Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer

Knowledge about the relationship between microbial community structure and hydrogeochemistry (e.g., pollution, redox and degradation processes) in landfill leachate-polluted aquifers is required to develop tools for predicting and monitoring natural attenuation. In this study analyses of pollutant and redox chemistry were conducted in parallel with culture-independent profiling of microbial communities present in a well-defined aquifer (Banisveld, The Netherlands). Degradation of organic contaminants occurred under iron-reducing conditions in the plume of pollution, while upstream of the landfill and above the plume denitrification was the dominant redox process. Beneath the plume iron reduction occurred. Numerical comparison of 16S ribosomal DNA (rDNA)-based denaturing gradient gel electrophoresis (DGGE) profiles of Bacteria and Archaea in 29 groundwater samples revealed a clear difference between the microbial community structures inside and outside the contaminant plume. A similar relationship was not evident in sediment samples. DGGE data were supported by sequencing cloned 16S rDNA. Upstream of the landfill members of the beta subclass of the class Proteobacteria (beta-proteobacteria) dominated. This group was not encountered beneath the landfill, where gram-positive bacteria dominated. Further downstream the contribution of gram-positive bacteria to the clone library decreased, while the contribution of delta-proteobacteria strongly increased and beta-proteobacteria reappeared. The beta-proteobacteria (Acidovorax, Rhodoferax) differed considerably from those found upstream (Gallionella, Azoarcus). Direct comparisons of cloned 16S rDNA with bands in DGGE profiles revealed that the data from each analysis were comparable. A relationship was observed between the dominant redox processes and the bacteria identified. In the iron-reducing plume members of the family Geobacteraceae made a strong contribution to the microbial communities. Because the only known aromatic hydrocarbon-degrading, iron-reducing bacteria are Geobacter spp., their occurrence in landfill leachate-contaminated aquifers deserves more detailed consideration.     

Microbial Distribution in a Hydrothermal Plume of the Southwest Indian Ridge

Hydrothermal plumes are widely distributed throughout the global spreading ridges, yet few of them are microbiologically explored. The ultraslow-spreading ridges, recently recognized as a unique, new class of mid-ocean-ridge system, have provided surprises and new insights in hydrothermal system research. A suite of water column samples including both hydrothermal plume samples and ambient seawater were collected at different depths from the ultraslow-spreading Southwest Indian Ridge (SWIR) in 2010. We use molecular approaches such as clone libraries, denaturing gradient gel electrophoresis (DGGE) and quantitative PCR to determine microbial community compositions and their spatial variability within the hydrothermal plume and seawater. Phylogenetic analysis showed that plume samples were mainly dominated by members of α-Proteobacteria and γ-Proteobacteria and members of marine group I group within the Crenarchaeota. Within the hydrothermal plume, archaeal populations were spatially homogeneous, while bacterial compositions were heterogeneous and remarkably distinct at different depths. Moreover, several lineages, closely related to known Mn(II) oxidizers were found to be abundant and even predominant within the plume bacterial communities. DGGE band patterns showed that there was no significant difference in microbial compositions between the samples of hydrothermal plume and ambient seawater. Taken together, we inferred that microbial communities in the SWIR hydrothermal plumes were sourced from ambient seawater rather than from seafloor vent-derived niches. This is the first report on the characteristics of microbial community structures in hydrothermal plume and ambient seawater in the Southwest Indian Ridge.     

Microbial Population Changes during Bioremediation of an Experimental Oil Spill

Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the α-proteobacteria and Flexibacter-Cytophaga-Bacteroides phylum. α-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained.     

Microbial population changes during bioremediation of an experimental oil spill.

Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the alpha-proteobacteria and Flexibacter-Cytophaga-Bacteroides phylum. alpha-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained.     

Bacterial Diversity of the Broadbalk ‘Classical’ Winter Wheat Experiment in Relation to Long-Term Fertilizer Inputs

With more than 160 years of contrasting fertilizer regimes, the Broadbalk winter wheat experiment represents a unique experimental resource for studying the effects of long-term fertilizer application on microbial population diversity. Using DGGE and clone library analysis, we report here on eubacterial species diversity (16S rRNA gene) and diversity within two sets of gene products associated with microbial N acquisition: NifH (nitrogen fixation) and AmtB (ammonium transport). Comparisons were made within and between soils treated with mineral N fertilizer, farmyard manure or receiving no fertilizer. Analysis of 16S rRNA gene DGGE profiles showed no clear patterns to qualitatively distinguish bacterial community structure between the three different treatments (P > 0.05), with all samples containing a range of eubacterial taxa similar to those that are characteristic of soil bacteria reported elsewhere. Intra-plot heterogeneity was high and of a similar magnitude to that between treatments. This lack of qualitative between plot differences was echoed in the representative sequences of 16S rRNA, nifH, and amtB genes in the various samples. Taken together, both phylogenetic and functional gene analyses showed bacterial communities in the Broadbalk-trial soil were very stable and relatively non-responsive to long-term management of balanced fertilizer inputs.     

Dynamic changes in the microbial community composition in microbial fuel cells fed with sucrose

The performance and dynamics of the bacterial communities in the biofilm and suspended culture in the anode chamber of sucrose-fed microbial fuel cells (MFCs) were studied by using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA genes followed by species identification by sequencing. The power density of MFCs was correlated to the relative proportions of species obtained from DGGE analysis in order to detect bacterial species or taxonomic classes with important functional role in electricity production. Although replicate MFCs showed similarity in performance, cluster analysis of DGGE profiles revealed differences in the evolution of bacterial communities between replicate MFCs. No correlation was found between the proportion trends of specific species and the enhancement of power output. However, in all MFCs, putative exoelectrogenic denitrifiers and sulphate-reducers accounted for approximately 24% of the bacterial biofilm community at the end of the study. Pareto–Lorenz evenness distribution curves extracted from the DGGE patterns obtained from time course samples indicated community structures where shifts between functionally similar species occur, as observed within the predominant fermentative bacteria. These results suggest the presence of functional redundancy within the anodic communities, a probable indication that stable MFC performance can be maintained in changing environmental conditions. The capability of bacteria to adapt to electricity generation might be present among a wide range of bacteria.     

Biodegradation processes in a laboratory-scale groundwater contaminant plume assessed by fluorescence imaging and microbial analysis

Flow reactors containing quartz sand colonized with biofilm were set up as physical model aquifers to allow degrading plumes of acetate or phenol to be formed from a point source. A noninvasive fluorescent tracer technique was combined with chemical and biological sampling in order to quantify transport and biodegradation processes. Chemical analysis of samples showed a substantial decrease in carbon concentration between the injection and outflow resulting primarily from dilution but also from biodegradation. Two-dimensional imaging of the aqueous oxygen [O2(aq)] concentration field quantified the depletion of O2(aq) within the contaminant plume and provided evidence for microbial respiration associated with biodegradation of the carbon source. Combined microbiological, chemical, and O2(aq) imaging data indicated that biodegradation was greatest at the plume fringe. DNA profiles of bacterial communities were assessed by temperature gradient gel electrophoresis, which revealed that diversity was limited and that community changes observed depended on the carbon source used. Spatial variation in activity within the plume could be quantitatively accounted for by the changes observed in active cell numbers rather than differences in community structure, the total biomass present, or the increased enzyme activity of individual cells. Numerical simulations and comparisons with the experimental data were used to test conceptual models of plume processes. Results demonstrated that plume behavior was best described by growth and decay of active biomass as a single functional group of organisms represented by active cell counts.     

A Shallow BTEX and MTBE Contaminated Aquifer Supports a Diverse Microbial Community

Microbial communities in subsurface environments are poorly characterized and the impacts of anthropogenic contamination on their structure and function have not been adequately addressed. The release of contaminant(s) to a previously unexposed environment is often hypothesized to decrease the diversity of the affected community. We characterized the structure of microbial communities along a gradient of benzene, toluene, ethylbenzene, and xylene (BTEX) and methyl-tert-butyl-ether (MTBE) contamination, resulting from a petroleum spill, within a shallow sandy aquifer at Vandenberg Air Force Base (VAFB) in Lompoc, CA. Differences in microbial community composition along the contaminant plume were assessed via a combinatorial approach utilizing denaturing gradient gel electrophoresis (DGGE), cloning and sequencing, intergenic transcribed spacer analysis (ITS), and comparative phylogenetic analysis of partial 16S rDNA sequences. Substantial bacterial sequence diversity, similar levels of species richness, and similar phylo-groups (including the Cytophaga–Flavobacterium–Bacteroidetes group and numerous members of the -, -, -, -, and -groups of the proteobacteria) were observed in both uncontaminated and contaminated regions of the aquifer. High-resolution measures (ITS fingerprinting and phylogenetic inference) readily separated communities impacted by the original petroleum spill (in source zone) from those in other parts of the aquifer and indicated that communities exposed to MTBE only were similar to communities in uncontaminated regions. Collectively, these data suggest that petroleum contamination alters microbial community structure at the species and subspecies level. Further study is required to determine whether these changes have an impact on the functioning of this subsurface ecosystem.     

Geobacteraceae community composition is related to hydrochemistry and biodegradation in an iron-reducing aquifer polluted by a neighboring landfill

Relationships between community composition of the iron-reducing Geobacteraceae, pollution levels, and the occurrence of biodegradation were established for an iron-reducing aquifer polluted with landfill leachate by using cultivation-independent Geobacteraceae 16S rRNA gene-targeting techniques. Numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles and sequencing revealed a high Geobacteraceae diversity and showed that community composition within the leachate plume differed considerably from that of the unpolluted aquifer. This suggests that pollution has selected for specific species out of a large pool of Geobacteraceae. DGGE profiles of polluted groundwater taken near the landfill (6- to 39-m distance) clustered together. DGGE profiles from less-polluted groundwater taken further downstream did not fall in the same cluster. Several individual DGGE bands were indicative of either the redox process or the level of pollution. This included a pollution-indicative band that dominated the DGGE profiles from groundwater samples taken close to the landfill (6 to 39 m distance). The clustering of these profiles and the dominance by a single DGGE band corresponded to the part of the aquifer where organic micropollutants and reactive dissolved organic matter were attenuated at relatively high rates.     

应用DGGE研究微生物群落时的常见问题分析

变性梯度凝胶电泳(DGGE)是通过核酸片段对微生物群落进行研究,可以监测未培养细菌及其功能基因,被广泛地应用于微生物群落多样性和动态分析,并成为微生物分子生态学研究中的重要手段之一。文中论述了DGGE操作过程中遇到的常见问题,并提出了相应的解决方法。全面分析了样品预处理过程和PCR扩增效果对DGGE分析的影响,探讨了DGGE图谱的优化过程和图谱分析方法,并对DGGE的应用前景进行了综述。     

Biodegradation Processes in a Laboratory-Scale Groundwater Contaminant Plume Assessed by Fluorescence Imaging and Microbial Analysis

Flow reactors containing quartz sand colonized with biofilm were set up as physical model aquifers to allow degrading plumes of acetate or phenol to be formed from a point source. A noninvasive fluorescent tracer technique was combined with chemical and biological sampling in order to quantify transport and biodegradation processes. Chemical analysis of samples showed a substantial decrease in carbon concentration between the injection and outflow resulting primarily from dilution but also from biodegradation. Two-dimensional imaging of the aqueous oxygen [O₂(aq)] concentration field quantified the depletion of O₂(aq) within the contaminant plume and provided evidence for microbial respiration associated with biodegradation of the carbon source. Combined microbiological, chemical, and O₂(aq) imaging data indicated that biodegradation was greatest at the plume fringe. DNA profiles of bacterial communities were assessed by temperature gradient gel electrophoresis, which revealed that diversity was limited and that community changes observed depended on the carbon source used. Spatial variation in activity within the plume could be quantitatively accounted for by the changes observed in active cell numbers rather than differences in community structure, the total biomass present, or the increased enzyme activity of individual cells. Numerical simulations and comparisons with the experimental data were used to test conceptual models of plume processes. Results demonstrated that plume behavior was best described by growth and decay of active biomass as a single functional group of organisms represented by active cell counts.     

Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil

In recent years, culture-independent methods have been used in preference to traditional isolation techniques for microbial community analysis. However, it is questionable whether uncultured organisms from a given sample are important for determining the impact of anthropogenic stress on indigenous communities. To investigate this, soil samples were taken from a site with patchy metal contamination, and the bacterial community structure was assessed with a variety of approaches. There were small differences in microscopic epifluorescence bacterial counts. Denaturing gradient gel electrophoresis (DGGE) profiles of 16S rRNA gene fragments (16S-DGGE) amplified directly from soil samples were highly similar. A clone library generated from the most contaminated sample revealed a diverse bacterial community, which showed similarities to pristine soil communities from other studies. However, the proportion of bacteria from the soil samples that were culturable on standard plate-counting media varied between 0.08 and 2.2%, and these values correlated negatively with metal concentrations. The culturable communities from each sample were compared by 16S-DGGE of plate washes and by fatty acid profiling of individual isolates. Each approach indicated that there were considerable differences between the compositions of the culturable communities from each sample. DGGE bands from both culture-based and culture-independent approaches were sequenced and compared. These data indicated that metal contamination did not have a significant effect on the total genetic diversity present but affected physiological status, so that the number of bacteria capable of responding to laboratory culture and their taxonomic distribution were altered. Thus, it appears that plate counts may be a more appropriate method for determining the effect of heavy metals on soil bacteria than culture-independent approaches.     

Cultivation-Dependent and -Independent Approaches for Determining Bacterial Diversity in Heavy-Metal-Contaminated Soil

In recent years, culture-independent methods have been used in preference to traditional isolation techniques for microbial community analysis. However, it is questionable whether uncultured organisms from a given sample are important for determining the impact of anthropogenic stress on indigenous communities. To investigate this, soil samples were taken from a site with patchy metal contamination, and the bacterial community structure was assessed with a variety of approaches. There were small differences in microscopic epifluorescence bacterial counts. Denaturing gradient gel electrophoresis (DGGE) profiles of 16S rRNA gene fragments (16S-DGGE) amplified directly from soil samples were highly similar. A clone library generated from the most contaminated sample revealed a diverse bacterial community, which showed similarities to pristine soil communities from other studies. However, the proportion of bacteria from the soil samples that were culturable on standard plate-counting media varied between 0.08 and 2.2%, and these values correlated negatively with metal concentrations. The culturable communities from each sample were compared by 16S-DGGE of plate washes and by fatty acid profiling of individual isolates. Each approach indicated that there were considerable differences between the compositions of the culturable communities from each sample. DGGE bands from both culture-based and culture-independent approaches were sequenced and compared. These data indicated that metal contamination did not have a significant effect on the total genetic diversity present but affected physiological status, so that the number of bacteria capable of responding to laboratory culture and their taxonomic distribution were altered. Thus, it appears that plate counts may be a more appropriate method for determining the effect of heavy metals on soil bacteria than culture-independent approaches.     

Geobacteraceae Community Composition Is Related to Hydrochemistry and Biodegradation in an Iron-Reducing Aquifer Polluted by a Neighboring Landfill

Relationships between community composition of the iron-reducing Geobacteraceae, pollution levels, and the occurrence of biodegradation were established for an iron-reducing aquifer polluted with landfill leachate by using cultivation-independent Geobacteraceae 16S rRNA gene-targeting techniques. Numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles and sequencing revealed a high Geobacteraceae diversity and showed that community composition within the leachate plume differed considerably from that of the unpolluted aquifer. This suggests that pollution has selected for specific species out of a large pool of Geobacteraceae. DGGE profiles of polluted groundwater taken near the landfill (6- to 39-m distance) clustered together. DGGE profiles from less-polluted groundwater taken further downstream did not fall in the same cluster. Several individual DGGE bands were indicative of either the redox process or the level of pollution. This included a pollution-indicative band that dominated the DGGE profiles from groundwater samples taken close to the landfill (6 to 39 m distance). The clustering of these profiles and the dominance by a single DGGE band corresponded to the part of the aquifer where organic micropollutants and reactive dissolved organic matter were attenuated at relatively high rates.     

PCR指纹图谱技术分析人体口腔内微生物菌群结构

目的 应用PCR-DGGE指纹图谱技术对人体口腔微生物菌群结构进行系统性研究.方法 对1例健康人唾液周期性采集的样品和8例健康人个体的唾液与牙菌斑采集的样品,进行微生物群落总DNA的抽提.以此为模板扩增16S rRNA V3可变区,产物经DGGE指纹图谱分析其组成结构,并运用UVIBAND/MAP等软件比较所得群落指纹图谱的相似性指数.结果 同一健康人个体不同采样时间的唾液菌群结构相似性系数＞74%,通过对不同健康个体口腔样本的研究,发现同一个体的唾液与牙菌斑菌群结构存在差异（84%～95%）.结论 同一健康个体其唾液微生物菌群在一定时间内基本稳定,仅有微小的变化;唾液与同个体牙菌斑的微生物组成虽然存在差异,但这种差异要明显小于个体间的差异.     

The impact of grassland management on archaeal community structure in upland pasture rhizosphere soil

The community structure of rhizosphere soil Archaea from three grassland types, associated with different management practices, was examined at a site in the Borders region of Scotland, by analysis of 16S rRNA gene fragments amplified from 16S rDNA and from rRNA. Denaturing gradient gel electrophoresis (DGGE) and sequence analysis of amplified products indicated high relative abundance within the archaeal community of two distinct lineages of non-thermophilic (group 1) Crenarchaeota. Grassland management practices influenced archaeal community structure, as characterized by both 16S rRNA- and 16S rDNA-derived DGGE profiles. One band dominated DGGE profiles in all three grassland types examined, and reproducible differences in the presence and intensity of bands were observed between profiles from managed and natural grassland sites. Analysis of 16S rRNA-derived amplicons from managed and natural grasslands at sites in the north of England and the north of Wales also indicated high relative abundance of non-thermophilic crenarchaeotes within the archaeal community. The band dominating the Scottish grassland site also dominated DGGE profiles from the English and Welsh sites, and similar differences were seen between profiles derived from soils subjected to different management regimes. The study indicates that grassland archaeal communities are dominated by Crenarchaeota, with closely related members of this lineage ubiquitous in distribution in UK upland pasture, and indicate that management practices influence the nature of the crenarchaeotal community.     

Assessing the impact of the biological control agent Bacillus thuringiensis on the indigenous microbial community within the pepper plant phyllosphere

Although biological control agents (BCAs) have been used extensively for controlling insects and pathogens of plants, little is known regarding the effects of such agents on the indigenous microbial communities within the plant phyllosphere. We assessed the effect of the BCA Bacillus thuringiensis (Bt) on the microbial communities within the pepper plant phyllosphere using culture-independent methodologies. Phospholipid fatty acid (PLFA) analysis suggested that the bacterial and fungal biomass were not significantly affected following Bt application. However, principal component analysis of PLFA data indicated that Bt did change the phyllosphere microbial community structure significantly. 16S rRNA gene-directed PCR with denaturing gradient gel electrophoresis (DGGE) also suggested a significant change in the phyllosphere bacterial community structure following Bt inoculation. Phylogenetic analysis of excised DGGE bands suggested a change in bacterial phyla; bands from untreated samples predominantly belonged to the Firmicutes, while Gammaproteobacteria abounded in the treated samples.     

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

The Deepwater Horizon oil spill in the Gulf of Mexico is the deepest and largest offshore spill in the United State history and its impacts on marine ecosystems are largely unknown. Here, we showed that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill. A variety of metabolic genes involved in both aerobic and anaerobic hydrocarbon degradation were highly enriched in the plume compared with outside the plume, indicating a great potential for intrinsic bioremediation or natural attenuation in the deep sea. Various other microbial functional genes that are relevant to carbon, nitrogen, phosphorus, sulfur and iron cycling, metal resistance and bacteriophage replication were also enriched in the plume. Together, these results suggest that the indigenous marine microbial communities could have a significant role in biodegradation of oil spills in deep-sea environments.     

Spatial and temporal changes in microbial community structure associated with recharge-influenced chemical gradients in a contaminated aquifer

In a contaminated water-table aquifer, we related microbial community structure on aquifer sediments to gradients in 24 geochemical and contaminant variables at five depths, under three recharge conditions. Community amplified ribsosomal DNA restriction analysis (ARDRA) using universal 16S rDNA primers and denaturing gradient gel electrophoresis (DGGE) using bacterial 16S rDNA primers indicated: (i). communities in the anoxic, contaminated central zone were similar regardless of recharge; (ii). after recharge, communities at greatest depth were similar to those in uncontaminated zones; and (iii). after extended lack of recharge, communities at upper and lower aquifer margins differed from communities at the same depths on other dates. General aquifer geochemistry was as important as contaminant or terminal electron accepting process (TEAP) chemistry in discriminant analysis of community groups. The Shannon index of diversity (H) and the evenness index (E), based on DGGE operational taxonomic units (OTUs), were statistically different across community groups and aquifer depths. Archaea or sulphate-reducing bacteria 16S rRNA abundance was not clearly correlated with TEAP chemistry indicative of methanogenesis or sulphate reduction. Eukarya rRNA abundance varied by depth and date from 0 to 13% of the microbial community. This contaminated aquifer is a dynamic ecosystem, with complex interactions between physical, chemical and biotic components, which should be considered in the interpretation of aquifer geochemistry and in the development of conceptual or predictive models for natural attenuation or remediation.     

Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds

The bacterial and fungal rhizosphere communities of strawberry (Fragaria ananassa Duch.) and oilseed rape (Brassica napus L.) were analysed using molecular fingerprints. We aimed to determine to what extent the structure of different microbial groups in the rhizosphere is influenced by plant species and sampling site. Total community DNA was extracted from bulk and rhizosphere soil taken from three sites in Germany in two consecutive years. Bacterial, fungal and group-specific (Alphaproteobacteria, Betaproteobacteria and Actinobacteria) primers were used to PCR-amplify 16S rRNA and 18S rRNA gene fragments from community DNA prior to denaturing gradient gel electrophoresis (DGGE) analysis. Bacterial fingerprints of soil DNA revealed a high number of equally abundant faint bands, while rhizosphere fingerprints displayed a higher proportion of dominant bands and reduced richness, suggesting selection of bacterial populations in this environment. Plant specificity was detected in the rhizosphere by bacterial and group-specific DGGE profiles. Different bulk soil community fingerprints were revealed for each sampling site. The plant species was a determinant factor in shaping similar actinobacterial communities in the strawberry rhizosphere from different sites in both years. Higher heterogeneity of DGGE profiles within soil and rhizosphere replicates was observed for the fungi. Plant-specific composition of fungal communities in the rhizosphere could also be detected, but not in all cases. Cloning and sequencing of 16S rRNA gene fragments obtained from dominant DGGE bands detected in the bacterial profiles of the Rostock site revealed that Streptomyces sp. and Rhizobium sp. were among the dominant ribotypes in the strawberry rhizosphere, while sequences from Arthrobacter sp. corresponded to dominant bands from oilseed rape bacterial fingerprints.