变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)因其具有可靠性强、易操作、可同时分析多个样品等优点,目前已经成为一种普遍的快速指纹分析分子技术,广泛应用于微生物群落组成、多样性及种群动态等研究。笔者综述了D...变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)因其具有可靠性强、易操作、可同时分析多个样品等优点,目前已经成为一种普遍的快速指纹分析分子技术,广泛应用于微生物群落组成、多样性及种群动态等研究。笔者综述了DGGE技术的基本原理和发展,以及该技术在土壤微生物生态学领域诸多方面的应用,并进一步对该技术在微生物生态学领域研究中存在的优势和局限性进行了讨论评价,最后对其应用前景进行了展望。展开更多
Cadmium (Cd) is ubiquitous in the human environment and has toxic effect on soil microbial biomass or its activity, including microbial biomass carbon (Cmic), dehydrogenase activity (DHA) and basal respiration (BR), e...Cadmium (Cd) is ubiquitous in the human environment and has toxic effect on soil microbial biomass or its activity, including microbial biomass carbon (Cmic), dehydrogenase activity (DHA) and basal respiration (BR), etc., Cmic, DHA, BR were used as bioindicators of the toxic effect of Cd in soil. This study was conducted to determine the effects of Cd on soil microbial biomass and its activity in a paddy soil. The inhibition of microbial biomass and its activity by different Cd concentrations was described by the kinetic model (M1) and the sigmoid dose-response model (M2) in order to calculate three ecological doses of Cd: ED50, ED10 and ED5. Results showed that M2 was better fit than M1 for describing the ecological toxicity dose effect of cadmium on soil microbial biomass and its activity in a paddy soil. M2 for ED values (mg/kg soil) of Cmic, DHA, BR best fitted the measured paddy soil bioindicators. M2 showed that all ED values (mg/kg) increased in turn with increased incubation time. ED50, ED10 and ED5 of Cmic with M2 were increased in turn from 403.2, 141.1, 100.4 to 1000.7, 230.9, 144.8, respectively, after 10 d to 60 d of incubation. ED50, ED10 and ED5 of DHA with M2 increased in turn from 67.6, 6.2, 1.5 to 101.1, 50.9, 41.0, respectively, after 10 d to 60 d of incubation. ED50, ED10 and ED5 of BR with M2 increased in turn from 149.7, 6.5, 1.8 to 156.5, 50.8, 35.5, respectively, after 10 d to 60 d of incubation. So the ecological dose increased in turn with increased incubation time for M2 showed that toxicity of cadmium to soil microbial biomass and its activity was decreased with increased incubation time.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
文摘变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)因其具有可靠性强、易操作、可同时分析多个样品等优点,目前已经成为一种普遍的快速指纹分析分子技术,广泛应用于微生物群落组成、多样性及种群动态等研究。笔者综述了DGGE技术的基本原理和发展,以及该技术在土壤微生物生态学领域诸多方面的应用,并进一步对该技术在微生物生态学领域研究中存在的优势和局限性进行了讨论评价,最后对其应用前景进行了展望。
基金Projects supported by the National Basic Research Program (973) ofChina (No. 2002CB410804) and the National Natural Science Foun-dation (No. 40201026) of China
文摘Cadmium (Cd) is ubiquitous in the human environment and has toxic effect on soil microbial biomass or its activity, including microbial biomass carbon (Cmic), dehydrogenase activity (DHA) and basal respiration (BR), etc., Cmic, DHA, BR were used as bioindicators of the toxic effect of Cd in soil. This study was conducted to determine the effects of Cd on soil microbial biomass and its activity in a paddy soil. The inhibition of microbial biomass and its activity by different Cd concentrations was described by the kinetic model (M1) and the sigmoid dose-response model (M2) in order to calculate three ecological doses of Cd: ED50, ED10 and ED5. Results showed that M2 was better fit than M1 for describing the ecological toxicity dose effect of cadmium on soil microbial biomass and its activity in a paddy soil. M2 for ED values (mg/kg soil) of Cmic, DHA, BR best fitted the measured paddy soil bioindicators. M2 showed that all ED values (mg/kg) increased in turn with increased incubation time. ED50, ED10 and ED5 of Cmic with M2 were increased in turn from 403.2, 141.1, 100.4 to 1000.7, 230.9, 144.8, respectively, after 10 d to 60 d of incubation. ED50, ED10 and ED5 of DHA with M2 increased in turn from 67.6, 6.2, 1.5 to 101.1, 50.9, 41.0, respectively, after 10 d to 60 d of incubation. ED50, ED10 and ED5 of BR with M2 increased in turn from 149.7, 6.5, 1.8 to 156.5, 50.8, 35.5, respectively, after 10 d to 60 d of incubation. So the ecological dose increased in turn with increased incubation time for M2 showed that toxicity of cadmium to soil microbial biomass and its activity was decreased with increased incubation time.
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.
