Soil microorganisms play a central role in decomposing organic matter, in determining the release of mineral nutrients, and in nutrient cycling. Recently, extensive studies have focused on soil microbial diversity. Ho...Soil microorganisms play a central role in decomposing organic matter, in determining the release of mineral nutrients, and in nutrient cycling. Recently, extensive studies have focused on soil microbial diversity. However, understanding the diversity of this complex microbial community in the soil environment is a challenging task. Thus, it is important to master and comprehend appropriate methods for studying soil microbial diversity. Concepts of soil microbial diversity and major methods of study are briefly introduced in this paper. Then, the application of biochemical-based and molecular-based techniques in this area, and their advantages and disadvantages are evaluated. Based on recent related research, perspectives for studying microbial diversity in soils are presented.展开更多
Soil samples were collected from both bare and vegetated mine railings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed （Phragmites communis） colonizatio...Soil samples were collected from both bare and vegetated mine railings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed （Phragmites communis） colonization. The structures of bacterial communities were investigated using culture-independent 16S rRNA gene sequencing method. The bacterial diversity in the bare mine tailing was lower than that of the vegetated mine tailing. The former was dominated by sulfur metabolizing bacteria, whereas the latter was by nitrogen fixing bacteria. The bare mine tailing was acidic （pH = 3.78）, whereas the vegetated mine tailing was near neutral （pH ： 7.28）. The contents of organic matter, total nitrogen, and ammonium acetate-extractable potassium in vegetated mine tailings were significantly higher than those in the bare mine railings （P 〈 0.01）, whereas available phosphorus and electrical conductivity were significantly lower than those in the bare mine tailings （P 〈 0.01）. The results demonstrated that 16S rRNA gene sequencing could be successfully used to study the bacterial diversity in mine tailings. The colonization of the mine tailings by reed significantly changed the bacterial community and the chemical properties of tailings. The complex interactions between bacteria and plants deserve further investigation.展开更多
The structure and diversity of the bacterial communities in rhizosphere soils of native Phragmites australis and Scirpus rnariqueter and alien Spartina alterniflora in the Yangtze River Estuary were investigated by co...The structure and diversity of the bacterial communities in rhizosphere soils of native Phragmites australis and Scirpus rnariqueter and alien Spartina alterniflora in the Yangtze River Estuary were investigated by constructing 16S ribosomal DNA （rDNA） clone libraries. The bacterial diversity was quantified by placing the clones into operational taxonomic unit （OTU） groups at the level of sequence similarity of 〉 97%. Phylogenetic analysis of the resulting 398 clone sequences indicated a high diversity of bacteria in the rhizosphere soils of these plants. The members of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria of the phylum Proteobacteria were the most abundant in rhizobacteria. Chao 1 nonpaxametric diversity estimator coupled with the reciprocal of Simpson＇s index （l/D） was applied to sequence data obtained from each library to evaluate total sequence diversity and quantitatively compare the level of dominance. The results showed that Phragmites, Scirpus, and Spartina rhizosphere soils contained 200, 668, and 382 OTUs, respectively. The bacterial communities in the Spartina and Phragraites rhizosphere soils displayed species dominance revealed by 1/D, whereas the bacterial community in Scirpus rhizosphere soil had uniform distributions of species abundance. Overall, analysis of 16S rDNA clone libraries from the rhizosphere soils indicates that the changes in bacterial composition may occur concomitantly with the shift of species composition in plant communities.展开更多
基金Project supported by the National Key Basic Research and Development Program of China (No. 2002CB111505).
文摘Soil microorganisms play a central role in decomposing organic matter, in determining the release of mineral nutrients, and in nutrient cycling. Recently, extensive studies have focused on soil microbial diversity. However, understanding the diversity of this complex microbial community in the soil environment is a challenging task. Thus, it is important to master and comprehend appropriate methods for studying soil microbial diversity. Concepts of soil microbial diversity and major methods of study are briefly introduced in this paper. Then, the application of biochemical-based and molecular-based techniques in this area, and their advantages and disadvantages are evaluated. Based on recent related research, perspectives for studying microbial diversity in soils are presented.
基金the National Natural Science Foundation of China (Nos.39830310 and 30070134)the NationalKey Basic Research Support Foundation (NKBRSF) of China (No.2002CB111504).
文摘Soil samples were collected from both bare and vegetated mine railings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed （Phragmites communis） colonization. The structures of bacterial communities were investigated using culture-independent 16S rRNA gene sequencing method. The bacterial diversity in the bare mine tailing was lower than that of the vegetated mine tailing. The former was dominated by sulfur metabolizing bacteria, whereas the latter was by nitrogen fixing bacteria. The bare mine tailing was acidic （pH = 3.78）, whereas the vegetated mine tailing was near neutral （pH ： 7.28）. The contents of organic matter, total nitrogen, and ammonium acetate-extractable potassium in vegetated mine tailings were significantly higher than those in the bare mine railings （P 〈 0.01）, whereas available phosphorus and electrical conductivity were significantly lower than those in the bare mine tailings （P 〈 0.01）. The results demonstrated that 16S rRNA gene sequencing could be successfully used to study the bacterial diversity in mine tailings. The colonization of the mine tailings by reed significantly changed the bacterial community and the chemical properties of tailings. The complex interactions between bacteria and plants deserve further investigation.
基金Project supported by the National Natural Science Foundation of China (Nos.30370235 and 30670330)Science and Technology Commission of Shanghai (No.04DZ19304)Ministry of Education of China (No.105063)
文摘The structure and diversity of the bacterial communities in rhizosphere soils of native Phragmites australis and Scirpus rnariqueter and alien Spartina alterniflora in the Yangtze River Estuary were investigated by constructing 16S ribosomal DNA （rDNA） clone libraries. The bacterial diversity was quantified by placing the clones into operational taxonomic unit （OTU） groups at the level of sequence similarity of 〉 97%. Phylogenetic analysis of the resulting 398 clone sequences indicated a high diversity of bacteria in the rhizosphere soils of these plants. The members of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria of the phylum Proteobacteria were the most abundant in rhizobacteria. Chao 1 nonpaxametric diversity estimator coupled with the reciprocal of Simpson＇s index （l/D） was applied to sequence data obtained from each library to evaluate total sequence diversity and quantitatively compare the level of dominance. The results showed that Phragmites, Scirpus, and Spartina rhizosphere soils contained 200, 668, and 382 OTUs, respectively. The bacterial communities in the Spartina and Phragraites rhizosphere soils displayed species dominance revealed by 1/D, whereas the bacterial community in Scirpus rhizosphere soil had uniform distributions of species abundance. Overall, analysis of 16S rDNA clone libraries from the rhizosphere soils indicates that the changes in bacterial composition may occur concomitantly with the shift of species composition in plant communities.
