共查询到20条相似文献，搜索用时 31 毫秒
1.
Mark R. Liles Brian F. Manske Jean-Marie Rouillard Teri Balser Robert M. Goodman 《Soil biology & biochemistry》2010,42(5):739-747
We designed an oligonucleotide microarray using probe sequences based upon a phylogenetic analysis of 16S rRNA genes recovered from members of the bacterial division Acidobacteria. A total of 42,194 oligonucleotide probes targeting members of the Acidobacteria division at multiple phylogenetic levels were included on a high-density microarray. Positive control hybridizations revealed a linear relationship between hybridization signal and template concentration, and a substantial decrease in non-specific hybridization was achieved through the addition of 2.5 M betaine to the hybridization buffer. A mean hybridization signal value was calculated for each Acidobacteria lineage, with the resultant lineage-specific hybridization data revealing strong predictive value for the positive control hybridizations. The Acidobacteria phylochip was then used to evaluate Acidobacteria rRNA genes from a Wisconsin soil and within a soil clay fraction. The Acidobacteria hybridization profile revealed the predominance of Acidobacteria subdivisions four and six, and also suggested a decrease in the abundance of subdivision six relative to subdivision four in the soil clay fraction. The change in relative abundance of these subdivisions in a soil clay fraction was supported by data from quantitative PCR. These results support the utility of a phylogenetic microarray in revealing changes in microbial population-level distributions in a complex soil microbial assemblage. 相似文献
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Sangkyu Park Mi Ja Seo Ji Eun Yeon Soon-Chun Jeong Chee Hark Harn 《Soil biology & biochemistry》2006,38(8):2344-2349
To assess the impact of a transgenic crop on soil environment, we compared soil bacterial communities from the rhizospheres of cucumber green mottle mosaic virus (CGMMV)-resistant transgenic watermelon (Citrullus vulgaris [Twinser] cv. Gongdae) and non-transgenic parental line watermelon at an experimental farm in Miryang, Korea. Soil microbial community structure was studied using terminal restriction fragment length polymorphism (T-RFLP) using HaeIII and HhaI enzymes on products from polymerase chain amplification reactions (PCR) of total DNA from rhizosphere. We used principal component analyses (PCA) to reduce dimensionality of T-RFLP profiles before comparison. On these PCA scores, we conducted discrimination analyses to compare soil microbial communities from the rhizosphere of transgenic and non-transgenic. Discriminant analyses indicate that microbial communities from rhizosphere of transgenic and non-transgenic watermelon did not differ with significance at 95% level. Our study could be used as a model case to assess the environmental risk assessment of transgenic crops on soil microbial organisms. 相似文献
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《Applied soil ecology》2011,47(3):372-382
The proper identification and quantification of F. oxysporum populations inhabiting soil and plant rhizosphere niches are of importance for soil microbial ecology and plant pathology. In this study, we report the improvement of a PCR protocol for the specific identification of the F. oxysporum species complex and its conversion into a real-time qPCR assay for the quantification up to 1 pg of the fungus DNA in soil and different plant tissues. The amplification efficiency, sensibility and reproducibility of qPCR assays were not influenced by presence of non-target DNA from either plant or soil. The applicability of the newly developed qPCR protocol for F. oxysporum population studies was demonstrated using the technique for quantifying the fungus in different complex environmental samples. The use of the qPCR protocol allowed to accurately quantify up to 25 pg of F. oxysporum/g of naturally infested field soil, as well as to identify significant differences in the amount of F. oxysporum DNA in roots of different chickpea cultivars grown in a field soil infested with diverse pathogenic and nonpathogenic F. oxysporum populations. This qPCR protocol may be especially important for studies on soil microbial ecology and plant pathology since it provides a new opportunity for analyzing F. oxysporum populations and their interactions with the soil microflora, environment and plant host genotypes. 相似文献
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A quantitative approach was devised to evaluate the influence of soil microbial activity as a sink for nutrients exuded by fungal spores as a factor in soil fungistasis. The approach was based on measuring the CO2 evolved from microbial respiration of 14C-labelled exudates from conidia of Cochliobolus victoriae incubated on soil. The amount of exudate lost by spores on soil was greater than the amount lost by spores incubated on a bed of sand undergoing leaching at a flow rate of 110 ml h?1. where restriction of germination was similar to that on soil. Increasing flow rates in the leaching system increased spore exudation and reduced germination. Germination of C. victoriae conidia on membrane filters floated on distilled water decreased as the volume of water increased. The results indicate that the microbial nutrient sink of soil is sufficient to impose soil fungistasis. 相似文献
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《Applied soil ecology》2007,35(1):79-93
Microbial diversity in soils is considered important for maintaining sustainability of agricultural production systems. However, the links between microbial diversity and ecosystem processes are not well understood. This study was designed to gain better understanding of the effects of short-term management practices on the microbial community and how changes in the microbial community affect key soil processes. The effects of different forms of nitrogen (N) on soil biology and N dynamics was determined in two soils with organic and conventional management histories that varied in soil microbial properties but had the same fertility. The soils were amended with equal amounts of N (100 kg ha−1) in organic (lupin, Lupinus angustifolius L.) and mineral form (urea), respectively. Over a 91-day period, microbial biomass C and N, dehydrogenase enzyme activity, community structure of pseudomondas (sensu stricto), actinomycetes and α proteobacteria (by denaturing gradient gel electrophoresis (DGGE) following PCR amplification of 16S rDNA fragments) and N mineralisation were measured. Lupin amendment resulted in a two- to five-fold increase in microbial biomass and enzyme activity, while these parameters did not differ significantly between the urea and control treatments. The PCR–DGGE analysis showed that the addition of mineral and organic compounds had an influence on the microbial community composition in the short term (up to 10 days) but the effects were not sustained over the 91-day incubation period. Microbial community structure was strongly influenced by the presence or lack of substrate, while the type of amendment (organic or mineral) had an effect on microbial biomass size and activity. These findings show that the addition of green manures improved soil biology by increasing microbial biomass and activity irrespective of management history, that no direct relationship existed among microbial structure, enzyme activity and N mineralisation, and that microbial community structure (by PCR–DGGE) was more strongly influenced by inherent soil and environmental factors than by short-term management practices. 相似文献
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In recent years, methods of molecular microbiology have been used for the investigation of soil microbial diversity. Fluorescence in situ hybridization (FISH) represents a method which allows a specific staining and enumeration of soil microorganisms by using fluorescent-labelled oligonucleotide probes. However, the detection of FISH-stained cells is often affected by strong autofluorescence of the background, especially in samples of the top soils.In this study a more efficient FISH-approach coupled with catalyzed reporter deposition (CARD) was adapted to soils. Due to tyramide signal amplification (TSA) the fluorescence intensity has been considerably increased at the target binding site of a probe.Six different soils were investigated to evaluate the effect of sample preparation and pre-treatments, TSA, and the procedure of detection. The results show that both cell permeabilization and TSA are two important factors which improve in situ hybridization of soil microorganisms. Soils with higher clay contents have shown better results when prepared on polycarbonate filters rather than on glass slides.Using specific fluorescence filter systems and dye combinations the detection of hybridized cells was extensively increased compared with the application of monolabelled oligonucleotide probes in regular FISH-analysis. As a result, CARD-FISH-stained cells were suitable for automated counting using digital image analysis. Nevertheless, the counterstain with DAPI had to be analyzed manually as it was strongly affected by autofluorescence. 相似文献
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猪粪施于土壤可能会对土壤微生物多样性造成影响,为选用同一种DNA提取方法用于土壤和猪粪微生物DNA的提取,该文采用了化学裂解法和试剂盒法同时从土壤和猪粪样品中提取微生物DNA,并对这两种方法的提取DNA的效果进行了比较。结果表明,试剂盒法不能用于提取土壤中的微生物DNA;可以从猪粪中提取到DNA,PCR扩增能得到目的产物,但重复性不高。化学裂解法提取的土壤微生物DNA浓度高但纯度低,纯化后纯度增加,但DNA有所损失,用于PCR扩增时结果不理想;处理猪粪样品,提取的DNA浓度较低但纯度较高,PCR扩增结果比较理想。由此可见,化学裂解法用来提取猪粪样品中的微生物DNA是可行的,但需寻求更好的土壤样品微生物DNA的提取方法。 相似文献
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Rhizoctonia solani AG-8 is a major root pathogen in wheat (Triticum aestivum L.) systems worldwide and while natural disease suppression can develop under continuous cropping, this is not always the case. The main aim of our work was to elucidate the rhizosphere microbial community underlying a Rhizoctonia suppressive soil (Avon, South Australia) and to investigate how this community may develop in agricultural soils conducive to disease and of different soil type (Galong and Harden, New South Wales). The Avon suppressive soil community included Asaia spp. and Paenibacillus borealis, which were absent from a paired non-suppressive site. At Galong, soil taken from inside and outside disease patches showed no evidence of suppression, and disease suppression could not be transferred from the suppressive soil to the conducive soil from a different soil type and climatic area. 16S rRNA microarray analysis revealed Pseudomonas spp. were significantly more abundant inside than outside three disease patches at Galong. However, a survey of 32 patches across a range of stubble and tillage treatments at a nearby site showed no correlation between Pseudomonas and disease incidence. R. solani levels were significantly lower when stubble was retained rather than burnt or when nutrients (N, P and S) were incorporated with stubble during the non-crop period. Our results suggest soil type is an important factor for suppressive capability and that where specific disease suppression is absent, agronomic practice to increase soil carbon can encourage a non-specific microbial response that limits disease severity. 相似文献
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Lichen phenolics that are known to leach out from lichen thalli during rainfall episodes are considered to be allelopathic or antimicrobial agents. On the other hand, small organic molecules originating from aboveground vegetation generally constitute an important C source for the soil microbial community. We studied the effects of leaching lichen acids on soil microbial processes by chemically removing usnic (UA) and perlatolic acid (PA) from the extracellular space of mat-forming lichen, Cladina stellaris, a dominant component of the ground vegetation in boreal oligotrophic forests. Removal of UA and PA did not affect the intracellular contents of the lichen. We hypothesized that if lichen acids have an adverse effect on soil biota, microbial respiration would increase underneath chemically manipulated lichen mats. In turn, if these substances provide energy source for the microorganisms, microbial respiration would decline under lichens from which PA and UA has been removed. Microbial metabolic activity, qCO2 was significantly lower under the lichens from which UA and PA had been removed, thus supporting the latter hypothesis. Removing UA and PA did not affect the amount of microbial C, N and P, or soil nutrient concentrations. Our results suggest that the microbial community in the soil under a lichen carpet is adapted to the presence of these lichen secondary metabolites and can utilize them as a C source. The approach of removing lichen substances from the system could be used as an effective research tool as it can overcome several problems that are often common in the studies on allelopathic interactions. 相似文献
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传统的分离培养和鉴定土壤微生物方法所具有的困难性和局限性 ,是造成难以深入了解土壤微生物生态学特性和多样性组成方面的主要障碍。本文运用分子生物学技术 ,以澳大利亚两种主要森林类型的土壤微生物多样性研究为实例 ,介绍了从土壤中直接提取土壤微生物DNA的方法以及末端限制性酶切片段长度多态性 (T RFLP)分析的基本原理和方法。作者认为 ,用该方法提取的土壤真菌DNA的纯度高 ,完全适合PCR扩增和T RFLP分析的要求。T RFLP已成为国外深入研究土壤微生物多样性的理想方法之一 相似文献
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Bin Zhang Huan Deng Hui-li Wang Rui Yin Bryan S. Griffiths Tim J. Daniell 《Soil biology & biochemistry》2010,42(5):850-859
Re-vegetation of eroded soil restores organic carbon concentrations and improves the physical stability of the soil, which may then extend the range of microhabitats and influence soil microbial activity and functional stability through its effects on soil bacterial community structure. The objectives of this study were (i) to evaluate the restorative effect of re-vegetation on soil physical stability, microbial activity and bacterial community structure; (ii) to examine the effects of soil physical microhabitats on bacterial community structure and diversity and on soil microbial functional stability. Soil samples were collected from an 18-year-old eroded bare soil restored with either Cinnamomum camphora (“Eroded Cc”) or Lespedeza bicolour (“Eroded Lb”). An uneroded soil planted with Pinus massoniana (“Uneroded Pm”) and an eroded bare soil served as references. The effect of microhabitats was assessed by physical destruction with a wet shaking treatment. Soil bacterial community structure and diversity were measured using a terminal restriction fragment length polymorphism (T-RFLP) approach, while soil microbiological stability (resistance and resilience) was determined by measuring short-term (28 days) decomposition rate of added barley (Hordeum vulgare) powder following copper and heat perturbations. The results demonstrated that re-vegetation treatment affected the recovery of physical and biological stability, microbial decomposition and the bacterial community structure. Although the restored soils overshot the Uneroded Pm sample in physical stability, they had lower microbial decomposition and less resilience to copper and heat perturbations than the Uneroded Pm samples. Soil physical destruction by shaking had the same effect on soil physical stability, but different effects on soil microbial functional stability. There were significant effects of vegetation treatment and perturbation type, and interactive effects among vegetation treatment, shaking and perturbation type on bacterial community structure. The destruction of aggregate structure increased resilience of the Eroded Lb sample and also altered its bacterial community structure. Both copper and heat perturbations resulted in significantly different community structure from the unperturbed controls, with a larger effect of copper than heat perturbation. Bacterial diversity (Shannon index) increased following the perturbations, with a more profound effect in the Uneroded Pm sample than in the restored soils. The interactive effects of vegetation treatment and shaking on microbial community and stability suggest that soil aggregation may contribute to the generation of bacterial community structure and mediation of biological stability via the protection afforded by soil organic carbon. Differential effects of re-vegetation treatment suggest that the long-term effects are mediated through changes in the quality and quantity of C inputs to soil. 相似文献
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Falin Chen Hua Zheng Kai Zhang Zhiyun Ouyang Yongfu Wu Qian Shi Huailin Li 《Journal of Soils and Sediments》2013,13(5):887-894
Purpose
Although it is generally accepted that planting exotic plant species alters metabolic function of soil microbial communities, its temporal dynamic is often ignored when evaluating ecological effects of associated land use changes. To investigate the dynamic impacts of successive Eucalyptus planting on carbon metabolic activities of soil microbial communities, we studied community-level physiological profiles of soil microbial communities in different generations of Eucalyptus plantations.Materials and methods
We studied community-level physiological profiles of soil microbial communities, using the Biolog? Ecoplates incubation, in adjacent first (G1), second (G2), third (G3), and fourth (G4) generation Eucalyptus plantations that were, respectively, aged 3, 8, 14, and 19 years in Guangxi province, southern China. We used the ‘space-for-time substitution’ approach to investigate the impact of stand age of exotic Eucalyptus plantations on carbon metabolic diversity and activities of soil microbial communities. For each Eucalyptus plantation generation, three experimental plots were randomly selected. In each plot, one composite soil sample from 0 to 10 cm in depth was obtained for the analyses.Results and discussion
Single carbon source utilization varied with Eucalyptus plantation stand age. Among preselected 31 carbon sources, utilization of 17 carbon sources changed significantly, which was best described by a quadratic function (ten carbon sources) and an exponential function (seven carbon sources). As a result, cumulative averaged metabolic activity and metabolic diversity of soil microbial communities showed quadratic and exponential changes relative to Eucalyptus plantation stand age. The order of cumulative averaged carbon metabolic activity and metabolic diversity were G1?>?G4, G3?>?G2 and G1?>?G2?>?G3, G4 (p?<?0.05), respectively. The factors contributing to carbon source utilization structure of soil microbial communities for different stand ages of Eucalyptus plantations were shrub richness, soil organic carbon content, microbial biomass carbon, C-to-N ratio, and N-to-P ratio.Conclusions
Eucalyptus plantation stand age has inconsistent non-linear impacts on two aspects of soil microbial metabolic function: (1) quadratic impacts on carbon metabolic efficiency and (2) exponential impacts on carbon metabolic diversity. The decreasing carbon metabolic diversity has no significant impact on carbon metabolic efficiency during successive Eucalyptus plantings. The results show that the importance of assessing long-term impacts of land use changes on soil microbial communities from exotic plantations by quantifying multi-aspect non-linear changes on soil microbial metabolic function. 相似文献16.
Microbial community PLFA and PHB responses to ecosystem restoration in tallgrass prairie soils 总被引：1，自引：0，他引：1
Native North American prairie grasslands are renowned for the richness of their soils, having excellent soil structure and very high organic content and microbial biomass. In this study, surface soils from three prairie restorations of varying ages and plant community compositions were compared with a nearby undisturbed native prairie remnant and a cropped agricultural field in terms of soil physical, chemical and microbial properties. Soil moisture, organic matter, total carbon, total nitrogen, total sulfur, C:N, water-holding capacity and microbial biomass (total PLFA) were significantly greater (p<0.05) in the virgin prairie remnant as well as the two long-term (21 and 24 year) prairie restorations, compared with the agricultural field and the restoration that was begun more recently (7 years prior to sampling). Soil bulk density was significantly greater (p<0.05) in the agricultural and recently restored sites. In most cases, the soil quality indicators and microbial community structures in the restoration sites were intermediate between those of the virgin prairie and the agricultural sites. Levels of poly-β-hydroxybutyrate (PHB) and PLFA indicators of nutritional stress were significantly greater (p<0.05) in the agricultural and recent restoration sites than in the long-term restorations or the native prairie. Samples could be assigned to the correct site by discriminant analysis of the PLFA data, with the exception that the two long-term restoration sites overlapped. Redundancy analysis showed that prairie age (p<0.005) was the most important environmental factor in determining the PLFA microbial community composition, with C:N (p<0.015) also being significant. These findings demonstrate that prairie restorations can lead to improved quality of surface soils. We predict that the conversion of farmland into prairie will shift the soil quality, microbial community biomass and microbial community composition in the direction of native prairies, but with the restoration methods tested it may take many decades to approach the levels found in a virgin prairie throughout the soil profile. 相似文献
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E. A. Soshnikova A. S. Cherobaeva A. L. Stepanov E. V. Lebedeva N. A. Manucharova P. A. Kozhevin 《Moscow University Soil Science Bulletin》2016,71(3):135-138
DNA isolation from soil samples and amplification of fragment of a key gene of nitrification, archaeal and bacterial amoA, revealed presence of the product in all investigated soil samples. Characteristics of ammonia-oxidizing microbial communities in agrocenoses and undisturbed soil were determined. Bacteria were predominant in agrocenoses (at circum-neurtal pH), whereas the share of representatives of domain Archaea (phylum Thaumarchaeota) increased in prokaryotic ammonia-oxidizing complexes of undisturbed forest ecosystems (at low pH). It was demonstrated that the contribution of taumarhaea in nitrous oxide emission from gray forest soil may reach 20–25%. 相似文献
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Lisbet Holm Bach John-Arvid Grytnes Mikael Ohlson 《Soil biology & biochemistry》2010,42(11):1934-1943
Biological communities differ over time and in space, and in the forest these communities often vary according to trees and tree gaps, mediated by mechanisms that are likely to change over time and as a tree are removed. In this paper we ask the questions: What is the influence of individual trees on soil microbial community structure? Does the soil microbial community change in the short-term when a tree is removed, and does this change depend on the initial influence of the tree? We use phospholipid fatty acid (PLFA) analysis and a geostatistical approach to study effects of trees and tree removal (thinning) on soil microbial community structure in a young boreal Norway spruce (Picea abies) forest. An experiment was setup where half (four) of the included trees were cut and soil was collected prior to (t0) and one month after (t1) tree felling. The samples were collected along two perpendicular transects originating from each of the eight study trees. A tree influence index was calculated for each sample point from the distances to neighbouring trees, weighted by tree diameter. We found that individual trees are important in structuring the soil microbial community as microbial community structure responded to the gradient in tree influence. Also strong spatial structure was found corresponding to the patch structure induced by trees. Changes in microbial community structure before and after tree felling (t0 and t1) was found to differ significantly between felled and non-felled trees: samples from felled trees came to resemble samples with a low value of tree influence and samples from below non-felled trees came to resemble samples with a high value for tree influence. We thus found that soil microbial community structure in a boreal forest is spatially structured by the distribution of single trees, and that soil microbial community structure varies seasonally and is affected by tree removal, in an intricate manner that reflects the initial influence of trees. 相似文献
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Microbial biomass is an important source of soil organic matter, which plays crucial roles in the maintenance of soil fertility and food security. However, the mineralization and transformation of microbial biomass by the dominant soil macrofauna earthworms are still unclear. We performed feeding trials with the geophagous earthworm Metaphire guillelmi using 14C-labelled bacteria (Escherichia coli and Bacillus megaterium) cells, fungal (Penicillium chrysogenum) cells, protein, peptidoglycan, and chitin. The mineralization rate of the microbial cells and cell components was significantly 1.2–4.0-fold higher in soil with the presence of M. guillelmi for seven days than in earthworm-free soil and 1–11-fold higher than in fresh earthworm cast material. When the earthworms were removed from the soil, the mineralization of the residual carbon of the microbial biomass was significantly lower than that in the earthworm-free soil, indicating that M. guillelmi affects the mineralization of the biomass in soil in two aspects: first stimulation and then reduction, which were attributed to the passage of the microbial biomass through the earthworm gut, and that the microorganisms in the cast could play only minor roles in the stimulated mineralization and residual stabilization of microbial biomass. Large amounts (8–29%) of radiolabel of the tested microbial biomass were assimilated in the earthworm tissue. Accumulation of fungal cells (11%) and cell wall component chitin (29%) in the tissue was significantly higher than that of bacterial cells (8%) and cell wall component peptidoglycan (15%). Feeding trails with 14C-lablled microbial cells and cell components provided direct evidence that microbial biomass is a food source for geophagous earthworm and fungal biomass is likely a more important food source for earthworms than bacterial biomass. Findings of this study have important implications for the roles of geophagous earthworms in the fate of microbial biomass in soil. 相似文献
20.
Impact of coloniser plant species on the development of decomposer microbial communities following deglaciation 总被引：1，自引：0，他引：1
The effects of coloniser plant species on microbial community growth and composition were investigated on recently deglaciated terrain at Glacier Bay, south-east Alaska. Analysis of microbial communities using phospholipids fatty acid analysis (PLFA) revealed that Alnus and Rhacomitrium had the greatest impact on microbial growth, increasing total PLFA by some 6-7 fold relative to bare soil, whereas Equisetum led to a 5.5 fold increase in total PLFA relative to bare soil. These coloniser species also had significant effects on the composition of their associated microbial communities. Rhacomitrium, Alnus, and Equisetum increased bacterial PLFA, a measure of bacterial biomass, relative to bare soil. Rhacomitrium and Alnus also dramatically increased the concentration of the fungal fatty 18:2ω6 in soil relative to bare soil, by 12-fold and 8-fold, respectively. The net effect of the above changes was a significant increase in the ratio of fungal: bacterial fatty acids in soil associated with Alnus and Rhacomitrium, but not Equisetum. Possible reasons for these effects of particular plants on microbial communities are discussed, as is their significance in relation to the development of microbial communities in relatively sterile, recently deglaciated ground. 相似文献