)National Natural Science Foundation of China(No.41471202,41171201,41230750,41430856)
基金supported by the Strategic Priority Research Program of Chinese Academy of Sciences(XDB15010300)the National Science Foundation of China(U1602234,41807316,41471218,41501282,and 31870467)+1 种基金the CAS 135 project(2017XTBG-F01)the National Key Research and Development Program(2016YFC0500702)。
文摘尽管微生物-气候的相互作用已得到越来越多的研究者和决策者的认可,但微生物的高多样性和对气候环境变化多变量的响应导致预测微生物在未来气候背景下的分布格局非常困难.本研究依托于中国土壤微生物组计划,基于采集自中国东部森林的1600多个样品的16S r RNA基因测序数据,首先证实了微生物群落组成和多样性的纬度分布规律且温度对微生物群落组成有显著的直接作用.其次,利用核心微生物代替整体群落来进行多样性的缩减,并将这些核心微生物根据其对环境的偏好性划分为不同的生态集群,这些生态集群在空间上的热点区域,即高丰度区域相互不重叠.此外,通过Cubist模型预测未来不同气候变化情景下(RCP2.6和RCP8.5)各生态集群的丰度变化并将其投影到中国森林生态系统分布区域,通过与现在的分布格局做对比得到增温驱动的生态集群空间分布格局的变化.这些变化一方面可以指示集群内微生物对未来气候变化的适应性,另一方面考虑到每一类生态集群所代表的环境偏好性,这些变化也可进一步用来指示未来气候变化背景下土壤属性的变化.
