Perturbation of maize rhizosphere microflora following seed bacterization with Burkholderia cepacia MCI 7

Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture

The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.

Stabilising fluoride in contaminated soils with monocalcium phosphate and municipal solid waste compost: microbial, biochemical and plant growth impact

This study evaluated the influence of a municipal solid waste compost (MSWC) and monocalcium phosphate (MCP), alone or combined, on the mobility, toxicity, bioavailability and health risk of fluoride (1000 mg F^-·kg^-1) in an artificially polluted soil (pH 7.85). The addition of MCP (0.2% w/w) and MSWC (1% w/w) (alone and combined) to the contaminated soil reduced water-soluble (e.g. by more than 50% in MCP and MCP + MSWC-treated soils) and exchangeable F^- fractions and increased the residual one. The addition of MSWC and MSWC + MCP to the contaminated soil significantly increased microbial biomass C (SMB-C; 1.3-3.6-fold) while all treatments increased the abundance of culturable heterotrophic bacteria (up to twofold in MSWC + MCP). Overall, dehydrogenase, β-glucosidase, urease and phosphomonoesterase activities were enhanced in treated soils and positively correlated with SMB-C, but not with labile F^-. All treatments increased carrot yield (up to 3.4-fold in MSWC + MCP), while bean growth was significantly enhanced only by MCP and MCP + MSWC (~ twofold). The opposite trend applied for F^- uptake which was especially reduced in the edible part of carrot after soil amendment. A limited influence of MCP and MSWC on hazard quotient (HQ), due to bean and carrot consumption, was also recorded (i.e. HQ generally > 1). Results suggest that MCP and MSWC can be used in the recovery of soil chemical, microbial and biochemical status of F-rich agricultural soils. They also indicate that the bean and carrot cultivars employed in this study are likely unsuitable in such soils due to high F^- uptake in edible parts.

Soil Microbiome Manipulation Gives New Insights in Plant Disease-Suppressive Soils from the Perspective of a Circular Economy: A Critical Review

This review pays attention to the newest insights on the soil microbiome in plant disease-suppressive soil (DSS) for sustainable plant health management from the perspective of a circular economy that provides beneficial microbiota by recycling agro-wastes into the soil. In order to increase suppression of soil-borne plant pathogens, the main goal of this paper is to critically discuss and compare the potential use of reshaped soil microbiomes by assembling different agricultural practices such as crop selection; land use and conservative agriculture; crop rotation, diversification, intercropping and cover cropping; compost and chitosan application; and soil pre-fumigation combined with organic amendments and bio-organic fertilizers. This review is seen mostly as a comprehensive understanding of the main findings regarding DSS, starting from the oldest concepts to the newest challenges, based on the assumption that sustainability for soil quality and plant health is increasingly viable and supported by microbiome-assisted strategies based on the next-generation sequencing (NGS) methods that characterize in depth the soil bacterial and fungal communities. This approach, together with the virtuous reuse of agro-wastes to produce in situ green composts and organic bio-fertilizers, is the best way to design new sustainable cropping systems in a circular economy system. The current knowledge on soil-borne pathogens and soil microbiota is summarized. How microbiota determine soil suppression and what NGS strategies are available to understand soil microbiomes in DSS are presented. Disturbance of soil microbiota based on combined agricultural practices is deeply considered. Sustainable soil microbiome management by recycling in situ agro-wastes is presented. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed.

Antifungal, plant growth-promoting, and mycotoxin detoxication activities of Burkholderia sp. strain XHY-12

A bacterial strain named XHY-12 was isolated from corn soil samples and identified as Burkholderia sp. based on 16S rDNA sequencing, it displayed high antagonistic activity against 12 fungal pathogens and the common fungal contaminant in grain Aspergillus flavus. Plate experiment showed that XHY-12 fermentation broth reduced the incidence of S. sclerotiorum on detached rape leaves (Brassica campestris L.) by 100%, and a greenhouse experiment showed that it could promote the growth of rape seedlings with significant increases in plant height, root length, and fresh weight. Furthermore, a novel funding was the reduction of aflatoxin B1 and B2 by over 85% in 60 h, and the decomposition enzymes should be extracellular. The results suggest that XHY-12 has a potential for commercial applications as biocontrol, mycotoxin detoxification agent or biofertilizer.

Alleviated Antibiotic-Resistant Genes in the Rhizosphere of Agricultural Soils with Low Antibiotic Concentration

The influence of the rhizosphere on the abundance and diversity of antibiotic resistance genes (ARGs) has been recognized but there is a lack of consensus because of broad ranges of plant species and antibiotic concentrations across different habitats and the elusive underlying mechanisms. Here, we profiled antibiotic concentrations and resistomes in the rhizosphere and bulk soils by cultivating 10 types of crops in manure-amended agricultural soils. Rhizosphere effects altered the antibiotic resistome structure, significantly increased the absolute abundance of the antibiotic resistome, and decreased their relative abundance, contrasting previous studies. Such plantation-driven variation in ARGs resulted from the boost of bacterial lineages with negative relationships with ARGs and the constraint of the potential ARG-hosts in the rhizosphere of plants cultivated in soils with low antibiotic concentrations as the selective pressure. This mechanism is not reported previously and deepens our understanding about the rhizosphere effects on ARGs.

Alterations in the Endophyte-Enriched Root-Associated Microbiome of Rice Receiving Growth-Promoting Treatments of Urea Fertilizer and Rhizobium Biofertilizer

We examined the bacterial endophyte-enriched root-associated microbiome within rice (Oryza sativa) 55 days after growth in soil with and without urea fertilizer and/or biofertilization with a growth-promotive bacterial strain (Rhizobium leguminosarum bv. trifolii E11). After treatment to deplete rhizosphere/rhizoplane communities, washed roots were macerated and their endophyte-enriched communities were analyzed by 16S ribosomal DNA 454 amplicon pyrosequencing. This analysis clustered 99,990 valid sequence reads into 1105 operational taxonomic units (OTUs) with 97% sequence identity, 133 of which represented a consolidated core assemblage representing 12.04% of the fully detected OTU richness. Taxonomic affiliations indicated Proteobacteria as the most abundant phylum (especially α- and γ-Proteobacteria classes), followed by Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, and several other phyla. Dominant genera included Rheinheimera, unclassified Rhodospirillaceae, Pseudomonas, Asticcacaulis, Sphingomonas, and Rhizobium. Several OTUs had close taxonomic affiliation to genera of diazotrophic rhizobacteria, including Rhizobium, unclassified Rhizobiales, Azospirillum, Azoarcus, unclassified Rhizobiaceae, Bradyrhizobium, Azonexus, Mesorhizobium, Devosia, Azovibrio, Azospira, Azomonas, and Azotobacter. The endophyte-enriched microbiome was restructured within roots receiving growth-promoting treatments. Compared to the untreated control, endophyte-enriched communities receiving urea and/or biofertilizer treatments were significantly reduced in OTU richness and relative read abundances. Several unique OTUs were enriched in each of the treatment communities. These alterations in structure of root-associated communities suggest dynamic interactions in the host plant microbiome, some of which may influence the well-documented positive synergistic impact of rhizobial biofertilizer inoculation plus low doses of urea-N fertilizer on growth promotion of rice, considered as one of the world's most important food crops.

Phenotypic and genotypic characterization of phosphate solubilizing bacteria and their efficiency on the growth of maize

Phosphate solubilizing bacteria (PSB) has ability to convert insoluble form of phosphorous to an available form. Applications of PSB as inoculants increase the phosphorus uptake by plant in the agriculture field. In this study, isolation and identification of PSB were carried out in Indian agriculture field (Nainital region, Uttarakhand). A total of 8 phosphate solubilizing bacterial colonies were isolated on the Pikovskaya’s (PKV) agar medium, containing insoluble tricalcium phosphate (TCP). The colonies showed clear halo zones around the bacterial growth were considered as phosphate solubilizers. Out of 8 bacterial isolates, 3 isolates showed high phosphate solubilization index (PSI) ranged from 4.88 ± 0.69 to 4.48 ± 0.30, lower pH ranging 3.08 ± 0.08 to 3.82 ± 0.12 and high phosphate solubilization varied from 305.49 ± 10 μg/ml to 277.72 ± 1.45 μg/ml, were selected for further characterization. Based on the 16 S rRNA gene sequence analysis A4 isolate and H6 isolate were closely related to Alcaligenes aquatilis (99%), and C1 isolate was closely related to Burkholderia cepacia (99%). In addition, pot examination also showed the greatest efficiency in promotion of maize growth compared to uninoculated plant. Isolated PSB were able to produce different organic acids (such as gluconic acids, formic acid, and citric acid) in the culture supernatant and may consider as the principle mechanism for phosphate solubilization. This study clearly indicates that A4, C1 and H6 isolates may use as a biofertilizers in ecological agricultural systems instead of synthetic chemicals and may help to sustain environmental health and soil productivity.

Biosafety Test for Plant Growth-Promoting Bacteria: Proposed Environmental and Human Safety Index (EHSI) Protocol

Plant growth-promoting bacteria (PGPB) colonize plants and enhance their growth by different mechanisms. Some of these microorganisms may represent a potential threat to human, animal or plant health; however, their use might be approved in parts of Europe if they have been recommended as plant growth enhancers. The current regulatory framework has resulted in a fragmented, contradictory system, and there is an urgent need to establish harmonized protocols for the predictability, efficiency, consistency and especially the safety of PGPB for human and animal health and for the environment. In response to current efforts to update biosafety policies and provide alternative methods to replace the use of vertebrate animals, we propose a panel of tests and an evaluation system to reliably determine the biosafety of bacterial strains used as PGPB. Based on the results of different tests, we propose a scoring system to evaluate the safety of candidates for PGPB within the limitations of the assays used.

Biodegradation of alachlor in liquid and soil cultures under variable carbon and nitrogen sources by bacterial consortium isolated from corn field soil

Alachlor, an aniline herbicide widely used in corn production, is frequently detected in water resources. The main objectives of this research were focused on isolating bacterial consortium capable of alachlor biodegradation, assessing the effects of carbon and nitrogen sources on alachlor biodegradation and evaluating the feasibility of using bacterial consortium in soil culture. Kavar corn field soil with a long history of alachlor application in Fars province of Iran has been explored for their potential of alachlor biodegradation. The influence of different carbon compounds (glucose, sodium citrate, sucrose, starch and the combination of these compounds), the effect of nitrogen sources (ammonium nitrate and urea) and different pH (5.5-8.5) on alachlor removal efficiency by the bacterial consortium in liquid culture were investigated. After a multi-step enrichment program 100 days of acclimation, a culture with the high capability of alachlor degradation was obtained (63%). Glucose and sodium citrate had the highest alachlor reduction rate (85%). Alachlor reduction rate increased more rapidly by the addition of ammonium nitrate (94%) compare to urea. Based on the data obtained in the present study, pH of 7.5 is optimal for alachlor biodegradation. After 30 days of incubation, the percent of alachlor reduction were significantly enhanced in the inoculated soils (74%) as compared to uninoculated control soils (17.67%) at the soil moisture content of 25%. In conclusion, bioaugmentation of soil with bacterial consortium may enhance the rate of alachlor degradation in a polluted soil.

Effect of on-field inoculation of Phaseolus vulgaris with rhizobia on soil bacterial communities

The aim of this study was to assess the impact of inoculation of Phaseolus vulgaris with two indigenous rhizobia strains on plant growth promotion, nitrogen turnover processes, richness and structure of the Rhizobiaceae and total bacterial communities in the bulk soil. Both strains used induced a significant increase in nodulation and grain yield. Analysis of bulk soil fertility showed positive, negative and strain-dependent effects of inoculation on nitrate, phosphorus and ammonium, respectively. Terminal-restriction fragment length polymorphism profiling demonstrated that inoculation significantly increased the phylotype richness of the bacterial communities. No significant difference in richness between the strains used and no additive effect of co-inoculation were observed. However, differences between both inoculants and a clear additive effect of co-inoculation on heterogeneity were found. This work gives original insights into the effect of rhizobial inoculation outside the restricted rhizospheric area. Effects on bacterial structure and diversity are clearly sensed in the neighbourhood of 25 cm and in a limited time course. Both Alpha- and Gammaproteobacteria, together with Firmicutes and Actinobacteria, were enhanced by inoculation, No evidence of terminal-restriction fragment inhibition was found. However, it remains to be answered how the impact on taxonomic groups can be related to effects on functional capabilities of soil microbial communities.

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.

Effects of inoculation with plant growth-promoting rhizobacteria on resident rhizosphere microorganisms

Plant growth-promoting rhizobacteria (PGPR) are exogenous bacteria introduced into agricultural ecosystems that act positively upon plant development. However, amendment reproducibility as well as the potential effects of inoculation upon plant root-associated microbial communities can be sources of concern. To address these questions, an understanding of mutual interactions between inoculants and resident rhizosphere microorganisms is required. Mechanisms used by PGPR can be direct or indirect; the former entails the secretion of growth regulators and the latter occurs through the production of antimicrobial compounds that reduce the deleterious effects of phytopathogens. The different modes of action may lead to different relationships between an inoculant and root microbial communities. Rhizobacterial communities are also affected by the plant, engineered genes, environmental stresses and agricultural practices. These factors appear to determine community structure more than an exogenous, active PGPR introduced at high levels.

A degradation product of the salicylic acid pathway triggers oxidative stress resulting in down-regulation of Bacillus subtilis biofilm formation on Arabidopsis thaliana roots

Bacillus subtilis, a plant growth promoting rhizobacteria (PGPR), induces growth response and protection against pathogenic organisms through colonization and biofilm formation on the Arabidopsis thaliana root surface. In the current investigation, we utilized various Arabidopsis defense pathway mutants in a series of studies and showed that the plants recognize B. subtilis by a chemical-dependent cascade, which is independent of the salicylic acid (SA), jasmonic acid (JA), or ethylene pathways. These experiments revealed the importance of root surface chemistry in colonization and biofilm formation by B. subtilis. It was found that B. subtilis FB17 could not form biofilms on the roots of NahG, a transgenic Arabidopsis line for salicylate hydroxylase that produces catechol as the degradation product of SA. These findings suggest that catechol may play a direct role in inhibiting B. subtilis FB17 biofilm formation on the NahG root surface, possibly through induction of reactive oxygen species (ROS) in the roots. Using both in vitro microtitre plate and in planta assays we confirmed that catechol inhibited biofilm formation, but not the planktonic growth, of B. subtilis. Inhibition of biofilm formation was shown to be the result of a physiological response by B. subtilis to the presence of catechol, which resulted in the down-regulation of transcription of the yqxM-sipW-tasA and epsA-O operons, both of which are required for biofilm formation by B. subtilis. These data indicate that the suppression of biofilm formation on NahG plants was strongly influenced by the root-derived catechol production through ROS-mediated down-regulation of B. subtilis biofilm genes.

Rhizosphere microbial community structure at different maize plant growth stages and root locations

The aims of the present work were (1) to determine the influence of plant growth stages on the population size of culturable bacteria and fungi associated with rhizoplane and endo-rhizosphere of maize grown in field and (2) to establish the community structure of total culturable bacteria and fungi. Density, diversity and community structure of culturable rhizoplane and endo-rhizosphere populations at different maize plant growth stages were estimated. Plant development did not have influence on total culturable microflora density but it selectively influenced some bacterial and fungal groups present in the rhizosphere. However, the microbial community structure changed markedly over time. This knowledge is relevant for exploring endophytic rhizobacteria potential in the promotion of plant-growth, protection against pathogens and to detect perturbations in natural agro ecosystems.

Behavior and fate of chlorpyrifos introduced into soil-crop systems by irrigation

The effect of chlorpyrifos added in irrigation water to a red soil from Central South China on the growth of wheat and oilseed rape seedlings, together with its uptake, was studied in a pot experiment. Addition of chlorpyrifos (1-10 microg g-1) in a single irrigation with distilled water resulted in absorption of chlorpyrifos by wheat (0.257-4.50 microg g-1) and also oilseed rape seedlings (0.249-2.02 microg g-1) during 20 d of plant growth. An initial concentration of chlorpyrifos in soil that is equivalent to or below 10 microg g-1 did not significantly influence the growth of wheat seedlings. Similarly, an initial concentration equivalent to or below 5 microg g-1 did not significantly influence the growth of oilseed rape seedlings. The degradation rate of chlorpyrifos was 1.4-4.2 times larger in oilseed rape rhizosphere soil than in unvegetated soil. The numbers of bacteria and fungi in oilseed rape rhizosphere soil were 3.18 times and 1.84 times larger, respectively, than those in unvegetated soil. This helps to explain the difference in degradation rates obtained.

Inoculation with the plant-growth-promoting rhizobacterium Azospirillum brasilense causes little disturbance in the rhizosphere and rhizoplane of maize (Zea mays)

Inoculation with Azospirillum brasilense exerts beneficial effects on plant growth and crop yields. In this study, a comparative analysis of maize (Zea mays) root inoculated or not inoculated with A. brasilense strains was performed in two soils. Colonization dynamics of the rhizobacteria were tracked in various root compartments using 16S rRNA-targeted probes and 4',6'diamidino-2-phenylindole staining, and the structure of bacterial populations in the same samples was analyzed by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction products of the 16S rRNA gene. Based on whole cell hybridization, a large fraction of the bacterial community was found to be active in both the rhizoplane-endorhizosphere and rhizosphere soil compartments, in both soil types. A DGGE fingerprint analysis revealed that plant inoculation with A. brasilense had no effect on the structural composition of the bacterial communities, which were also found to be very similar at the root tip and at zones of root branching. However, rhizobacterial populations were strongly influenced by plant age, and their complexity decreased in the rhizoplane-endorhizosphere in comparison to rhizosphere soil. A clone library generated from rhizosphere DNA revealed a highly diverse community of soil and rhizosphere bacteria, including an indigenous Azospirillum-like organism. A large proportion of these clones was only distantly related to known species.

Biocontrol of Bacillus subtilis against Fusarium verticillioides in vitro and at the maize root level

Bacillus species as a group offer several advantages over other bacteria for protection against root pathogens because of their ability to form endospores, and because of the broad-spectrum activity of their antibiotics. The objectives of this work were to determine the ability of strains of Bacillus to inhibit Fusarium verticillioides growth and fumonisin B(1) accumulation in vitro, and to evaluate the ability of the best bacterium for preventing rhizosphere and endorhizosphere colonization by F. verticillioides. Bacterial populations from the maize rhizoplane were obtained, and the capacity of ten Bacillus strains to inhibit fungal growth and fumonisin B(1) accumulation in vitro was assayed. According to these results, B. subtilis CE1 was selected as the best antagonist for testing maize root colonization of F. verticillioides. Bacillus subtilis CE1 at 10(8) and 10(7) CFU ml(-1) inocula was able to reduce rhizoplane and endorhizosphere colonization of F. verticillioides in greenhouse trials. The strain B. subtilis CE1 could be a potential biological control agent against F. verticillioides at the root level.

Symbiotic microorganisms, a key for ecological success and protection of plants

Plant-associated microbial diversity encompasses symbionts, protecting their host against various aggressions. Mycorrhizal and rhizospheric microorganisms buffer effects of soil toxic compounds and soil-borne pathogens. Endophytic bacteria and fungi, some of which are vertically inherited through seeds, take part in plant protection by acting directly on aggressive factors (mainly pathogens and herbivores) or by enhancing plant responses. Plant protective microbial symbionts determine the ecological success of plants; they drastically modify plant communities and related trophic webs. This review suggests approaches to improve the inventory of diversity and functions of in situ plant-associated microorganisms.

Effect of a Sinorhizobium meliloti strain with a modified putA gene on the rhizosphere microbial community of alfalfa

The success of a rhizobial inoculant in the soil depends to a large extent on its capacity to compete against indigenous strains. M403, a Sinorhizobium meliloti strain with enhanced competitiveness for nodule occupancy, was recently constructed by introducing a plasmid containing an extra copy of a modified putA (proline dehydrogenase) gene. This strain and M401, a control strain carrying the same plasmid without the modified gene, were used as soil inoculants for alfalfa in a contained field release experiment at León, Spain. In this study, we determined the effects of these two strains on the indigenous microbial community. 16S rRNA genes were obtained from the rhizosphere of alfalfa inoculated with strain M403 or strain M401 or from noninoculated plants by amplification of DNA from soil with bacterial group-specific primers. These genes were analyzed and compared by restriction fragment length polymorphism and temperature gradient gel electrophoresis. The results allowed us to differentiate between alterations in the microbial community apparently caused by inoculation and by the rhizosphere effect and seasonal fluctuations induced by the alfalfa plants and by the environment. Only moderate inoculation-dependent effects could be detected, while the alfalfa plants appeared to have a much stronger influence on the microbial community.

Culture-based and non-growth-dependent detection of the Burkholderia cepacia complex in soil environments

Burkholderia cepacia complex (Bcc) bacteria reside in soil, plant rhizospheres, and water, but their prevalence and distribution in outdoor environments is not clear. We sampled a variety of soil and rhizosphere environments with which people may have contact: playgrounds, athletic fields, parks, hiking trails, residential yards, and gardens. A total of 91 sites was sampled in three large U.S. cities. In the first phase of the study, putative Bcc isolates were recovered on Burkholderia cepacia selective agar and trypan blue tetracycline medium and subsequently examined for biochemical reactivity and growth at 32 and 22 degrees C. Isolates were further examined by PCR assays targeting Bcc-specific ribosomal DNA and recA gene sequences. Among the 1,013 bacterial isolates examined, 68 were identified as Bcc; 14 (15%) of 91 sampled sites yielded Bcc isolates. In the second phase, DNA was extracted directly from soil samples and examined with PCR assays targeting Bcc 16S rRNA gene sequences. Either 82 or 93% of the soil samples were positive for at least one Bcc genomovar, depending on the PCR assay system used. Cloning and sequencing were performed to check the specificity of the PCR assays. Sequence analysis of the 463-bp 16S rRNA inserts from eight clones indicated that all were from members of the Bcc. The four soil samples from which these clones were generated did not yield isolates identified as Bcc. Based on PCR detection, Bcc appears to be prevalent in soil from urban and suburban environments. Culture-based recovery of Bcc may underestimate environmental populations.

Combined use of a specific probe and PCAT medium to study Burkholderia in soil

Due to its pathogenic traits and agricultural benefits, there is some challenge in detecting Burkholderia in the soil environment. In this perspective, an existing semi-selective medium, (PCAT), was combined with a Burkholderia specific molecular probe. Using the complete 16S rRNA sequences of all available Burkholderia species type strains, we selected the following sequence: 5'-ACCCTCTGTTCCGACCATTGTATGA-3'. The probe was validated against GenBank sequences, with dot blots and colony hybridization tests. A diversity study of all strains growing on a PCAT plate after plating a soil dilution (75 strains) was carried out with ARDRA analysis and colony hybridization tests. All the hybridizing strains belonged to genus Burkholderia. The major type of non-hybridizing isolates belonged to Pseudomonas (16S rRNA sequencing). Both tools were combined to compare the Burkholderia populations in a rhizosphere (maize) and a non-rhizosphere soil. Based on hybridizing PCAT isolates, we were able to show an increase in Burkholderia populations in the maize rhizosphere. This genus represented 2% and 16% of the total cultivable microflora in the non-rhizosphere and rhizosphere soils, respectively. Although PCAT was shown not to be appropriate to routinely enumerate Burkholderia populations in soil, it allowed environmental investigations at the genus level, when combined with a molecular specific probe.

Burkholderia, a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution

The genus Burkholderia comprises 19 species, including Burkholderia vietnamiensis which is the only known N(2)-fixing species of this bacterial genus. The first isolates of B. vietnamiensis were recovered from the rhizosphere of rice plants grown in a phytotron, but its existence in natural environments and its geographic distribution were not reported. In the present study, most N(2)-fixing isolates recovered from the environment of field-grown maize and coffee plants cultivated in widely separated regions of Mexico were phenotypically identified as B. cepacia using the API 20NE system. Nevertheless, a number of these isolates recovered from inside of maize roots, as well as from the rhizosphere and rhizoplane of maize and coffee plants, showed similar or identical features to those of B. vietnamiensis TVV75(T). These features include nitrogenase activity with 10 different carbon sources, identical or very similar nifHDK hybridization patterns, very similar protein electrophoregrams, identical amplified 16S rDNA restriction (ARDRA) profiles, and levels of DNA-DNA reassociation higher than 70% with total DNA from strain TVV75(T). Although the ability to fix N(2) is not reported to be a common feature among the known species of the genus Burkholderia, the results obtained show that many diazotrophic Burkholderia isolates analyzed showed phenotypic and genotypic features different from those of the known N(2)-fixing species B. vietnamiensis as well as from those of B. kururiensis, a bacterium identified in the present study as a diazotrophic species. DNA-DNA reassociation assays confirmed the existence of N(2)-fixing Burkholderia species different from B. vietnamiensis. In addition, this study shows the wide geographic distribution and substantial capability of N(2)-fixing Burkholderia spp. for colonizing diverse host plants in distantly separated environments.

Impact of 2,4-diacetylphloroglucinol-producing biocontrol strain Pseudomonas fluorescens F113 on intraspecific diversity of resident culturable fluorescent pseudomonads associated with the roots of field-grown sugar beet seedlings

The impact of the 2,4-diacetylphloroglucinol-producing biocontrol agent Pseudomonas fluorescens F113Rif on the diversity of the resident community of culturable fluorescent pseudomonads associated with the roots of field-grown sugar beet seedlings was evaluated. At 19 days after sowing, the seed inoculant F113Rif had replaced some of the resident culturable fluorescent pseudomonads at the rhizoplane but had no effect on the number of these bacteria in the rhizosphere. A total of 498 isolates of resident fluorescent pseudomonads were obtained and characterized by molecular means at the level of broad phylogenetic groups (by amplified ribosomal DNA restriction analysis) and at the strain level (with random amplified polymorphic DNA markers) as well as phenotypically (55 physiological tests). The introduced pseudomonad induced a major shift in the composition of the resident culturable fluorescent Pseudomonas community, as the percentage of rhizoplane isolates capable of growing on three carbon substrates (erythritol, adonitol, and L-tryptophan) not assimilated by the inoculant was increased from less than 10% to more than 40%. However, the pseudomonads selected did not display enhanced resistance to 2,4-diacetylphloroglucinol. The shift in the resident populations, which was spatially limited to the surface of the root (i.e., the rhizoplane), took place without affecting the relative proportions of phylogenetic groups or the high level of strain diversity of the resident culturable fluorescent Pseudomonas community. These results suggest that the root-associated Pseudomonas community of sugar beet seedlings is resilient to the perturbation that may be caused by a taxonomically related inoculant.

16S rDNA fingerprinting of rhizosphere bacterial communities associated with healthy and Phytophthora infected avocado roots

Molecular techniques employing 16S rDNA profiles generated by PCR-DGGE were used to detect changes in bacterial community structures of the rhizosphere of avocado trees during infection by Phytophthora cinnamomi and during repeated bioaugmentation with a disease suppressive fluorescent pseudomonad. When the 16S rDNA profiles were analyzed by multivariate analysis procedures, distinct microbial communities were shown to occur on healthy and infected roots. Bacterial communities from healthy roots were represented by simple DNA banding profiles, suggestive of colonization by a few predominant species, and were approximately 80% similar in structure. In contrast, roots that were infected with Phytophthora, but which did not yet show visible symptoms of disease, were colonized by much more variable bacterial communities that had significantly different community structures from those of healthy roots. Root samples from trees receiving repeated applications of the disease suppressive bacterium Pseudomonas fluorescens st. 513 were free of Phytophthora infection, and had bacterial community structures that were similar to those of nontreated healthy roots. Sequence analysis of clones generated from four predominant bands cut from the DGGE gels revealed the presence of pseudomonads, as well as several previously unidentified bacteria. Differentiation of 16S rDNA profiles for healthy and infected roots suggests that rhizosphere bacterial community structure may serve as an integrative indicator of changes in chemical and biological conditions in the plant rhizosphere during the infection process.

Effect of field inoculation with Sinorhizobium meliloti L33 on the composition of bacterial communities in rhizospheres of a target plant (Medicago sativa) and a non-target plant (Chenopodium album)-linking of 16S rRNA gene-based single-strand conformation polymorphism community profiles to the diversity of cultivated bacteria

Fourteen weeks after field release of luciferase gene-tagged Sinorhizobium meliloti L33 in field plots seeded with Medicago sativa, we found that the inoculant also occurred in bulk soil from noninoculated control plots. In rhizospheres of M. sativa plants, S. meliloti L33 could be detected in noninoculated plots 12 weeks after inoculation, indicating that growth in the rhizosphere preceded spread into bulk soil. To determine whether inoculation affected bacterial diversity, 1,119 bacteria were isolated from the rhizospheres of M. sativa and Chenopodium album, which was the dominant weed in the field plots. Amplified ribosomal DNA restriction analysis (ARDRA) revealed plant-specific fragment size frequencies. Dominant ARDRA groups were identified by 16S rRNA gene nucleotide sequencing. Database comparisons indicated that the rhizospheres contained members of the Proteobacteria (alpha, beta, and gamma subgroups), members of the Cytophaga-Flavobacterium group, and gram-positive bacteria with high G+C DNA contents. The levels of many groups were affected by the plant species and, in the case of M. sativa, by inoculation. The most abundant isolates were related to Variovorax sp., Arthrobacter ramosus, and Acinetobacter calcoaceticus. In the rhizosphere of M. sativa, inoculation reduced the numbers of cells of A. calcoaceticus and members of the genus Pseudomonas and increased the number of rhizobia. Cultivation-independent PCR-single-strand conformation polymorphism (SSCP) profiles of a 16S rRNA gene region confirmed the existence of plant-specific rhizosphere communities and the effect of the inoculant. All dominant ARDRA groups except Variovorax species could be detected. On the other hand, the SSCP profiles revealed products which could not be assigned to the dominant cultured isolates, indicating that the bacterial diversity was greater than the diversity suggested by cultivation.