RNA- and DNA-based profiling of soil fungal communities in a native Australian eucalypt forest and adjacent Pinus elliotti plantation     

Brigitte A. Bastias  Zhihong Xu 《Soil biology & biochemistry》2007,39(12):3108-3114

Total and active soil fungal communities in a native eucalypt forest and first rotation Pinus elliotti plantation were investigated by direct extraction of DNA and RNA from soil. Terminal restriction fragment length polymorphism (T-RFLP) analysis of internal transcribed spacer (ITS) and 18S rRNA profiles indicated that total and active fungal communities differed significantly in both forest types. This was supported by DGGE profile analysis on an individual plot basis for both forest types and when groups in the canonical analysis were redefined to allow comparison between forest types. Analyses of both ITS and 18S T-RFLP profiles indicated that conversion from native eucalypt forest to P. elliottii plantation may significantly alter total and active soil fungal communities. ITS DGGE (DNA) and 18S (RNA) profiles also suggested differences in fungal communities in the two forest types. No significant separation of the fungal communities in the two forest types was observed, however, when ITS DGGE (RNA) profiles were compared. Overall, the data suggest that conversion from native eucalypt forest to P. elliottii plantation at the Beerburrum State Forest in subtropical Australia has significantly altered soil fungal communities.  相似文献   

Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh     

Barbara Kraigher  Janez Hacin  Ivan Mahne  Ines Mandic-Mulec 《Soil biology & biochemistry》2006,38(9):2762-2771

Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled from the Ljubljana Marsh under different seasonal conditions. Substrate-induced respiration and dehydrogenase activity were used as indicators of total microbial activity. Both methods indicated higher microbial activities in the fen soil with the higher SOC content on all dates of sampling. To determine whether the differences in microbial activity were associated with differences in the microbial community structures, terminal restriction fragment length polymorphism (T-RFLP) of bacterial 16S rRNA genes was performed. Comparison of the T-RFLP profiles revealed very similar community structures in both fens and in the two seasonal extremes investigated. This suggested a stable community structure in the two fens, which is not affected by the SOC content or seasonal variation. In addition, a bacterial 16S ribosomal RNA gene based clone library was prepared from the fen soil with the higher SOC content. Out of 114 clones analysed, approximately 53% belonged to the Proteobacteria, 23% to the Acidobacteria, 21% to a variety of other taxa, and less than 3% were affiliated with the Firmicutes.  相似文献   

DNA and RNA in soil–What can we see through them? 7. Analysis of soil microbial community structure (Part 3). Multiple enzyme restriction fragment length polymorphism analysis and terminal restriction fragment length polymorphism analysis – their principles and applications     

Katsuji WATANABE  Masao SAKAI 《Soil Science and Plant Nutrition》2006,52(1):137-138

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Assessing the relationship between patch type and soil mites: A molecular approach     

Karen Gibb  Jennifer Beard  Peter O&#x;Reagain  Keith Christian  Valeria Torok  Kathy Ophel-Keller 《Pedobiologia》2008,51(5-6):445-461

An urgent need exists for indicators of soil health and patch functionality in extensive rangelands that can be measured efficiently and at low cost. Soil mites are candidate indicators, but their identification and handling is so specialised and time-consuming that their inclusion in routine monitoring is unlikely. The aim of this study was to measure the relationship between patch type and mite assemblages using a conventional approach. An additional aim was to determine if a molecular approach traditionally used for soil microbes could be adapted for soil mites to overcome some of the bottlenecks associated with soil fauna diversity assessment. Soil mite species abundance and diversity were measured using conventional ecological methods in soil from patches with perennial grass and litter cover (PGL), and compared to soil from bare patches with annual grasses and/or litter cover (BAL). Soil mite assemblages were also assessed using a molecular method called terminal-restriction fragment length polymorphism (T-RFLP) analysis. The conventional data showed a relationship between patch type and mite assemblage. The Prostigmata and Oribatida were well represented in the PGL sites, particularly the Aphelacaridae (Oribatida). For T-RFLP analysis, the mite community was represented by a series of DNA fragment lengths that reflected mite sequence diversity. The T-RFLP data showed a distinct difference in the mite assemblage between the patch types. Where possible, T-RFLP peaks were matched to mite families using a reference 18S rDNA database, and the Aphelacaridae prevalent in the conventional samples at PGL sites were identified, as were prostigmatids and oribatids. We identified limits to the T-RFLP approach and this included an inability to distinguish some species whose DNA sequences were similar. Despite these limitations, the data still showed a clear difference between sites, and the molecular taxonomic inferences also compared well with the conventional ecological data. The results from this study indicated that the T-RFLP approach was effective in measuring mite assemblages in this system. The power of this technique lies in the fact that species diversity and abundance data can be obtained quickly because of the time taken to process hundreds of samples, from soil DNA extraction to data output on the gene analyser, can be as little as 4 days.  相似文献   

Rearrangement of bacterial community structure during peat diagenesis     

Andrei L. Barkovskii  Hirokazu Fukui  Johannes Leisen  Terence L. Marsh 《Soil biology & biochemistry》2009,41(1):135-143

The relationship between microbial diagenesis of Sphagnum peat (SP) and reed-sedge peat (RSP) and the spatial organization of peat bacterial communities was studied. Peats were aerobically incubated at 18-22 °C for 4 months. Changes in molecular composition of peat organic matter were monitored with solid-state ¹³C NMR, and the respective amount of functional groups was determined by integration of corresponding peaks. No abiotic peat transformation was detected. SP diagenesis caused about a 4% loss of parent materials with a similar yield of ketones, phenols, aromatic, and carbonyl compounds; whereas about 20% of RSP carbohydrates, along with ketones and methoxyl compounds were gradually transformed into carbonyl and aliphatic compounds. SP and RSP substantially varied in bacterial composition. To address spatial community structure, bacterial populations were dissected by a differential elution technique into three fractions based on the degree of their attachment to peat. Community composition was surveyed with T-RFLP (HhaI, MspI, and RsaI). The fragments were further attributed to freely-dispersed (FD), particle-associated (PA), or omnipresent (OMN) bacterial fractions. In both peats, bacterial communities have gradually shifted with the progress of diagenesis. In SP, numbers of exclusively FD or PA bacteria slightly decreased while in RSP their numbers more than doubled after 4-month incubation, and the number of OMN bacteria respectively decreased. The substantially greater changes in the spatial structure of RSP bacterial community compared to SP were consistent with the chemical transformations detected in these peats suggesting the diagenesis-driven divergence of RSP bacterial community into FD and PA sub-communities.  相似文献   

Differences in the activity and bacterial community structure of drained grassland and forest peat soils     

Luka Ausec  Barbara Kraigher  Ines Mandic-Mulec   《Soil biology & biochemistry》2009,41(9):1874-1881

The microbial activity and bacterial community structure were investigated in two types of peat soil in a temperate marsh. The first, a drained grassland fen soil, has a neutral pH with partially degraded peat in the upper oxic soil horizons (16% soil organic carbon). The second, a bog soil, was sampled in a swampy forest and has a very high soil organic carbon content (45%), a low pH (4.5), and has occasional anoxic conditions in the upper soil horizons due to the high water table level. The microbial activity in the two soils was measured as the basal and substrate-induced respiration (SIR). Unexpectedly, the SIR (μl CO₂ g⁻¹ dry soil) was higher in the bog than in the fen soil, but lower when CO₂ production was expressed per volume of soil. This may be explained by the notable difference in the bulk densities of the two soils. The bacterial communities were assessed by terminal restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNA genes and indicated differences between the two soils. The differences were determined by the soil characteristics rather than the season in which the soil was sampled. The 16S rRNA gene libraries, constructed from the two soils, revealed high proportions of sequences assigned to the Acidobacteria phylum. Each library contained a distinct set of phylogenetic subgroups of this important group of bacteria.  相似文献   

Environmental and spatial characterisation of bacterial community composition in soil to inform sampling strategies     

Kate L. Baker  Silke Langenheder  Graeme W. Nicol  Dean Ricketts  Kenneth Killham  Colin D. Campbell  James I. Prosser 《Soil biology & biochemistry》2009,41(11):2292-2298

Soil physicochemical properties and microbial communities are highly heterogeneous and vary widely over spatial scales, necessitating careful consideration of sampling strategies to provide representative and reproducible soil samples across field sites. To achieve this, the study aimed to establish appropriate sampling methodology and to determine links between the variability of parameters, utilising two sampling strategies. The first (design 1) involved extracting 25 cores from random locations throughout the field and pooling them into five sets of five cores. The second (design 2) involved a further 25 cores within five 1 m² sub-plots. Sub-samples from each sub-plot were pooled in order to determine between and within sub-plot variability. All samples were analysed independently and as pooled sub-samples. Results indicate that pooling spatially separated samples significantly reduced the variability in pH, compared to individual samples. Pooling samples from a small area resulted in lower within sub-plot variability than between sub-plots for pH and bacterial community composition assessed by terminal-restriction fragment length polymorphism analysis. Following multivariate statistical analysis, a large amount of variation in community composition was explained by soil pH, which is remarkable given the relatively small size of the sampling area and minor differences in pH. Moisture content was also important in determining bacterial communities in the random design (design 1). In the 1 m² sub-plot design (design 2), the spatial location of the plots explained a large degree of the variation in bacterial community composition between plots, which was due to spatial autocorrelation of pH and possible additional environmental parameters. This study emphasises the importance of sampling design for obtaining representative samples from soil.  相似文献   

牛场肥水灌溉对土壤氨氧化微生物的影响   总被引：1，自引：0，他引：1  

王婷  刘丽丽  张克强  沈仕洲  冯洁  王风  杜会英  高文萱 《农业环境科学学报》2015,34(9):1737-1746

以不同牛场肥水灌溉制度下河北省徐水县梁家营长期定位施肥试验田为研究对象,通过构建氨氧化细菌和氨氧化古菌的amoA 基因克隆文库,利用T-RFLP方法研究了5种施肥处理(CK:不施肥;CF:300 kg N·hm^-2,120 kg P₂O·hm^-2,75 kg K₂O·hm^-2;T4:105 kg N·hm^-2,39 kg P₂O₅·hm^-2;T5:210 kg N·hm^-2,78 kg P₂O₅·hm^-2; T11:317 kg N·hm^-2,117 kg P₂O₅·hm^-2)下土壤中氨氧化细菌及氨氧化古菌的多样性及其群落结构演变。氨氧化细菌T-RFLP结果显示,T5 处理土壤中氨氧化细菌的 Shannon-Wiener指数(H')和 Pielou指数(E)均最高, T11处理最低,表明T5处理增加了土壤中氨氧化细菌的多样性和丰富度,T11处理一定程度上降低了氨氧化细菌的多样性和丰富度。基于amoA基因建立的系统进化树显示,土壤中氨氧化细菌主要属于Nitrosospira 和Nitrosomanas。氨氧化古菌T-RFLP结果显示,T11处理氨氧化古菌Shannon-Wiener指数(H')、Simpson 指数(Ds)和Pielou指数(E)均最高,表明T11处理增加了土壤中氨氧化古菌的多样性和丰富度。氨氧化古菌的系统发育树显示大部分氨氧化古菌amoA序列与 Cluster S 聚为一类,且占主导地位,少数序列为Unclassified-Archaea(未分类古菌)。最大优势菌与来自中国荷斯坦奶牛瘤胃样品的氨氧化古菌Clone属于同种,推测牛场肥水灌溉增加了土壤的氨氧化古菌的群落多样性。  相似文献   

生防木霉菌Th2和T4对甜瓜根围土壤微生态的影响   总被引：3，自引：1，他引：2  

郁雪平  朱伟杰  高观朋  王伟 《植物保护学报》2009,36(6):522-528

利用平板计数、微生物量碳和末端标记限制性片段长度多态性分析(terminal restriction fragment length polymorphism,T-RFLP)相结合的方法研究了2株生防菌哈茨木霉Th2和T4对甜瓜根围土壤微生态的影响.结果表明,生防菌Th2和T4对根围土壤细菌有明显的促生作用,而对真菌和放线菌有明显的抑制作用.T-RFLP数据统计学分析表明,Th2和T4的引入可以增加土壤细菌的多样性.其中对开花期土壤细菌菌群影响最显著,Th2对TRF251和TRF513菌群有显著的促生作用,含量是对照的3.7倍和4.5倍,T4对TRF251和TRF513菌群含量也比对照高4倍和5.6倍,而2株生防菌对TRF60菌群均有显著的抑制作用,其含量分别为对照的51.6%和64.3%.在果熟期生防菌对土壤细菌菌群的影响减弱,表明土壤的缓冲功能发挥了作用.研究结果还表明,Th2和T4对土壤细菌菌群有着相似的促生和抑制作用,且不会破坏土壤微生态的稳定性.  相似文献   

Investigations concerning the role of Chalara fraxinea in declining Fraxinus excelsior     

R. Bakys  R. Vasaitis  P. Barklund  K. Ihrmark  J. Stenlid 《Plant pathology》2009,58(2):284-292

A study was carried out to clarify the role of the fungus Chalara fraxinea in decline of Fraxinus excelsior , which is observed on a large scale in central and northern Europe with high incidence of tree mortality. The aims of this work were: (i) to check for the presence of C. fraxinea in various tissues of declining F. excelsior by agar culture isolations and by direct analysis of plant tissues using molecular techniques (DNA extraction, ITS-PCR, cloning, ITS sequencing and T-RFLP); (ii) to study fungal communities inhabiting tissues with symptoms; and (iii) to test the pathogenicity of C. fraxinea to F. excelsior . Chalara fraxinea was isolated from 93% of stem cankers, 91% of necrotic leaf stalks, 27–28% of bark wounds and 30% of visually healthy leaf stalks. Molecular analyses of necrotic leaves, leaf stalks and bark revealed the presence of 25 different fungal taxa, 14 of which were detected in all three types of tissue sample. Chalara fraxinea was the second most common species (61% of samples), and only Cryptococcus foliicola occurred more often (70%). All eight of the tested C. fraxinea isolates induced necroses in bark and cambium on each of 86 inoculated trees, and all controls remained healthy. Average length of necroses caused by different C. fraxinea strains varied from 4·2 to 8·9 cm, but the differences were statistically insignificant. Instead, differences in resistance of individual trees to C. fraxinea were observed.  相似文献