高黎贡山不同土地利用方式对土壤 微生物数量和多样性的影响

测定了高黎贡山不同利用方式土壤中微生物的数量、小型真菌的多样性和属的分布,分析了上述指标在不同利用方式土壤中的分布与人为干扰和环境因素之间的相互关系。结果表明微生物数量和真菌的多样性在不同利用方式土壤中的分布是,原生林(次生林(幼杉木纯林;耕作通常使条件更有利于土壤微生物生长繁殖,成熟人工纯林和旱地的土壤微生物数量及真菌多样性均较高;在五类利用方式中,土壤微生物数量及真菌多样性以原生林最高,荒地最低。     

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.     

Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities.     

Soil Microbial Diversity in the Vicinity of Desert Shrubs

Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0–10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon–Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.     

辣椒青枯病罹病与健康植株根际土壤微生物群落多样性研究

系统研究和分析辣椒青枯病常发地发病与健康植株土壤微生物群落结构特征,为辣椒青枯病的绿色防治提供理论依据.基于16SrDNA基因高通量测序技术,对辣椒青枯病发病和健康植株根际土壤微生物群落结构和组成进行分析,同时采用biologyeco平板培养技术研究其土壤微生物群落代谢多样性和功能多样性的特征.结果表明,辣椒青枯病发病和健康植株根际土壤微生物群落组成之间存在显著差异,辣椒青枯病发病土壤的OTU为4566个,辣椒青枯病健康土壤的OTU为4167个.依据OTU所属细菌物种信息对土壤细菌群落结构进行分析,变形菌门在发病和健康土壤中均为优势细菌类群,其次为放线菌门类群.其中健康植株根际土壤中芽单胞菌门(Gemmatimonadetes)、装甲菌门(Armatimonadetes)的相对丰度比发病植株的分别高出了4.37,3.87倍,而发病植株根际土壤中厚壁菌门(Firmicutes)的相对丰度比健康植株的高出了3.87倍.辣椒青枯病发病土壤和健康土壤的土壤微生物代谢多样性也存在显著差异,同时,健康土壤中其微生物群落代谢得到显著增强,特别是对酚类化合物的利用显著增多,对辣椒抗病性存在显著的影响.研究表明,辣椒青枯病发病和健康植株根际土壤微生物群落组成和结构之间存在显著差异,并且健康土壤的微生物群落对酚类化合物的利用显著增强.     

Spatial and Resource Factors Influencing High Microbial Diversity in Soil

To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach. While microbial communities in low-carbon, saturated, subsurface soils showed dominance, microbial communities in low-carbon surface soils showed remarkably uniform distributions, and all species were equally abundant. Two diversity indices, the reciprocal of Simpson’s index (1/D) and the log series index, effectively distinguished between the dominant and uniform diversity patterns. For example, the uniform profiles characteristic of the surface communities had diversity index values that were 2 to 3 orders of magnitude greater than those for the high-dominance, saturated, subsurface communities. In a site richer in organic carbon, microbial communities consistently exhibited the uniform distribution pattern regardless of soil water content and depth. The uniform distribution implies that competition does not shape the structure of these microbial communities. Theoretical studies based on mathematical modeling suggested that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure. Carbon resource heterogeneity may explain the uniform diversity patterns observed in the high-carbon samples even in the saturated zone. Very high levels of chromium contamination (e.g., >20%) in the high-organic-matter soils did not greatly reduce the diversity. Understanding mechanisms that may control community structure, such as spatial isolation, has important implications for preservation of biodiversity, management of microbial communities for bioremediation, biocontrol of root diseases, and improved soil fertility.     

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.     

Effects of Plant Diversity,Functional Group Composition,and Fertilization on Soil Microbial Properties in Experimental Grassland

BackgroundLoss of biodiversity and increased nutrient inputs are two of the most crucial anthropogenic factors driving ecosystem change. Although both received considerable attention in previous studies, information on their interactive effects on ecosystem functioning is scarce. In particular, little is known on how soil biota and their functions are affected by combined changes in plant diversity and fertilization.Conclusions/SignificanceOur study highlights the role of plant species and functional group diversity as well as interactions between plant community composition and fertilizer application for soil microbial functions. Our results suggest soil microbial stoichiometry to be a powerful indicator of microbial functioning under N limited conditions. Although our results support the notion that plant diversity and fertilizer application independently affect microbial functioning, legume effects on microbial N limitation were superimposed by fertilization, indicating significant interactions between the functional composition of plant communities and nutrient inputs for soil processes.     

Microbial Diversity and Structure Are Drivers of the Biological Barrier Effect against Listeria monocytogenes in Soil

Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.     

Land Consolidation with Seedling Cultivation Could Decrease Soil Microbial PLFA Diversity

The impact of land consolidation on the soil microbial PLFA diversity is of great importance for understanding the effective arable land usage, improving agricultural ecological conditions and environment. In this study, we collected the soil samples (0–20 cm) in experimental plots with 0 (Z₀), 1 (Z_1a) and 4 (Z_4a) years of land consolidation in the forest station of Ningbo City, Zhejiang Province, southeastern China. The results were analyzed using ANOVA for randomized block design. Compared with control (Z₀), the soil pH value under Z_1a treatment increased by 14.6%, soil organic carbon (SOC) content decreased by 65.4%, so did the PLFA contents and relative abundance of all the microbial PLFA diversity (P < 0.05), respectively. Meanwhile, for the Z_1a treatment, the ratio of fungi to bacteria (F/B) significantly decreased by 35.9% (P < 0.05), while the ratio of Gram-positive bacteria to Gram-negative bacteria (G+/G−) signific antly increased by 56.1%. This was strongly related to the increased soil pH values and the decrease of SOC. The Shannon index (H) and evenness index (E) of soil microbial PLFA diversity were significantly decreased after land consolidation (P < 0.05). Compared to the Z₁ treatment, the microbial PLFA diversity was improved slightly. Therefore, the land consolidation could significantly affect the composition of soil microbial PLFA diversity, and decrease the soil ecosystem stability.     

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。     

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.     

新疆叶城两种主栽红枣土壤养分、微生物多样性与营养品质的比较分析

比较新疆叶城两种主栽红枣—骏枣与灰枣的土壤养分、微生物多样性和枣营养品质之间的差异,分析土壤养分、微生物与枣营养品质之间的相关性,从土壤养分、微生物角度研究枣营养品质的影响因素。通过化学分析法测定叶城骏枣与灰枣土壤养分、枣营养品质指标,高通量测序分析土壤微生物多样性,将土壤养分和微生物优势门属微生物进行冗余分析,研究枣营养品质指标与土壤养分、微生物功能类群的相关性。结果显示,新疆叶城两种主栽红枣土壤的全氮、速效氮、有机质含量显著不同;细菌群落变化的主要原因是土壤TN(全氮)值,真菌群落变化的主要原因是土壤AN(速效氮)值。两种主栽红枣土壤微生物多样性显示,骏枣土壤微生物在细菌水平上具有更高的物种丰富性和多样性,薄壁杆菌属(Gracilibacillus)、芽胞杆菌目(Bacillales)等溶磷微生物、固氮微生物等功能土壤微生物相对丰度和占比较高,差异显著;枣营养品质,尤其是不可溶膳食纤维、Fe、K、Zn的含量差异明显。而不可溶膳食纤维、K、蔗糖含量与TP(全磷)、OM(有机质)存在显著负相关;Fe、Zn含量与薄壁杆菌属、芽胞杆菌目等九类功能微生物存在显著正相关;Mg、可溶性糖、可溶性...     

DNA指纹图谱技术在土壤微生物多样性研究中的应用

土壤中的微生物多样性是十分丰富的,传统培养方法对土壤微生物多样性的研究有很大局限性。近年来,各种基于16S rDNA基因的指纹图谱分析技术取得了长足的进步,并广泛应用于土壤微生物多样性的研究。这些技术主要有变性梯度凝胶电泳(DGGE)/温度梯度凝胶电泳(TGGE)、单链构象多态性(SSCP)、随机引物扩增多态性DNA(RAPD)、限制性片段长度多态性(RFLP)和扩增核糖体DNA限制性分析(ARDRA)等。对这些技术近年来在土壤微生物多样性研究领域的应用予以简短综述,并初步探讨未来几年土壤微生物分子生态学发展的方向。     

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

The long-term application of excessive chemical fertilizers has resulted in the degeneration of soil quality parameters such as soil microbial biomass, communities, and nutrient content, which in turn affects crop health, productivity, and soil sustainable productivity. The objective of this study was to develop a rapid and efficient solution for rehabilitating degraded cropland soils by precisely quantifying soil quality parameters through the application of manure compost and bacteria fertilizers or its combination during maize growth. We investigated dynamic impacts on soil microbial count, biomass, basal respiration, community structure diversity, and enzyme activity using six different treatments [no fertilizer (CK), N fertilizer (N), N fertilizer + bacterial fertilizer (NB), manure compost (M), manure compost + bacterial fertilizer (MB), and bacterial fertilizer (B)] in the plowed layer (0–20 cm) of potted soil during various maize growth stages in a temperate cropland of eastern China. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. The Shannon index of bacterial and fungi communities displayed the highest value in the MB treatments and the lowest in the N treatment at the maize mature stage. Changes in soil microorganism community structure and diversity after different fertilizer treatments resulted in different microbial properties. Adding manure compost significantly increased the amount of cultivable microorganisms and microbial biomass, thus enhancing soil respiration and enzyme activities (p<0.01), whereas N treatment showed the opposite results (p<0.01). However, B and NB treatments minimally increased the amount of cultivable microorganisms and microbial biomass, with no obvious influence on community structure and soil enzymes. Our findings indicate that the application of manure compost plus bacterial fertilizers can immediately improve the microbial community structure and diversity of degraded cropland soils.     

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.     

不同药用植物根际土壤原核微生物多样性研究

为研究不同药用植物根际土壤中的原核微生物多样性,分别采集白术(Atractylodes macrocephala)、白芍(Paeonia sterniana)、牡丹(Paeonia suffruticosa)、玄参(Scrophularia ningpoensis)四种药用植物的根际土壤以及非种植区的土壤,针对16S rRNA基因的V3～V4区进行测序,分析土壤细菌群落的组成。结果表明,药用植物根际土壤中的细菌群落多样性指数显著高于非种植区土壤。五组样本的优势类群差异不大,总体相对丰度较高的有变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)、芽单胞菌门(Gemmatimonadetes)、绿弯菌门(Chloroflexi)等,药用植物根际中的放线菌相对丰度高于非种植区。属水平上四种药用植物根际细菌和非种植区的群落结构有较大差异,四种中药材的根际土壤中各自富集了特异性的有益细菌属。药用植物根际土壤中的NMD1、Dongia、Gaiella、Streptomyces等相对丰度高于非种植区,而非种植区土壤中Lysoba...     

Assessment of the Bacterial Diversity in Fenvalerate-Treated Soil

The impact of the pesticide fenvalerate on the diversity of the bacterial community in soil was investigated in this study. After treatment with 0.1, 0.5 or 1.0 mg fenvalerate g^–1 soil in three soils and incubation for a 40-day period, the changes in diversity were monitored by two different methods. The cultivable heterotrophic diversity was investigated by colony morphology on solid LB medium. Genetic diversity was measured as bands on denaturing gradient gel electrophoresis (DGGE) gels by total genomic DNA extraction and purification, PCR-amplification of bacterial 16S rDNA fragments. The Shannon–Wiener index of diversity (H), richness (S) and evenness (E _H) were used to measure changes in the bacterial community in the soils. The results of the cultivable heterotrophic diversity and genetic diversity showed that there was an obvious decrease in diversity due to the application of fenvalerate to the soils, and the different amounts added had different impacts on the diversity. Bands appearing to be either enhanced or inhibited as a result of the fenvalerate treatments were excized and sequenced. Sequencing of excized DGGE bands indicated that application of fenvalerate had an obvious impact on several Pseudomonas spp., or Xanthomonas campestrisor Streptomyces avermitilis. This revealed that microbial community changes can occur due to the application of fenvalerate to soil.     

Long-Term Phosphorus Fertilization Impacts Soil Fungal and Bacterial Diversity but not AM Fungal Community in Alfalfa

Soil function may be affected by cropping practices impacting the soil microbial community. The effect of different phosphorus (P) fertilization rates (0, 20, or 40 kg P₂O₅ ha⁻¹) on soil microbial diversity was studied in 8-year-old alfalfa monocultures. The hypothesis that P fertilization modifies soil microbial community was tested using denaturing gradient gel electrophoresis and phospholipids fatty acid (PLFA) profiling to describe soil bacteria, fungi, and arbuscular mycorrhizal (AM) fungi diversity. Soil parameters related to fertility (soil phosphate flux, soluble P, moisture, phosphatase and dehydrogenase assays, and carbon and nitrogen content of the light fraction of soil organic matter) were also monitored and related to soil microbial ribotype profiles. Change in soil P fertility with the application of fertilizer had no effect on crop yield in 8 years, but on the year of this study was associated with shifts in the composition of fungal and bacterial communities without affecting their richness, as evidenced by the absence of effect on the average number of ribotypes detected. However, variation in soil P level created by a history of differential fertilization did not significantly influence AM fungi ribotype assemblages nor AM fungi biomass measured with the PLFA 16:1ω5. Fertilization increased P flux and soil soluble P level but reduced soil moisture and soil microbial activity, as revealed by dehydrogenase assay. Results suggest that soil P fertility management could influence soil processes involving soil microorganisms. Seasonal variations were also recorded in microbial activity, soil soluble P level as well as in the abundance of specific bacterial and fungal PLFA indicators of soil microbial biomass.