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1.
土壤微生物多样性影响因素及研究方法的现状与展望   总被引:37,自引:0,他引:37  
周桔  雷霆 《生物多样性》2007,15(3):306-311
土壤微生物是土壤生态系统的重要组成部分,在土壤有机物质分解和养分释放、能量转移等生物地化循环中起着重要作用。随着人们对生物多样性重要性认识的不断深入及研究方法的不断改进,土壤微生物多样性,尤其是功能多样性的研究工作逐渐受到生态学家的重视。本文从土壤微生物多样性的影响因素以及研究方法等方面阐述了目前国内外土壤微生物多样性的研究现状,并对其未来研究方向进行了展望。  相似文献   

2.
入侵植物根际土壤微生物是地下生态系统的重要组成部分。外来植物入侵到新的栖息地后能够促进其根际土壤微生物群落结构的演替、改变土壤理化性质,强化微生物群落功能的发挥,进而创造更适合外来植物生长的土壤微环境,促进外来种的入侵进程。从外来入侵植物根际土壤微生物的研究方法、外来入侵植物对根际土壤微生物群落影响以及从地下生态学对外来植物入侵的影响等方面进行了综述。土壤微生物研究方法主要包括微生物计数法、微生物生理生化指标方法及分子技术3类;入侵植物对根际土壤微生物的影响主要体现在对其生物量、多样性以及功能微生物菌群等方面。在今后的研究中,应当注重对同一区域外来入侵植物和近缘本土种、及其伴生种的根际土壤微生物进行比较研究;加强入侵植物根际微生物功能机理、环境因子与微生物间关联性的研究;同时在研究方法上应注重传统方法与生物标记法及其与分子技术的结合。  相似文献   

3.
宏基因组学:土壤微生物研究的新策略   总被引:8,自引:0,他引:8  
土壤中多数微生物不可培养,这限制了微生物资源的开发利用。宏基因组学方法在开发和利用不可培养微生物资源方面有巨大潜力,可以将其运用到土壤微生物学研究中。对土壤宏基因组DNA的提取、宏基因组文库的构建和筛选等方面的研究现状和进展进行了简要综述。  相似文献   

4.
【目的】通过对一处经过长期使用贝壳砂进行改良的土壤中的反硝化细菌的多样性和细菌分离分析,研究该土壤中反硝化细菌的组成特征。【方法】采用454焦磷酸测序的方法分析了土壤样品中微生物群落的组成,选用Giltay培养基培养、鉴定从土壤中挑选的分离物的反硝化能力,并对具有反硝化能力的微生物进行了16S rRNA基因鉴定。【结果】该土壤样品中占据优势地位的为Proteobacteria、Acidobacteria、Bacteroidetes、Chloroflexi等门的微生物,属的水平上则有近70%尚未确立分类地位。所分离的细菌中,共得到12株厌氧条件下具有较高硝酸盐去除效率的微生物,分属Pseudomonas、Aeromonas、Serratia和Acinetobacter,均为γ变形菌纲的微生物。【结论】该土壤中具有较高的微生物多样性,包括很多未知类型的微生物和众多类型的反硝化细菌;分离到了11株具有反硝化能力的菌株,可用于该土壤的反硝化过程的进一步研究。  相似文献   

5.
研究确定土壤微生物基因组DNA提取方法、PCR扩增条件、DGGE电泳条件,为进一步研究分析土壤中微生物结构变化规律提供理论依据。土壤微生物基因组DNA提取采用直接法和间接法进行比较; PCR扩增条件调整扩增体系、DGGE电泳条件调整变性剂范围,并对其结果进行比较分析。通过对DGGE电泳相关条件的研究,结果显示,土壤中粗基因组DNA采用直接法提取,然后进行纯化; PCR扩增体系中加入BSA,DGGE电泳系统组成中变性剂浓度范围为35%~55%。确定了土壤微生物基因组DNA提取方法、PCR扩增条件、DGGE电泳条件,为后续的相关研究提供理论依据。  相似文献   

6.
[目的]揭示盐碱土壤微生物量与土壤因子间的关系.[方法]选择河西走廊不同盐碱程度的11个样点在春季进行采样,研究了土壤的微生物数量、酶活和理化性质,并对其进行方差分析、简单相关分析、逐步回归分析和主成分分析.[结果]河西地区原生盐碱地、次生盐碱地与农田土在土壤理化性质和土壤微生物数量等方面均有差异;河西地区土壤较贫瘠,土壤微生物数量较低,且分布有规律性,即原生盐碱土<次生盐碱土<农田土;放线菌、真菌、碱性磷酸酶、脲酶和有效磷5个因子是引起土壤微生物数量、酶活性与理化因子之间相关性的主要因素.[结论]结果证实河西地区盐碱土壤中磷的循环很大程度上影响着土壤微生物数量.  相似文献   

7.
【目的】评估土壤长期保存(4个月)对土壤微生物群落代谢活性的影响。【方法】采用Biolog? EcoPlateTM生态板研究4 °C风干保存和?20 °C低温冻存的农田土壤和森林土壤中微生物群落的碳源利用模式。【结果】与新鲜土壤样品相比,长期保存的土壤样品的微生物群落对碳源的利用能力大大降低,其多样性、均匀度和Simpson指数均降低;风干保存和低温冻存两者对土壤微生物的碳源利用的影响没有显著差异;除风干保存的土壤样品中利用多聚物类的微生物类群的代谢活性外,两种保存方法显著降低微生物群落的代谢活性,降低幅度为54.5%–99.8%。【结论】长期保存土壤可能会导致对微生物群落信息的低估,土壤微生物代谢活性研究的最佳样品为新鲜 土壤。  相似文献   

8.
3 次连续重复提取DNA 能较好反映土壤微生物丰度   总被引:7,自引:1,他引:6  
【目的】研究同一个土壤需要反复提取几次才能在最大程度上反映土壤微生物的丰度,探讨风干土壤代替新鲜土壤用于微生物丰度研究的可行性。【方法】针对两种理化性质具有较大差异的旱地和稻田新鲜土壤及其风干土壤,分别对土壤微生物进行5次连续裂解提取DNA。通过实时荧光定量PCR技术分析连续反复提取对土壤古菌和细菌16S rRNA gene数量、氨氧化古菌和细菌功能基因amoA数量的影响。【结果】3次连续提取DNA占5次提取DNA总量的76%以上,氨氧化古菌、氨氧化细菌、古菌和细菌4类微生物的3次连续提取最低回收率为77.5%;与新鲜土壤相比,风干处理导致氨氧化古菌、氨氧化细菌、古菌、细菌的数量分别降低84.3%、81.2%、12.5%和90.3%,然而,2种土壤风干过程中主要微生物类群的数量变化规律基本一致,表明土壤微生物对风干处理的响应可能受土壤类型的影响较小。【结论】土壤微生物连续3次裂解能较好反映微生物丰度。与新鲜土壤相比,风干过程显著降低了土壤微生物丰度,然而,通过风干土壤中微生物丰度的变化趋势反映新鲜土壤中微生物数量变化规律具有一定的可行性。  相似文献   

9.
【目的】揭示盐碱土壤微生物量与土壤因子间的关系。【方法】选择河西走廊不同盐碱程度的11个样点在春季进行采样,研究了土壤的微生物数量、酶活和理化性质,并对其进行方差分析、简单相关分析、逐步回归分析和主成分分析。【结果】河西地区原生盐碱地、次生盐碱地与农田土在土壤理化性质和土壤微生物数量等方面均有差异;河西地区土壤较贫瘠,土壤微生物数量较低,且分布有规律性,即原生盐碱土<次生盐碱土<农田土;放线菌、真菌、碱性磷酸酶、脲酶和有效磷5个因子是引起土壤微生物数量、酶活性与理化因子之间相关性的主要因素。【结论】结果证实河西地区盐碱土壤中磷的循环很大程度上影响着土壤微生物数量。  相似文献   

10.
农田生态系统耕作方式显著影响土壤微生物群落结构和功能,进而影响土壤微生物介导的土壤碳循环过程。以免耕结合作物秸秆还田为核心的保护性耕作是提升土壤碳汇功能和肥力的重要措施,其中土壤微生物发挥了关键作用。尽管有较多关于保护性耕作下微生物群落结构与功能的研究,但由于土壤系统的复杂性、环境因素以及微生物群落评价方法的差异性,尚未形成对保护性耕作下土壤微生物群落响应规律的系统认知。此外,研究多关注土壤微生物作为分解者的作用以及植物源碳对土壤碳库形成的贡献,而忽略了微生物源碳对土壤碳库形成和稳定的贡献。本文在归纳土壤有机质形成和稳定理论体系演变的基础上,梳理了土壤微生物研究方法的进展,重点阐述了保护性耕作对土壤微生物生物量、群落多样性和组成、碳代谢活性以及微生物源有机碳截获的影响,并对未来该领域的研究方向进行展望,以期为探索农田生态系统土壤微生物群落响应规律及其介导的土壤碳循环功能提供参考。  相似文献   

11.
Cultivation independent analyses of soil microbial community structures are frequently used to describe microbiological soil characteristics. This approach is based on direct extraction of total soil DNA followed by PCR amplification of selected marker genes and subsequent genetic fingerprint analyses. Semi-automated genetic fingerprinting techniques such as terminal restriction fragment length polymorphism (T-RFLP) and ribosomal intergenic spacer analysis (RISA) yield high-resolution patterns of highly diverse soil microbial communities and hold great potential for use in routine soil quality monitoring, when rapid high throughput screening for differences or changes is more important than phylogenetic identification of organisms affected. Our objective was to perform profound statistical analysis to evaluate the cultivation independent approach and the consistency of results from T-RFLP and RISA. As a model system, we used two different heavy metal treated soils from an open top chamber experiment. Bacterial T-RFLP and RISA profiles of 16S rDNA were converted into numeric data matrices in order to allow for detailed statistical analyses with cluster analysis, Mantel test statistics, Monte Carlo permutation tests and ANOVA. Analyses revealed that soil DNA-contents were significantly correlated with soil microbial biomass in our system. T-RFLP and RISA yielded highly consistent and correlating results and both allowed to distinguish the four treatments with equal significance. While RISA represents a fast and general fingerprinting method of moderate cost and labor intensity, T-RFLP is technically more demanding but offers the advantage of phylogenetic identification of detected soil microorganisms. Therefore, selection of either of these methods should be based on the specific research question under investigation.  相似文献   

12.
A survey of the available literature on methods most frequently used for the identification and characterization of microbial strains, communities, or consortia is presented. The advantages and disadvantages of the various methodologies were examined from several perspectives including technical, economic (time and cost), and regulatory. The methods fall into 3 broad categories: molecular biological, biochemical, and microbiological. Molecular biological methods comprise a broad range of techniques that are based on the analysis and differentiation of microbial DNA. This class of methods possesses several distinct advantages. Unlike most other commonly used methods, which require the production of secondary materials via the manipulation of microbial growth, molecular biological methods recover and test their source materials (DNA) directly from the microbial cells themselves, without the requirement for culturing. This eliminates both the time required for growth and the biases associated with cultured growth, which is unavoidably and artificially selective. The recovered nucleic acid can be cloned and sequenced directly or subpopulations can be specifically amplified using polymerase chain reaction (PCR), and subsequently cloned and sequenced. PCR technology, used extensively in forensic science, provides researchers with the unique ability to detect nucleic acids (DNA and RNA) in minute amounts, by amplifying a single target molecule by more than a million-fold. Molecular methods are highly sensitive and allow for a high degree of specificity, which, coupled with the ability to separate similar but distinct DNA molecules, means that a great deal of information can be gleaned from even very complex microbial communities. Biochemical methods are composed of a more varied set of methodologies. These techniques share a reliance on gas chromatography and mass spectrometry to separate and precisely identify a range of biomolecules, or else investigate biochemical properties of key cellular biomolecules. Like the molecular biological methods, some biochemical methods such as lipid analyses are also independent of cultured growth. However, many of these techniques are only capable of producing a profile that is characteristic of the microbial community as a whole, providing no information about individual members of the community. A subset of these methodologies are used to derive taxonomic information from a community sample; these rely on the identification of key subspecies of biomolecules that differ slightly but characteristically between species, genera, and higher biological groupings. However, when the consortium is already growing in chemically defined media (as is often the case with commercial products), the rapidity and relatively low costs of these procedures can mitigate concerns related to culturing biases. Microbiological methods are the most varied and the least useful for characterizing microbial consortia. These methods rely on traditional tools (cell counting, selective growth, and microscopic examination) to provide more general characteristics of the community as a whole, or else to narrow down and identify only a small subset of the members of that community. As with many of the biochemical methods, some of the microbiological methods can fairly rapidly and inexpensively create a community profile, which can be used to compare 2 or more entire consortia. However, for taxonomic identification of individual members, microbiological methods are useful only to screen for the presence of a few key predetermined species, whose preferred growth conditions and morphological characteristics are well defined and reproducible.  相似文献   

13.
Soil is a repository of diverse microorganisms, which has frequently been used to isolate and exploit microbes for industrial, environmental and agricultural applications. Knowledge about the structure and dynamics of bacterial communities in soil has been limited as only a small fraction of bacterial diversity is accessible to culture methods. Traditional enrichment techniques and the pure culture approach for microbiological studies have offered only a narrow portal for examining the soil microbial flora due to their limited selectivity. Therefore, the morphological and nutritional criteria used to describe bacterial community failed to provide a natural taxonomic order according to evolutionary relationship. Molecular methods under an emerging discipline of biology "molecular microbial ecology" are now helping in getting these constraints removed to some extent. Nucleic acid extraction from soil is the first crucial step in the application of most of the molecular techniques, which have largely been dominated by diverse variations of PCR. Due to its rapidity, sensitivity and specificity, PCR-based finger printing techniques have proved extremely useful in assessing the changes in microbial community structure. Such techniques can yield complex community profiles and can also provide useful phylogenetic information. Fluorescent in situ hybridization (FISH) can be used to evaluate the distribution and function of bacterial population in situ. DNA microarray techniques have also been developed and being frequently used for the evaluation of ecological role and phylogenetic affiliations of bacterial populations in the soil.  相似文献   

14.
Cultivation-independent analyses of soil microbial community structures are frequently used to describe microbiological soil characteristics. Semi-automated terminal restriction fragment length polymorphism (T-RFLP) analyses yield high-resolution genetic profiles of highly diverse soil microbial communities and hold great potential for use in routine soil quality monitoring. A serious limitation of T-RFLP analyses has been the inability to reliably affiliate observed terminal restriction fragments (T-RF) to phylogenetic groups. In the study presented here, we were able to overcome this limitation of T-RFLP. With a combination of adapter ligation, fragment size selection, and re-amplification with adapter site specific PCR, we were able to isolate a T-RF-fraction of a narrow size-range containing a T-RF that was significantly more abundant in heavy metal amended soils. Cloning the size-selected T-RF fraction allowed for the efficient isolation of clones containing this specific T-RF. Sequence determination and phylogenetic inference in RDP-II affiliated the sequence to unclassified cyanobacteria. Specific primer design and PCR amplification from bulk soil DNA allowed for independent confirmation of the results from bacterial T-RFLP and T-RF cloning. Our results show that specific T-RFs can be efficiently isolated and identified, and that the adapter ligation approach holds great potential for genetic profiling and for identification of community components of interest.  相似文献   

15.
Summary There is an immense literature on biological and biochemical analyses of soils. Such analyses have revealed the enormous richness of species in soil and their vast range of metabolic potentials and ecological diversity. Accordingly, the approaches used to investigate the soil biota and its biochemistry usually have to be modified or adapted depending upon the purpose of the investigation.Studies of micro-organisms in the soil environment, are complicated because microbial cells are commonly attached to surfaces where they live side-by-side with other populations in consortia usually containing different morphological and physiological types. Such assemblages of organisms cannot be described quantitatively using cultural techniques, such as plate counts, which underestimate both cell numbers and viable biomass. The development of more powerful observational and staining techniques has improved our knowledge of the diverse morphological and biochemical composition of soil micro-communities. Such findings have been amplified at a grosser level by laboratory studies with multi-component systems (microcosms) to mimic field situations and to assess the range of biochemical potentials of microbial consortia.But despite notable advances in analytical methods we are still, with a few exceptions, unable to detect or identify those microorganisms which carry out specific biochemical transformations or determine whether particular cells are alive, dormant or dead at the time of observation.Considerable work has been done to define some of the fundamental ecological attributes of microbial assemblages in soil. Productive work on the metabolic activities of the soil microbiota, specially geochemical transformations of C, N, S and P, has been under way for more than a century. But only in more recent years have more sensitive and reproducible analytical methods become available to measure viable biomass in soil. This will enable some insight to be gained into the role that microbial biomass plays as a labile source and sink for plant nutrients.Introductory lecture  相似文献   

16.
A combination of geochemical, microbiological and isotopic methods were used to evaluate in-situ bioremediation of petroleum hydrocarbons at one site contaminated with refinery waste and a second site contaminated with aviation gasoline at Alameda Point, California. At each site, geochemical and microbiological characteristics from four locations in the contaminated zone were compared to those from two uncontaminated background locations. At both sites, the geochemical indicators of in-situbiodegradation includeddepleted soil gas and groundwater oxygen, elevated groundwater alkalinity, and elevated soil gas carbon dioxide and methane in the contaminated zone relative to the background. Radiocarbon content of methane and carbon dioxide measured in soil gas at both sites indicated that they were derived from hydrocarbon contaminant degradation. Direct microscopy of soil core samples using cell wall stains and activity stains, revealed elevated microbial numbers and enhanced microbial activities in contaminated areas relative to background areas, corroborating geochemical findings. While microbial plate counts and microcosm studies using soil core samples provided laboratory evidence for the presence of some microbial activity and contaminant degradation abilities, they did not correlate well with either contaminant location, geochemical, isotopic, or direct microscopy data.  相似文献   

17.
The impact of long-term heavy metal contamination on soil communities was assessed by a number of methods. These included plate counts of culturable bacteria, community level physiological profiling (CLPP) by analysis of the utilization of multiple carbon sources in BIOLOG plates, community fatty acid methyl ester (C-FAME) profiling and dehydrogenase enzyme activity measurements. These approaches were complemented with microscopic assessments of the diversity of the nematode community. Samples from two sites with different histories of heavy-metal input were assessed. Major differences in microbial and meiofaunal parameters were observed both between and within the sites. There was a large degree of congruence between each of the microbiological approaches. In particular, one sample appeared to be distinguished by a reduction in culturable bacteria (especially pseudomonads), limited response to carbon sources in CLPP, and major differences in extracted fatty acid profiles. The use of multivariate analysis to examine the relationship between microbial and physicochemical measurements revealed that CLPP and plate counts were useful for determining the gross effect of metals on soil microbial communities, whereas proportions of metal-resistant bacteria and dehydrogenase activity differentiated between the two sites. Copper and zinc concentrations and pH all showed significant correlation with the microbial parameters. Nematode community structure was affected to a greater extent by soil pH than by metal content, but the within-site rankings were the same as those achieved for microbiological analyses. The use of these methods for field evaluation of the impact of industrial pollution may be possible provided care is taken when interpreting the data.  相似文献   

18.
污染土壤微生物群落结构多样性及功能多样性测定方法   总被引:18,自引:0,他引:18  
陈承利  廖敏  曾路生 《生态学报》2006,26(10):3404-3412
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.  相似文献   

19.
土壤微生物多样性研究方法   总被引:43,自引:8,他引:35  
概述了研究土壤微生物多样性的主要方法.传统上,土壤微生物群落的分析依赖于培养技术,使用各种培养基最大限度地培养各种微生物群体,但仍只能培养和分离出一小部分土壤微生物群落.使用Biolog分析、磷脂脂肪酸分析和核酸分析等方法,可研究和表征那些现在还不能够被培养的土壤微生物。从而获取关于土壤微生物群落多样性的更多和更完整的信息.  相似文献   

20.
Until recently, our understanding of microbial community development in soil ecosystems exposed to different inorganic and organic pollutants has been limited to culturable microorganisms because of the techniques available. The discovery that most soil microorganisms are non-culturable but potentially viable and metabolically active accelerated the application of different culture-independent methods for structural diversity assessments of the microbial community. This review examines the results of recent studies on the impact of heavy metals and organic pollutants on the diversity of the microflora obtained with methods based on analyses of signature biomarkers such as nucleic acids and fatty acids. The application of these techniques allowed researchers to pinpoint reduction of microbial diversity in contaminated soil, and significant shifts in the community structure, leading to the dominance of only a few populations (species) and the disappearance of others, some of which were never isolated by conventional methods (e.g. an increase in Acidobacterium or a decrease in terrestrial non-thermophilic Crenarchaeota). Although the new techniques are not free from limitations, they allow the monitoring of the virtual impact of stressors on soil microorganisms and the direction of resuscitation of the microbial community during natural or induced bioremediation, especially when using combined approaches.  相似文献   

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