Search of environmental descriptors to explain the variability of the bacterial diversity from maize rhizospheres across a regional scale

The regional scale variability of the bacterial community inhabiting the rhizosphere was studied with soil collected from maize fields located in the Santo Domingo Valley (SDV; Baja California Sur, Mexico), a semi-arid agricultural ecosystem of approximately 200 km². The bacterial community structure was visualized by single-strand conformation polymorphism (SSCP) profiles of PCR-amplified partial 16S rRNA genes of directly extracted rhizosphere soil DNA. SSCP profiles of different SDV sites and an external field site in Germany were evaluated for their similarities and the contributing bacteria were characterized by DNA sequence analyses. SSCP profiles from each site were significantly different from the others, as revealed by permutation of pairwise similarities (P < 0.05). In comparison to the German site, SSCP profiles from SDV were more similar to each other despite contrasting soil salinity levels. Correspondence analysis revealed that among SDV sites, salinity levels, soil organic carbon and calcium (Ca²⁺) were most influential on the bacterial community structure. Depending on the phylogenetic group analyzed (Bacteria, Alphaproteobacteria, Pseudomonas), the importance of these soil variables varied. Interestingly, the East–West direction also revealed an effect, suggesting that future explorations of bacterial diversity patterns should also consider landscape topography in search of explaining patterns of bacterial diversity in soils.     

Structural differences in the rhizosphere communities of legumes are not equally reflected in community-level physiological profiles

The relationship of structural diversity and differences in the functional potentials of rhizosphere communities of alfalfa, common bean and clover was investigated in microcosms. PCR-SSCP (single strand conformation polymorphism) analysis of 16S rRNA genes revealed significant differences in the composition of the leguminous rhizosphere communities at the shoot stage of plants grown in the same soil. Sequencing of dominant SSCP-bands indicated the presence of plant specific organisms. The partial rRNA gene sequences were related to members of the α- and γ-Proteobacteria, Bacteroidetes and Actinobacteria. Besides the plant species, the soil also affected the structural diversity in rhizospheres. The dominant bacterial populations of alfalfa grown in soils with different agricultural histories were assigned to different taxonomic groups. Addressing the functional potentials, community-level physiological profiles (CLPP) were generated using BIOLOG GN^®. The three leguminous rhizosphere communities could be differentiated by principle component analysis, though the overall analysis indicated that the metabolic potential of all rhizosphere samples was similar. The functional variation examined in rhizospheres of alfalfa was minor in response to the soil origin and was found not to be significant different at different growth stages. The results indicate that similar functional potentials may be provided by structurally different bacterial communities.     

Influence of management practices on the diversity of pseudomonads in rhizosphere soil of wheat cropping system

The composition and diversity of the bacterial communities associated with plant root is influenced by various biotic and abiotic factors. In this study, effect of soil management practices, conventional (pf) and raised bed (rb), are compared for bacterial diversity in rhizosphere of wheat (Triticum aestivum) var. UP2338, taking pseudomonads as a biomarker. Microbial diversity was assessed employing culturable and unculturable approaches. Amplified rDNA restriction analysis showed that soil management practices and site of sampling (rhizosphere-RS and rhizoplane-RP) affected the composition of microbial communities. Sample from conventional management showed a higher Pseudomonas diversity (H′ = 3.7) than that from raised bed (H′ = 2.78). However, total bacterial diversity (SSCP data) was more complex in rb than pf management. Dominant members of both pf and rb were γ-proteobacteria as Pseudomonas was dominant over other forms, while Bacillus species were only present as low numbers in rb.     

Resistance of bacterial communities in the potato rhizosphere to disturbance and its application to agroecology

Soil bacteria have the ability to increase agricultural sustainability through the production of biopesticides and biofertilizers. Application of bacteria to field crops often results in sporadic colonization and unpredictable crop performance. This research sought to understand the colonization of the potato (Solanum tuberosum L.) rhizosphere using reciprocal transplants. Plants were grown in a forest or an agricultural soil and then transplanted into either the same soil or the opposite soil. Bacterial communities were profiled using terminal restriction fragment length polymorphism (TRFLP) and analyzed using pairwise comparisons. The results revealed that the bacterial community that colonized the rhizosphere in the first soil remained mostly intact for 30 days after the plants were transplanted into another soil in which the soil bacteria community differed from that found in the original soil. The concept that it may be possible to establish a functional microbiota and to deliver it to an agricultural environment was tested. A nitrogen-fixing bacterial community was established on plants grown under tissue culture conditions and the plants were transplanted into a field soil. Plants inoculated with eight separate nitrogen-fixing communities showed an average fivefold increase in dry biomass when compared to mock-inoculated plants and the microbial profiles remained distinct at 30 days after transplantation. These results demonstrate that the plant rhizosphere is a resistant community and that the first bacterial community that becomes established on the root remains with the plant even when the plant is placed into soil with a vastly different microbiota.     

Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils

A number of studies have reported species specific selection of microbial communities in the rhizosphere by plants. It is hypothesised that plants influence microbial community structure in the rhizosphere through rhizodeposition. We examined to what extent the structure of bacterial and fungal communities in the rhizosphere of grasses is determined by the plant species and different soil types. Three grass species were planted in soil from one site, to identify plant-specific influences on rhizosphere microbial communities. To quantify the soil-specific effects on rhizosphere microbial community structure, we planted one grass species (Lolium perenne L.) into soils from three contrasting sites. Rhizosphere, non-rhizosphere (bulk) and control (non-planted) soil samples were collected at regular intervals, to examine the temporal changes in soil microbial communities. Rhizosphere soil samples were collected from both root bases and root tips, to investigate root associated spatial influences. Both fungal and bacterial communities were analysed by terminal restriction fragment length polymorphism (TRFLP). Both bacterial and fungal communities were influenced by the plant growth but there was no evidence for plant species selection of the soil microbial communities in the rhizosphere of the different grass species. For both fungal and bacterial communities, the major determinant of community structure in rhizospheres was soil type. This observation was confirmed by cloning and sequencing analysis of bacterial communities. In control soils, bacterial composition was dominated by Firmicutes and Actinobacteria but in the rhizosphere samples, the majority of bacteria belonged to Proteobacteria and Acidobacteria. Bacterial community compositions of rhizosphere soils from different plants were similar, indicating only a weak influence of plant species on rhizosphere microbial community structure.     

Stenotrophomonas rhizophila DSM14405T promotes plant growth probably by altering fungal communities in the rhizosphere

Stenotrophomonas rhizophila DSM14405^T is of high biotechnological interest as plant growth stimulator, especially for salinated conditions. The objective of this study was to determine the effect of plant species (cotton, tomato, and sweet pepper) on colonisation and plant growth promotion of this beneficial bacterium in gnotobiotic systems and in non-sterile soil. All plant structures (leaves, stems, and roots) were densely colonised by DSM14405^T reaching up to 10⁹ cells g^?1 fresh weight; under gnotobiotic conditions the abundances were 4–5 orders of magnitude higher than in non-sterile soil. Under non-sterile conditions and ambient humidity, tomato shoots were more densely colonised than shoots of sweet pepper and cotton. S. rhizophila DSM14405^T was shown to grow endophytically and colonise the vicinity of root hairs of tomato. Plant growth promotion was particularly apparent in tomato. In general, the impact of plant species on colonisation and plant growth promotion was more pronounced in soil than under gnotobiotic conditions and likely due to the control of diseases and deleterious microorganisms. S. rhizophila DSM14405^T was shown to control diseases in sweet pepper and in cotton. Molecular profiling via single strand conformation polymorphism of internal transcribed spacers and 16S rRNA genes (PCR-single strand conformational polymorphism (SSCP)) revealed that S. rhizophila DSM14405^T strongly affected fungal, but not bacterial communities in the rhizosphere of tomato and sweet pepper. Major SSCP bands related to uncultured fungi and Candida subhashii, disappeared in tomato rhizosphere after Stenotrophomonas treatment. This suggests an indirect, species-specific plant growth promotion effect of S. rhizophila via the elimination of deleterious rhizosphere organisms.     

Bacterial diversity in cucumber (Cucumis sativus) rhizosphere in response to salinity, soil pH, and boron

Soil salinity is a major factor relating microbial communities to environmental stress in the microbial selection process as stress can reduce bacterial diversity. In the San Joaquin Valley (SJV) of California, the problem of increasing salinity and consequently, decreasing crop productivity, due to reuse of saline drainage water are major concerns. An experiment was conducted in a closed, recirculating volumetric lysimeter system (VLS) consisting of 24 experimental plant growth units to determine the interactive effects of salinity, boron and pH on rhizosphere and non-rhizosphere microbial composition of cucumber (Cucumis sativus L. cv. Seminis Turbo hybrid). Plants in the VLS were irrigated from individual reservoirs containing a modified half-strength Hoagland's nutrient solution combined with salinity, boron (B), and pH treatments. The results indicated that salinity and pH were the most influential factors affecting the growth of plants and the effect of boron on the plant was more severe under slightly acidic conditions. Total bacterial DNA was extracted from rhizosphere and non-rhizosphere samples, and a 236-bp DNA fragment in the V3 region of the small subunit ribosomal RNA genes of eubacteria was amplified. The 16S rRNA and the products were subjected to denaturing gradient gel electrophoresis (DGGE) and sequencing. Analyses of bacterial diversity showed that the effects of salinity, boron, and pH were more severe on the rhizosphere bacterial population during the first week of growing cucumber, with decreasing impacts with plant growth. However, there was no salinity-B-pH interaction effects on plant biomass, but the effects were seen in the number of heterotrophic bacteria in the rhizosphere and on species richness and diversity during week seven of the study. These suggest that the effects of salinity-B-pH interactions may influence microorganisms first before plants and may pose long term effects on soil quality.     

Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition

The relative importance of specific plant properties versus soil characteristics in shaping the bacterial community structure of the rhizosphere is a topic of considerable debate. Here, we report the results of a study on the bacterial composition of the rhizosphere of the wild plant Carex arenaria (sand sedge) growing at 10 natural sites in The Netherlands. The soil properties of the sandy soils at these sites were highly disparate, most notably in pH, chloride and organic matter content. Rhizosphere and bulk soil bacterial communities were examined by culture-independent means, namely, 16S rDNA-directed PCR-DGGE profiling. Large differences were observed between the bacterial communities of the different sites for both bulk and rhizosphere soil. Cluster analysis of bacterial profiles revealed that the rhizosphere community of each site was generally more closely related to the bulk soil community of that site rather than to rhizosphere communities of other sites. Hence, bacterial community structure within the rhizosphere of C. arenaria appeared to be determined to a large extent by the bulk soil community composition. This conclusion was supported by a reciprocal planting experiment, where C. arenaria shoots of different sites yielded highly similar rhizosphere communities when planted in the same soil.     

Amendment of degraded desert soil with wastewater debris containing immobilized Chlorella sorokiniana and Azospirillum brasilense significantly modifies soil bacterial community structure, diversity, and richness

The main goal of this study was to expand our knowledge of what happens to the soil bacterial community in an eroded desert soil when improvement of soil fertility is derived from the application of debris of tertiary wastewater treatment containing immobilized microalgae Chlorella sorokiniana and the plant growth-promoting bacterium (PGPB) Azospirillum brasilense. We hypothesized that an “improved” non-agricultural desert soil will exhibit substantial changes in the structure of the bacterial community in a relatively short time after amendment. To assess the effect of the amendments, microalgae and PGPB alone or combined, on the structure of the rhizosphere bacterial community, changes in species richness and bacterial diversity over time were based on sequence differences in the 16S rRNA gene, performed with PCR–denaturing gradient gel electrophoresis (DGGE) and then analyzed by similarity test and non-metric multidimensional scaling analysis. Root surface colonization and persistence in the rhizosphere of A. brasilense was monitored by fluorescent in situ hybridization and sequencing of DGGE bands. Application of waste debris significantly changed the rhizosphere bacterial population structure, whether comparisons were made over time, between inoculated and non-inoculated soil, and among different inoculated microorganisms. Species richness and diversity increased when the waste debris contained the microalgae–bacteria association and also over time. Even as its secondary role as an inoculant after wastewater treatment, A. brasilense colonized the root surface profusely and persisted within the rhizosphere bacterial community. This study demonstrated that small organic amendment to desert soil significantly changed soil bacterial community compared to the original soil and also 2 months after amendments were added.     

Comparison of root system architecture and rhizosphere microbial communities of Balsas teosinte and domesticated corn cultivars

The progenitor of maize is Balsas teosinte (Zea mays subsp. parviglumis) which grows as a wild plant in the valley of the Balsas river in Mexico. Domestication, primarily targeting above-ground traits, has led to substantial changes in the plant's morphology and modern maize cultivars poorly resemble their wild ancestor. We examined the hypotheses that Balsas teosinte (accession PI 384071) has a) a different root system architecture and b) a structurally and functionally different rhizosphere microbial community than domesticated cultivars sweet corn (Zea mays subsp. mays accession PI 494083) and popping corn (Zea mays subsp. mays accession PI 542713). In a greenhouse experiment, five plants from each corn variety were grown in individual pots containing a Maury silt loam – perlite (2:1) mixture and grown to the V8 growth stage at which rhizosphere bacterial and fungal community structure was assessed using terminal restriction fragment length polymorphism and fatty acid methyl ester analysis. Functional characteristics of the rhizosphere were assayed by examining the potential activity of seven extracellular enzymes involved in carbon, nitrogen and phosphorus cycling. Root system architecture was characterized by root scans of sand grown plants at the V5 growth stage. Compared to the control the sweet corn rhizosphere had different bacterial and fungal community structure, decreased fungal diversity and increased bacterial abundance. Teosinte caused a significant change in the rhizosphere bacterial and fungal community structure and increased bacterial abundance, but no significant decrease in bacterial or fungal diversity where the former was found to be significantly greater than in the sweet corn rhizosphere. Popping corn did not trigger significant changes in the bacterial or fungal diversity and bacterial abundance in the soil. The individual popping corn plants changed the bacterial and fungal communities in different directions and the overall effect on community structure was significant, but small. Of the enzymes analyzed, potential N-acetylglucosaminidase (NAG) activity was found to contributed most to the differentiation of teosinte rhizosphere samples from the other corn varieties. The teosinte root system had proportionally more very fine (diameter < 0.03 mm) roots than popping corn and sweet corn and it developed the highest root to shoot dry weight ratio, followed by popping corn. Sweet corn had significantly lower average root diameter than popping corn and teosinte and grew proportionally the least below-ground dry mass. The results allude to functional and structural differences in the rhizosphere microbial communities of the corn varieties that, with additional research, could lead to useful discoveries on how corn domestication has altered rhizosphere processes and how plant genotype influences nutrient cycling.     

Effect of <Emphasis Type="Italic">Silene vulgaris</Emphasis> and Heavy Metal Pollution on Soil Microbial Diversity in Long-Term Contaminated Soil

In this study, we analysed the impact of heavy metals and plant rhizodeposition on the structure of indigenous microbial communities in rhizosphere and bulk soil that had been exposed to heavy metals for more than 150 years. Samples of the rhizosphere of Silene vulgaris and non-rhizosphere soils 250 and 450 m from the source of emission that had different metal concentrations were collected for analyses. The results showed that soils were collected 250 m from the smelter had a higher number of Cd-resistant CFU compared with the samples that were collected from 450 m, but no significant differences were observed in the number of total and oligotrophic CFU or the equivalent cell numbers between rhizosphere and non-rhizosphere soils that were taken 250 and 450 m from the emitter. Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis of the denaturing gradient gel electrophoresis (DGGE) profiles, as well as a cluster analysis that was generated on the phospholipid fatty acid (PLFA) profiles, showed that the bacterial community structure of rhizosphere soils depended more on the plant than on the distance and metal concentrations. The sequencing of the 16S rDNA fragments that were excised from the DGGE gel revealed representatives of the phyla Bacteroidetes, Acidobacteria, Gemmatimonadetes, Actinobacteria and Betaproteobacteria in the analysed soil with a predominance of the first three groups. The obtained results demonstrated that the presence of S. vulgaris did not affect the number of CFUs, except for those of Cd-resistant bacteria. However, the presence of S. vulgaris altered the soil bacterial community structure, regardless of the sampling site, which supported the thesis that plants have a higher impact on soil microbial community than metal contamination.     

Impact of fresh root material and mature crop residues of oilseed rape (Brassica napus) on microbial communities associated with subsequent oilseed rape

Glasshouse bioassays were conducted to assess the impact of different inputs of oilseed rape plant material on soil and rhizosphere microbial diversity associated with subsequently grown oilseed rape (Brassica napus) plants. The first bioassay focussed on the effect of oilseed rape rhizodeposits and fresh detached root material on microbial communities, in a rapid-cycling experiment in which oilseed rape plants were grown successively in pots of field soil for 4 weeks at a time, with six cycles of repeated vegetative planting in the same pot. Molecular analyses of the microbial communities after each cycle showed that the obligate parasite Olpidium brassicae infected the roots of oilseed rape within 4 weeks after the first planting (irrespective of the influence of rhizodeposits alone or in the presence of fresh detached root material), and consistently dominated the rhizosphere fungal community, ranging in relative abundance from 43 to 88 % when oilseed rape was grown more than once in the same soil. Fresh detached root material also led to a reduction in diversity within the soil fungal community, due to the increased relative abundance of O. brassicae. In addition, rhizosphere bacterial communities were found to have a reduced diversity over time when fresh root material was retained in the soil. In the second glasshouse experiment, the effect of incorporating mature, field-derived oilseed rape crop residues (shoots and root material) on microbial communities associated with subsequently grown oilseed rape was investigated. As before, molecular analyses revealed that O. brassicae dominated the rhizosphere fungal community, despite not being prevalent in either the residue material or soil fungal communities.     

Plant nitrogen uptake drives rhizosphere bacterial community assembly during plant growth

When plants establish in novel environments, they can modify soil microbial community structure and functional properties in ways that enhance their own success. Although soil microbial communities are influenced by abiotic environmental variability, rhizosphere microbial communities may also be affected by plant activities such as nutrient uptake during the growing season. We predicted that during the growing season, plant N uptake would explain much of the variation in rhizosphere microbial community assembly and functional traits. We grew the invasive C₃ grass Bromus tectorum and three commonly co-occurring native C₃ grasses in a controlled greenhouse environment, and examined rhizosphere bacterial community structural and functional characteristics at three different plant growth stages. We found that soil N availability and plant tissue N levels strongly correlated with shifts in rhizosphere bacterial community structure. It also appeared that the rapid drawdown of soil nutrients in the rhizosphere during the plant growing season triggered a selection event whereby only those microbes able to tolerate the changing nutrient conditions were able to persist. Plant N uptake rates inversely corresponded to microbial biomass N levels during periods of peak plant growth. Mechanisms which enable plants to influence rhizosphere bacterial community structure and function are likely to affect their competitive ability and fitness. Our study suggests that plants can alter their rhizosphere microbiomes through influencing nutrient availability. The ways in which plants establish their rhizosphere bacterial communities may now be viewed as a selection trait related to intrinsic plant species nutrient demands.     

Bacillus amyloliquefaciens BNM122, a potential microbial biocontrol agent applied on soybean seeds,causes a minor impact on rhizosphere and soil microbial communities

The increase in soybean productivity has contributed to a greater use of agrochemicals, which cause major problems, such as soil and water pollution and reduction of biodiversity, and have a negative impact on non-target species. The development of microbial biocontrol agents for soybean diseases can help to reduce pesticide abuse. Bacillus amyloliquefaciens BNM122 is a potential microbial biocontrol agent able to control the damping-off caused by Rhizoctonia solani when inoculated in soybean seeds, both in a plant growth chamber and in a greenhouse. In this study, we report the effect of soybean seed treatments with strain BNM122 or with two fungicides (thiram and carbendazim) on the structure and function of the bacterial community that colonizes the soybean rhizosphere. Also, soybean root nodulation by Bradyrhizobium japonicum, mycorrhization by arbuscular mycorrhizal fungi and plant growth were evaluated. We used the r- and K-strategist concept to evaluate the ecophysiological structure of the culturable bacterial community, community-level physiological profiles (CLPP) in Biolog? EcoPlates to study bacterial functionality, and the patterns of 16S RNA genes amplified by PCR and separated by denaturing gradient gel electrophoresis (PCR–DGGE) to assess the genetic structure of the bacterial community. Neither the ecophysiological structure nor the physiological profiles of the soybean rhizosphere bacterial community showed important changes after seed inoculation with strain BNM122. On the contrary, seed treatment with fungicides increased the proportions of r-strategists and altered the metabolic profiles of the rhizosphere culturable bacterial community. The genetic structure of the rhizosphere bacterial community did not show perceptible changes between treated and non-treated seeds. Regarding the bacterial and fungal symbioses, seed treatments did not affect soybean nodulation, whereas soybean mycorrhization significantly decreased (P < 0.05) in plants obtained from seeds treated with strain BNM122 or with the fungicides. However, a higher negative effect was observed in plants which seeds were treated with the fungicides. Plant growth was not affected by seed treatments.It can be concluded that soybean seed treatment with B. amyloliquefaciens BNM122 had a lesser effect on soil microbial community than that with the fungicides, and that these differences may be attributed to the less environmental persistence and toxic effects of the strain, which deserve further studies in order to develop commercial formulations.     

<Emphasis Type="Italic">p</Emphasis>-Coumaric can alter the composition of cucumber rhizosphere microbial communities and induce negative plant-microbial interactions

Phenolics from root exudates or decaying residues are usually referred as autotoxins of several plant species. However, how phenolics affect soil microbial communities and their functional significances are poorly understood. Rhizosphere bacterial and fungal communities from cucumber (Cucumis sativus L.) seedlings treated with p-coumaric acid, an autotoxin of cucumber, were analyzed by high-throughput sequencing of 16S rRNA gene and internal transcribed spacer amplicons. Then, feedback effects of the rhizosphere biota on cucumber seedlings were evaluated by inoculating non-sterilized and sterilized rhizosphere soils to sterilized background soils. p-Coumaric acid decreased the bacterial diversity of rhizosphere but increased fungal diversity and altered the compositions of both the bacterial and fungal communities. p-Coumaric acid increased the relative abundances of microbial taxa with phenol-degrading capability (such as Chaetomium, Humicola, and Mortierella spp.) and microbial taxa which contained plant pathogens (such as Fusarium spp.). However, p-coumaric acid inhibited the relative abundances of Lysobacter, Haliangium, and Gymnoascus spp., whose species can have pathogen-antagonistic and/or plant-growth-promoting effects. The positive effect of cucumber rhizosphere microbiota on cucumber seedling growth was reduced by p-coumaric acid. Overall, our results showed that, besides its direct phytotoxicity, p-coumaric acid can inhibit cucumber seedling growth through generating negative plant-soil microbial interactions.     

Screening of rhizobacteria isolated from maize (Zea mays L.) in Rio Grande do Sul State (South Brazil) and analysis of their potential to improve plant growth

Plant growth-promoting rhizobacteria (PGPR) are considered to have a beneficial effect on host plants and may facilitate plant growth by different mechanisms. In this work, the influence of different soil types on the bacterial diversity and the stimulatory effects of selected PGPR on two cultivars of maize were investigated. A set of 292 strains was isolated from the roots and rhizosphere soil of maize cultivated in five different areas of the Rio Grande do Sul State in Brazil. 16S rDNA-PCR-RFLP and 16S rDNA partial sequencing were used for identification, and the Shannon–Weaver index was used to evaluate bacterial diversity. We evaluated the ability of each isolate to produce indole acetic acid (IAA), siderophores and solubilize phosphates. On the basis of multiple PGP traits, six isolates were selected to test their potential as plant growth-promoting rhizobacteria on maize plants. In both the roots and the rhizospheric soil of maize, the dominant bacterial genera identified were Klebsiella and Burkholderia. IAA producers were distributed widely among isolates, regardless of the sampling site. Approximately 42% of the isolates exhibited at least two attributes, and 24% showed all three PGP traits. Three strains, identified as Achromobacter, Burkholderia, and Arthrobacter, were effective as PGPR in both of the cultivars evaluated.     

Soil bacterial community response to sulfadiazine in the soil–root zone

Sulfonamide antibiotics reach soil via manure and adversely affect microbial diversity. Clear effects of these bacteriostatic, growth‐inhibiting antibiotics occur in the presence of a parallel input of microbial activity stimulating manure. Natural hot spots with already increased soil microbial activity are located in the rhizosphere, comprising microorganism such as Pseudomonas with plant growth promoting and pathogenic strains. The hypothesis was therefore that the antibiotic activity of sulfonamides is promoted in the rhizosphere even in the absence of manure, followed by shifts of the natural plant‐specific microbial community structure. This was evaluated by a laboratory experiment with Salix fragilis L. and Zea mays L. After 40 d of incubation, sub‐areas such as non‐rhizosphere soil, rhizosphere soil and plant roots were sampled. Effects on microbial community structure were analyzed using 16S rRNA gene fragment patterns of total bacteria community and Pseudomonas. Selected exoenzymes of N‐, P‐, and C‐cycling were used to test effects on microbial functions. Compared to the factors soil sub‐area and sulfadiazine (SDZ) content, plant species had the largest influence on the bacterial community structure and soil exoenzyme activity pattern. This was also reflected by an up to 1.5‐fold higher acid phosphatase activity in samples from maize‐ compared to willow‐planted soil. We conclude that antibiotic effects on the bacterial community structures are influenced by the antibiotic concentration and root influence.     

Interactions of arbuscular-mycorrhizal fungi and Bacillus strains and their effects on plant growth,microbial rhizosphere activity (thymidine and leucine incorporation) and fungal biomass (ergosterol and chitin)

The effects of two Bacillus strains (Bacillus pumillus and B. licheniformis) on Medicago sativa plants were determined in single or dual inoculation with three arbuscular-mycorrhizal (AM) fungi and compared to P-fertilization. Shoot and root plant biomass, values of thymidine and leucine incorporation as well as ergosterol and chitin in rhizosphere soil were evaluated to estimate metabolic activity and fungal biomass, respectively, according to inoculation treatments. For most of the plant parameters determined, the effectiveness of AM fungal species was influenced by the bacterial strain associated. Dual inoculation of Bacillus spp. and AM fungi did not always significantly increase shoot biomass compared to single AM-colonized plants. The most efficient treatment in terms of dry matter production was the dual Glomus deserticola plus B. pumillus inoculation, which produced similar shoot biomass and longer roots than P-fertilization and a 715% (shoot) and 190% (root length) increase over uninoculated control. The mycorrhizas were more important for N use-efficiency than for P use-efficiency, which suggests a direct mycorrhizal effect on N nutrition not mediated by P uptake. Both chemical and biological treatments affected thymidine and leucine incorporation in the rhizosphere soil differently. Thymidine was greater in inoculated than in control rhizospheres and B. licheniformis was more effective than B. pumillus in increasing thymidine. Non-inoculated rhizospheres showed the lowest thymidine and leucine values, which shows that indigenous rhizosphere bacteria increased with introduced inocula. The highest thymidine and leucine values found in P-fertilized soils indicate that AM plants are better adapted to compete with saprophytic soil bacteria for nutrients than P-amended plants. Chitin was only increased by coinoculation of B. licheniformis and G. intraradices. B. pumillus increased ergosterol (indicative of active saprophyte fungal populations) in the rhizosphere of AM plants and particularly when colonized by G. mosseae. The different AM fungi have different effects on bacterial and/or fungal saprophytic populations and for each AM fungus, this effect was specifically stimulated or reduced by the same bacterium. This is an indication of ecological compatibilities between microorganisms. Particular Glomus–bacterium interactions (in terms of effect on plant growth responses or rhizosphere population) do not seem to be related to the percentage of AM colonization. The effect on plant growth and stimulation of rhizosphere populations, as a consequence of selected microbial groups, may be decisive for the plant establishment under limiting soil conditions.     

Effect of Capsicum annuum cultivated in sub-alkaline soil on bacterial community and activities of cultivable plant growth promoting bacteria under field conditions

In literature, it remains little explored the soil–plant relationships within Capsicum agroecosystem. We studied how chili peppers plants contribute to influence microbial diversity. Across the bulk and rhizosphere soils of three genotypes of Capsicum annuum, the structure, the diversity and the abundance of bacteria was evaluated by means of DNA-based culture-independent approach. Furthermore, 515 bacterial strains isolated from the bulk and rhizosphere soil, were used to investigate the effect of C. annuum on four plant growth promoting bacteria (PGPB) abilities. Our results indicated that the three genotypes influence differently the physical-chemical and microbial properties of soil around the roots. Bacterial abundance resulted in increasing with different trend rhizospheres to bulk soil ratio; however, bacterial diversity was significantly higher only in the rhizosphere of one genotype. Only the indolic compounds production was stimulated in the rhizosphere of the three cultivars. Inhibition of Fusarium oxysporum was stimulated just with one genotype, where 53 of rhizosphere isolates showed more than 10% of inhibition. 165 of isolates produced siderophores and the major part belonged to the high production level. Interactions between PGPB features revealed that anti-phytopathogenic activity was not associated with the others characteristics; however, phosphate solubilization was associated with both siderophores and indolic compounds productions.     

Microbial community composition and functioning in the rhizosphere of three Banksia species in native woodland in Western Australia

Annual plant species differ in their rhizosphere microbial community composition. However, rhizosphere communities are often investigated under controlled conditions, and it is unclear if perennial plants growing in the field also have rhizosphere communities that are specific to a particular plant species. The aim of our study was to determine the bacterial community composition of three species of Banksia (B. attenuata R. Brown, B. ilicifolia R. Brown and B. menziesii R. Brown) growing in close proximity in a native woodland in Western Australia and to relate community structure to function. All three species are small trees that produce cluster roots in the field following winter rains. Cluster roots and rhizosphere soil were sampled in early spring (August 2001) and again four weeks later (September 2001). Many new cluster roots were formed in the period between the August and the September sampling. Rhizosphere soil pH, percent soil moisture and C and N content did not differ significantly among species or sampling times. However, the bacterial community composition on the cluster roots and in the rhizosphere soil, studied by denaturing gradient gel electrophoresis (DGGE), differed among the three species, with cluster root age class (young or mature to senescing) and also between sampling times. These changes in community composition were accompanied by changes in the activity of some of the enzymes studied. The activities of β-glucosidase and protease increased over time. The three species differed in asparaginase activity, but not in the activity of acid and alkaline phosphatase in the rhizosphere. These results suggest a relationship between the changes in composition and function of bacterial communities.