植被对土壤微生物群落结构的影响

研究了不同土壤及覆盖其上的植被与土壤微生物群落结构和多样性的关系．植被使土壤中的微生物种类更丰富,群落多样性更高．表层土壤微生物群落中没有明显的优势种群,种间竞争作用较弱．并介绍了研究土壤微生物群落的分子生物学方法．     

污染土壤微生物群落结构多样性及功能多样性测定方法

土壤微生物在促进土壤质量和植物健康方面发挥着重要的作用,土壤微生物群落结构和组成的多样性及其变化在一定程度上反映了土壤质量.为了更好地了解土壤健康状况,非常有必要发展有效的方法来研究污染土壤微生物的多样性、分布以及行为等.回顾了近年来国内外污染土壤微生物群落结构多样性及功能多样性的测定方法,包括生物化学技术和分子生物学技术,现将它们的原理、优缺点、实用性及其发展动态作一阐述,同时指出结合这两种技术可为微生物群落分析提供一个更全面的、精确的方法.     

Effect of above-ground plant species on soil microbial community structure and its impact on suppression of Rhizoctonia solani AG3

The extent of soil microbial diversity is seen to be critical to the maintenance of soil health and quality. Different agricultural practices are able to affect soil microbial diversity and thus the level of suppressiveness of plant diseases. In a 4-year field experiment, we investigated the microbial diversity of soil under different agricultural regimes. We studied permanent grassland, grassland turned into arable land, long-term arable land and arable land turned into grassland. The diversity of microbial communities was described by using cultivation-based and cultivation-independent methods. Both types of methods revealed differences in the diversities of soil microbial communities between different treatments. The treatments with higher above-ground biodiversity generally maintained higher levels of microbial diversity. Moreover, a positive correlation between suppression of Rhizoctonia solani AG3 and microbial diversity was observed. Permanent (species-rich) grassland and grassland turned into maize stimulated higher microbial diversities and higher levels of suppressiveness of R. solani AG3 compared with the long-term arable land. Effects of agricultural practices on Bacillus and Pseudomonas communities were also observed and clear correlations between the levels of suppressiveness and the diversities of these bacterial groups were found. This study highlighted the importance of agricultural management regime for soil microbial community structure and diversity as well as the level of soil suppressiveness.     

红树林土壤总DNA不同提取方法比较研究

获得高浓度、大片段、无偏好的土壤微生物总DNA是土壤微生物分子生态学研究和宏基因组文库构建的基础。本研究采用了5种方法从红树林土壤中提取DNA,并对5种方法提取出的DNA的质量和产量进行比较评价。结果表明,5种方法均可从土壤中提取到DNA,但不同方法提取到DNA的产量和质量存在明显差异。Bio101FastPrep?SPINKit(forSoil)抽提到的DNA得率最高,适合分子生态学研究;SDS-GITC-PEG法提取的DNA纯度最高,所得到的DNA片段较大(>48kb),有利于构建宏基因组文库。     

Efficiency of DNA extraction methods on the evaluation of soil microeukaryotic diversity

The evaluation of microbial molecular diversity has been mainly based on the extraction of total DNA from environmental samples. The indirect extraction methods, which have been used for prokaryotes, have never been used to recover soil microeukaryotic DNA. We evaluated the efficiency of an improved indirect DNA extraction protocol developed herein and the direct lysis (the sodium dodecyl sulfate (SDS)-based method and commercial DNA extraction kit) on estimating the molecular diversity of soil microbial eukaryotes. DNA quality and quantity as well as denaturing gradient gel electrophoresis (DGGE) profiles were determined using three soil samples from different stations. The indirect method detected the highest DGGE bands in spite of the low DNA yield. The commercial kit detected a lower number of DGGE bands than the indirect method. The SDS-based method produced the lowest DGGE bands and DNA purity but the highest yield. Using the indirect method, we further evaluated the effect of freezing and air-dried preservations on estimating the microeukaryotic diversity. In spite of the low DNA yield obtained from the air-dried preservation, no significant differences were found in either the number of DGGE bands or the DNA purity between two manners. Our results indicate that the improved indirect method could obtain a high purity of intracellular DNA and high efficiency in the estimation of molecular diversity of soil microbial eukaryotes.     

植物、土壤及土壤管理对土壤微生物群落结构的影响

土壤微生物是土壤生态系统的重要组成部分,对土壤微生物群落结构多样性的研究是近年来土壤生态学研究的热点。本文综述了有关植物、土壤类型以及土壤管理措施对土壤微生物群落结构影响的最新研究结果,指出植物的作用因植物群落结构多样性、植物种类、同种植物不同的基因型,甚至同一植物不同根的区域而异;而土壤的作用与土壤质地和有机质含量等因素有关;植物和土壤类型在对土壤微生物群落结构影响上的作用存在互作关系。不同的土壤管理措施对土壤微生物群落结构影响较大,长期连作、大量的外援化学物质的应用降低了土壤微生物的多样性;而施用有机肥、免耕可以增加土壤微生物群落结构多样性,有利于维持土壤生态系统的功能。     

Microbial diversity and function in soil: from genes to ecosystems

Soils sustain an immense diversity of microbes, which, to a large extent, remains unexplored. A range of novel methods, most of which are based on rRNA and rDNA analyses, have uncovered part of the soil microbial diversity. The next step in the era of microbial ecology is to extract genomic, evolutionary and functional information from bacterial artificial chromosome libraries of the soil community genomes (the metagenome). Sophisticated analyses that apply molecular phylogenetics, DNA microarrays, functional genomics and in situ activity measurements will provide huge amounts of new data, potentially increasing our understanding of the structure and function of soil microbial ecosystems, and the interactions that occur within them. This review summarizes the recent progress in studies of soil microbial communities with focus on novel methods and approaches that provide new insight into the relationship between phylogenetic and functional diversity.     

土壤微生物群落多样性解析法:从培养到非培养

土壤微生物群落多样性是土壤微生物生态学和环境科学的重点研究内容之一.传统的土壤微生物群落多样性解析技术是指纯培养分离法(平板分离和形态分析法以及群落水平生理学指纹法).后来,研究者们建立了多样性评价较为客观的生物标记法(磷脂脂肪酸法和呼吸醌指纹法).随着土壤基因组提取技术和基因片段扩增(PCR)技术的发展,大量的现代分子生物学技术不断地涌现并极大地推动了土壤微生物群落多样性的研究进程.这些技术主要包括:G+C％含量、DNA复性动力学、核酸杂交法(FISH和DNA芯片技术)、土壤宏基因组学以及DNA指纹图谱技术等.综述了这些技术的基本原理、比较了各种技术的优缺点并且介绍了他们在土壤微生物群落多样性研究中的应用,展望了这些技术的发展方向.     

土壤管理措施及环境因素对土壤微生物多样性影响研究进展

本文综述了土壤管理措施及环境因素对土壤微生物多样性影响的研究进展,并介绍了土壤微生物多样性的研究方法,土壤微生物多样性包括微生物物种多样性、遗传多样性和生态多样性。传统上,土壤微生物群落的分析依赖于培养技术,但使用该技术只能培养和分离出一部分土壤微生物群落。现在国际上普遍使用Biolog分析、磷脂脂肪酸(PLFA)分析和核酸分析等多种现代技术研究和表征土壤微生物多样性。土壤微生物多样性受土壤管理措施和多种环境因素的影响。农药可能使土壤微生物多样性减少或改变其结构和功能;施有机肥有利于维持土壤微生物的多样性及活性;但在施用无机肥的影响上目前的报道有矛盾之处。农业土壤减少耕作可能增加微生物多样性和生物量;轮作可能比单一栽培耕作更有利于维持土壤微生物的多样性及活性。土壤微生物多样性也受土壤有机质、植被、季节变化等因素的影响,且通常遭受干旱、过度放牧、营养缺乏等的胁迫作用。     

红树林土壤微生物的研究：过去、现在、未来

红树林土壤生境的独特性决定了其中微生物的多样性及其资源的珍稀性,对于红树林土壤微生物的研究正在成为热点。然而由于传统研究方法等因素的限制,至今人们对红树林土壤微生物的系统了解仍较为有限。近年来,基于16S rRNA,18S rRNA基因的各种分子微生物学技术的迅速发展,红树林土壤微生物的研究亦面临着崭新的局面。文中主要从红树林土壤微生物物种的多样性、生理生化类型的多样性及其在治理污染环境、生物修复作用中的可能性、有效性等方面阐述了红树林土壤微生物的研究进展,并以更合理、有效地开发利用红树林土壤微生物资源为目标,展望了21世纪,以新理念、新技术、新方法进行红树林土壤微生物研究及资源开发的巨大前景。     

A Molecular Comparison of Plumage and Soil Bacteria Across Biogeographic,Ecological, and Taxonomic Scales

We used molecular methods to determine the microbial community of soil and avian plumage across biogeographic, ecological, and taxonomic scales. A total of 17 soil and 116 feather samples were collected from five avian species across multiple habitat types within one Neotropical and one temperate locality. Hypotheses regarding patterns of microbial composition relative to acquisition and dispersal of plumage bacteria in the ecosystem were tested by comparing microbial communities within and between soil and plumage. Samples from the plumage of American Redstarts (Setophaga ruticilla) were collected across both habitat types and geographic scales for intraspecific comparisons. The microbial diversity in avian plumage was moderately diverse and was dominated by Pseudomonas species. Despite a highly significant individual bird effect on microbial composition of the plumage, we detected significant biogeographic and type of habitat effects. Pseudomonas species were more abundant on the temperate site when all avian species were included in the analysis, and Bacillus subtilis and Xanthomonas groups were more abundant on the Neotropical site for redstarts alone. However, 16S rDNA sequence libraries were not significantly different between Jamaican and Maryland redstarts. Biogeographic and habitat effects were significant and more pronounced for soil samples indicating lower dispersal of soil microbiota. We detected a significant difference between soil and plumage microbial communities suggesting that soil plays a small role in plumage bacterial acquisition. Our results suggest bacterial communities on the plumage of birds are dynamic and may change at different stages in a bird’s annual cycle.     

冬季火对川西亚高山草地土壤微生物功能多样性及其强度的短期影响

为可持续管理川西亚高山草地生态系统, 全面地了解火后土壤微生物功能的多样性和强度的变化及其恢复状况, 基于2010年“12·5”冬草场的火烧事件, 以川西亚高山草地为研究对象, 对比了火烧和未火烧区域0-20 cm土层土壤中7种酶(β-葡糖苷酶、酸性磷酸酶、碱性磷酸酶、脲酶、蔗糖酶、蛋白酶和过氧化氢酶)的活性变化, 分析了土壤微生物功能多样性及其强度对火处理的响应。结果发现, 7种酶的潜在活性在0-5 cm土层中皆有所增加, 但对火处理、土层深度和两者交互作用的响应有所差异; 其中, 碱性磷酸酶在指示该区域火后微生物功能多样性和强度短期内的变化时具有较好的灵敏性和指示性。火在一定程度上促进了表土层微生物功能的发挥, 但是土壤微生物功能多样性及其强度对火和土层深度(0-20 cm)的响应并不显著。因此, 为能更好地揭示干扰行为对微生物生物多样性的影响机制, 未来应加强土壤微生物群落功能稳定性的研究。     

五大连池新期火山熔岩台地不同植被类型土壤微生物群落的功能多样性

土壤微生物群落是陆地生态系统的重要生物活性成分,其结构和功能多样性直接影响到系统的碳、氮等生态过程,微生物群落功能多样性与地上植被类型变化密切相关,开展植被类型对土壤微生物群落功能多样性的影响研究具有重要意义。以五大连池新期火山熔岩台地苔藓、草本、灌丛、矮曲林、针阔混交林5种典型植被类型为对象,利用BIOLOG微孔板法研究不同演替阶段植被类型土壤微生物群落功能多样性特征。结果表明：不同植被类型土壤微生物群落功能多样性存在显著差异。平均颜色变化率（AWCD）随培养时间延长而逐渐增加,大小顺序为：苔藓 > 针阔混交林 > 矮曲林 > 草本 > 灌丛。灌丛土壤微生物多样性指数与其他植被类型间差异显著。主成分分析结果表明,主成分1和主成分2分别能解释变量方差的56.24%和29.59%,不同植被类型下土壤微生物的碳源利用格局差异主要是由氨基酸类和带磷基糖类引起,二者合计解释总变异量的47.51%。冗余分析表明,速效磷、铵态氮、C：N和pH对微生物功能多样性具有显著的影响,羧酸类、氨基酸类、酯类和胺类的降解更易受到环境因素的影响。研究结果为进一步探讨植被类型与土壤微生物之间在植被演替过程中的关系提供参考。     

Short-term effects of a winter wildfire on diversity and intensity of soil microbial function in the subalpine grassland of western Sichuan,China

为可持续管理川西亚高山草地生态系统, 全面地了解火后土壤微生物功能的多样性和强度的变化及其恢复状况, 基于2010年“12·5”冬草场的火烧事件, 以川西亚高山草地为研究对象, 对比了火烧和未火烧区域0-20 cm土层土壤中7种酶(β-葡糖苷酶、酸性磷酸酶、碱性磷酸酶、脲酶、蔗糖酶、蛋白酶和过氧化氢酶)的活性变化, 分析了土壤微生物功能多样性及其强度对火处理的响应。结果发现, 7种酶的潜在活性在0-5 cm土层中皆有所增加, 但对火处理、土层深度和两者交互作用的响应有所差异; 其中, 碱性磷酸酶在指示该区域火后微生物功能多样性和强度短期内的变化时具有较好的灵敏性和指示性。火在一定程度上促进了表土层微生物功能的发挥, 但是土壤微生物功能多样性及其强度对火和土层深度(0-20 cm)的响应并不显著。因此, 为能更好地揭示干扰行为对微生物生物多样性的影响机制, 未来应加强土壤微生物群落功能稳定性的研究。     

土壤病毒之奥秘:研究进展、挑战及未来展望

土壤病毒是土壤生物多样性的重要组成部分,数量繁多,在调控微生物多样性、群落组成和养分循环等方面具有重要的生态功能。然而,由于土壤自身的复杂性及其动态变化特征,病毒在土壤生态系统中发挥的功能及其作用机理,一直是该研究领域的薄弱环节,也是当前土壤生物学、微生态学和环境科学等领域的研究热点和前沿。近年来,分子生物学技术的突破及生态学理论的广泛应用极大地推动了土壤病毒研究领域的发展。为客观全面地分析土壤病毒研究领域的动态和热点,本研究借助文献计量分析方法,对土壤病毒研究现状及热点进行了综述,展示了土壤病毒研究的发展态势,并结合土壤环境特征,对土壤病毒研究领域未来发展方向进行了展望,主要包括土壤病毒多样性、生物学特征、环境影响因素、作用机制及其在农业上的应用。随着多学科交叉融合及研究技术手段的进步,土壤病毒研究迎来了一个高速发展阶段,而土壤病毒研究在养分循环、生态系统服务及生物调控等方面所取得的重要成果,可以更好地服务于土壤健康以及碳中和计划。     

海洋微生物多样性及其分子生态学研究进展

海洋微生物多样性的深入研究将有助于微生物资源更好的开发和利用,海洋微生物多样性有很大的研究价值和研究空间。海洋中大多数微生物处于未可培养状态,在分子生态学基础上对海洋未可培养微生物进行研究是当今微生物多样性研究的主要方向。近年来相关研究进展迅速,研究方法不断更新。主要从分子生态学角度对微生物多样性研究现状进行概述并详细分析探讨了相关的研究方法,而且从分子生态学与海洋微生物多样性研究相结合的层面,对本领域的研究进行展望。旨在为海洋微生物多样性的研究及海洋资源的可持续开发与利用提供参考。     

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.     

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。     

Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape

Background

The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution.

Methodology/Principal Findings

Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat-specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta-diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity.

Conclusions/Significance

Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation.