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Background: The erratic alterations in climate being experienced in agriculture, such as extended periods of drought or heavy rainfalls, are bringing increasing concerns about nitrogen (N) management. Even in high-input farming systems, unpredictable weather patterns can cause N deficiencies and result in nutrient losses that contribute to major pollution issues in groundwater, lakes, and even the oceans. Our present understanding of the beneficial interactions between N-deficient-challenged plants and plant-associated bacteria (PAB), mainly of the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria, is largely based on studies performed at the level of whole-plant fitness and impacts of crop yields via the abilities of bacteria to synthesize indole acetic acid and/or produce the enzyme 1-aminocyclopropane-1-carboxylate deaminase which reduces endogenous ethylene levels. Much less is known about the complex interaction that occur from the PAB’s abilities to produce N ureide (allantoin and allantoate) and how these purine intermediaries function as an N source and prime stress signals for the growth of both partners.Methods: This review examines the noteworthy progress made on understanding the bacterial ureide pathway with the aim to elaborate possible scenarios to unravel the complex nature of PAB-plant interactions at the purine level. Tables with updated information on PAB growth-promoting activities, N metabolism, and abilities to hydrolyze purine intermediates as well as allantoin for colony growth are included.Results: As in plants, the metabolism of ureides in PAB covers the pathways from the deamination of the nucleobase guanine up to its conversion into glyoxylate, NH4+, and/or NH3 to recycle C and N. More important, in PAB, the full set of riboswitch-modulated genes encoding the enzymes involved in the synthesis and catabolism of ureides, as well as purine transporters, is expressed primarily under stressful conditions leading to N deficiency. Thus, PAB might act as a stress-induced source of purines for the plant N metabolism, or could become scavengers of the plant-synthesized purines for colony replication. Consumption of purine intermediaries or ureides by PAB may hinder the symbiotic efficiency of rhizobia-nodulated N2-fixing legumes. The impact of soil xanthine, hypoxanthine, and allantoin pools on the plants or PAB ureide synthesis is also discussed.Conclusions: Given widespread concerns for crop losses due to the drastically changing climate and prevailing agricultural practices, the understanding of the interactive signaling for the purine metabolisms between PAB and plants takes on a major importance, as it may support management decisions necessary to maintain PAB biodiversity and the agricultural services provided by PAB to crops. [ABSTRACT FROM AUTHOR]

Potato plantlets inoculated with strain PsJN of the bacterium Burkholderia phytofirmans exhibit consistent and significant increases in plant growth under in vitro conditions, when compared with uninoculated plants. The greatest influence on the degree and type of growth enhancement that develops has been shown to be mediated by the sugar concentration in the agar media. Bacterial growth promotion has been suggested in other studies to be regulated by the sugar sensor enzyme hexokinase1, the role of which is activation of glucose phosphorylation. In this present study, we examined the co-relationship between root and stem development in potato plants treated with PsJN and the activity of hexokinase1. Plants grown in the presence of 1.5% and 3% sucrose showed increased levels of hexokinase1 activity only in the roots of inoculated plants, suggesting that the increased enzyme levels may be associated with root growth. Analysis for mRNA using reverse transcriptase did not reveal any significant differences in transcription levels of the gene between inoculated and uninoculated plants. When PsJN-inoculated plants were grown in 1.5% and 3% concentrations of glucose and fructose, stem height and mass, leaf number, root mass, and overall biomass increased. No growth promotion occurred when PsJN-inoculated plants were grown in 3% maltose. Subsequently, a hexokinase1 activity assay showed that PsJN-induced growth of potato plants was found to only occur when plants were grown in the presence of sugars that are recognized by the plant hexokinase1. The results suggest that PsJN may enhance sugar uptake in plants by direct or indirect stimulation of hexokinase1 activity in roots and this results in enhanced overall plant growth. [ABSTRACT FROM AUTHOR]

Phytophthora blight or crown or root rot (Phytophthora capsici Leonian) is an important disease of a wide range of plant species including peppers, tomatoes, cucumbers and other cucurbits in Canada and worldwide. We have previously demonstrated the effectiveness of a new liquid formulation of AG3 phosphonate (Calirus 150, Bromine Compounds Ltd., Beer Sheva, Israel) in suppressing pythium damping-off of cucumbers and clubroot of bok choy and cabbage. In this study, the effectiveness of AG3 phosphonate formulation to suppress phytophthora damping-off and root rot of cucumber (Cucumis sativus L.) seedlings or phytophthora blight of bell pepper (Capsicum annuum L.) plants was determined in a peat-based mix or sandy-loam soil artificially infested with soil inoculum of P. capsici under growth room conditions. In an infested peat-based mix, AG3 phosphonate preplanting amendment or postplanting drench treatments (0.05%, 0.1% and 0.2% a.i.) and a 10-min seed-soak treatment (10.45% a.i.) significantly increased the percentage of healthy cucumber seedlings and reduced damping-off and root rot severity. The seed-soak and 0.2% treatments were the most effective treatments that consistently suppressed damping-off and root rot of cucumber even in a peat-based mix infested with high inoculum levels of P. capsici. Disease severity on cucumber plants was also significantly less in the AG3 phosphonate treatments. The single drench applications of AG3 phosphonate (0.05%, 0.1% and 0.2% a.i.) significantly reduced the incidence and severity of phytophthora blight of bell pepper plants in an infested peat-based mix or a sandy-loam soil compared with the control plants receiving no treatment. The best control of phytophthora blight of bell pepper was achieved with the higher rate (0.2% a.i.) in both peat-based mix and soil with 90% of the plants remaining healthy compared with none in the control. The disease protection increased with increasing concentrations of AG3 phosphonate in both bell peppers and cucumbers without any phytotoxicity. [ABSTRACT FROM AUTHOR]

Fish emulsion (FE) added to a sandy-loam soil at 1 and 2% rates reduced the viability of Verticillium dahliae microsclerotia by 39 and 74% in 1 day, 87 and 98% in 3 days, and 95 and 99% in 6 days, respectively. The immediate kill of microsclerotia indicated that FE contains toxic substances. We found in FE high concentrations (400 mmol/liter) of organic acids, including some known toxicants. Glycolic, acetic, formic, n-butyric, and propionic acids were the major organic acids detected in FE at the proportions of 52.5, 26.9, 7.9, 7.2, and 4.7%, respectively. In solution assays, the viability of V. dahliae microsclerotia treated for 24 h in 1, 2, 5, and 10% FE (pH 3.6 to 3.0) or a mixture of organic acids (pH 4.1 to 3.9) equivalent to the proportions in FE was reduced by 74, 94, 97, and 99% or 81, 91, 98, and 99%, respectively. The viability of microsclerotia was increased when the treatment solutions were buffered to pH 6.0. The organic acids mixtures and formic (0.025%) and acetic (0.1%) acids were toxic to Pythium ultimum. A mixture of organic acids (1, 2, and 4%) provided immediate protection of cucumber seedlings from damping-off in P. ultimum-infested muck and sandy-loam soils but not in peat-based mix. FE (1 and 2%) provided immediate protection of cucumber seedlings from damping-off in an infested muck soil, and disease protection was consistent when planting was delayed for 7, 14, and 28 days after adding FE. FE (1, 2, and 4%) did not provide immediate protection of cucumber seedlings from damping-off in a P. ultimum- infested peat-based mix; however, disease suppression was evident when planting was delayed for 7, 14, and 21 days after adding FE. Real-time polymerase chain reaction analyses of the peat-based mix indicated that the P. ultimum populations in the FE-amended mix declined over time. This study suggests that these organic acids in FE played a major role in pathogen or disease suppression, depending on the soil and substrate. [ABSTRACT FROM AUTHOR]

The article presents a study which examines the toxicity of condensed distiller's solubles (CDS) to pathogen-infested soils and disease suppression. It states that the study found that CDS contains moderate levels of organic acids, minor concentrations of isobutyric and propionic acids. Moreover, the study suggests that the organic acids component of CDS enables to suppress the disease in muck and sandy-loam soils.

In order to determine possible relationships between geocaulosphere soil properties and severity of common scab of potato caused by Sireptomyces scabies, soils were collected from representative commercial potato fields in Canada: in Simcoe and Dufferin Counties, Ontario and across Prince Edward Island (PEI) in August 2004. Soils immediately adjacent to tubers were sampled and analyzed for select edaphic factors and for pathogen presence using polymerase chain reaction (PCR) tests with primers that amplify a region of the TxIA gene involved in regulating the biosynthesis of the thaxtomin toxin family. Individual tubers were assessed visually for scab severity. The relationships between soil chemical factors and disease severity were investigated for each region to detect the strongest relationships. Principal component analysis revealed a distinctive clustering of samples with respect to disease severity in PEI but not in Ontario soils. Total and percent saturation of K (%K) were the only factors found associated with high disease severity in soils from both provinces. In PEE soils, pH, Mg, Ca, Cu, and %K, %Mg. %Ca, and %Na were associated with high disease severity, whereas cation exchange capacity (CEC) and Al were correlated with low disease severity soils. In Ontario, high Mn content was strongly correlated with low disease severity soils, whereas %K and organic matter content were correlated with disease severity. Partitioning samples into presence or absence of the TxtA PCR product with corresponding high or low severity showed further significant relationships in the data. There was an excellent correlation between Sireptomyces spp. presence as detected by PCR and disease severity in PEI soils; however, the relationship was not as clear in Ontario soils, where many PCR-positive soils had low disease incidence. Principal component and partial least square analysis indicated that disease severity was predicted by soil factors such as organic matter, CEC, pH, Al, %Ca, %Mg, and %K for PEI but not for Ontario soils. The data reveal that the relationship between scab severity and soil chemical components is complex and potentially soil specific. [ABSTRACT FROM AUTHOR]

Alcohol production from corn is gaining importance in Ontario, Canada, and elsewhere. A major cost of corn production is the cost of chemical fertilizers and these continue to increase in price. The competitiveness of alcohol with fossil fuels depends on access to low-cost corn that allows growers to earn a sustainable income. In this study we set out to determine if we can identify root-associated microorganisms from Ontario-grown corn that can enhance the nutrient flow to corn roots, directly or indirectly, and help minimize the use of extraneous fertilizer. Bacteria were isolated from corn rhizosphere and screened for their capacity to enhance corn growth. The bacteria were examined for their ability to fix nitrogen, solubilize phosphate, and produce indole acetic acid (IAA) and antifungal substances on potato dextrose agar. Bacterial suspensions were applied to pregerminated seed of four corn varieties (39D82, 39H84, 39M27, and 39T68) planted in sterilized sand and unsterilized cornfield soil. The plants were grown under greenhouse conditions for 30 days. Three isolates were identified as having growth-promoting effect. These bacteria were identified as to species by biochemical tests, fatty acid profiles, and 16S rDNA sequence analysis. Corn rhizosphere isolates, Gluconacetobacter azotocaptans DS1, Pseudomonas putida CQ179, and Azospirillum lipoferum N7, provided significant plant growth promotion expressed as increased root/shoot weight when compared to uninoculated plants, in sand and/or soil. All strains except P. putida CQ179 were capable of nitrogen fixation and IAA production. Azospirillum brasilense, however, produced significantly more IAA than the other isolates. Although several of the strains were also able to solubilize phosphate and produce metabolites inhibitory to various fungal pathogens, these properties are not considered as contributing to growth promotion under the conditions used in this study. These bacteria will undergo field tests for their effect on corn growth. [ABSTRACT FROM AUTHOR]

Reports on results of a mail survey of growers to estimate potato common scab prevalence and economic loss in Canada. Survey feasibility; Overall response rate; Mean prevalence of scab.

Determines the potential for spreading Streptomyces on seed tubers into field soil. Enumeration of populations of pathogens on diseased and healthy tuber surfaces; Use of colony polymerase chain reaction to detect gene of the thaxtomin biosynthetic pathway;Decline in the density of pathogenic populations.

In previous studies we showed that adding meat and bone meal (MBM) to a sandy soil resulted in the death of microsclerotia (MS) of the fungal wilt pathogen Verticillium dahliae. No effect on MS was found when the same quantity of MBM was added to a loam soil. MS mortality in the sandy soil was attributed to the accumulation of ammonia (NH3) or nitrous acid (HNO2), products that did not accumulate to lethal levels in the loam soil. The objective of this study was to identify soil properties associated with the accumulation of NH3 and HNO2. Using a microcosm system we tracked the survival of MS and changes in pH and concentrations of NH3 and HNO2 over a 29-day incubation period in 12 soils from diverse regions and amended with MBM (0 or 2% (w/w) dry soil). Prior to the initiation of the study, and at periodic intervals after amendment, we also determined numerous biological, chemical, and physical soil factors possibly influencing NH3 and HNO2 accumulation. The results showed that MS died within 7 days in four soils due to NH3 accumulation. In six soils where NH3 levels were <20 mM, MS germination was reduced, but the effects were only fungistatic as germination returned when NH3 dissipated. In two acid soils, HNO2 was lethal at levels exceeding 0.02 mM but not in four soils of basic pH which also accumulated similar levels of this gas. The influence of acidity in enhancing the lethal effect of HNO2 was confirmed in an aqueous exposure assay. Germination of MS was unaffected in four soils where neither NH3 nor HNO2 accumulated. Univariate and multivariate statistical analyses corroborated that NH3 toxicity occurred in soils with low rates of nitrification, low levels of cation exchange capacity, moisture levels, organic carbon contents, but high bulk density and sand contents. The results indicate that soil properties are related to the effectiveness of MBM and likely other nitrogenous amendments in reducing the viability of soilborne pathogens by influencing the accumulation and lethal effect of NH3 or HNO2. The results of this and other studies in our laboratories examining the effect of individual soil properties indicate simply measuring such properties as organic carbon content and pH may be sufficient to predict where MBM will be effective to control Verticillium wilt. [Copyright &y& Elsevier]

The use of chemical fertilizers strongly promotes productivity in agricultural crops; therefore, large amounts of chemical fertilizers have been used. The use of plant growth-promoting bacteria may be a strategy to reduce the use of chemical fertilizers; however, little is known about the effect of chemical fertilization on the performance of these bacteria through plant–microbe interactions. The present study aimed to verify the performance of Bacillus subtilis, Azospirillum brasilense, B. pumilus, B. amyloliquefaciens, Herbaspirillum seropedicae, Gluconacetobacter diazotrophicus, and the mixtures A. brasilense + B. subtilis, B. pumilus + B. amyloliquefaciens, and H. seropedicae + G. diazotrophicus on parameters such as nitrogen and phosphorus extraction from soil, the concentrations of these nutrients in maize plants, and plant growth in both fertilized and unfertilized soil. The results showed that H. seropedica increased the nitrogen content by 6.6 g kg−1 in leaves and 2.2 g kg−1 in the root when comparing the unfertilized with the fertilized condition. G. diazotrophicus increased the nitrogen content by 3.7 g kg−1 in leaves and 2.4 g kg−1 in the root. B. pumilus increased the phosphorous content by 1.7 g kg−1 in leaves, and B. amyloliquefaciens increased the phosphorous content by 0.61 g kg−1. The present study showed that even though the bacteria presented good performance related to plant growth under fertilized conditions, H. seropedicae, G. diazotrophicus, B. pumilus, and B. amyloliquefaciens could be used in the maize crop with a reduced chemical fertilization dose. [ABSTRACT FROM AUTHOR]

Tomato vine decline (TVD) in south-western Ontario is a disease with symptoms that include premature plant senescence, root browning and rotting, and fruit yield reduction. Soilborne fungi cause similar vine decline symptoms in melons and potatoes. To identify which potential pathogens might be associated with TVD, we undertook both a DNA and culture based survey of the fungi found in roots and rhizospheres of field and lab grown plants. DNA finger printing revealed that roots are colonized by significantly different fungal populations than those found in rhizospheres or the soil in which they are grown. The fungal species associated with TVD resistant ‘Beaufort’ and ‘RST-04–105-T’ rootstocks were also consistently different from those in the TVD susceptible commercial variety ‘Heinz 2401ʹ. Mycobiomes in ‘Heinz 2401ʹ roots and rhizospheres changed significantly when plants were grown in sterile sand, TVD infested soil, or in the same soil that had been amended with molasses. Internal transcribed spacer (ITS) region sequences derived from PCR product clones or fungal cultures isolated from roots identified 53 different fungal species. Annotated DNA fingerprints showed that roots of all plants grown in soil containedVerticillium dahliae, a destructive vascular pathogen of tomatoes, while only susceptible ‘Heinz 2401ʹ roots were infected with the obligate parasiteOlpidium virulentus. While these two pathogens may both be reducing tomato yields in Ontario, it appears that existing tomato rootstock varieties may be resistant to infection byO. virulentus. This poorly characterized soil-transmitted Chrytidiomycete may be contributing to TVD. [ABSTRACT FROM PUBLISHER]

Background and aims To assess the impacts of soil microbes and plant genotype on the composition of maize associated bacterial communities. Methods Two genotypes of Brazilian maize were planted indoors on sterile sand, a deep underground subsoil, and a nutrient-rich topsoil from the Amazon jungle (terra preta). DNA was extracted from rhizospheres, phyllospheres, and surface sterilized roots for 16S rDNA fingerprinting and next generation sequencing. Results Neither plant genotype nor soil type appeared to influence bacterial diversity in phyllospheres or endospheres. Rhizospheres showed strikingly similar 16S rDNA ordination of both fingerprinting and sequencing data, with soil type driving grouping patterns and genotype having a significant impact only on sterile sand. Rhizospheres grown in non-sterile soils contained greater bacterial diversity than sterile-sand grown ones, however the dominant OTUs (species of Proteobacteria and Bacteroidetes) were found in all rhizospheres suggesting seeds as a common source of inoculum. Rhizospheres of the commercial hybrid appeared to contain less bacterial diversity than the landrace. Conclusions Maize rhizospheres receive diverse bacteria from soil, are influenced by the genotype or treatment of the seed, and are dominated by species of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. As many dominant 16S rDNA sequences were observed in rhizospheres grown in both sterile and non-sterile substrate, we conclude that the most common bacterial cells in juvenile maize rhizospheres are seed transmitted. [ABSTRACT FROM AUTHOR]

Development of agronomic practices that maximize the use of natural resources to improve soil health and crop productivity is critical for long-term sustainability of agricultural technologies. In Ontario, Canada, the most conventional maize production practice follows a 3-year rotation with soybeans and ploughing of the land before planting and after harvesting. This technology yields 8-10 t ha of maize. We became aware of a long-term no-till strip row farming system developed by an Ontario grower where maize yields are double that of the average for the province. This study set out to identify what factors contribute to such a massive yield increase and the basis for this superior method of maize production. In a 2-year field study, we compared a variety of biotic and abiotic factors associated with yields at this highly productive site with those of two average yielding sites. The no-till strip row farming system grew maize and soybeans in alternate strips rotated yearly and had higher plant populations, better root architecture, higher plant biomass, and 75 % greater (18.35 t ha) grain yield compared to a nearby farm that used conventional production practices. About 21 % of the yield increase resulted from early planting, greater number of seeds planted, and healthier ears/seeds. The remaining 54 % increase was linked to larger ears, which we tentatively attribute to beneficial effects conferred by the microorganisms that develop in this unique agro-ecosystem. The average net return at the no-till site was estimated to be CDN (Canadian) $2000 ha, which was 400 % higher than the net returns of the conventional sites. The study concludes that no-till management where soil remains undisturbed when combined with yearly rotations of an appropriate legume crop, growing crops exactly on the same cropping rows every year, and optimization of plant density creates a sustainable technology for maximizing maize yields. [ABSTRACT FROM AUTHOR]

Background: Endophytes are microbes that live within plants such as maize (corn, Zea mays L.) without causing disease. It is generally assumed that most endophytes originate from soil. If this is true, then as humans collected, domesticated, bred and migrated maize globally from its native Mexico, they moved the species away from its native population of endophyte donors. The migration of maize persists today, as breeders collect wild and exotic seed (as sources of diverse alleles) from sites of high genetic diversity in Mexico for breeding programs on distant soils. When transported to new lands, it is unclear whether maize permits only selective colonization of microbes from the Mexican soils on which it co-evolved, tolerates shifts in soil-derived endophytes, or prevents colonization of soil-based microbes in favour of seed-transmitted microbes. To test these hypotheses, non-sterilized seeds of three types of maize (pre-domesticated-Mexican, ancient-Mexican, modern-temperate) were planted side-by-side on indigenous Mexican soil, Canadian temperate soil or sterilized sand. The impact of these soil swaps on founder bacterial endophyte communities was tested using 16S-rDNA profiling, culturing and microbial trait phenotyping. Results: Multivariate analysis showed that bacterial 16S-rDNA TRFLP profiles from young, surface-sterilized maize plants were more similar when the same host genotype was grown on the different soils than when different maize genotypes were grown on the same soil. There appeared to be two reasons for this result. First, the largest fraction of bacterial 16S-signals from soil-grown plants was shared with parental seeds and/or plants grown on sterilized sand, suggesting significant inheritance of candidate endophytes. The in vitro activities of soil-derived candidate endophytes could be provided by bacteria that were isolated from sterile sand grown plants. Second, many non-inherited 16S-signals from sibling plants grown on geographically-distant soils were shared with one another, suggesting maize can select microbes with similar TRFLP peak sizes from diverse soils. Wild, pre-domesticated maize did not possess more unique 16S-signals when grown on its native Mexican soil than on Canadian soil, pointing against long-term co-evolutionary selection. The modern hybrid did not reject more soil-derived 16S-signals than did ancestral maize, pointing against such rejection as a mechanism that contributes to yield stability across environments. A minor fraction of 16S-signals was uniquely associated with any one soil. Conclusion: Within the limits of TRFLP profiling, the candidate bacterial endophyte populations of pre-domesticated, ancient and modern maize are partially buffered against the effects of geographic migration --- from a Mexican soil associated with ancestral maize, to a Canadian soil associated with modern hybrid agriculture. These results have implications for understanding the effects of domestication, migration, ex situ seed conservation and modern breeding, on the microbiome of one of the world’s most important food crops. [ABSTRACT FROM AUTHOR]

The objective of this study was to isolate and characterize genera of bacteria that had been identified as being the most common residents in the rhizosphere of potato using cpn60 pyrosequencing analysis. Using various semi-selective media targeted to specific genera of interest, 200 isolates of bacteria were collected from rhizosphere soil and the rhizoplane of potatoes grown in soils obtained from a potato farm in Prince Edward Island and Ontario. The procedures employed were successful in selecting out representative bacteria suggested by pyrosequencing to be common in the potato rhizoplane. Results of 16S rRNA sequencing showed that 44 % of the isolates represented new species. All isolates were tested for biological and biochemical activities including phosphate solubilization, phytohormone metabolism, nitrogen fixation, antibiosis, exoenzyme production, and production of acyl-homoserine lactones. Massilia spp. and Chryseobacterium spp. showed the strongest exoenzyme activities. A greater proportion of Agrobacterium tumefaciens rhizosphere strains produced acyl-homoserine lactones compared to rhizoplane strains. Pseudomonas spp. and Lysobacter capsici had the greatest antagonistic activity on laboratory media towards six potato pathogens, and also significantly decreased disease in plants grown in pathogen-infested soil. Four isolates significantly increased growth of potato nodal explants in tissue culture. By using preliminary results derived from next generation sequencing technology and a targeted cultural technique, we were able to gain a better understanding of the biological activities of the most abundant bacterial species in the rhizosphere and rhizoplane of a cultivated crop. [ABSTRACT FROM AUTHOR]

The efficacy of condensed distiller's solubles (CDS), a co-product of ethanol production from corn, rich in organic matter, and high in carbon to nitrogen ratio, was tested as a pre-plant amendment against Verticillium wilt of eggplant and potato scab in potato soils from commercial fields and against damping-off diseases of radish and cucumber seedlings in a peat-based mix and muck soil. Eggplants grown in a potato soil amended with CDS (1% mass/mass) showed less Verticillium wilt and increased fresh (37-54%) and dry (31-45%) plant biomass compared to the control in the greenhouse. In a potato soil with medium levels of disease, CDS (1 or 2%) increased the percentage of marketable tubers by 116% under greenhouse, 119% under micro-plot and 75% under field conditions. In the growth room, CDS (1, 2, and 4%) amendment to a peat-based mix infested with Rhizoctonia solani 1 week before planting seeds improved the percentage of healthy radish seedlings (22-72% healthy seedlings compared to 2% in the control). Levels of disease suppression increased with the incubation time prior to planting. Disease control effect of CDS was not consistent between different batches of peat-based mix. In a non-suppressive batch of peat-based mix, disease suppression by CDS was enhanced by a bio-control agent, Trichoderma hamatum 382. In muck soil from a commercial field naturally-infested with Pythium spp., CDS (0.25, 0.5, and 1%) provided protection of cucumber seedlings from damping-off immediately after incorporation, but the maximum protection was seen after 1 week with all three rates. The number of total bacteria was enhanced in the CDS-amended muck soil. In the micro-plots, CDS (0.5 and 1%) as an amendment to muck soil 2 weeks before planting improved the percentage of healthy cucumber seedlings and fresh plant weight compared to the control. CDS is not toxic to the pathogens and disease suppression is believed to be due to biological activity stimulated by CDS in the substrate. [ABSTRACT FROM AUTHOR]

Burkholderia sp. strain PsJN stimulates root growth of potato explants compared to uninoculated controls under gnotobiotic conditions. In order to determine the mechanism by which this growth stimulation occurs, we used Tn5 mutagenesis to produce a mutant, H41, which exhibited no growth-promoting activity but was able to colonize potato plants as well as the wild-type strain. The gene associated with the loss of growth promotion in H41 was shown to exhibit 65% identity at the amino acid level to the nadC gene encoding quinolinate phosphoribosyltransferase (QAPRTase) in Ralstonia solanacearum. Complementation of H41 with QAPRTase restored growth promotion of potato explants by this mutant. Expression of the gene identified in Escherichia coli yielded a protein with QAPRTase activities that catalyzed the de novo formation of nicotinic acid mono-nucleotide (NaMN). Two other genes involved in the same enzymatic pathway, nadA and nadB, were physically linked to nadC. The nadA gene was cotranscribed with nadC as an operon in wild-type strain PsJN, while the nadB gene was located downstream of the nadA-nadC operon. Growth promotion by H41 was fully restored by addition of NaMN to the tissue culture medium. These data suggested that QAPRTase may play a role in the signal pathway for promotion of plant growth by PsJN. [ABSTRACT FROM AUTHOR]

In previous studies, liquid swine manure (LSM) was sometimes shown to reduce Verticillium wilt of potato caused by Verticillium dahliae. We also observed that microsclerotia of this fungus died within 1 day, or between 3 and 6 weeks, after addition of LSM to some acid soils and within 1 week in some alkaline soils. In this study, we demonstrated that a volatile fatty acid (VFA) mixture with an identical concentration of VFAs as that found in an effective LSM reduced germination in an acid soil (pH 5,1) to the same extent as the LSM after 1 day of exposure. Germination was reduced by 45, 75, and 90% in the 10, 20, and 40% ([wt/wt] soil moisture) treatments, respectively, with the latter being equivalent to an application of 80 hl/ha. Addition to this acid soil of 19 LSMs (30% [wt/wt] soil moisture) collected from different producers resulted in complete kill of microsclerotia with 12 manures. Effective manures had a total concentration of nonionized forms of VFAs in soil solution of 2.7 mM or higher. In some acid soils (pH 5.8), addition of LSM (40% [wt/wt] soil moisture) did not kill microscierotia until 3 to 6 weeks later. Here, a reduction in viability of microsclerotia was attributed to the accumulation of 0.06 mM nitrous acid in the soil solution at 4 weeks. When an LSM was added (40% [wt/wt} soil moisture) to an alkaline soil (pH 7.9) where VFAs are not toxic, microsclerotia germination was reduced by 80% after 1 week. Here the pH increased to 8.9 and the concentration of ammonia reached 30 mM in the soil solution. An ammonium chloride solution having an equivalent concentration of ammonium as the manure was shown to have the same spectrum of toxicity as the manure in assays ranging from pH 7 to 9, both in solutions and above the solutions. At pH 9, the concentration of ammonia reached 18 mM and 100% mortality of microsclerotia occurred. Thus, in acid soils, LSM can kill microsclerotia of V dahliae by VFA and/or nitrous acid toxicity and in alkaline soils by ammonia toxicity. In order to take advantage of these mechanisms for disease reduction, the manure chemical composition, rate of addition, and soil characteristics need to be determined for each instance of use. [ABSTRACT FROM AUTHOR]

Investigates the suppression of Rhizoctonia and Pythium damping-off of radish and cucumber seedlings by adding fish emulsion to peak mix or soil. Focus on the efficacy of fish emulsion in enhancing plant growth and suppressing seedling damping-off diseases; Results suggesting that fish emulsion may not be toxic to the pathogens but may create a biological climate in peat substrate or soil that is suppressive to the disease.

Plant-associated bacteria play an important role in the enhancement of plant growth and productivity. Gluconacetobacter azotocaptans is an exceptional bacterium considering that till today it has been isolated and reported only from Mexico and Canada. It is a plant growth-promoting bacterium and can be used as biofertilizer for different crops and vegetables. The objective of the current study was to evaluate the inoculation effect of Gluconacetobacter azotocaptans DS1, Pseudomonas putida CQ179, Azosprillium zeae N7, Azosprillium brasilense N8, and Azosprillium canadense DS2, on the growth of vegetables including cucumber, sweet pepper, radish, and tomato. All strains increased the vegetables' growth; however, G. azotocaptans DS1 showed better results as compared to other inoculated and control plants and significantly increased the plant biomass of all vegetables. Therefore, the whole genome sequence of G. azotocaptans DS1 was analyzed to predict genes involved in plant growth promotion, secondary metabolism, antibiotics resistance, and bioremediation of heavy metals. Results of genome analysis revealed that G. azotocaptans DS1 has a circular chromosome with a size of 4.3 Mbp and total 3898 protein-coding sequences. Based on functional analysis, genes for nitrogen fixation, phosphate solubilization, indole acetic acid, phenazine, siderophore production, antibiotic resistance, and bioremediation of heavy metals including copper, zinc, cobalt, and cadmium were identified. Collectively, our findings indicated that G. azotocaptans DS1 can be used as a biofertilizer and biocontrol agent for growth enhancement of different crops and vegetables. [ABSTRACT FROM AUTHOR]

This study aimed to identify possible relationships between corn (Zea mays L.) productivity and its endosphere microbial community. Any insights would be used to develop testable hypotheses at the farm level. Sap was collected from 14 fields in 2014 and 10 fields in 2017, with a yield range of 10.1 to 21.7 tonnes per hectare (t/ha). The microbial sap communities were analyzed using terminal restriction fragment length polymorphism (TRFLP) and identified using an internal pure culture reference database and BLAST. This technique is rapid and inexpensive and is suitable for use at the grower level. Diversity, richness, and normalized abundances of each bacterial population in corn sap samples were evaluated to link the microbiome of a specific field to its yield. A negative trend was observed (r = –0.60), with higher-yielding fields having lower terminal restriction fragment (TRF) richness. A partial least square regression analysis of TRF intensity and binary data from 2014 identified 10 TRFs (bacterial genera) that positively, or negatively, correlated with corn yields, when either absent or present at certain levels or ratios. Using these observations, a model was developed that accommodated criteria for each of the 10 microbes and assigned a score for each field out of 10. Data collected in 2014 showed that sites with higher model scores were highly correlated with larger yields (r = 0.83). This correlation was also seen when the 2017 data set was used (r = 0.87). We were able to conclude that a positive significant effect was seen with the model score and yield (adjusted R2 = 0.67, F[1,22] = 46.7, p < 0.001) when combining 2014 and 2017 data. The results of this study are being expanded to identify the key microbes in the corn sap community that potentially impact corn yield, regardless of corn variety, geographic factors, or edaphic factors. [ABSTRACT FROM AUTHOR]

Background Plant growth promoting rhizobacteria (PGPR) are functionally diverse group of bacteria having immense potential as biofertilizers and biopesticides. Depending upon their function, they may serve as partial replacements for chemical fertilizer or pesticides as an eco-friendly and cost-effective alternatives as compared to their synthetic counterparts. Therefore, isolation, characterization and practical evaluation of PGPRs having the aforementioned multifaceted beneficial characteristics, are essentially required. This study describes the detailed polyphasic characterization of Bacillus sp. strain RMB7 having profound broad spectrum antifungal activity and plant growth promoting potential. Results Based on 16S rRNA gene sequencing, strain RMB7 was identified as Bacillus specie. This strain exhibited the production of 8 mg. L-1 of indole-3-acetic acid (IAA) in tryptophansupplemented medium. It was able to solubilize 50.6 mg. L-1 tri-calcium phosphate, reduced 601ɳmol acetylene h-1/vial and inhibited >70% growth of nine fungal phytopathogens tested in vitro. Under natural pathogen pressure, inoculation with strain RMB7 and RMB7- supernatant conferred resistance by arugula plant against Pythium irregulare with a concurrent growth improvement over non-inoculated plants. The T-RFLP analysis based on 16S rRNA gene showed that inoculation with RMB7 or its supernatant have a major impact on the indigenous rhizosphere bacterial population. Mass spectrometric analysis revealed the production of lipopeptide surfactins as well as iturin A presence in crude extract of RMB7. PCR-amplification further confirmed the presence of genes involved in the biosynthesis of these two bioactive lipopeptide compounds. Conclusions The data show that Bacillus sp. strain RMB7 has multifaceted beneficial characteristics. It may be an ideal plant growth promoting as well as biocontrol agent, for its integrated use in disease and nutrient management strategies. [ABSTRACT FROM AUTHOR]

Abstract: Fertilizer costs are a major component of corn production. The use of biofertilizers may be one way of reducing production costs. In this study we present isolation and identification of three plant growth promoting bacteria that were identified as Enterobacter cloacae (CR1), Pseudomonas putida (CR7) and Stenotrophomonas maltophilia (CR3). All bacterial strains produced IAA in the presence of 100mgl−1 of tryptophan and antifungal metabolites to several soilborne pathogens. S. maltophilia and E. cloacae had broad spectrum activity against most Fusarium species. The only strain that was positive for nitrogen fixation was E. cloacae and it, and P. putida, were also positive for phosphate solubilization. These bacteria and the corn isolate Sphingobacterium canadense CR11, and known plant growth promoting bacterium Burkholderia phytofirmans E24 were used to inoculate corn seed to examine growth promotion of two lines of corn, varieties 39D82 and 39M27 under greenhouse conditions. When grown in sterilized sand varieties 39M27 and 39D82 showed significant increases in total dry weights of root and shoot of 10–20% and 13–28% and 17–32% and 21–31% respectively. Plants of the two varieties grown in soil collected from a corn field had respective increases in dry weights of root and shoot of 10–30% and 12–35% and 11–19% and 10–18%. In sand, a bacterial mixture was highly effective whereas in soil individual bacteria namely P. putida CR7 and E. cloacae CR1 gave the best results with 39M27 and 39D82 respectively. These isolates and another corn isolate, Azospirillum zeae N7, were tested in a sandy soil with a 55 and 110kgha−1 of nitrogen fertility at the Delhi research Station of Agriculture and Agri-Food Canada over two years. Although out of seven bacterial treatments, no treatment provided a statistically significant yield increase over control plots but S. canadense CR11 and A. zeae N7 provided statistically significant yield increase as compared to other bacteria. The 110kg rate of nitrogen provided significant yield increase compared to the 55kg rate in both years. [Copyright &y& Elsevier]

A new nylon membrane bag (NMB) assay was developed for studies to determine the effect of chemicals added to soil on survival of soilborne plant pathogens. The rapid and effective assay can be used to study organisms for which there are no selective media or for which a selective medium is expensive or difficult to prepare. This assay consists of placing pathogens inside a bag made of small-pore (0.22-μm) nylon filtration membrane, which is placed in soil and later retrieved to determine survival of the pathogens on nonselective media. Chemicals but not other microorganisms can enter the bag from the soil. Using this assay, Streptomyces scabies, Fusarium oxysporum f. sp. lycopersici race 3, and Ralstonia solanacearum were successfully recovered from soil after 72 h as demonstrated by growth on a semiselective Streptomyces medium (S. scabies) or nonselective potato dextrose agar medium (F oxysporum f. sp. lycopersici race 3 and R. solanacearum) with minimal microbial contamination. Addition of acetic acid (200 mM) to soil killed 100% of S. scabies. SPK (a mixture of organic chemicals) at a concentration of 1,500 mg kg-1 of soil killed 83.3% of F oxysporum f. sp. lycopersici race 3 culture plugs, 100% of F oxysporum f. sp. lycopersici race 3 spores, and 97.2% of R. solanacearum cells. SPK at 1,000 mg kg-1 of soil killed 50% of F oxysporum f. sp. lycopersici race 3 culture plugs, 68.2% of F oxysporum f. sp. lycopersici race 3 spores, and 12% of R. solanacea rum. Benlate (500 to 1,500 mg kg-1 of soil) did not kill the culture plugs of F oxysporum f. sp. lycopersici race 3 but reduced the growth rate of F oxysporum f. sp. lycopersici race 3. Benlate (500, 1,000, and 1,500 mg kg-1 of soil) reduced F oxysporum f. sp. lycopersici race 3 spore germination by 39.4, 49.3, and 50.4%, respectively. Streptomycin sulfate (1,500, 800, 400, and 200 mg kg' of soil) caused 75.3, 21, 11.9, and 0.9% mortality, respectively, of R. solanacea rum. [ABSTRACT FROM AUTHOR]

In this study, we report on the isolation, identification, and characterization of seven fluorescent pseudomonads isolated from the roots, shoots, and rhizosphere soil of sugarcane and their impacts on the growth of sugarcane plantlets. 16S rRNA gene sequence of five isolates showed close homology with Pseudomonas putida, one with Pseudomonas graminis, and one with Pseudomonas fluorescens. Physiological and biochemical characterizations were determined using API50CH and QTS24 identification kits. The isolates were also subjected to tests for various known growth promoting properties including production of indole acetic acid, the ability to fix nitrogen via the presence of the nifH gene, and ability to solubilize phosphate. Biological control potential was determined from agar diffusion assays of HCN production and production of antifungal compounds against local isolates of Colletotrichum falcatum (that induces red-rot disease of sugarcane). Direct plant growth promoting effects were tested on sugarcane plantlets in tissue culture under gnotobiotic conditions. All seven isolates provided significant increases in fresh and dry masses but only five strains increased shoot height. [ABSTRACT FROM AUTHOR]

• Green fluorescent protein (GFP) labeling of bacteria has been used to study their infection of and localization in plants, but strong autofluorescence from leaves and the relatively weak green fluorescence of GFP-labeled bacteria restrict its broader application to investigations of plant–bacterial interactions. • A stable and broad-host-range plasmid vector (pDSK-GFPuv) that strongly expresses GFPuv protein was constructed not only for in vivo monitoring of bacterial infection, localization, activity, and movement at the cellular level under fluorescence microscopy, but also for monitoring bacterial disease development at the whole-plant level under long-wavelength ultraviolet (UV) light. • The presence of pDSK-GFPuv did not have significant impact on the in vitro or in planta growth and virulence of phytobacteria. A good correlation between bacterial cell number and fluorescence intensity was observed, which allowed us to rapidly estimate the bacterial population in plant leaf tissue. We demonstrated that GFPuv-expressing bacteria can be used to screen plants that are compromised for nonhost disease resistance and Agrobacterium attachment. • The use of GFPuv-labeled bacteria has a wide range of applications in host–bacterial interaction studies and bacterial ecology-related research. [ABSTRACT FROM AUTHOR]

Of several hundred microorganisms randomly selected from the environment, only a fungal isolate identified as Aspergillus niger van Tiegham var. niger was found to transform the phytotoxin thaxtomin A to much less toxic metabolites. The rate and extent of transformation of thaxtomin A was tested under a variety of conditions, including different growth media, biomass concentrations, incubation periods, and shaker speeds. Under optimum conditions the fungus converted thaxtomin A into two major and five minor metabolites. The two major metabolites and three of the five minor metabolites were fully characterized by a combination of mass spectral and nuclear magnetic resonance techniques. When assayed on aseptically produced mini-tubers, the major metabolites proved to be much less phytotoxic than thaxtomin A. [ABSTRACT FROM AUTHOR]

This study investigated strain-dependent variability in Escherichia coli survival in soil, and strain-dependent responses to variations in some soil conditions. Collections of E. coli were isolated from swine manure slurry, and from manured soil following 6 days of incubation in the laboratory. The bacteria were fingerprinted by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). During the course of the incubation the composition of the E. coli community changed dramatically suggesting that E. coli phylotypes, distinguishable by ERIC-PCR fingerprinting, varied significantly in their ability to survive in soil under these conditions. A representative isolate from one ERIC group which increased in abundance in soil (designated strain C279) and one which decreased (designated strain C278) were chosen for comparison. These strains persisted comparatively when inoculated into loam soil. However, when added into a loam soil or a sandy soil supplemented with 10% (v/v) swine manure slurry, strain C279 increased in abundance 10-fold, whereas strain C278 did not. At 4°C, or in a clay loam soil, manure slurry did not support the growth of strain C279. These results indicate that the community composition of E. coli populations in manured soils can be very dynamic, and that strains able to proliferate in manured soils can have a selective advantage. [Copyright &y& Elsevier]

Forty-three Fusarium oxysporum strains and one Fusarium solani strain were analyzed for genetic diversity. These strains represent a wide range of geographic locations and were collected primarily from tomato (Lycopersicon esculentum) roots. Among all 43 F. oxysporum strains, 21 were not pathogenic to tomato, 20 were pathogenic, including 13 strains of Fusarium oxysporum lycopersici and seven strains of Fusarium oxysporum radicis-lycopersici, and two were other formae speciales of the fungus. Genetic diversity of all 43 strains was assessed by vegetative compatibility group (VCG), sequence analysis of the rDNA internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene, and amplified fragment length polymorphism (AFLP). Most of the F. o. lycopersici strains were assigned to VCG 0030, while most nonpathogenic ones were incompatible with each other. ITS region analysis grouped the strains into four clusters. The nonpathogenic F. oxysporum strains were in two groups, while the pathogenic strains were placed in two different groups. Pathogenic and nonpathogenic strains were also separated into different clusters based on AFLP data, although some nonpathogenic strains grouped with pathogenic strains. The population of pathogenic strains was less diverse than that of the nonpathogenic strains, suggesting that the pathogenic strains were possibly of monophyletic origin. For both pathogenic and nonpathogenic F. oxysporum strains, no relationship was observed between the genetic profiles and geographic origin; this may indicate that pathogens did not originate independently at each locality.Key words: Fusarium oxysporum, VCG, rDNA (ITS) sequence, AFLP.Les auteurs ont analysé la diversité génétique chez 43 souches du Fusarium oxysporum et une souche du Fusarium solani. Ces souches proviennent d'un grand nombre de localités géographiques et ont été récoltées surtout sur des racines de tomate (Lycopersicon esculentum). Sur l'ensemble des 43 souches du F. oxysporum, 21 ne sont pas pathogènes pour la tomate, 20 sont pathogènes, incluant 13 souches du Fusarium oxysporum lycopersici et sept souches de Fusarium oxysporum radicis-lycopersici, alors que deux autres constituent des formae speciales du champignon. La diversité génétique de l'ensemble des 43 souches a été évaluée selon les groupes de compatibilité végétative (VCG), par l'analyse séquentielle de l'ADNr des espaceurs internes transcrits (ITS1 et ITS2) et de l'ARNr du gène 5,8S, ainsi que par l'amplification du polymorphisme de la longueur des fragments (AFLP). La plupart des souches du F. o. lycopersici appartiennent au VCG 0030, alors que la majorité des souches non-pathogènes sont incompatibles les unes avec les autres. L'analyse des régions ITS regroupe les souches en quatre ensembles. Les souches non-pathogènes du F. oxysporum constituent deux groupes, alors que les souches pathogènes se retrouvent dans deux groupes différents. Les souches pathogènes et non-pathogènes se retrouvent également dans des ensembles différents sur la base des données de l' AFLP, bien que certaines souches non-pathogènes se regroupent avec des souches pathogènes. La population des souches pathogènes est moins diversifiée que celle des souches non-pathogènes, ce qui suggère que les souches pathogènes sont possiblement d'origine monophylétique. Pour les souches pathogènes aussi bien que non-pathogènes du F. oxysporum, on ne perçoit pas de relation entre les profiles génétiques et l'origine géographique, ce qui peut indiquer que ces champignons pathogènes n'ont pas d'origine indépendante dans chaque localitéMots clés : Fusarium oxysporum, VCG, séquence de l'ADNr (ITS), AFLP.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

Soils with highly uniform textural, physical, and chemical characteristics still give rise to crop stand variability. Seed quality is one of the factors adding to yield variability and has become a concern for corn growers. Hybrid seed producers claim that their seeds provide a uniformity in crop emergence and productivity, but they do not always provide detailed studies to support this claim. Based on growers' concerns, we examined fields planted with three different hybrid varieties and found that 25% to 50% of the stand had relatively weak vigor, where seed variety A showed 15% of seedlings with lower vigor, and varieties B and C had 30% of seedlings with low vigor. These apparent differences in plant vigor prompted us to initiate a cursory investigation to identify how seed size influenced seedling vigor and if the seedling's microbial profile played a role in the early growth stages of three commonly grown corn hybrids in Ontario. Seeds were separated based on size, prior to conducting a growth room study. Different sizes of seeds from the same seed lot showed significant differences in vigor capacity and related biometric components. Significant differences were also found in their nutritional composition and microbial profiles within the different seed sizes and the roots and shoots of seedlings derived from such seeds. The results clearly indicate that seed size greatly impacts the plant growth and its microbiome, resulting in seedlings with different plant vigor, microbiomes, and performance. [ABSTRACT FROM AUTHOR]

This study describes the biocontrol potential of rhizobacteria against a range of fungal phytopathogens. Out of 227 bacteria isolated from the rhizosphere of maize, rice, wheat, potato, sunflower and soybean crops cultivated in different agro-ecological regions of Pakistan, 48 exhibited >60 % antifungal activity against Fusarium oxysporum, Fusarium moniliforme, Rhizoctonia solani, Colletotrichum gloeosporioides, Colletotrichum falcatum, Aspergillus niger, and Aspergillus flavus. The rhizobacteria inhibiting >65 % pathogen growth were selected for detailed molecular and in planta studies most of which were identified as Pseudomonas and Bacillus species based on 16S rRNA gene sequence analysis. Antifungal metabolites produced by these rhizobacteria analyzed through LCMS were identified as antibiotics (iturin, surfactins, fengycin, DAPG, Phenazine, etc.), cell wall degrading enzymes (protease, chitinase, and cellulase), plant growth promotion enzymes and hormones (indole-3-acetic acid, ACC-deaminase, phosphates, nitrogen fixation), N-acyl-homoserine lactones and siderophores. The growth room experiment validated the potential of these bacteria as biofertilizer and biopesticide agents. Of all, P. aeruginosa strain FB2 and B. subtilis strain RMB5 showed significantly higher potential as antagonistic plant-beneficial bacteria effective against a range of fungal phytopathogens. Both these bacteria can be used to develop a dual-purpose bacterial inoculum as biopesticide and biofertilizer. Rest of the antagonistic PGPR may be exploited for disease control in less-infested soils. [ABSTRACT FROM AUTHOR]