Effect of monoculture soybean on soil microbial community in the Northeast China

Monoculture (MC) soybean, a common practice in the Northeast China, causes significant declines in soybean yield and quality. The objective of this study was to evaluate the responses of the soil microbial community and soybean yield to different soybean cropping systems. Three cropping systems were compared, (1) corn-soybean rotation (corn-corn-soybean, CS), (2) MC soybean for 3 years (S3), (3) MC soybean for 9 years (S9). Both bulk and rhizosphere soil samples were collected at three growth stages: two trifoliate (V2), full bloom (R2), and full seed (R6), respectively. Soil microbial DNA was analyzed using polymerase chain reaction (PCR)—denaturing gradient gel electrophoresis (DGGE) to assess changes in composition of bacterial and fungal communities. Prominent DGGE bands were excised and sequenced to gain insight into the identities of the predominant microbial populations. Some prominent differences were observed in bacterial DGGE patterns of amplified 16S rDNA (V3 region) among rhizosphere soils. These major differences included one DGGE band (showing 100% similarity to Arthrobacter sp.) that was enriched at R2 stages in CS and S9, and another band with 97% sequence similarity to an uncultured actinobacterium was detected at R6 stage in CS, and at R2 and R6 stages in S9. The bacterial community from bulk soil showed no significant band change in DGGE patterns among different cropping systems. In fungal DGGE patterns of the amplified 18S rDNA partial fragment, one specific band (showing 98% similarity to Trichoderma viride) occurred in rhizosphere soil of treatment CS at V2 and R6 stages and treatment S9 at R6 stage. None of the above bands were detected in treatment S3. The soybean yields and plant heights from CS and S9 were greater than those from S3. Moreover, catalase activities from CS and S9 at V2 and R2 stages were higher than those tested from S3 at the corresponding times in rhizosphere soil. The present results showed that DGGE patterns were not able to detect significant differences in diversity or evenness among microbial communities, but significant differences were found in the composition of bacterial and fungal community structures. Some distinguished bands from bacterial and fungal DGGE patterns were only enriched in CS and S9 soil, which could potentially play an important role in soybean growth development.     

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.     

Dynamics of Fungal Communities in Bulk and Maize Rhizosphere Soil in the Tropics

The fungal population dynamics in soil and in the rhizospheres of two maize cultivars grown in tropical soils were studied by a cultivation-independent analysis of directly extracted DNA to provide baseline data. Soil and rhizosphere samples were taken from six plots 20, 40, and 90 days after planting in two consecutive years. A 1.65-kb fragment of the 18S ribosomal DNA (rDNA) amplified from the total community DNA was analyzed by denaturing gradient gel electrophoresis (DGGE) and by cloning and sequencing. A rhizosphere effect was observed for fungal populations at all stages of plant development. In addition, pronounced changes in the composition of fungal communities during plant growth development were found by DGGE. Similar types of fingerprints were observed in two consecutive growth periods. No major differences were detected in the fungal patterns of the two cultivars. Direct cloning of 18S rDNA fragments amplified from soil or rhizosphere DNA resulted in 75 clones matching 12 dominant DGGE bands. The clones were characterized by their HinfI restriction patterns, and 39 different clones representing each group of restriction patterns were sequenced. The cloning and sequencing approach provided information on the phylogeny of dominant amplifiable fungal populations and allowed us to determine a number of fungal phylotypes that contribute to each of the dominant DGGE bands. Based on the sequence similarity of the 18S rDNA fragment with existing fungal isolates in the database, it was shown that the rhizospheres of young maize plants seemed to select the Ascomycetes order Pleosporales, while different members of the Ascomycetes and basidiomycetic yeast were detected in the rhizospheres of senescent maize plants.     

Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics

The fungal population dynamics in soil and in the rhizospheres of two maize cultivars grown in tropical soils were studied by a cultivation-independent analysis of directly extracted DNA to provide baseline data. Soil and rhizosphere samples were taken from six plots 20, 40, and 90 days after planting in two consecutive years. A 1.65-kb fragment of the 18S ribosomal DNA (rDNA) amplified from the total community DNA was analyzed by denaturing gradient gel electrophoresis (DGGE) and by cloning and sequencing. A rhizosphere effect was observed for fungal populations at all stages of plant development. In addition, pronounced changes in the composition of fungal communities during plant growth development were found by DGGE. Similar types of fingerprints were observed in two consecutive growth periods. No major differences were detected in the fungal patterns of the two cultivars. Direct cloning of 18S rDNA fragments amplified from soil or rhizosphere DNA resulted in 75 clones matching 12 dominant DGGE bands. The clones were characterized by their HinfI restriction patterns, and 39 different clones representing each group of restriction patterns were sequenced. The cloning and sequencing approach provided information on the phylogeny of dominant amplifiable fungal populations and allowed us to determine a number of fungal phylotypes that contribute to each of the dominant DGGE bands. Based on the sequence similarity of the 18S rDNA fragment with existing fungal isolates in the database, it was shown that the rhizospheres of young maize plants seemed to select the Ascomycetes order Pleosporales, while different members of the Ascomycetes and basidiomycetic yeast were detected in the rhizospheres of senescent maize plants.     

间作大豆对甘蔗根际土壤细菌及固氮菌多样性的影响

为探讨间作大豆(Glycine max)对甘蔗(Saccharum officinarum)根际土壤细菌及固氮细菌多样性的影响, 收集和开发固氮菌资源, 筛选高效甘蔗联合固氮体系, 选用3个甘蔗栽培品种‘ROC22’、‘GT21’、‘B8’与大豆品种‘Guizao 2’进行间种栽培, 采用巢式PCR特异扩增细菌16S rRNA基因片段和固氮细菌nifH基因片段, 并结合变性梯度凝胶电泳(DGGE)技术, 对间作大豆的甘蔗根际土壤细菌及固氮细菌进行系统演化和多样性分析。聚类分析结果显示, 间作大豆改变了甘蔗根际土壤细菌及固氮细菌原来的群落组成结构, 尤其对固氮菌群落组成的改变更大, 但对群落物种的优势度影响较小。Shannon-Wiener多样性指数和Simpson多样性指数分析结果表明, 甘蔗-大豆间作显著影响甘蔗根际土壤中细菌和固氮菌的多样性, 其中对固氮细菌多样性的影响较大。不同甘蔗品种的根际土壤细菌和固氮菌在间作大豆条件下表现出不同的多样性, ‘ROC22’和‘GT21’间作处理甘蔗根际土壤固氮细菌的Shannon-Wiener多样性指数显著高于单作处理, 而‘ROC22’与大豆间作处理的甘蔗根际土壤固氮菌多样性最为丰富。在大豆生长盛期, 间作处理的甘蔗根际土壤细菌多样性最为丰富, 不同处理间的差异也最大, 随后下降。总体来看, 甘蔗-大豆间作显著地影响根际土壤细菌和固氮菌的群落结构和群落多样性, 有助于对甘蔗合理间作栽培模式的认识和筛选高效甘蔗联合固氮体系。     

Assessment of differences in ascomycete communities in the rhizosphere of field-grown wheat and potato

To assess effects of plant crop species on rhizosphere ascomycete communities in the field, we compared a wheat monoculture and an alternating crop rotation of wheat and potato. Rhizosphere soil samples were taken at different time points during the growing season in four consecutive years (1999-2002). An ascomycete-specific primer pair (ITS5-ITS4A) was used to amplify internal transcribed spacer (ITS) sequences from total DNA extracts from rhizosphere soil. Amplified DNA was analyzed by denaturing gradient gel electrophoresis (DGGE). Individual bands from DGGE gels were sequenced and compared with known sequences from public databases. DGGE gels representing the ascomycete communities of the continuous wheat and the rotation site were compared and related to ascomycetes identified from the field. The effect of crop rotation exceeded that of the spatial heterogeneity in the field, which was evident after the first year. Significant differences between the ascomycete communities from the rhizospheres of wheat in monoculture and one year after a potato crop were found, indicating a long-term effect of potato. Sequencing of bands excised from the DGGE gels revealed the presence of ascomycetes that are common in agricultural soils.     

轮套作对黄瓜根际土壤细菌种群的影响

以黄瓜为试材,采用PCR-DGGE技术研究了小麦、大豆、毛苕子、三叶草和苜蓿与黄瓜轮作及大蒜、毛葱与黄瓜套作对黄瓜根际土壤细菌种群的影响.结果表明:轮套作对黄瓜根际土壤细菌种群的种类、数量和黄瓜产量具有一定的影响,提高了土壤细菌种群多样性指数、均匀度指数和黄瓜产量.对DGGE条带进行测序的结果表明,它们大多与不可培养的细菌种属具有较高的同源性,大多为鞘氨醇杆菌属（Sphingobacterium）和变形细菌纲（Proteobacteria）, High bacterium G+C只在以毛葱为套作作物的黄瓜根际中出现.不同轮套作中细菌种群多样性随黄瓜生育期的变化而变化,在盛瓜期达最高值.以小麦为轮作作物和以毛葱为套作作物的黄瓜轮套作栽培模式最佳.     

Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5

The genetic structure of bacterial and fungal communities was characterized in the rhizosphere of Medicago truncatula Gaertn. cv. Jemalong line J5 at five developmental stages (three vegetative and two reproductive stages), and in three compartments (bulk soil, rhizosphere soil and root tissues). The genetic structure of microbial communities was determined by cultivation-independent methods using directly extracted DNA that was characterized by automated ribosomal intergenic spacer analysis (ARISA). Principal component analyses (PCA) indicate that, for all developmental stages, the genetic structure of microbial communities differed significantly by compartment, with a major shift in the community in root tissues corresponding to the most intimate compartment with the plant. Differences were also recorded during plant development, the most significant being observed during the transition between vegetative and reproductive stages. Throughout this period, plants were shown to establish the highest level of symbiotic association (mycorrhization, nodulation) with arbuscular mycorrhizal fungi and Rhizobia. During the reproductive stages, the dynamics of the genetic structure differed between bacterial and fungal communities. At the last reproductive stage, the genetic structure of bacterial communities became close to that recorded during the first vegetative stages, suggesting a resilience phenomenon, whereas the genetic structure of fungal communities remained different from the vegetative stages and also from the early reproductive stages, suggesting a persistence of the rhizosphere effect.     

内生真菌发酵提取物和植物生长调节剂对大豆根际细菌多样性的影响

为了研究内生真菌发酵提取物和植物生长调节剂对大豆根际细菌多样性的影响,采用PCR-DGGE技术分析了各处理中不同发育期的大豆根际细菌群落变化。结果发现发酵提取液和植物生长调节剂能增加部分优势菌群的数量,但对根际细菌类群结构影响并不明显;生育周期也是影响根际细菌数量的重要因素。另外割胶测序发现优势菌群主要是Proteobacteria(变形菌门)、Acidobacteria(酸杆菌纲)、Nitrospira(硝化螺旋菌属)、Bradyrhizobium(慢生根瘤菌属)等,这些也都是大豆根际比较常见的细菌类群。     

Seasonal and substrate preferences of fungi colonizing leaves in streams: traditional versus molecular evidence

Aquatic hyphomycetes are the main fungal decomposers of plant litter in streams. We compared the importance of substrate (three leaf species, wood) and season on fungal colonization. Substrates were exposed for 12 4-week periods. After recovery, mass loss, fungal biomass and release of conidia by aquatic hyphomycetes were measured. Fungal communities were characterized by counting and identifying released conidia and by extracting and amplifying fungal DNA (ITS2), which was subdivided into phylotypes by denaturing gradient gel electrophoresis (DGGE) and terminal-restriction fragment length polymorphism (T-RFLP). Mass loss, fungal biomass and reproduction were positively correlated with stream temperature. Conidial diversity was highest between May and September. Numbers of different phylotypes were more stable. Principal coordinate analyses (PCO) and canonical analyses of principal coordinates (CAP) of presence/absence data (DGGE bands, T-RFLP peaks and conidial species) showed a clear seasonal trend (Por=0.88). Season was also a significant factor when proportional similarities of conidial communities or relative intensities of DGGE bands were evaluated (P相似文献   

RISA、DGGE和2D-PAGE技术对大豆根际土壤细菌多样性分析的比较

采用基于PCR扩增的核糖体间隔区分析(RISA)、变性梯度凝胶电泳(DGGE)和双向电泳(2D-PAGE)3种分子生态学技术对大豆根际土壤细菌多样性比对分析.结果表明:2D-PAGE技术得到的土壤细菌多样性(基因点)最丰富,其次为DGGE技术(基因片段),RISA技术(基因片段)最低.RISA技术得到的条带数最少,但结...     

Comparing activated sludge fungal community population diversity using denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism

We compared the relative values of denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) for profiling fungal communities in wastewater treatment plants using both ITS and 18S rRNA gene fragments as phylogenetic markers. A similar number of fungal ribotypes was obtained with both methods for the same treatment plant when the ITS primer set was used, while a greater number of ribotypes was obtained with T-RFLP compared to DGGE with the 18S rRNA primer set. Non-metric multi-dimensional scaling of presence/absence data and analysis of similarity showed that both methods could distinguish between the different plant communities at a statistically significant level (p < 0.05), regardless of which phylogenetic marker was used. The data suggest that both methods can be used preferably together to profile activated sludge fungal communities. A comparison of profiles generated with both these phylogenetic markers based on the number of ribotypes/bands, suggests that the 18S rRNA region is more discriminatory than the ITS region. Detected differences in fungal community compositions between plants probably reflect differences in their influent compositions and operational parameters.     

Diversity of fungi in organic soils under a moorland--Scots pine (Pinus sylvestris L.) gradient

The conservation and regeneration of native Scots pine (Pinus sylvestris L.) woodlands is being actively encouraged by conservation agencies in the UK because of their high biodiversity value. In the present study, the consequences of regeneration on terrestrial fungal communities was determined in three parallel transects running from open moorland, through an intermediate zone showing seedling colonization, into a mature Scots pine forest at Abernethy Forest, Cairngorm, Scotland. Soil cores were taken at 18 m intervals along each 180 m transect, and the diversity of the soil fungal community was investigated by DGGE and sequence analysis of ITS fragments PCR-amplified from DNA extracted from soil. Analysis of DGGE profiles generated for two of the three transects indicates a clear shift in the community from the moorland region of the transects to the forest region. Whereas a few bands were present at all sampling points across the transects, the majority of bands were unique to either the moorland or forest samples. FASTA database searches of ITS sequence data generated from excised DGGE bands revealed the closest species match for each band. In some cases, the similarity of ITS sequences to database sequences was poor, but the remaining sequences were most closely related to ITS sequences of both mycorrhizal and non-mycorrhizal fungi. The data are discussed in relation to the effect of native pine woodland expansion on the soil fungal community.     

Toxic and nontoxic microcystis colonies in natural populations can be differentiated on the basis of rRNA gene internal transcribed spacer diversity

Assessing and predicting bloom dynamics and toxin production by Microcystis requires analysis of toxic and nontoxic Microcystis genotypes in natural communities. We show that genetic differentiation of Microcystis colonies based on rRNA internal transcribed spacer (ITS) sequences provides an adequate basis for recognition of microcystin producers. Consequently, ecological studies of toxic and nontoxic cyanobacteria are now possible through studies of rRNA ITS genotypic diversity in isolated cultures or colonies and in natural communities. A total of 107 Microcystis colonies were isolated from 15 lakes in Europe and Morocco, the presence of microcystins in each colony was examined by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and they were grouped by rRNA ITS denaturing gradient gel electrophoresis (DGGE) typing. Based on DGGE analysis of amplified ITSa and ITSc fragments, yielding supplementary resolution (I. Janse et al., Appl. Environ. Microbiol. 69:6634-6643, 2003), the colonies could be differentiated into 59 classes. Microcystin-producing and non-microcystin-producing colonies ended up in different classes. Sequences from the rRNA ITS of representative strains were congruent with the classification based on DGGE and confirmed the recognition of microcystin producers on the basis of rRNA ITS. The rRNA ITS sequences also confirmed inconsistencies reported for Microcystis identification based on morphology. There was no indication for geographical restriction of strains, since identical sequences originated from geographically distant lakes. About 28% of the analyzed colonies gave rise to multiple bands in DGGE profiles, indicating either aggregation of different colonies, or the occurrence of sequence differences between multiple operons. Cyanobacterial community profiles from two Dutch lakes from which colonies had been isolated showed different relative abundances of genotypes between bloom stages and between the water column and surface scum. Although not all bands in the community profiles could be matched with isolated colonies, the profiles suggest a dominance of nontoxic colonies, mainly later in the season and in scums.     

Community Structure of Arbuscular Mycorrhizal Fungi in Rhizospheric Soil of a Transgenic High-Methionine Soybean and a Near Isogenic Variety

The use of transgenic plants in agriculture provides many economic benefits, but it also raises concerns over the potential impact of transgenic plants on the environment. We here examined the impact of transgenic high-methionine soybean ZD91 on the arbuscular mycorrhizal (AM) fungal community structure in rhizosphere soil. Our investigations based on clone libraries were conducted in field trials at four growth stages of the crops each year from 2012 to 2013. A total of 155 operational taxonomic units (OTUs) of AM fungi were identified based on the sequences of small subunit ribosomal RNA (SSU rRNA) genes. There were no significant differences found in AM fungal diversity in rhizosphere soil during the same growth stage between transgenic soybean ZD91 and its non-transgenic parental soybean ZD. In addition, plant growth stage and year had the strongest effect on the AM fungal community structure while the genetically modified (GM) trait studied was the least explanatory factor. In conclusion, we found no indication that transgenic soybean ZD91 cultivation poses a risk for AM fungal communities in agricultural soils.     

Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields

Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.     

Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere

Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely-studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2. Fungal species diversity was found to decrease from bulk soil to rhizosphere to endosphere. A significant effect of plant genotype on fungal community composition was detected only in the endosphere compartment. Despite A. thaliana being a non-mycorrhizal plant, it hosts a number of known mycorrhiza fungi in its endosphere compartment, which is also colonized by endophytic, pathogenic and saprotrophic fungi. Species in the Archaeorhizomycetes were most abundant in rhizosphere samples suggesting an adaptation to environments with high nutrient turnover for some of these species. We conclude that A. thaliana endosphere fungal communities represent a selected subset of fungi recruited from soil and that plant genotype has small but significant quantitative and qualitative effects on these communities.     

大豆不同生育期根际土壤细菌群落结构的变化

为了解大豆根际细菌群落结构多样性及根际细菌群落结构的变化,该研究以大豆苗期和成熟期的根际土壤为材料,采用Illumina高通量测序技术测定细菌16S rRNA V3+V4区序列,探究大豆不同生育期根际土壤细菌群落结构的变化。对原始数据进行拼接、过滤、去除嵌合体序列和聚类分析等数据处理,并对OTU进行分类学注释。在此基础上运用ANOVA分析物种组成变化,Alpha多样性指数研究细菌多样性变化。结果表明:细菌丰富度和多样性在不同生育期有显著变化,其中成熟期土壤中的细菌丰富度和多样性指数均明显高于苗期; 变形菌、放线菌、酸杆菌是大豆根际的优势菌门,其含量在不同生育期也有显著变化; 假诺卡氏菌属、糖丝菌属、鞘氨醇单胞菌属是大豆根际的优势菌属,这些菌属中的部分菌群属于根际促生菌,具有潜在的促生效应。这些结果证实大豆的生育期对根际土壤细菌群落结构有重要影响。     

中国中部太白山不同海拔杜鹃兰根部内生真菌多样性

本研究以太白山自然保护区蒿坪站杜鹃兰Cremastra appendiculata为材料,采用菌丝团和根组织分离法进行真菌分离,并用ITS序列分子鉴定;用变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)分析根部内生真菌多样性,研究海拔和根际土理化性质对真菌多样...     

Bacterial and fungal communities in bulk soil and rhizospheres of aluminum-tolerant and aluminum-sensitive maize (Zea mays L.) lines cultivated in unlimed and limed Cerrado soil

Liming of acidic soils can prevent aluminum toxicity and improve crop production. Some maize lines show aluminum (Al) tolerance, and exudation of organic acids by roots has been considered to represent an important mechanism involved in the tolerance. However, there is no information about the impact of liming on the structures of bacterial and fungal communities in Cerrado soil, nor if there are differences between the microbial communities from the rhizospheres of Al-tolerant and Al-sensitive maize lines. This study evaluated the effects of liming on the structure of bacterial and fungal communities in bulk soil and rhizospheres of Al-sensitive and Al-tolerant maize (Zea mays L.) lines cultivated in Cerrado soil by PCR-DGGE, 30 and 90 days after sowing. Bacterial fingerprints revealed that the bacterial communities from rhizospheres were more affected by aluminum stress in soil than by the maize line (Al-sensitive or Al-tolerant). Differences in bacterial communities were also observed over time (30 and 90 days after sowing), and these occurred mainly in the Actinobacteria. Conversely, fungal communities from the rhizosphere were weakly affected either by liming or by the rhizosphere, as observed from the DGGE profiles. Furthermore, only a few differences were observed in the DGGE profiles of the fungal populations during plant development when compared with bacterial communities. Cloning and sequencing of 16S rRNA gene fragments obtained from dominant DGGE bands detected in the bacterial profiles of the Cerrado bulk soil revealed that Actinomycetales and Rhizobiales were among the dominant ribotypes.