Fatty acid methyl ester (FAME) profiles as measures of soil microbial community structure

Analysis of fatty acid methyl ester (FAME) profiles extracted from soils is a rapid and inexpensive procedure that holds great promise in describing soil microbial community structure without traditional reliance on selective culturing, which seems to severely underestimate community diversity. Interpretation of FAME profiles from environmental samples can be difficult because many fatty acids are common to different microorganisms and many fatty acids are extracted from each soil sample. We used principal components (PCA) and cluster analyses to identify similarities and differences among soil microbial communities described using FAME profiles. We also used PCA to identify particular FAMEs that characterized soil sample clusters. Fatty acids that are found only or primarily in particular microbial taxa-marker fatty acids-were used in conjunction with these analyses. We found that the majority of 162 soil samples taken from a conventionally-tilled corn field had similar FAME profiles but that about 20% of samples seemed to have relatively low, and that about 10% had relatively high, bacterial:fungal ratios. Using semivariance analysis we identified 21:0 iso as a new marker fatty acid. Concurrent use of geostatistical and FAME analyses may be a powerful means of revealing other potential marker FAMEs. When microbial communities from the same samples were cultured on R2A agar and their FAME profiles analyzed, there were many differences between FAME profiles of soil and plated communities, indicating that profiles of FAMEs extracted from soil reveal portions of the microbial community not culturable on R2A. When subjected to PCA, however, a small number of plated communities were found to be distinct due to some of the same profile characteristics (high in 12:0 iso, 15:0 and 17:1 ante A) that identified soil community FAME profiles as distinct. Semivariance analysis indicated that spatial distributions of soil microbial populations are maintained in a portion of the microbial community that is selected on laboratory media. These similarities between whole soil and plated community FAME profiles suggest that plated communities are not solely the result of selection by the growth medium, but reflect the distribution, in situ, of the dominant, culturable soil microbial populations.     

Microbial Diversity in Soil,Sand Dune and Rock Substrates of the Thar Monsoon Desert,India

A culture-independent diversity assessment of archaea, bacteria and fungi in the Thar Desert in India was made. Six locations in Ajmer, Jaisalmer, Jaipur and Jodhupur included semi-arid soils, arid soils, arid sand dunes, plus arid cryptoendolithic substrates. A real-time quantitative PCR approach revealed that bacteria dominated soils and cryptoendoliths, whilst fungi dominated sand dunes. The archaea formed a minor component of all communities. Comparison of rRNA-defined community structure revealed that substrate and climate rather than location were the most parsimonious predictors. Sequence-based identification of 1240 phylotypes revealed that most taxa were common desert microorganisms. Semi-arid soils were dominated by actinobacteria and alpha proteobacteria, arid soils by chloroflexi and alpha proteobacteria, sand dunes by ascomycete fungi and cryptoendoliths by cyanobacteria. Climatic variables that best explained this distribution were mean annual rainfall and maximum annual temperature. Substrate variables that contributed most to observed diversity patterns were conductivity, soluble salts, Ca²⁺ and pH. This represents an important addition to the inventory of desert microbiota, novel insight into the abiotic drivers of community assembly, and the first report of biodiversity in a monsoon desert system.     

贺兰山不同海拔典型植被带土壤微生物多样性

土壤微生物多样性在海拔梯度的分布格局研究近年来受到和植物动物一样的重视程度,但是干旱风沙区微生物多样性在海拔梯度上的多样性分布规律尚未揭示。本研究以处于干旱风沙区的贺兰山不同海拔的六个典型植被带（荒漠草原带、山地旱生灌丛带、温性针叶林带、针阔混交林带、寒温性针叶林带和亚高山草甸带）土壤为研究对象,利用Biolog微平板法和磷脂脂肪酸甲酯法(FAMEs)系统研究微生物多样性群落特征以及在不同植被带分布规律。结果表明：土壤微生物功能多样性随海拔增加发生变化,且微生物群落结构存在显著差异。Biolog分析显示土壤微生物群落代谢活性依次是：亚高山草甸>寒温性针叶林>针阔混交林>温性针叶林>山地旱生灌丛>荒漠草原,随海拔的升高土壤微生物群落物种丰富度指数（H）和均匀度指数（E）总体上均表现出增大的趋势,差异显著（P＜0.05）;FAMEs分析表明不同海拔的微生物区系发生了一定程度的变化,寒温性针叶林土壤微生物磷酸脂肪酸生物标记的数量和种类均最高,且细菌、真菌特征脂肪酸相对含量也最高;土壤微生物群落结构多样性次序是：寒温性针叶林带>针阔混交林带>温性针叶林带>亚高山草甸>山地旱生灌丛>荒漠草原。本研究结果表明贺兰山海拔梯度的微生物多样性分布规律不同于已有的植物多样性“中部膨胀”研究结果,这说明在高海拔地区有更多的适合该生境的微生物存在,这对维持干旱风沙区的生态系统功能稳定性具有重要意义。     

古尔班通古特沙漠生物土壤结皮对氨氧化微生物生态位的影响

生物结皮作为荒漠地表的重要覆被类型, 在荒漠生态系统的氮素循环中扮演重要角色。融雪期为古尔班通古特沙漠生物结皮的复苏和生长提供了充足的水分, 也成为该沙漠氮素固定和转化的重要时期, 但该时期生物结皮如何影响驱动氨氧化转化的微生物群落动态尚未明确。因此, 我们利用荧光定量PCR (fluorescent quantitative PCR, qPCR)方法分析融雪期生物结皮与去除结皮不同土层(0-2, 2-5, 5-10和10-20 cm)氨氧化菌群丰度特征, 结合潜在硝化速率和土壤理化参数, 探究融雪期生物结皮对荒漠土壤氮素转化作用。结果表明: 氨氧化古菌(ammonia-oxidizing archaea, AOA)是古尔班通古特沙漠土壤优势氨氧化菌, 生物结皮对0-2 cm层土壤中AOA、氨氧化细菌(ammonia-oxidizing bacteria, AOB) amoA基因丰度具有显著抑制作用(P < 0.01), 对10-20 cm层土壤中AOA amoA基因丰度具有显著促进作用(P < 0.01)。冗余分析(redundancy analysis, RDA)表明, AOA、AOB amoA基因丰度主要受土壤含水量和铵态氮含量的影响, 占总条件效应的54.90%。氨氧化速率分析发现, 去除生物结皮显著降低古尔班通古特沙漠土壤硝化作用潜力(P < 0.001), 证实生物结皮对荒漠土壤氮素转化具有重要的调控作用。综上所述, 古尔班通古特沙漠氨氧化微生物的分布规律受环境因子调控, 特别是生物结皮可以通过调节土壤含水量和铵态氮含量影响AOA和AOB的空间生态位分化, 促进沙漠土壤的硝化作用。     

脂肪酸甲酯法检测空心莲子草入侵影响土壤微生物群落结构的初步研究

空心莲子草是我国2003年公布的第一批外来入侵物种。为了进一步了解该植物的入侵机制,采集湖北咸宁、仙桃和武汉三地的土样,采用土壤脂肪酸甲酯谱图分析的方法探讨该植物入侵对土壤微生物的影响。结果显示：空心莲子草入侵后土壤可培养细菌、真菌的数量显著增加,而放线菌的数量显著下降。脂肪酸分析表明土壤微生物群落结构发生一定程度的改变,但其变化因土壤的不同而有差异。     

Assessment of the spatial distribution of soil microbial communities in patchy arid and semi-arid landscapes of the Negev Desert using combined PLFA and DGGE analyses

Arid and semi-arid ecosystems are often characterized by vegetation patchiness and variable availability of resources. Phospholipid fatty acid (PLFA) and 16S rRNA gene fragment analyses were used to compare the bulk soil microbial community structure at patchy arid and semi-arid landscapes. Multivariate analyses of the PLFA data and the 16S rRNA gene fragments were in agreement with each other, suggesting that the differences between bulk soil microbial communities were primarily related to shrub vs intershrub patches, irrespective of climatic or site differences. This suggests that the mere presence of a living shrub is the dominant driving factor for the differential adaptation of the microbial communities. Lipid markers suggested as indicators of Gram-positive bacteria were higher in soils under the shrub canopies, while markers suggested as indicators of cyanobacteria and anaerobic bacteria were elevated in the intershrub soils. Secondary differences between soil microbial communities were associated with intershrub characteristics and to a lesser extent with the shrub species. This study provides an insight into the multifaceted nature of the factors that shape the microbial community structure in patchy desert landscapes. It further suggests that these drivers not only act in concert but also in a way that is dependent on the aridity level.     

长期施肥对灰漠土生物群落和酶活性的影响

长期定位试验表明:施肥对灰漠土生物类群、酶活性有一定影响,同时生物类群和酶活性也改变了土壤生态环境.(1) 施肥对灰漠土动物个体及类群数的影响显著,长期单施化肥对土壤动物优势度作用较大,化肥配施有机肥丰富了土壤动物组成,化肥配施秸秆有利于增加土壤动物的丰度,尤其是疣跳科和等节跳科动物个体数量增加近10倍,长期不施肥土壤动物均匀性较高,但优势类群数较低;(2)灰漠土微生物组成以细菌为主,特殊微生物生理类群是以固氮菌和氨化细菌数量居多.长期单施化肥不利于土壤微生物生长,几种菌类数量均较低,化肥配施有机物料增加了土壤微生物类群数量,比对照增加15%～44%,长期不施肥土壤微生物数量高于单施化肥处理.(3) 灰漠土自身过氧化氢酶含量较高,蔗糖酶次之.土壤4种酶活性中除过氧化氢酶与土壤养分之间呈负相关以外,其余3种酶活性与土壤速效养分均呈正相关或显著正相关.长期单施化肥土壤脲酶、磷酸酶活性降低,长期不施肥土壤脲酶、磷酸酶活性高于单施化肥处理,化肥配施有机肥或秸秆的土壤脲酶、蔗糖酶、磷酸酶活性比长期不施肥增加了24%～31%.因此,化肥配施有机物料增加了土壤酶活性,加速了土壤熟化,改变了土壤生态环境.     

宁夏荒漠草原不同植物群落微斑块内土壤微生物区系特征

植物群落斑块化是天然放牧草地最基本的特征之一.为探索植物群落斑块化对土壤微生物群落组成及多样性的影响,本研究以宁夏荒漠草原为研究对象,采用磷脂脂肪酸(PLFA)法对比分析了不同植物群落微斑块内土壤微生物生物量和群落结构特征的变化.结果表明: 1) 4种植物群落微斑块内土壤微生物种类丰富,且都表现为细菌含量最高,真菌和放线菌含量较少,革兰氏阳性菌含量高于革兰氏阴性菌;2)4种植物群落中,甘草微斑块的土壤微生物总量显著高于猪毛蒿、苦豆子和黄芪;3)冗余分析表明,磷脂脂肪酸总量、革兰氏阳性菌、革兰氏阴性菌、真菌、厌氧菌、真菌/细菌均与土壤有机碳呈显著正相关,与pH呈显著负相关,表明土壤有机碳、pH是荒漠草原土壤微生物生长和发育的重要影响因素.     

Factors determining soil microbial biomass and nutrient immobilization in desert soils

We examined the 10-day response of soil microbial biomass-N to additions of carbon (dextrose) and nitrogen (NH₄NO₃) to water-amended soils in a factorial experiment in four plant communities of the Chihuahuan desert of New Mexico (U.S.A.). In each site, microbial biomass-N and soil carbohydrates increased and extractable soil N decreased in response to watering alone. Fertilization with N increased microbial biomass-N in grassland soils; whereas, fertilization with C increased microbial biomass-N and decreased extractable N and P in all communities dominated by shrubs, which have invaded large areas of grassland in the Chihuahuan desert during the last 100 years. Our results support the hypothesis that the control of soil microbial biomass shifts from N to C when the ratio of C to N decreases during desertification.     

Microbial community in the rhizosphere of young maize seedlings is susceptible to the impact of introduced pseudomonads as indicated by FAME analysis

Two species of Pseudomonas (i.e. P. chlororaphis or P. putida) derived from a maize rhizosphere were studied for their impact on the structure of the microbial community in the rhizosphere of young maize seedlings after inoculation. The culturable bacteria and total microbial communities were analyzed based on profiles of whole-cell fatty acid methyl esters (MIDI-FAME). The introduction of Pseudomonas species resulted in the shift from the Gram-positive dominated culturable community in the rhizosphere of uninoculated maize to more Gram-negative populations in the rhizospheres of the inoculated plants. For the total rhizosphere communities, 43, 47 and 42 FAMEs were detected in the uninoculated maize and the samples inoculated with P. chlororaphis or P. putida, respectively. In contrast to the culturable communities, low concentrations of marker FAMEs for Gram-positives (i15:0, a15:0, i16:0) were found in the profiles of the total rhizosphere communities. The maize inoculations resulted in an enrichment of some Gram-negative isolates; however, Gram-positive bacteria, Cytophaga/Flavobacterium and saprophytic fungi were found in the uninoculated rhizosphere.     

Amino Acid Analyses of Desert Varnish from the Sonoran and Mojave Deserts

There has long been a debate as to whether desert varnish deposits are microbially mediated or are deposited by inorganic processes. Several researchers have cultured bacteria from the surface of desert varnish suggesting that bacteria are intimately associated with varnish coatings and may play a role in their formation. To test this hypothesis, we have collected scrapings of desert varnish from the Sonoran Desert in Arizona and the Mojave Desert in California and analyzed them for amino acids. Thirteen amino acids were found in desert varnish indicating a biogenic component of these varnishes. Two protein amino acids that were not detected in any of the varnishes are cysteine and tryptophan. Two nonprotein amino acids,β-alanine andγ-amino butyric acid, were found. These are known to be formed by enzymatic decarboxylation, thereby indicating possible organismal activity in varnish. Some D -enantiomers of the amino acids were also found. In addition to small amounts of the D -enantiomer of aspartic acid, which is rapidly formed by racemization and was present in most samples, D -alanine and D -glutamic acid were found. These latter two amino acids are components of the peptidoglycan cell wall material of bacteria. L -lysine was also detected, but not diaminopimelic acid. The combination of L -lysine, D -alanine, and D -glutamic acid is characteristic of the peptidoglycan from Gram-positive bacteria. Although the presence of these biomarkers does not prove that Gram-positive bacteria produce the coatings, finding them is consistent with the hypothesis that they may play a role in desert varnish formation.     

Early Development of Soil Microbial Communities on Rehabilitated Quarries

The ecological development of soil microbial communities was studied in terms of microbial composition and structure at different rehabilitated phases on three quarries, namely Turret Hill Quarry (TH), Lam Tei Quarry (LT), and Shek O Quarry (SO), in Hong Kong. Using individual fatty acid methylesters (FAMEs) as biomarkers, Gram^? bacteria dominated at all sites, in which cy19:0 represented more than 15% of the total extracted FAMEs in all soils tested. Redundancy analysis showed that the abundance of Gram^? bacteria and Gram⁺ bacteria correlated significantly with woody species richness, native species richness, organic C, total N, and extractable NO₃‐N. Fungi (18:1w9c and 18:2w6) and arbuscular mycorrhizal (AM) fungi (16:1w5c) decreased in abundance with increasing age in SO and LT, which were positively correlated with grass coverage, soil pH, extractable NH₄‐N, and extractable P. Our study suggested that soil aeration and C availability in soils played a dominant role driving the changes in the composition and structure of Gram^? bacteria and Gram⁺ bacteria communities. Available P was the limiting factor for regulating the fungal and AM fungal communities on our local quarries.     

The Dry Limit of Microbial Life in the Atacama Desert Revealed by Calorimetric Approaches

The Atacama desert in Chile is one of the driest and most lifeless environments on Earth. It rains possibly once a decade. NASA examined these soils as a model for the Martian environment by comparing their degradation activity with Martian soil and looking for “the dry limit of life”. The existence of heterotrophic bacteria in Atacama soil was demonstrated by DNA extraction and by the isolation of microorganisms. So far, however, no data have been available about the metabolic activities in these soils due to the limitations of the existing methodologies when applied to desert soils. Calorimetry was used to obtain information on the metabolic and thermal properties of eleven soil samples collected at different sites in the Atacama desert. Differential scanning calorimetry and isothermal calorimetry were employed to determine the pyrolysis properties of the carbon‐containing matter and to measure biomass and microbial metabolism. They were compared to other soil properties such as total carbon and nitrogen, carbon to nitrogen ratio and pH. There was measurable organic matter in nine of the eleven samples and the heat of pyrolysis of those soils was correlated to the carbon content. In five of the eleven samples no biomass could be detected and the existence of basal microbial metabolism could not be established because all samples showed endothermic activity, probably from inorganic reactions with water. Six samples showed microbial activation after the addition of glucose. Carbon content, nitrogen content and the microbial activity after glucose amendment were correlated to the altitude and to the average minimum temperature of the sampling sites calculated from meteorological data. The detectable microbial metabolism was more dissipative with increasing altitude and decreasing temperature.     

极端干旱区防护林地土壤微生物多样性

土壤微生物在森林土壤中有重要功能.采用传统培养、脂肪酸鉴定和PCR-DGGE 3种方法分别研究了塔里木沙漠公路防护林地土壤微生物数量、脂肪酸种类和细菌DNA片段的多样性,从微生物学角度为塔里木沙漠公路防护林的管理提供理论依据.结果表明,塔里木沙漠公路防护林的建设促进了风沙土土壤微生物的发育,随着防护林定植年限的增加,土壤微生物数量、脂肪酸和细菌DNA片段的多样性指数明显增大;土壤微生物区系组成中,细菌是优势类群,占微生物总数80%以上,而真菌很少,不到微生物总数1%,但在不同土层间有所差异;传统培养法与现代生物标记和分子生物学方法对塔里木沙漠公路防护林地土壤微生物多样性的研究结果基本一致,说明塔里木沙漠公路防护林的建设使林地土壤生物活性有所增强,有利于林地土壤养分循环与利用.     

Microbial 13C utilization patterns via stable isotope probing of phospholipid biomarkers in Mojave Desert soils exposed to ambient and elevated atmospheric CO2

Changes in plant inputs under changing atmospheric CO₂ can be expected to alter the size and/or functional characteristics of soil microbial communities which can determine whether soils are a C sink or source. Stable isotope probing was used to trace autotrophically fixed ¹³C into phospholipid fatty acid (PLFA) biomarkers in Mojave Desert soils planted with the desert shrub, Larrea tridentata. Seedlings were pulse‐labeled with ¹³CO₂ under ambient and elevated CO₂ in controlled environmental growth chambers. The label was chased into the soil by extracting soil PLFAs after labeling at Days 0, 2, 10, 24, and 49. Eighteen of 29 PLFAs identified showed ¹³C enrichment relative to nonlabeled control soils. Patterns of PLFA enrichment varied temporally and were similar for various PLFAs found within a microbial functional group. Enrichment of PLFA ¹³C generally occurred within the first 2 days in general and fungal biomarkers, followed by increasingly greater enrichment in bacterial biomarkers as the study progressed (Gram‐negative, Gram‐positive, actinobacteria). While treatment CO₂ level did not affect total PLFA‐C concentrations, microbial functional group abundances and distribution responded to treatment CO₂ level and these shifts persisted throughout the study. Specifically, ratios of bacterial‐to‐total PLFA‐C decreased and fungal‐to‐bacterial PLFA‐C increased under elevated CO₂ compared with ambient conditions. Differences in the timing of ¹³C incorporation into lipid biomarkers coupled with changes in microbial functional groups indicate that microbial community characteristics in Mojave Desert soils have shifted in response to long‐term exposure to increased atmospheric CO₂.     

Bacterial Diversity of Terrestrial Crystalline Volcanic Rocks, Iceland

Bacteria inhabiting crystalline rocks from two terrestrial Icelandic volcanic lava flows of similar age and from the same geographical region, but differing in porosity and mineralogy, were characterised. Microarray (PhyloChip) and clone library analysis of 16S rRNA genes revealed the presence of a diverse assemblage of bacteria in each lava flow. Both methods suggested a more diverse community at the Dómadalshraun site (rhyolitic/andesitic lava flow) than that present at the Hnausahraun site (basaltic lava flow). Proteobacteria dominated the clone library at the Dómadalshraun site, while Acidobacteria was the most abundant phylum in the Hnausahraun site. Although analysis of similarities of denaturing gradient gel electrophoresis profiles suggested a strong correlation of community structure with mineralogy, rock porosity may also play an important role in shaping the bacterial community in crystalline volcanic rocks. Clone sequences were most similar to uncultured microorganisms, mainly from soil environments. Of these, Antarctic soils and temperate rhizosphere soils were prominent, as were clones retrieved from Hawaiian and Andean volcanic soils. The novel diversity of these Icelandic microbial communities was supported by the finding that up to 46% of clones displayed <85% sequence identities to sequences currently deposited in the RDP database.     

Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development

The origins of the biological complexity and the factors that regulate the development of community composition, diversity and richness in soil remain largely unknown. To gain a better understanding of how bacterial communities change during soil ecosystem development, their composition and diversity in soils that developed over c. 77 000 years of intermittent aeolian deposition were studied. 16S rRNA gene clone libraries and fatty acid methyl ester (FAME) analyses were used to assess the diversity and composition of the communities. The bacterial community composition changed with soil age, and the overall diversity, richness and evenness of the communities increased as the soil habitat matured. When analysed using a multivariate Bray-Curtis ordination technique, the distribution of ribotypes showed an orderly pattern of bacterial community development that was clearly associated with soil and ecosystem development. Similarly, changes in the composition of the FAMEs across the chronosequence were associated with biomarkers for fungi, actinomycetes and Gram-positive bacteria. The development of the soil ecosystem promoted the development of distinctive microbial communities that were reminiscent of successional processes often evoked to describe change during the development of plant communities in terrestrial ecosystems.     

Spatial distribution of microbial communities associated with dune landform in the Gurbantunggut Desert,China

The microbial community compositions and potential ammonia oxidation in the topsoil at different positions of sand dune (stoss slope, crest, lee slope, and interdune) from the Gurbantunggut Desert, the largest semi-fixed desert in China, were investigated using several molecular methods. Actinobacteria and Proteobacteria (especially Alphaproteobacteria) were commonly the dominant taxa across all soil samples. Bacterial communities were similar in soils collected from the stoss slopes and interdunes (HC-BSCs, biological soil crusts with a high abundance of cyanobacteria), containing more abundant cyanobacterial populations (16.9–24.5%) than those (0.2–0.7% of Cyanobacteria) in the crests and lee slopes (LC-BSCs, biological soil crusts with a low abundance of cyanobacteria). The Cyanobacteria were mainly composed of Microcoleus spp., and quantitative PCR analysis revealed that 16S rRNA gene copy numbers of Cyanobacteria (especially genus Microcoleus) were at least two orders of magnitude higher in HC-BSCs than in LC-BSCs. Heterotrophic Geodermatophilus spp. frequently occurred in HC-BSCs (2.5–8.0%), whereas genera Arthrobacter, Bacillus, and Segetibacter were significantly abundant in LC-BSC communities. By comparison, the desert archaeal communities were less complex, and were dominated by Nitrososphaera spp. The amoA gene abundance of ammonia-oxidizing archaea (AOA) was higher than that of ammonia-oxidizing bacteria (AOB) in all soil samples, particularly in the interdunal soils (10⁶–10⁸ archaeal amoA gene copies per gram dry soil), indicating that AOA possibly dominate the ammonia oxidation at the interdunes.     

Physiology and microbial community structure in soil at extreme water content

A sandy loam soil was brought to 6 water contents (13-100% WHC) to study the effects of extreme soil moistures on the physiological status of microbiota (represented by biomass characteristics, specific respiration, bacterial growth, and phospholipid fatty acid, PLFA, stress indicators) and microbial community structure (assessed using PLFA fingerprints). In dry soils, microbial biomass and activity declined as a consequence of water and/or nutrient deficiency (indicated by PLFA stress indicators). These microbial communities were dominated by G+ bacteria and actinomycetes. Oxygen deficits in water-saturated soils did not eliminate microbial activity but the enormous accumulation of poly-3-hydroxybutyrate by bacteria showed the unbalanced growth in excess carbon conditions. High soil water content favored G bacteria.     

Impact of fumigants on soil microbial communities.

Agricultural soils are typically fumigated to provide effective control of nematodes, soilborne pathogens, and weeds in preparation for planting of high-value cash crops. The ability of soil microbial communities to recover after treatment with fumigants was examined using culture-dependent (Biolog) and culture-independent (phospholipid fatty acid [PLFA] analysis and denaturing gradient gel electrophoresis [DGGE] of 16S ribosomal DNA [rDNA] fragments amplified directly from soil DNA) approaches. Changes in soil microbial community structure were examined in a microcosm experiment following the application of methyl bromide (MeBr), methyl isothiocyanate, 1,3-dichloropropene (1,3-D), and chloropicrin. Variations among Biolog fingerprints showed that the effect of MeBr on heterotrophic microbial activities was most severe in the first week and that thereafter the effects of MeBr and the other fumigants were expressed at much lower levels. The results of PLFA analysis demonstrated a community shift in all treatments to a community dominated by gram-positive bacterial biomass. Different 16S rDNA profiles from fumigated soils were quantified by analyzing the DGGE band patterns. The Shannon-Weaver index of diversity, H, was calculated for each fumigated soil sample. High diversity indices were maintained between the control soil and the fumigant-treated soils, except for MeBr (H decreased from 1.14 to 0.13). After 12 weeks of incubation, H increased to 0.73 in the MeBr-treated samples. Sequence analysis of clones generated from unique bands showed the presence of taxonomically unique clones that had emerged from the MeBr-treated samples and were dominated by clones closely related to Bacillus spp. and Heliothrix oregonensis. Variations in the data were much higher in the Biolog assay than in the PLFA and DGGE assays, suggesting a high sensitivity of PLFA analysis and DGGE in monitoring the effects of fumigants on soil community composition and structure. Our results indicate that MeBr has the greatest impact on soil microbial communities and that 1,3-D has the least impact.