Phylogenetic Diversity Of Bacterial Communities Research Articles

Little environmental adaptation and high stability of bacterial communities in rhizosphere rather than bulk soils in rice fields

The rhizosphere harbors complex bacterial communities, which are critical for plant growth and health. Significant differences exist between bacterial communities in the rhizosphere and bulk soils, however, limited research has explored co-occurrence patterns, environmental adaptations, and assembly mechanisms of rhizosphere bacterial communities. Using 16S rRNA high-throughput sequencing, we investigated the taxonomic and phylogenetic diversity of bacterial communities in both rhizosphere and bulk soils from a rice cropping experimental system in China. In addition to investigating differences in bacterial composition, we examined co-occurrence patterns, estimated environmental breadth and phylogenetic signals, and analyzed community assembly processes in these environments. Significant differences were observed between rhizosphere composition and bulk soil (p < 0.05) even some bacteria in the rice rhizosphere may come from the bulk soil around roots. The distribution patterns and ecological functions between communities in the rice rhizosphere and bulk soil were also significantly different. Lower β-diversity values among bacterial communities in the rice rhizosphere indicated that they had a higher stability than those in the bulk soils. In addition, rice rhizosphere communities had a wider phylogenetic diversity and lower functional redundancy when compared with bulk soils. Moreover, the results of environmental breadth analysis revealed that communities in bulk soils were more environmentally constrained than rhizosphere communities. Our null model revealed that deterministic processes drove community assembly in bulk soils (59.57%), whereas stochastic processes determined those in the rice rhizosphere (53.85%). Available potassium was decisive in determining the balance between stochasticity and determinism in both communities. Our study provides insights on the mechanisms underlying the assembly and maintenance of bacterial diversity in rice cropping soils, in response to environmental changes.

Survey of Bacterial Phylogenetic Diversity During the Glacier Melting Season in an Arctic Fjord.

To understand bacterial biogeography in response to the hydrographic impact of climate change derived from the Arctic glacier melting, we surveyed bacterial diversity and community composition using bacterial 16S rRNA gene metabarcoding in the seawaters of Kongsfjorden, Svalbard, during summer 2016. In the present study, bacterial biogeography in the Kongsfjorden seawaters showed distinct habitat patterns according to water mass classification and habitat transition between Atlantic and fjord surface waters. Moreover, we estimated phylogenetic diversity of bacterial communities using the net relatedness, nearest taxon, and beta nearest taxon indices. We found the influence of freshwater input from glacier melting in shaping bacterial assemblage composition through the stochastic model. We further evaluated bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) using a quantitative PCR (qPCR) measurement with demethylation (dmdA) and cleavage (dddP) genes of two fundamentally different processes. Our qPCR results imply that bacterial DMSP degradation follows the Atlantic inflow during summer in Kongsfjorden. These findings suggest that the Atlantic inflow and glacial melting influence bacterial community composition and assembly processes and thus affect the degradation of phytoplankton-derived organic matter in an Arctic fjord.

Carbon-to-nitrogen ratio influence on the performance of bioretention for wastewater treatment.

Bioretention cell (BRC), bioretention cell with microbial fuel cell (BRC-MFC), and an enhanced combined BRC-MFC system with bimetallic zero-valent iron (BRC-MFC-BZVI) were implemented in current study to treat the domestic wastewater. Nitrogen removal characteristics of three systems were investigated by adjusting influent carbon/nitrogen ratio (C/N ratio of 2.54-19.36). Results revealed that the nitrification and denitrification performances were mainly influenced by organic matter and system combination, which further affected nitrogen removal. When the influent C/N ratio was between 2 to 3, compared with BRC system, in BRC-MFC and BRC-MFC-BZVI system, chemical oxygen demand (COD), total nitrogen (TN), and ammonical nitrogen (NH4+-N) removal efficiencies were still reached to 83.04%, 61.06%, and 42.26% and 86.53%, 43.61%, and 50.99% respectively, which simultaneously achieved high-efficiency of organic matter and nitrogen removal. The efficient supply of electrons in the BRC-MFC and BRC-MFC-BZVI processes was the main reason to achieve profound denitrification removal under the condition of low C/N. Removal rates of nitrate (NO3--N) and nitrite (NO2--N) were relatively higher due to microbial-driven redox reactions caused by driving electrons to flow in the closed circuit of metal wire connection. Moreover, phylogenetic diversity of bacterial communities mainly induced the catalytic iron, which further enhanced biological nitrogen reduction. The maximum efficient removal of organic matter (OM), TN, and NH4 + -N were obtained in the BRC-MFC-BZVI system, which were 98.42% (C/N = 10.42), 55.61% (C/N = 4.16), and 61.13% (C/N = 4.16), respectively.

Nitrogen removal performance of microbial fuel cell enhanced bioretention system

Abstract Bioretention cell (BRC) and an enhanced system combining bioretention cell with microbial fuel cell (BRC-MFC) were used to treat domestic wastewater. Nitrogen removal characteristics and permeation characteristics of two systems were investigated by adjusting influent carbon/nitrogen ratio (C/N = 2–20). Results showed that nitrification and denitrification performances were mainly influenced by organic matter and system combination, which further effected the nitrogen removal. When optimal operating parameters were: electrode space of 30 cm, hydraulic load of 1.0 m3/(m2·d) and inlet/reaction time of 1/8 in BRC-MFC system, chemical oxygen demand (COD), total nitrogen (TN) and NH4+ removal efficiencies still reached 97.63, 64, and 42.26%, respectively and achieved high removal efficiency of organic matter and nitrogen simultaneously compared to the BRC system. Efficient supply of electron and phylogenetic diversity of bacterial communities in BRC-MFC process was the main reason to achieve deep denitrification removal. After the V3-V4 variable region of 16S rRNA gene was sequenced by the Miseq high-throughput sequencing method, introduction of MFC enhancement technology affected the microbial community structure in the system. The presence of MFC contributed to an increase in community diversity (from 14 to 19 phyla). The results provide a simple method without kinetic energy for simultaneous denitrification and steady infiltration of bioretention.

Analysis of the diversity of aerobic, thermophilic endospore-forming bacteria in two Algerian hot springs using cultural and non-cultural methods

Terrestrial hot environments are important resources for isolation of thermophilic microorganisms. Few studies have been made on microbial diversity of Algerian geothermal sites. This paper reports the diversity of thermophilic, aerobic endospore-forming bacteria from water and sediment samples taken from Hammam Ouled Ali and Hammam Debagh, two hot springs with a wide range of temperatures and a very rich mineral composition, located in the region of Guelma, north-east of Algeria using culture-dependent and culture-independent approaches Sequences of the V4 region of the 16S rRNA gene from environmental DNA extracted from sediment samples were analyzed and a set of isolates from water and sediment have been characterized by phenotypic and molecular methods. Phylogenetic surveys using environmental DNA sequences indicated that three families dominated the two hot springs: Planococcaceae, Bacillaceae, and Paenibacillaceae. Phenotypic characterization revealed the morphological, biochemical, and physiological properties of these microorganisms, all of which exhibited a range of common extracellular enzymatic activities. Amplified ribosomal DNA restriction analysis (ARDRA) was used to cluster isolates into different phylotypic groups and phylogenetic analysis of 16S rRNA gene sequences of selected isolates showed that all were closely related to four genera of thermophilic Bacilli: Bacillus, Anoxybacillus, Geobacillus, and Brevibacillus. Our results provide important insights into the microbial ecology of Guelma hot springs. They showed that the phylogenetic diversity of bacterial communities within the two studied hot springs was mostly aerobic, with the presence of taxonomic groups of great biotechnological interest. Bioprospection of thermozymes and other biomolecules within these communities will probably provide a data basis for their industrial exploitation.

Acclimation of Culturable Bacterial Communities under the Stresses of Different Organic Compounds.

The phylogenetic diversity of bacterial communities in response to environmental disturbances such as organic pollution has been well studied, but little is known about the way in which organic contaminants influence the acclimation of functional bacteria. In the present study, tolerance assays for bacterial communities from the sediment in the Pearl River Estuary were conducted with the isolation of functional bacteria using pyrene and different estrogens as environmental stressors. Molecular ecological networks and phylogenetic trees were constructed using both 16S rRNA gene sequences of cultured bacterial strains and 16S rRNA gene-based pyrosequencing data to illustrate the successions of bacterial communities and their acclimations to the different organic compounds. A total of 111 bacterial strains exhibiting degradation and endurance capabilities in response to the pyrene estrogen-induced stress were successfully isolated and were mainly affiliated with three orders, Pseudomonadales, Vibrionales, and Rhodobacterales. Molecular ecological networks and phylogenetic trees showed various adaptive abilities of bacteria to the different organic compounds. For instance, some bacterial OTUs could be found only in particular organic compound-treated groups while some other OTUs could tolerate stresses from different organic compounds. Furthermore, the results indicated that some new phylotypes were emerged under stresses of different organic pollutions and these new phylotypes could adapt to the contaminated environments and contribute significantly to the microbial community shifts. Overall, this study demonstrated a crucial role of the community succession and the acclimation of functional bacteria in the adaptive responses to various environmental disturbances.

토판염전 결정지 내 세균군집의 계통학적 다양성 및 Culturomics법을 이용한 고도 호염균의 분리

토판염전 결정지 내 세균군집의 계통학적 다양성 및 Culturomics법을 이용한 고도 호염균의 분리

Soil microbial responses to wood ash addition and forest fire in managed Ontario forests

Wood ash is typically applied to soils to counteract acidification and base cation depletion, but the effects of this ash on the organic layer microbial community are rarely studied. We analyzed microbial responses to ash addition in two field-scale experiments in Ontario, Canada. One experiment was in a young boreal forest soil and the other was in an uneven-aged hardwood north-temperate forest soil. We also investigated the effects of a natural forest fire near the boreal experiment. In both cases, ash addition had no effect on overall microbial biomass and respiration, but increased the phylogenetic diversity of bacterial communities and the relative abundance of Bacteroidetes taxa, though effects on other bacterial taxa were site-specific. Eukaryotic effects also varied by experiment; at the boreal site, ash increased eukaryotic phylogenetic diversity and decreased the fungi:bacteria ribosomal marker ratio, but at the temperate site ash decreased eukaryotic diversity and did not affect the fungi:bacteria ratio. There was limited additional effect on the boreal soil microbial community of increasing ash addition from 0.7 to 5.7tha−1, as determined by T-RFLP analysis, though soil pH in both experiments increased with higher addition rates. At the temperate site, ash effects were consistently stronger for fly ash than for bottom ash. In both experiments, only 14 unique bacterial taxa were found after ash addition, and the strongest driver of overall community composition was the forest type, not ash treatment. In contrast, the soil microbial community observed at the forest fire site was clearly different. Overall, these results indicate that wood ash addition has only minimal effects on the composition of the soil microbial community in sites across two distinct global forest biomes.

High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes.

We carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4-10.1) by 16S rRNA gene tag sequencing. Relative Archaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (PCR) mixture, and we detected 769 operational taxonomic units (OTUs; grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the data set (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota-Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata and ammonia-oxidizing thaumarchaeota (AOA) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, Bathyarchaeota and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota having the smallest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.

Phylogenetic diversity of bacterial communities associated with bioremediation of crude oil in microcosms

Bioremediation, mainly by indigenous bacteria, has been regarded as an effective way to clean up oil pollution after an oil spill. In order to obtain a systematic understanding of the succession of bacterial communities associated with oil bioremediation, sediments collected from the Penglai 19-3 oil platform were co-incubated with crude oil. Oil biodegradation was assessed on the basis of changes in oil composition monitored by GC–MS. Changes in the bacterial community structure were detected by two 16S rRNA gene based culture-independent methods, denaturing gradient gel electrophoresis (DGGE) and clone library. The results suggested that crude oil was rapidly degraded during the 30-day bioremediation period. Bacteria affiliated with the genus Pseudomonas dominated all three clone libraries. But dramatic changes were also detected in the process of biodegradation of crude oil. The “professional hydrocarbonocastic bacteria” (e.g., Alcanivorax) became abundant in the two samples during the bioremediation period. Meanwhile, δ-proteobacteria was only detected in the two samples. Information on the bacterial community revealed in this study will be useful in developing strategies for bioremediation of crude oil dispersed in the marine ecosystem.

Phylogenetic diversity of bacterial communities inhabiting the sediment of Lake Hévíz — A comparison of cultivation and cloning

Lake Hévíz is the largest natural warm water lake of Europe. The curative mud of the lake comprises volcanic and marsh components although their species composition is hardly known yet. The aim of the present study was to gain information about the distribution and species diversity of bacterial communities inhabiting the sediment of Lake Hévíz using cultivation-based and molecular cloning methods. Samples from two depths and locations were taken in 2004 and 2007. Representatives of the altogether 255 bacterial isolates were affiliated with the phyla Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes. The most abundant groups belonged to the genus Bacillus (Firmicutes). Many of Lake Hévíz isolates showed the highest sequence similarity to bacteria known to be plant associated or members of normal human microbiota as well as participating in decomposition of highly resistant organic materials. In the three clone libraries, phylotypes belonging to altogether different phyla (Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria, Chlorobi, Chloroflexi, Deferribacteres, Nitrospirae, Spirochaetes and Verrucomicrobia) were revealed from which members of Gammaproteobacteria and Cyanobacteria proved to be the most abundant. Regardless of the sampling times and methodology used, high spatial heterogeneities of bacterial community structures were characteristic of the sediment of Lake Hévíz.

Culturable bacteria community development in postglacial soils of Ecology Glacier, King George Island, Antarctica

Glacier forelands are excellent sites in which to study microbial succession because conditions change rapidly in the emerging soil. Development of the bacterial community was studied along two transects on lateral moraines of Ecology Glacier, King George Island, by culture-dependent and culture-independent approaches (denaturating gradient gel electrophoresis). Environmental conditions such as cryoturbation and soil composition affected both abundance and phylogenetic diversity of bacterial communities. Microbiocenosis structure along transect 1 (severe cryoturbation) differed markedly from that along transect 2 (minor cryoturbation). Soil physical and chemical factors changed along the chronosequence (time since exposure) and influenced the taxonomic diversity of cultivated bacteria, particularly along transect 2. Arthrobacter spp. played a pioneer role and were present in all soil samples, but were most abundant along transect 1. Cultivated bacteria isolated from transect 2 were taxonomically more diverse than those cultivated from transect 1; those from transect 1 tended to express a broader range of enzyme and assimilation activities. Our data suggest that cryoturbation is a major factor in controlling bacterial community development in postglacial soils, shed light on microbial succession in glacier forelands, and add a new parameter to models that describe succession phenomena.

Comparison of soil microbial communities from two distinct karst areas in Hungary

Karst areas belong to the most exposed terrestrial ecosystems, therefore their study have a priority task in Hungary, as well. The aim of this study was to compare the structure, activity and diversity of soil microbial communities from two distinct Hungarian karst areas (Aggtelek NP and Tapolca-basin). Soil samples were taken three times from 6 distinct sites, from different depths. Soil microbial biomass C (MBC), microbial biomass N (MBN), basal respiration (BRESP) and substrate induced respiration (SIR) were measured. The phylogenetic diversity of bacterial communities was compared by Denaturing Gradient Gel Electrophoresis (DGGE). The highest MBC, MBN, BRESP and SIR values were measured in the rendzina soil from Aggtelek. On the basis of biomass and respiration measurements, microbial communities differentiated mainly according to soil depths whereas DGGE profiles of bacterial communities resulted in groups mainly according to sampling sites.

Phylogenetic Diversity of Bacterial Communities Associated with Sulfurous Karstic Well Waters of a Hungarian Spa

The composition of bacterial communities associated with waters of one thermal and three sulfurous lukewarm wells of cavernous limestone aquifers in the Southwestern part of Hungary was studied in 2007 and 2008 by microscopy and culture-independent clone library analysis targeting the 16S rRNA gene. The presence of Thiothrix-like filamentous bacteria was observed by microscopy in the lukewarm samples. From the clone libraries, a high proportion of phylotypes belonging to Proteobacteria (Rhodobacter, Sphingopyxis, Phenylobacterium, Ochrobactrum, Methylobacterium, Sulfuritalea, Thiobacillus, Limnobacter, Acidovorax, Xanthomonadaceae, Thiothrix, Lysobacter, Pseudoxanthomonas, Desulfopila, Desulfocapsa, Desulforhopalus, Sulfuricurvum, Sulfurimonas, Sulfurospirillum) was revealed. In addition, phylotypes of Acidobacteria, Chloroflexi, Sphingobacteria, Clostridia, Aquificae, Deferribacteres and Chlorobi were detected. On the basis of their habitat preference 21 out of a total of 39 different phylotypes represented mesophilic and thermophilic sulfur bacteria. From the lukewarm samples large numbers of clones were affiliated with uncultured Epsilonproteobacteria clones common in sulfurous hydrothermal vents. From the thermal sample, several clones were in the closest relationship to the Sulfuritalea hydrogenivorans, a novel sulfur-oxidizing Betaproteobacterium.

Microbial communities at the borehole observatory on the Costa Rica Rift flank (Ocean Drilling Program Hole 896A)

The microbiology of subsurface, hydrothermally influenced basaltic crust flanking mid-ocean ridges has remained understudied, due to the difficulty in accessing the subsurface environment. The instrumented boreholes resulting from scientific ocean drilling offer access to samples of the formation fluids circulating through oceanic crust. We analyzed the phylogenetic diversity of bacterial communities of fluid and microbial mat samples collected in situ from the observatory at Ocean Drilling Program Hole 896A, drilled into ~6.5 million-year-old basaltic crust on the flank of the Costa Rica Rift in the equatorial Pacific Ocean. Bacterial 16S rRNA gene sequences recovered from borehole fluid and from a microbial mat coating the outer surface of the fluid port revealed both unique and shared phylotypes. The dominant bacterial clones from both samples were related to the autotrophic, sulfur-oxidizing genus Thiomicrospira. Both samples yielded diverse gamma- and alphaproteobacterial phylotypes, as well as members of the Bacteroidetes, Planctomycetes, and Verrucomicrobia. Analysis of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes (cbbL and cbbM) from the sampling port mat and from the borehole fluid demonstrated autotrophic carbon assimilation potential for in situ microbial communities; most cbbL genes were related to those of the sulfur-oxidizing genera Thioalkalivibrio and Thiomicrospira, and cbbM genes were affiliated with uncultured phylotypes from hydrothermal vent plumes and marine sediments. Several 16S rRNA gene phylotypes from the 896A observatory grouped with phylotypes recovered from seawater-exposed basalts and sulfide deposits at inactive hydrothermal vents, but there is little overlap with hydrothermally influenced basaltic boreholes 1026B and U1301A on the Juan de Fuca Ridge flank, suggesting that site-specific characteristics of Hole 896A (i.e., seawater mixing into borehole fluids) affect the microbial community composition.

Phylogenetic diversity of bacterial communities in bovine rumen as affected by diets and microenvironments

Phylogenetic analysis was conducted to examine ruminal bacteria in two ruminal fractions (adherent fraction vs. liquid fraction) collected from cattle fed with two different diets: forage alone vs. forage plus concentrate. One hundred forty-four 16S rRNA gene (rrs) sequences were obtained from clone libraries constructed from the four samples. These rrs sequences were assigned to 116 different operational taxonomic units (OTUs) defined at 0.03 phylogenetic distance. Most of these OTUs could not be assigned to any known genus. The phylum Firmicutes was represented by approximately 70% of all the sequences. By comparing to the OTUs already documented in the rumen, 52 new OTUs were identified. UniFrac, SONS, and denaturing gradient gel electrophoresis analyses revealed difference in diversity between the two fractions and between the two diets. This study showed that rrs sequences recovered from small clone libraries can still help identify novel species-level OTUs.

Phylogenetic diversity of bacterial communities in South China Sea mesoscale cyclonic eddy perturbations

Eddy pumping drives a set of biogeochemical processes by lifting deep waters into the euphotic zone. To address the potential effect of such physical processes upon the bacterial community, phylogenetic diversity was determined in two cold-core cyclonic eddies in the South China Sea. 16S rDNA terminal restriction fragment length polymorphism analysis of the microbial communities through the whole water column showed a wider depth range for the intermediate transition water mass at sites inside the eddies than for those outside. This water mass contained a relatively more complex community than the euphotic and deep-water zones. Stratification of prokaryotic populations between the surface and chlorophyll maximum layer of eddy-related sites versus homogeneity of communities in the euphotic zone of the reference site, revealed by statistical analysis of 16S rDNA libraries, is most likely a reflection of isopycnal displacement induced by differing water movement inside and outside eddies. Phylogenetic analysis revealed that eddy center sites were characterized by deep-water group Alteromonadales-affiliated clones, the psychrophilic genus Octadecabacter cluster and the nitrogen-fixing phototrophic Rhodospirillaceae cluster, while Paracoccus, an important functional group, abundantly existed at the reference site outside eddies. Our analysis revealed that bacterial community structure was significantly influenced by cyclonic eddy perturbations.

Temporal bacterial diversity and detection of putative methanotrophs in surface mats of Lonar crater lake

The phylogenetic diversity of bacterial communities in microbial mats of two different seasons from saline and hyperalkaline Lonar Lake was investigated using 16S rRNA gene library analysis. Arthrospira (Cyanobacteria) related clones (>80% of total clones) dominated libraries of both the seasons. Clear differences were found in both the seasons as the operational taxonomic units (OTUs) related to Fusibacter (LAI-1 and LAI-59) and Tindallia magadiensis (LAI-27) found in post-monsoon were not found in the pre-monsoon library. Likewise, OTUs related to Planococcus rifietensis (LAII-67), Bordetella hinzii (LAII-2) and Methylobacterium variabile (LAII-25) found in the pre-monsoon were not found in post-monsoon. The study was extended to identify methanotrophs in the surface mats. Libraries constructed with type I and type II methanotroph specific 16S rRNA gene primers showed the presence of clones (LAMI-99 and LAMII-2) closely related to Methylomicrobium buryaticum and Beijerinckiaceae family members. Denaturing gradient gel electrophoresis (DGGE) fingerprinting based on protein-coding genes (pmoA and mxaF) further confirmed the detection of Methylomicrobium sp. Hence, we report here for the first time the detection of putative methanotrophs in surface mats of Lonar Lake. The finding of clones related to organisms with interesting functional attributes such as assimilation of C(1) compounds (LAII-25, LAMI-39, LAMI-99 and LAMII-2), non-sulfur photosynthetic bacteria (LAMII-43) and clones distantly affiliated to organisms of heavily polluted environments (LAI-59 and LAMII-52), is of significant note. These preliminary results would direct future studies on the functional dynamics of microbial mat associated food web chain in the extreme environment.

Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots

The rhizosphere of Trifolium repens and Lolium perenne was divided into three fractions: the bulk soil; the soil adhering to the roots; and the washed roots (rhizoplane and endorhizosphere). After isolation and purification of DNA from these fractions, 16S rDNA was amplified by PCR and cloned to obtain a collection of 16S rRNA genes representative of the bacterial communities of these three fractions. The cloned 16S rRNA genes were then partially sequenced and analysed by a molecular phylogenetic approach. Our data show a high diversity in the bulk soil, which is dominated by clones related to Gram-positive, Cytophaga–Flexibacter–Bacteroides, Proteobacteria, and Holophaga–Acidobacterium groups. The ubiquity of members of the Holophaga–Acidobacterium group, which is composed of sequences of yet-uncultivated microorganisms, is confirmed. The plant roots have a selective effect towards the gamma Proteobacteria, to the detriment of the Gram-positive and the Holophaga–Acidobacterium bacteria, leading to a dominance of Pseudomonas. This work shows by a culture independent approach that the phylogenetic diversity decreases in the proximity of plant roots.