Microbial Diversity and Community Structure in Two Different Agricultural Soil Communities

Abstract In this study, two different agricultural soils were investigated: one organic soil and one sandy soil, from Stend (south of Bergen), Norway. The sandy soil was a field frequently tilled and subjected to crop rotations. The organic soil was permanent grazing land, infrequently tilled. Our objective was to compare the diversity of the cultivable bacteria with the diversity of the total bacterial population in soil. About 200 bacteria, randomly isolated by standard procedures, were investigated. The diversity of the cultivable bacteria was described at phenotypic, phylogenetic, and genetic levels by applying phenotypical testing (Biolog) and molecular methods, such as amplified rDNA restriction analysis (ARDRA); hybridization to oligonucleotide probes; and REP-PCR. The total bacterial diversity was determined by reassociation analysis of DNA isolated from the bacterial fraction of environmental samples, combined with ARDRA and DGGE analysis. The relationship between the diversity of cultivated bacteria and the total bacteria was elucidated. Organic soil exhibited a higher diversity for all analyses performed than the sandy soil. Analysis of cultivable bacteria resulted in different resolution levels and revealed a high biodiversity within the population of cultured isolates. The difference between the two agricultural soils was significantly higher when the total bacterial population was analyzed than when the cultivable population was. Thus, analysis of microbial diversity must ultimately embrace the entire microbial community DNA, rather than DNA from cultivable bacteria.     

Effect of Metal Oxide Nanoparticles on Microbial Community Structure and Function in Two Different Soil Types

Increased availability of nanoparticle-based products will, inevitably, expose the environment to these materials. Engineered nanoparticles (ENPs) may thus find their way into the soil environment via wastewater, dumpsters and other anthropogenic sources; metallic oxide nanoparticles comprise one group of ENPs that could potentially be hazardous for the environment. Because the soil bacterial community is a major service provider for the ecosystem and humankind, it is critical to study the effects of ENP exposure on soil bacteria. These effects were evaluated by measuring bacterial community activity, composition and size following exposure to copper oxide (CuO) and magnetite (Fe₃O₄) nanosized (<50 nm) particles. Two different soil types were examined: a sandy loam (Bet-Dagan) and a sandy clay loam (Yatir), under two ENP concentrations (1%, 0.1%). Results indicate that the bacterial community in Bet-Dagan soil was more susceptible to change due to exposure to these ENPs, relative to Yatir soil. More specifically, CuO had a strong effect on bacterial hydrolytic activity, oxidative potential, community composition and size in Bet-Dagan soil. Few effects were noted in the Yatir soil, although 1% CuO exposure did cause a significant decreased oxidative potential and changes to community composition. Fe₃O₄ changed the hydrolytic activity and bacterial community composition in Bet-Dagan soil but did not affect the Yatir soil bacterial community. Furthermore, in Bet-Dagan soil, abundance of bacteria annotated to OTUs from the Bacilli class decreased after addition of 0.1% CuO but increased with 1% CuO, while in Yatir soil their abundance was reduced with 1% CuO. Other important soil bacterial groups, including Rhizobiales and Sphingobacteriaceae, were negatively affected by CuO addition to soil. These results indicate that both ENPs are potentially harmful to soil environments. Furthermore, it is suggested that the clay fraction and organic matter in different soils interact with the ENPs and reduce their toxicity.     

Microbial Diversity and Community Structure on Corroding Concretes

The objective of this study was to analyze bacterial diversity in two different concrete samples to understand the dominant types of bacteria that may contribute to concrete corrosion. Two concrete samples, HN-1 from the sunny side and HN-2 from dark and damp side, were collected from Zijin Mountain in Nanjing and genomic DNA was extracted. The partial bacterial 16S rRNA gene fragment was PCR amplified and two clone libraries were constructed. Amplified ribosomal DNA restriction analysis (ARDRA) was performed by digestion of the 16S rRNA gene and each unique restriction fragment polymorphism pattern was designated as an operational taxonomic unit (OTU). Phylogenetic trees of bacterial 16S rDNA nucleotide sequences were constructed. Sample HN-1 and HN-2 contained 21 OTUs and 26 OTUs, respectively. Proteobacteria and Planctomycetes were the predominant bacteria in both samples, and they are distributed among Herbaspirillum, Archangium, Phyllobacteriaceae and Planctomycetaceae. Cyanobacteria and Rubrobacter sp. are dominant in HN-1; while Acidobacteriaceae, Adhaeribacter sp. and Nitrospira sp. are predominant in HN-2. This distribution pattern was consistent with local environmental conditions of these two samples. The inferred physiological characteristics of these bacteria, based on relatedness of the DNA clone sequences to cultivated species, revealed different mechanisms of concrete corrosion depending on the local environmental conditions.     

高寒地区不同海拔梯度西北小檗生境土壤微生物群落结构及多样性分析

以青海高原2 300～4 000 m海拔范围的6处西北小檗(Berberis vernae)生境土壤为试材,采用高通量测序方法,分析不同海拔梯度西北小檗生境土壤微生物群落结构及多样性。研究结果表明:(1)在西北小檗生境土壤中,细菌群落组成主要包括10个细菌门21个细菌属,真菌群落由子囊菌门、担子菌门等8个真菌门59个真菌属组成。(2)低海拔位置的海东乐都1号样点(hdld1) 0～20 cm土层的细菌群落丰富性及多样性均最高,黄南泽库样点(hnzk) 0～20 cm土层的真菌群落丰富度最高,西宁大通样点(xndt) 0～20 cm土层的真菌群落多样性最高;随着海拔的升高,0～20 cm、40～60 cm土层的细菌群落丰富度及多样性呈现出先降低再升高再降低的趋势,20～40 cm土层的细菌群落丰富度及多样性则呈现出先升高后降低的趋势,0～20 cm、20～40 cm土层土壤微生物真菌群落丰富度呈现出先升高再降低再升高的趋势,0～20 cm、40～60 cm土层真菌群落多样性呈现先升高再降低的趋势,40～60 cm土层的真菌丰富度及20～40 cm土层的真菌多样性的变化趋势不明显。(3)硝态氮、速效磷和速效钾对土壤微生物群落的影响较明显。综上可知,高寒地区不同海拔梯度西北小檗生境土壤微生物群落结构多样性呈现出一定的海拔差异趋势,其海拔差异主要受到环境条件、土壤理化性质和植被分布的影响。     

不同施肥处理对玉米-小麦轮作土壤微生物群落功能多样性的影响

土壤微生物多样性能反应土壤的肥力,不同的施肥措施对土壤微生物的种群和功能多样性也会产生重要的影响。以山东德州连续两年小麦季和玉米季收获后土壤为研究对象,利用Biolog技术研究了6种不同施肥处理对土壤微生物群落功能多样性的影响。结果表明:其中各个施肥处理的平均颜色变化率(average well color development,AWCD)差异显著,常规氮磷钾肥+全量秸秆还田+秸秆腐熟剂(FS)处理代谢活性最高;物种丰富度指数(H)和均匀度指数(E)也表明各施肥方式均能够维持微生物种群的多样性,其中FS和30%猪粪+70%常规氮磷钾肥(OF)处理物种丰富度指数(H)和均匀度指数(E)最高;PCA及RDA分析显示,OF和FS处理微生物功能多样性相似,且其微生物功能多样性与有机质(Soil organic matter,SOM)、全氮(Total N,TN)、速效磷(Available P,AP)和速效钾(Available K,AK)密切相关。猪粪堆肥有机无机复合肥3 600 kg/hm2(OI2)处理与猪粪堆肥有机无机复合肥1 800 kg/hm2(OI1)处理相似,其功能多样性比常规施肥(CF)处理稍高。综上所述,OF处理和FS处理的土壤微生物群落功能多样性程度高于其他处理,说明秸秆还田+秸秆腐熟剂和有机肥部分替代氮磷钾肥能够显著提高土壤微生物功能多样性,有利于保护土壤微生态。     

乌鲁木齐地区不同生境下土壤跳虫群落结构及多样性研究

为了解乌鲁木齐地区不同生境土壤跳虫群落结构及其多样性,研究土壤跳虫群落结构特征,了解不同生境差异对土壤跳虫群落结构的影响,分别在2008年4月、7月、9月和11月中旬对该区自然榆林、防护林、植物园、草地、居民点、废弃地及菜地等7种典型生境土壤跳虫群落特征进行了调查。共采集跳虫3728只,隶属于4目13科27属,其中伪亚跳属Pseudachorutes、球角跳属Hypogastrura、棘跳属Onychiurus、等节跳属Isotoma为优势类群,分别占总数的13.25%、12.31%、11.40%、10.03%,共占总数的47.00%。跳虫属Podura、长跳属Entomobrya、原等跳属Proisotoma、土跳属Tullbergia、驼跳属Cyphoderus、裸长角跳属Sinella、钩圆跳属Bourletiella、德跳属Desoria、小等节跳属Isotomiella、疣跳属Neanura、类符跳属Folsomina、符跳属Folsomia、刺驼跳属Cyphoderopsis及缺弹跳属Anuropho-rus等14属为常见类群,共占总数的47.65%,其余9属均为稀有类群,共占总数的5.35%。不同生境土壤跳虫的个体数和类群数差异较大(P<0.05),其中个体数顺序为自然榆林>防护林>草地>植物园>居民点>废弃地>菜地。跳虫个体密度和类群数在不同季节间差异明显(P<0.05),其中个体数顺序为9月>7月>4月>11月,Shan-non-Wiener多样性指数(H)在不同生境间均有显著差异(P<0.05),其顺序为植物园>防护林>自然榆林>草地>居民点>废弃地>菜地。Simpson优势度指数(C)为菜地>居民点>废弃地>草地>自然榆林>植物园>防护林。各生境间土壤跳虫群落的相似性较差,仅少数生境间相似性达到相似水平。研究表明不同生境植被类型是影响该区跳虫群落结构和多样性的主要因素。     

Changes in Soil Microbial Community Structure Influenced by Agricultural Management Practices in a Mediterranean Agro-Ecosystem

Agricultural practices have proven to be unsuitable in many cases, causing considerable reductions in soil quality. Land management practices can provide solutions to this problem and contribute to get a sustainable agriculture model. The main objective of this work was to assess the effect of different agricultural management practices on soil microbial community structure (evaluated as abundance of phospholipid fatty acids, PLFA). Five different treatments were selected, based on the most common practices used by farmers in the study area (eastern Spain): residual herbicides, tillage, tillage with oats and oats straw mulching; these agricultural practices were evaluated against an abandoned land after farming and an adjacent long term wild forest coverage. The results showed a substantial level of differentiation in the microbial community structure, in terms of management practices, which was highly associated with soil organic matter content. Addition of oats straw led to a microbial community structure closer to wild forest coverage soil, associated with increases in organic carbon, microbial biomass and fungal abundances. The microbial community composition of the abandoned agricultural soil was characterised by increases in both fungal abundances and the metabolic quotient (soil respiration per unit of microbial biomass), suggesting an increase in the stability of organic carbon. The ratio of bacteria:fungi was higher in wild forest coverage and land abandoned systems, as well as in the soil treated with oat straw. The most intensively managed soils showed higher abundances of bacteria and actinobacteria. Thus, the application of organic matter, such as oats straw, appears to be a sustainable management practice that enhances organic carbon, microbial biomass and activity and fungal abundances, thereby changing the microbial community structure to one more similar to those observed in soils under wild forest coverage.     

Community Structure Analyses Are More Sensitive to Differences in Soil Bacterial Communities than Anonymous Diversity Indices

Changes in the diversity and structure of soil microbial communities may offer a key to understanding the impact of environmental factors on soil quality in agriculturally managed systems. Twenty-five years of biodynamic, bio-organic, or conventional management in the DOK long-term experiment in Switzerland significantly altered soil bacterial community structures, as assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. To evaluate these results, the relation between bacterial diversity and bacterial community structures and their discrimination potential were investigated by sequence and T-RFLP analyses of 1,904 bacterial 16S rRNA gene clones derived from the DOK soils. Standard anonymous diversity indices such as Shannon, Chao1, and ACE or rarefaction analysis did not allow detection of management-dependent influences on the soil bacterial community. Bacterial community structures determined by sequence and T-RFLP analyses of the three gene libraries substantiated changes previously observed by soil bacterial community level T-RFLP profiling. This supported the value of high-throughput monitoring tools such as T-RFLP analysis for assessment of differences in soil microbial communities. The gene library approach also allowed identification of potential management-specific indicator taxa, which were derived from nine different bacterial phyla. These results clearly demonstrate the advantages of community structure analyses over those based on anonymous diversity indices when analyzing complex soil microbial communities.     

The Influence of Tropical Plant Diversity and Composition on Soil Microbial Communities

There is growing interest in understanding the linkages between above- and belowground communities, and very little is known about these linkages in tropical systems. Using an experimental site at La Selva Biological Station, Costa Rica, we examined whether plant diversity, plant community composition, and season influenced microbial communities. We also determined whether soil characteristics were related to differences in microbial communities. Phospholipid fatty acid (PLFA) composition revealed that microbial community composition differed across a plant diversity gradient (plots contained 1, 3, 5, or over 25 species). Plant species identity also was a factor influencing microbial community composition; PLFA composition significantly varied among monocultures, and among three-species combinations that differed in plant species composition. Differences among treatments within each of these comparisons were apparent in all four sampling dates of the study. There was no consistent shift in microbial community composition between wet and dry seasons, although we did see significant changes over time. Of all measured soil characteristics, soil C/N was most often associated with changes in microbial community composition across treatment groups. Our findings provide evidence for human alteration of soil microbial communities via the alteration of plant community composition and diversity and that such changes are mediated in part by changes in soil carbon quality.     

Relationships between Soil Organic Status and Microbial Community Density and Genetic Structure in Two Agricultural Soils Submitted to Various Types of Organic Management

The effects of soil organic management on indigenous microorganisms were studied by comparing mulching straw (S), conifer compost (CC), and conifer bark (CB) as well as grass landing with grass (G), clover (Cl), and fescue (F) in a silty–clay soil (Macon), and by incorporating vine shoot (VS) and single and double doses of farmyard manure (FM) and mushroom manure (MM) in a calcareous sandy soil (Chinon). Soil physicochemical and microbial characteristics were assessed at each site at two depths by sampling at 0–5 and 5–20 cm for the Macon site and 0–10 and 10–20 cm for the Chinon site. Changes in the quantity of soil organic matter (SOM), through an increase in C_org and N_org contents, and in its quality, through modifications in the C/N and humic acid/fulvic acid ratios, were essentially recorded at the surface layer of treated plots with differential magnitudes according to the inputs and soil type. Quantitative modifications in microbial communities were assessed by means of C-biomass measurements and resulted in an increase in microbial densities fitted with the increase of C_org and N_org contents. However, the deduced C incorporation in microbial biomass was negatively correlated with the C/N ratio, demonstrating a strong influence of the type of organic management on the rate of microbial processes. Qualitative modifications in microbial communities were evaluated by the characterization of the genetic structure of bacterial and fungal communities from DNA directly extracted from the soil, using bacterial and fungal automated ribosomal intergenic spacer analysis. Organic amendments led to changes in the bacterial and fungal communities of both sites. However, the magnitude and the specificity of these changes were different between sites, organic amendments, and microorganisms targeted, revealing that the impact of organic management is dependent on the soil and organic input types as well as on the particular ecology of microorganisms. A co-inertia analysis was performed to specify the role of the quantity and quality of SOM on the modifications of the genetic structure. A significant costructure was only observed for Macon plots at 0–5 cm between the bacterial genetic structure and the SOM characteristics, demonstrating the influence of the relative amount of the different humic substances (humic and fulvic acids) on microbial composition.     

An Integrated Study to Analyze Soil Microbial Community Structure and Metabolic Potential in Two Forest Types

Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (P<0.05) at natural secondary forest site. The regression analysis showed that a strong positive (P<0.05) correlation was existed between the soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (P<0.05) to the relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can''t directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.     

Microbial Diversity During Cellulose Decomposition in Different Forest Stands: I. Microbial Communities and Environmental Conditions

We studied the effect of forest tree species on a community of decomposers that colonize cellulose strips. Both fungal and bacterial communities were targeted in a native forest dominated by beech and oak and 30-year-old beech and spruce plantations, growing in similar ecological conditions in the Breuil-Chenue experimental forest site in Morvan (France). Microbial ingrowths from the 3rd to 10th month of strip decomposition (May to December 2004) were studied. Community composition was assessed using temperature gradient gel electrophoresis with universal fungal (ITS1F, ITS2) and bacterial (1401r, 968f) primers. Soil temperature and moisture as well as fungal biomass were also measured to give additional information on decomposition processes. Changing the dominant tree species had no significant influence in the number of decomposer species. However, decomposer community composition was clearly different. If compared to the native forest, where community composition highly differed, young monocultures displayed similar species structure for fungi and bacteria. Both species numbers and community composition evolved during the decay process. Time effect was found to be more important than tree species. Nevertheless, the actual environmental conditions and seasonal effect seemed to be even more determining factors for the development of microbial communities. The course and correlations of the explored variables often differed between tree species, although certain general trends were identified. Fungal biomass was high in summer, despite that species richness (SR) decreased and conversely, that high SR did not necessarily mean high biomass values. It can be concluded that the growth and development of the microbiological communities that colonized a model material in situ depended on the combination of physical and biological factors acting collectively and interdependently at the forest soil microsite.     

Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity

The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another by a shrub (Rhamnus davurica), and the third by a tree (Ailanthus altissima). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen cycling bacteria and functions are important factors in plant invasions. Whether the changes in microbial communities are driven by direct plant microbial interactions or a result of plant-driven changes in soil properties remains to be determined.     

Microbial Community Structure and Carbon-Utilization Diversity in a Mine Tailings Revegetation Study

Restoration of metals‐contaminated environments requires a functional microbial community for successful plant community establishment, soil development, and biogeochemical cycling. Our research measured microbial community structure and carbon‐utilization diversity in treatment plots from a mine waste revegetation project near Butte, Montana. Treatments included two controls (raw tailings) either (1) with or (2) without tilling, (3) shallow‐tilled lime addition, (4) deep‐tilled lime addition, (5) lime slurry injection, (6) topsoil addition, and (7) an undisturbed area near the tailings. Microbial community structural differences were assayed by plate counts of heterotrophic bacteria, actinomycetes, fungi, and bacterial endospores, and quantification of arbuscular mycorrhizae colonization. Metabolic diversity differences were assessed by carbon‐utilization profiles generated with Biolog microtiter plates. Heterotrophic bacteria counts were significantly higher in the limed and topsoil treatment plots than the control plots, and the actinomycete and fungal counts increased in the tilled control plot as well. Endospore counts were significantly higher in the topsoil addition and the undisturbed plots than the other treatment plots. Carbon‐utilization activity was very low in untreated plots, intermediate in lime‐treated plots, and very high in topsoil and undisturbed plots. Arbuscular mycorrhizae (AM) colonization levels of two grass species showed low levels of colonization on control, shallow‐limed, and lime slurry‐injected plots, and high levels on the deep‐limed and topsoil‐addition plots. Plant and soil system components increased across the treatment plots, but individual components responded differently to changing environmental conditions.     

不同植茶年限茶树根际土壤细菌多样性及群落结构研究

运用传统培养法和高通量测序技术研究不同植茶年限(5年、10年、20年)茶树根际土壤细菌的多样性、结构和组成,并分析茶树土壤理化性质与细菌群落的相关性,为改善茶树的土壤和提高茶树产量提供参考。结果表明:两种方法均指出不同植茶年限下的根际细菌群落结构存在显著性差异,5年和10年茶树细菌多样性显著高于20年茶树细菌;培养法得出厚壁菌门(Firmicutes)和芽孢杆菌属(Bacillus)为优势门属,高通量测序技术得出酸杆菌门(Acidobacteria)、变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)和Candidatus_Udaeobacter属为优势门属;总氮(TN)、总钾(TK)、总磷(TP)、pH是影响茶树细菌群落的关键理化因子;随着植茶年限增加,要采取措施防止土壤酸化,适当增施氮肥和磷肥。     

克拉玛依石油污染土壤微生物群落结构及其代谢特征

为了分析克拉玛依油区内土壤中正构烷烃含量间的差异,微生物群落生理多样性、微生物代谢活性在不同石油污染梯度土壤中的变化规律。本研究采用GC、平板稀释法、Biolog微平板技术探讨了土壤微生物群落特征在3种不同污染程度下的变化情况。研究表明,石油污染土壤烷烃含量与微生物代谢活性呈显著负相关(r=-0.783, p<0.05)。随着石油污染程度增加微生物数量呈下降趋势,不同石油污染土壤中细菌数量占决定优势,细菌>真菌>放线菌。不同石油污染土壤微生物群落对6大碳源的利用体现出差异。主成分分析(PCA)表明,清洁土壤与石油污染土壤对底物利用有明显差异。石油污染严重土样碳源利用率为"酯类>酸类>胺类>氨基酸类>单糖/糖苷/聚合糖类>醇类"。本研究成果为后期修复污染土壤时调整投入的碳源底物等提供科学帮助。     

The Structure of Microbial Communities in Soil and the Lasting Impact of Cultivation

The structure of microbial communities was examined as a function of community composition and the relative abundance of specific microbial groups to examine the effects that plant community composition and land-use history have on microbial communities in the soil. The sites sampled were part of the Long Term Ecological Research (LTER) project in agricultural ecology at the W.K. Kellogg Biological Station of Michigan State University (Hickory Corners, MI) and included both active and abandoned agricultural fields as well as nearby fields that had never been cultivated. Microbial community structure was assessed by extracting total RNA from soil samples and using 16S rRNA-targeted oligonucleotide probes to quantify the abundance of rRNA from the alpha, beta, and gamma Proteobacteria, the Actinobacteria (Gram positive bacteria with a high mol % G+C genome), the Bacteria, and the Eukarya. In addition, soil microbial communities were characterized by examining fluorescently tagged terminal restriction fragment length polymorphisms (T-RFLP) in PCR amplified 16S rDNA. Microbial community structure was observed to be remarkably similar among plots that shared a long-term history of agricultural management despite differences in plant community composition and land management that have been maintained on the plots in recent years. In contrast, microbial community structure differed significantly between fields that had never been cultivated and those having a long-term history of cultivation.     

Effects of Agricultural Chemicals on DNA Sequence Diversity of Soil Microbial Community: A Study with RAPD Marker

Abstract The DNA sequence diversities for microbial communities in four soils affected by agricultural chemicals (mainly triadimefon and ammonium bicarbonate and their intermediates) were evaluated by Random Amplified Polymorphic DNA (RAPD) analysis. Fourteen random primers were used to amplify RAPDs from four soil microbial community DNAs. The products of 12 primers were separated in gel and generated 155 reliable fragments, of which 134 were polymorphic. The richness, modified richness, Shannon–Weaver index, and a similarity coefficient of DNA were calculated to quantify the diversity to access DNA sequence diversities for four soil microbial communities. The results showed that agricultural chemicals affected soil microbial community diversity at the DNA level. The four soil microbial communities were distinguishable in terms of DNA sequence richness, modified richness, Shannon–Weaver index, and coefficient of DNA similarity. Analysis also showed that the amounts of organic C and microbial biomass C were low in the soil polluted by pesticide (mainly triadimefon and its intermediates), but high in the soil polluted by chemical fertilizer (mainly ammonium bicarbonate and its intermediates). The above results combined may indicate that pesticide pollution caused a decrease in the soil microbial biomass but kept high diversity at DNA level, compared with the control without chemical pollution. In contrast, chemical fertilizer pollution caused an increase in the soil biomass but decrease in the DNA diversity. The RAPD marker technique combined with analysis of soil microbial biomass appears to be an effective approach for studying the diversity of soil microbial communities, although the effects of PCR bias on community composition, such as dominating and rare populations in soils, on the diversity needed to be addressed further.