Variation of Pythium-induced cocoyam root rot severity in response to soil type

In Cameroon, andosols are suspected to be suppressive to cocoyam (Xanthosoma sagittifolium) root rot disease (CRRD) caused by the Oomycete pathogen Pythium myriotylum. To determine factors involved in disease suppressiveness, andosols were studied in comparison to ferralsols known to be disease-conducive. Soil samples were collected from six sites of which three were in andosols around Mount Cameroon (Boteva, Njonji, and Ekona) and the three others in ferralsols (Bakoa, Lapkwang, and Nko’o canane). Greenhouse plant experiments were used to assess soil suppressiveness. Soils were artificially infested with two levels of P. myriotylum inoculum (100 and 300 mycelia strands g⁻¹ soil) prior to planting cocoyam. Disease severity was significantly higher in ferralsols than in andosols. Andosols partly lost their suppressiveness as a result of autoclaving and could recover suppressiveness following recolonisation by their original microflora. Soil microbial groups implicated in the disease suppression were investigated by assessing the effect of fungicide, bactericide, and pasteurisation on andosol suppressiveness. Andosols suppressiveness was significantly reduced following pasteurisation and treatment with fungicide and bactericide. The possible influence of microbial biomass on andosol suppressiveness was investigated by comparing microbial populations of suppressive andosols to those in andosols that had lost suppressiveness. A comparative analysis of suppressive and conducive soil properties was performed to identify soil variables, which may contribute to soil suppressiveness. Soil chemical analysis results showed that organic matter content was higher in andosols than in ferralsols. In addition, the content of mineral nutrients such as Ca, K, Mg and N, was higher in andosols than in ferralsols. These soil variables negatively correlated with disease severity. By contrast, sand and clay, which were higher in ferralsols than in andosols, were positively related to disease severity. This study has confirmed the suppressive nature of andosols from Mount Cameroon to CRRD. The results suggest that high organic matter content is likely mediating P. myriotylum suppression in andosols by improving soil structure, increasing soil nutrient content and microbial biomass, and sustaining microbial activity.     

Re-establishment of suppressiveness to soil- and air-borne diseases by re-inoculation of soil microbial communities

The aim of this study was to investigate the potentials and limitations in restoring soil suppressiveness in disturbed soils. Soils from three sites in UK and Switzerland (STC, REC, THE) differing in their level of suppressiveness to soil-borne and air-borne diseases were γ-irradiated and this soil matrix was re-inoculated with 1% (w/w) of either parent native soil or native soil from the other sites (‘soil inoculum’). Suppressiveness to air-borne and soil-borne diseases was quantified by means of the host-pathogen systems Lepidium sativum (cress)-Pythium ultimum, an oomycete causing root rot and seedling damping-off, and Arabidopsis thaliana-Hyaloperonospora parasitica, an oomycete causing downy mildew. Soil microbial biomass, activity and community structure, as determined by phospholipid fatty acid (PLFA) profiles, were measured in native, γ-irradiated, and re-inoculated soils. Both, L. sativum and A. thaliana were highly susceptible to the pathogens if grown on γ-irradiated soils. Re-inoculation completely restored suppressiveness of soils to the foliar pathogen H. parasitica, independently of soil matrix or soil inoculum, whereas suppressiveness to P. ultimum depended on the soil matrix and, to a lesser extent, on the soil inoculum. However, the soil with the highest inherent suppressiveness did not reach the initial level of suppressiveness after re-inoculation. In addition, native microbial populations as defined by microbial biomass, activity and community structure, could not be fully restored in re-inoculated soils. As for suppressiveness to P. ultimum, the soil matrix, rather than the source of soil inoculum was identified as the key factor for re-establishing the microbial community structure. Our data show that soils do not or only slowly fully recover from sterilisation by γ-irradiation, indicating that agricultural soil management practices such as soil fumigation or heat treatments frequently used in vegetable cropping should be avoided.     

Effect of successive cauliflower plantings and Rhizoctonia solani AG 2-1 inoculations on disease suppressiveness of a suppressive and a conducive soil

Disease suppressiveness against Rhizoctonia solani AG 2-1 in cauliflower was studied in two marine clay soils with a sandy loam texture. The soils had a different cropping history. One soil had a long-term (40 years) cauliflower history and was suppressive, the other soil was conducive and came from a pear orchard not having a cauliflower crop for at least 40 years. These two soils were subjected to five successive cropping cycles with cauliflower or remaining fallow in a greenhouse experiment. Soils were inoculated with R. solani AG 2-1 only once or before every crop. Disease decline occurred in all treatments cropped with cauliflower, either because of a decreased pathogen population or increased suppressiveness of the soil. Disease suppressiveness tests indicated that the conducive soil became suppressive after five subsequent cauliflower crops inoculated each cycle with R. solani AG 2-1. Suppressiveness of all treatments was measured in a seed germination test (pre-emergence damping-off) as well as by measuring the spread of R. solani symptoms in young plants (post-emergence damping-off). Results showed that suppressiveness was significantly stimulated by the successive R. solani inoculations; presence of the cauliflower crop had less effect. Suppressiveness was of biological origin, since it disappeared after sterilization of the soil. Moreover, suppressiveness could be translocated by adding 10% suppressive soil into sterilized soil. The suppressive soil contained higher numbers of culturable filamentous actinomycetes than the conducive soil, but treatments enhancing suppressiveness did not show an increased actinomycetes population. The suppressiveness of the soil samples did also not correlate with the number of pseudomonads. Moreover, no correlation was found with the presence of different mycoparasitic fungi, i.e. Volutella spp., Gliocladium roseum, Verticillium biguttatum and Trichoderma spp. The suppressive soil contained a high percentage of bacteria with a strong in vitro inhibition of R. solani. These bacteria were identified as Lysobacter (56%), Streptomyces (23%) and Pseudomonas (21%) spp. A potential role of Lysobacter in soil suppressiveness was confirmed by quantitative PCR detection (TaqMan), since a larger Lysobacter population was present in suppressive cauliflower soil than in conducive pear orchard soil. Our experiments showed that successive cauliflower plantings can cause a decline of the damage caused by R. solani AG 2-1, and that natural disease suppressiveness was most pronounced after subsequent inoculations with the pathogen. The mode of action of the decline is not yet understood, but antagonistic Lysobacter spp. are potential key organisms.     

Effect of sewage sludge on suppressiveness to soil-borne plant pathogens

The objective of this study was to evaluate the effect of sewage sludge on soil suppressiveness to the pathogens Fusarium oxysporum f. sp. lycopersici on tomato, Sclerotium rolfsii on bean, Sclerotinia sclerotiorum on tomato, Rhizoctonia solani on radish, Pythium spp. on cucumber, and Ralstonia solanacearum on tomato. Soil samples were collected from an experimental corn field in which sewage sludge had been incorporated once a year, since 1999. Sludge from two sewage treatment stations in Brazil (Franca and Barueri, SP) were applied at the rates of one (1N), two (2N), four (4N) and eight (8N) times the N recommended doses for the corn crop. Soil suppressiveness was evaluated by methods using indicator host plants, baits and mycelial growth. There was no effect of sewage sludge on soil suppressiveness to Fusarium oxysporum f. sp. lycopersici in tomato plants. For S. rolfsii, reduction of the disease in bean was inversely proportional to the dose of Franca sludge. The incidence of dead plants, caused by S. sclerotiorum, was directly proportional to sludge doses applied. For R. solani and R. solanacearum, there was a linear trend with reduction in plant death in soils treated with increasing amounts of sludge from Franca. There was an increase in the pathogen community of Pythium spp., proportional to the amounts of sewage applied. The effects of sewage sludge varied depending on the pathogen, methodology applied and on the time interval between the sewage sludge incorporation and soil sampling.     

Influence of soil type and indigenous pathogenic fungi on bean hypocotyl rot caused by Rhizoctonia solani AG4 HGI in Cuba

Calcisol, ferralsol and vertisol soils, representative of different bean production areas of Villa Clara province in Cuba, were selected to determine the impact of soil type on bean hypocotyl rot severity caused by Rhizoctonia solani AG4 HGI (isolate CuVC-Rs7). In inoculated autoclaved soil, hypocotyl rot was most severe in calcisol soil, followed by ferralsol soils and then vertisol soils. In inoculated natural soils, disease severity was lower in vertisol and calcisol soils and higher in ferralsol soil, indicating that biological factors are suppressing or stimulating the pathogenic efficiency of R. solani. Native binucleate Rhizoctonia AGF, Sclerotium rolfsii and R. solani AG 4 HGI were isolated from bean plants grown in natural calcisol, vertisol and ferralsol soils, respectively. Subsequent studies about the interaction between these fungi and R. solani indicated that they were involved in the variability of disease severity caused by R. solani. The addition of R. solani AG4 HGI (isolate CuVC-Rs7) into each autoclaved soil inoculated with binucleate Rhizoctonia or S. rolfsii resulted in a reduction of disease severity caused by this pathogen while in soils inoculated with native R. solani AG4 HGI, disease severity increased. Irrespective of fungal interactions, calcisol was always the most disease conducive soil and vertisol the most disease repressive soil. The mechanisms by which native pathogenic fungi could influence disease severity caused by R. solani are discussed.     

Size, symbiotic effectiveness and genetic diversity of field pea rhizobia (Rhizobium leguminosarum bv. viciae) populations in South Australian soils

Field pea (Pisum sativum L.) is widely grown in South Australia (SA), often without inoculation with commercial rhizobia. To establish if symbiotic factors are limiting the growth of field pea we examined the size, symbiotic effectiveness and diversity of populations of field pea rhizobia (Rhizobium leguminosarum bv. viciae) that have become naturalised in South Australian soils and nodulate many pea crops. Most probable number plant infection tests on 33 soils showed that R. l. bv. viciae populations ranged from undetectable (six soils) to 32×10³ rhizobia g⁻¹ of dry soil. Twenty-four of the 33 soils contained more than 100 rhizobia g⁻¹ soil. Three of the six soils in which no R. l. bv. viciae were detected had not grown a host legume (field pea, faba bean, vetch or lentil). For soils that had grown a host legume, there was no correlation between the size of R. l. bv. viciae populations and either the time since a host legume had been grown or any measured soil factor (pH, inorganic N and organic C). In glasshouse experiments, inoculation of the field pea cultivar Parafield with the commercial Rhizobium strain SU303 resulted in a highly effective symbiosis. The SU303 treatment produced as much shoot dry weight as the mineral N treatment and more than 2.9 times the shoot dry weight of the uninoculated treatment. Twenty-two of the 33 naturalised populations of rhizobia (applied to pea plants as soil suspensions) produced prompt and abundant nodulation. These symbioses were generally effective at N₂ fixation, with shoot dry weight ranging from 98% (soil 21) down to 61% (soil 30) of the SU303 treatment, the least effective population of rhizobia still producing nearly double the growth of the uninoculated treatment. Low shoot dry weights resulting from most of the remaining soil treatments were associated with delayed or erratic nodulation caused by low numbers of rhizobia. Random amplified polymorphic DNA (RAPD) polymerase chain reaction (PCR) fingerprinting of 70 rhizobial isolates recovered from five of the 33 soils (14 isolates from each soil) showed that naturalised populations were composed of multiple (5-9) strain types. There was little evidence of strain dominance, with a single strain type occupying more than 30% of trap host nodules in only two of the five populations. Cluster analysis of RAPD PCR banding patterns showed that strain types in naturalised populations were not closely related to the current commercial inoculant strain for field pea (SU303, ≥75% dissimilarity), six previous field pea inoculant strains (≥55% dissimilarity) or a former commercial inoculant strain for faba bean (WSM1274, ≥66% dissimilarity). Two of the most closely related strain types (≤15% dissimilarity) were found at widely separate locations in SA and may have potential as commercial inoculant strains. Given the size and diversity of the naturalised pea rhizobia populations in SA soils and their relative effectiveness, it is unlikely that inoculation with a commercial strain of rhizobia will improve N₂ fixation in field pea crops, unless the number of rhizobia in the soil is very low or absent (e.g. where a legume host has not been previously grown and for three soils from western Eyre Peninsula). The general effectiveness of the pea rhizobia populations also indicates that reduced N₂ fixation is unlikely to be the major cause of the declining field pea yields observed in recent times.     

Denaturing gradient gel electrophoretic analysis of dominant 2,4-diacetylphloroglucinol biosynthetic phlD alleles in fluorescent Pseudomonas from soils suppressive or conducive to black root rot of tobacco

In Switzerland, similar types of rhizosphere pseudomonads producing the biocontrol compound 2,4-diacetylphloroglucinol (Phl) have been found in soils suppressive to Thielaviopsis basicola-mediated black root rot of tobacco as well as in conducive soils. However, most findings were based on the analysis of a limited number of Pseudomonas isolates, obtained from a single experiment and only from T. basicola-inoculated plants. Here, an approach based on denaturing gradient gel electrophoresis (DGGE) of dominant phlD alleles from tobacco rhizosphere provided different phlD migration patterns. Sequencing of phlD-DGGE bands revealed a novel phylogenetic cluster of phlD sequences found in both suppressive and conducive soils in addition to previously-documented phlD alleles. phlD-DGGE bands and alleles differed little from one plant to the next but more extensively from one sampling to the next during the three-year study. Three of the 13 bands and 12 of the 31 alleles were only found in suppressive soil, whereas five bands and 13 alleles were found exclusively in conducive soil. The population structure of phlD⁺ pseudomonads depended more on the individual soil considered and its suppressiveness status than on inoculation of tobacco with T. basicola. In conclusion, phlD-DGGE revealed additional phlD diversity compared with earlier analyses of individual Pseudomonas isolates, and showed differences in phlD⁺Pseudomonas population structure in relation to disease suppressiveness.     

Screening of bacterial isolates from various European soils for in vitro antagonistic activity towards Rhizoctonia solani and Fusarium oxysporum: Site-dependent composition and diversity revealed

A cultivation-based approach was used to determine the in vitro antagonistic potential of soil bacteria towards Rhizoctonia solani AG3 and Fusarium oxysporum f. sp. lini (Foln3). Four composite soil samples were collected from four agricultural sites with previous documentation of disease suppression, located in France (FR), the Netherlands (NL), Sweden (SE) and the United Kingdom (UK). Similarly, two sites from Germany (Berlin, G-BR; and Braunschweig, G-BS) without documentation of disease suppression were sampled. Total bacterial counts were determined by plating serial dilutions from the composite soil samples onto R2A, AGS and King's B media. A total of 1,788 isolates (approximately 100 isolates per medium and site) was screened for antifungal activity, and in vitro antagonists (327 isolates) were found amongst the dominant culturable bacteria isolated from all six soils. The overall proportion of antagonists and the number of isolates with inhibitory activity against F. oxysporum were highest in three of the suppressive soils (FR, NL and SE). Characterization of antagonistic bacteria revealed a high phenotypic and genotypic diversity. Siderophore and protease activity were the most prominent phenotypic traits amongst the antagonists. The composition and diversity of antagonists in each soil was site-specific. Nevertheless, none of the antimicrobial traits of bacteria potentially contributing to soil suppressiveness analyzed in this study could be regarded as specific to a given site.     

Identifying the characteristics of organic soil amendments that suppress soilborne plant diseases

Application of organic amendments has been proposed as a strategy for the management of diseases caused by soilborne pathogens. However, inconsistent results seriously hinder their practical use. In this work we use an extensive data set of 2423 studies derived from 252 papers to explore this strategy. First, we assess the capability of a specific organic amendment to control different diseases; second, we investigate the influence of organic matter (OM) decomposition on disease suppressiveness; and third, we search for physical, chemical and biological parameters able to identify suppressive OM. OM was found to be consistently suppressive to different pathogens in only a few studies where a limited number of pathogens were tested. In the majority of studies a material suppressive to a pathogen was ineffective or even conducive to other pathogens, suggesting that OM suppressiveness is often pathogen-specific. OM decomposition in many studies (73%, n = 426) emerged as a crucial process affecting suppressiveness. During decomposition, disease suppression either increased, decreased, was unchanged or showed more complex responses, such as ‘hump-shaped’ dynamics. Peat suppressiveness generally decreased during decomposition, while responses of composts and crop residues were more complex. However, due to the many interactions of contributing factors (OM quality, microbial community composition, pathosystem tested and decomposition time), it was difficult to identify specific predictors of disease suppression. Among the 81 parameters analysed, only some of the 643 correlations showed a consistent relationship with disease suppression. The response of pathogen populations to OM amendments was a reliable feature only for some organic matter types (e.g. crop residues and organic wastes with C-to-N ratio lower than ∼15) and for pathogens with a limited saprophytic ability (e.g., Thielaviopsis basicola and Verticillium dahliae). Instead, population responses of the pathogenic fungi Phytophthora spp., Rhizoctonia solani and Pythium spp. appeared unrelated to disease suppression. Overall, enzymatic and microbiological parameters, rather than chemical ones, were much more informative for predicting suppressiveness. The most useful features were FDA activity, substrate respiration, microbial biomass, total culturable bacteria, fluorescent pseudomonads and Trichoderma populations. We conclude that the integration of different parameters (e.g. FDA hydrolysis and chemical composition by ¹³C NMR) may be a promising approach for identification of suppressive amendments.     

The Effects of Soil Solarization and Compost on Soil Suppressiveness against Fusarium Oxysporum f. sp. Melonis

Soil suppressiveness against Fusarium was tested using solarized and non-solarized soils combined with composts of three maturation levels, and a non-amended control. The soils were sampled on three dates: after previous year solarization but before current year solarization (0 weeks), at the end of the solarization period of the current year (4 weeks), and 4 weeks later (recovery time). Melon seedlings were inoculated with Fusarium spores and disease severity was assessed. The study showed a reduction of soil suppressiveness capacity against Fusarium oxysporum f. sp. melonis after 1 year of solarization (0 weeks). Fusarium disease severity in artificially inoculated melon plants, expressed by area under the disease progress curve, was higher in solarized soil than in non-solarized soil. Compost addition lowered the disease severity, both in the solarized and in the non-solarized soils. However, suppression was not obtained at the end of the solarization period, whereas compost beneficial effect was found at this time.     

Soil suppressiveness and functional diversity of the soil microflora in organic farming systems

Arable fields of 10 organic farms from different locations in The Netherlands were sampled in three subsequent years. The soil samples were analysed for disease suppressiveness against Rhizoctonia solani AG2.2IIIB in sugar beet, Streptomyces scabies in radish and Verticillium longisporum in oilseed rape. In addition, a variety of microbial, chemical and physical soil characteristics were assessed. All data were correlated by multiple regression and multivariate analyses with the objective to find correlations between soil suppressiveness and biotic or abiotic soil characteristics. Significant differences in soil suppressiveness were found between the fields for all three diseases. Multiple regression indicated a significant correlation between suppressiveness against Rhizoctonia and the number of antagonistic Lysobacter spp., as well as with % active fungi and bacterial diversity. Grass-clover stimulated Rhizoctonia suppression as well as the presence of antagonistic Lysobacter spp. (mainly L. antibioticus and L. gummosus) in clay soils. Streptomyces suppression correlated with the number of antagonistic Streptomyces spp., % of active fungi and bacterial population size. The presence of antagonistic Streptomyces spp. correlated with a high fungal/bacterial biomass ratio. Verticillium suppression was only measured in 2004 and 2005, due to the inconsistent suppressiveness along the years. Nevertheless, a significant correlation with pH, potential nitrogen mineralization and bacterial biomass was found. Bacterial and fungal PCR-denaturing gel electrophoresis fingerprinting of bacterial and fungal communities, in general, did not significantly correlate with disease suppression. Highly significant explanatory factors of the composition of the dominating bacterial and fungal populations were % lutum, pH, C/N quotient, biomass and growth rate of bacteria. Additionally, the % of organic matter and years of organic farming were explaining significantly the composition of the bacterial population.Thus, significant correlations between several soil characteristics and suppressiveness of different soil-borne pathogens were found. For two of the three pathogens, suppression correlated with biotic soil characteristics combined with the presence of specific bacterial antagonists. Probably the soil suppressiveness measured in the organic fields is a combined effect of general and specific disease suppression.     

Evaluating soil sodium indices in soils of volcanic nature conducive or suppressive to Fusarium wilt of banana

The ability of three soil Na indices to predict soil conduciveness or suppressiveness to disease caused by the soil fungus Fusarium oxysporum f. sp. cubense was evaluated in seven banana plantations from the Canary Islands (Spain). These indices were exchangeable sodium percentage (ESP), soluble Na (SS₀) and sodium adsorption ratio (SAR₀) in 1:2.5 soil-water extracts (SAR_w and total cationic concentration (TCC_w)=0. Sodium selectivity coefficients (K_G0,K₀) and TCC₀ were calculated from soil exchange and solution data. The effects of ESP, SAR₀, SS₀, TCC₀, K_G0 and K₀ on soil available iron (Fe extracted from soil by DTPA) and aggregate stability in water (water-stable aggregates (WSA), 200-2000 μm) were also studied. Our results showed that SAR₀ calculated using cationic concentrations in 1:2.5 extracts might be a good indication of a relationship between SS₀ and soluble divalent cations in conducive and suppressive volcanic soils to Fusarium. Both TCC₀ and dispersion-flocculation concentrations seem to be not linked to soil suppressiveness or conduciveness to Fusarium wilt. These results suggested that soil physical properties seem to be not controlled by Na behaviour in these type of soils and, therefore, sodicity and salinity should not be a problem from a physical point of view. Moreover, SS₀ and SAR₀ were always greater in suppressive areas than in conducive areas. SAR₀ was significantly correlated with SS₀ but correlations between ESP against SS₀ and SAR₀ were weak. For SAR₀ values above 2.5 (mmol_c l⁻¹)^1/2 and ESP values below 15%, the exchangeable Na did not seem to be related to the capacity of suppressive areas to release more Na to soil solution. Larger values of SS₀ were observed in suppressive areas for these values of SAR₀ and ESP. It implies a lower quantity of soluble Na salts in conducive samples. A high Na salt content in soil can produce an increase of soil pH, which exerts a negative influence on available Fe release to soil solution. A clear separation between conducive and suppressive samples from relations between SS₀ and SAR₀ against WSA and Fe-DTPA showed that SS₀ and SAR₀ can be satisfactory indices to study the influence of Na concentrations on the incidence of Fusarium wilt. The mass of WSA increase in conducive areas might be favoured by the smaller amounts of soil solution Na found in these samples. In conclusion, our data provide evidence that release of Na to soil solution could favour soil suppressiveness to Fusarium wilt limiting soil aggregation and the availability of Fe, at least in soils of volcanic nature that are not affected by salinity or sodicity processes.     

Partitioning the spatial and environmental variation of Sclerotinia stem rot on soybean

The variance in survival of Sclerotinia sclerotiorum's sclerotia, carpogenic germination (apothecia) as well as Sclerotinia stem rot (SSR) severity (Disease Severity Index (DSI)) on soybean was partitioned among canopy, soil physico-chemistry and microbiology, cultural practices (2 or 3-y-corn rotation/soybean monoculture and mineral fertilization/urban compost), and spatial matrices in two soils. Partial multiple regression was used to partition the individual SSR variables variance while partial canonical redundancy analysis partitioned the DSI-apothecia and apothecia-survival variance. In clay loam, the sclerotial survival and apothecia variance were mainly explained by the spatial structure of soil physico-chemistry while the DSI did not share this spatial structure and was largely explained by the effects of 3-y-corn rotation on canopy and soil, i.e. lower weed biomass, enhanced soybean yield and fewer apothecia were correlated with disease suppressiveness. In sandy loam, the DSI variance was mostly explained by the spatial structure of canopy and physico-chemistry. Disease suppressiveness, by the interaction of 3-y-corn rotation with urban compost, was largely explained by the enhancement of soil properties, i.e. higher aggregate stability, microbial activity and soil solution concentration in exchangeable ions correlated negatively with carpogenic germination. Partitioning the SSR variance among four matrices of spatial and environmental factors allowed for the first time to interpret and quantify the variance of disease development explained by cultural practices in interaction with the main characteristics of this agroecosystem.     

Soil fungal community structure along a soil health gradient in pea fields examined using deep amplicon sequencing

Soil fungi and oomycetes (syn. peronosporomycetes) are the most common causes of pea diseases, and these pathogens often occur in complexes involving several species. Information on the dynamics within this complex of pathogens, and also between the complex of pathogens and other fungi in the development of root disease is limited. In this study, next-generation sequencing of nuclear ribosomal internal transcribed spacer-1 was used to characterize fungal communities in agricultural soils from nine pea fields, in which pea roots showed different degrees of disease. Fungal species richness, diversity, and community composition were analyzed and compared among the different pea soils. After filtering for quality and excluding non-fungal sequences, 55,460 sequences clustering into 434 operational taxonomic units (OTUs), were obtained from the nine soil samples. These sequences were found to correspond to 145–200 OTUs in each soil. The fungal communities in the nine soils were strongly dominated by Ascomycota and Basidiomycota. Phoma, Podospora, Pseudaleuria, and Veronaea, at genus level, correlated to the disease severity index of pea roots; Phoma was most abundant in soils with diseased plants, whereas Podospora, Pseudaleuria, and Veronaea were most abundant in healthy soils. No correlation was found between the disease severity index and the abundance of some of the other fungi and oomycetes normally considered as root pathogens in pea.     

The abundance and efficacy of Rhizobium leguminosarum bv. viciae in cultivated soils of the eastern Canadian prairie

For optimum production, the use of commercial rhizobial inoculant on pea (Pisum sativum L.) at seeding is necessary in the absence of compatible rhizobial strains or when rhizobial soil populations are low or symbiotically ineffective. Multiple site experiments were conducted to characterize the abundance and effectiveness of resident populations of Rhizobium leguminosarum bv. viciae (Rlv) in eastern Canadian prairie soils. A survey of 20 sites across a broad geographical range of southern Manitoba was carried out in 1998 and was followed by more intensive study of five of the sites in 1999 and 2000. Appreciable nodulation of uninoculated pea was observed at all sites which had previously grown inoculated pea. However, uninoculated pea grown at two sites, which had not previously grown pea, had negligible nodulation. Likewise, wild Lathyrus sp. and Vicia sp. plants collected from uncultivated areas adjacent to agricultural sites were poorly nodulated. In the more intensively studied sites, there was a tendency towards higher nodulation in pea plants receiving commercial inoculant containing Rlv strain PBC108 across all site-years (e.g., 4.7% in nodulation and 22% in nodule mass), but the effect was significant at only 2 of 10 site-years. Despite a relatively high range of soil pH (6-8), regression analysis indicated that decreasing soil pH resulted in lower nodulation rates. Likewise, electrical conductivity (EC) was correlated to nodulation levels, however the effect of EC was likely more indicative of the influence of soil texture and organic matter than salinity. As with nodulation, commercial inoculation tended to increase above-ground dry matter (DM) and fixed-N (estimated by the difference method) at the early pod-filling stage, but again the effects were significant at only 2 of 10 site-years. Specifically, above-ground DM and fixed-N levels were up to 29 and 51% greater, respectively, in inoculated compared to non-inoculated treatments at these sites. Addition of N-fertilizer at a rate of 100 kg N ha⁻¹ decreased nodulation at almost all site-years (by as much as 70% at one site), but rarely resulted in increases in above-ground DM compared to inoculated plots. The study indicates for the first time that populations of infective, and generally effective strains of Rlv occur broadly in agricultural soils across the eastern Canadian prairie, but that there is a tendency for increased symbiotic efficiency with the use of commercial inoculant.     

Increase in soil pH due to Ca-rich organic matter application causes suppression of the clubroot disease of crucifers

Clubroot disease of cruciferous plants caused by the soil-borne pathogen Plasmodiophora brassicae is difficult to control because the pathogen survives for a long time in soil as resting spores. Disease-suppressive and conducive soils were found during the long-term experiment on the impact of organic matter application to arable fields and have been studied to clarify the biotic and abiotic factors involved in the disease suppression. The fact that a large amount of organic matter, 400 t ha⁻¹ yr⁻¹ farmyard manure (FYM) or 100 t ha⁻¹ yr⁻¹ food factory sludge compost (FSC), had been incorporated for more than 15 yr in the suppressive soils and these soils showed higher pH and Ca concentration than the disease conducive soil led us to hypothesize that an increase in soil pH due to the long-term incorporation of Ca-rich organic matter might be the primary cause of the disease suppression. We have designed a highly reproducible bioassay system to examine this hypothesis. The suppressive and conducive soils were mixed with the resting spores of P. brassicae at a rate of 10⁶ spore g⁻¹ soil, and Brassica campestris was grown in a growth chamber for 8 d. The number of root hair infections was assessed on a microscope. It was found that the incorporation of FYM and FSC at 2.5% (w/w) to the conducive soil suppressed the infection and that the finer particles (?5 mm) of FSC inhibited the infection and increased soil pH more effectively. Neutralization of the conducive soil by Ca(OH)₂, CaCO₃ and KOH suppressed the infection, but the effectiveness of KOH was less than those of Ca(OH)₂ and CaCO₃. Acidification of the suppressive soils by H₂SO₄, promoted the infection. The involvement of soil biota in the disease suppression was investigated using the sterilized (γ-ray irradiation) suppressive soils with respect to soil pH. The γ-ray irradiation promoted the infection at pH 5.5, but no infection was observed at pH 7.4 irrespective of the sterilization status. All these observations suggest that soil pH is a major factor in disease suppression by organic matter application and that Ca and soil biota play certain roles in the suppression under the influence of soil pH.     

Variations in soil characteristics affecting the occurrence of Aphanomyces root rot of sugar beet - Risk evaluation and disease control

Damping off and chronic root rot of sugar beet caused by Aphanomyces cochlioides is a major constraint in cultivation of sugar beet, with occurrence of the disease in Sweden being concentrated to specific areas. This study examined soil factors that can be used for risk assessment of Aphanomyces root rot. Soils from 134 field plots were assessed over three years for Aphanomyces root rot potential in bioassays and analysed for easily measured soil factors such as soluble nutrients, pH and soil electrical conductivity (EC). Classification of the field plots into four groups with increasing disease severity index (DSI) according to the bioassay revealed that the group with the lowest DSI (<39) had an average soil calcium (Ca) content of 430 mg/100 g and a soil EC of 1.12 mS/cm, which were significantly higher than in the groups with DSI >40. From these results, we concluded that soil Ca concentration is an easily measured factor that can be used to identify soils with an increased risk of Aphanomyces root rot. We suggest that the Ca content should be above 250 mg Ca/100 g soil to avoid problems with Aphanomyces root rot in sugar beet. To gain a more thorough understanding of the geographical variation in Aphanomyces root rot and its connection to the geological origin of the soils, a number of other soil factors were analysed in the field plots, including clay mineralogy, CEC, and particle size distribution. Aphanomyces root rot was very rare in soils with a high proportion of smectite and vermiculite relative to illite and kaolin minerals, here predominantly calcareous soils developed on clay till in south-western Scania.     

Soil texture and irrigation influence the transport and the development of Pasteuria penetrans, a bacterial parasite of root-knot nematodes

The transport of the spores of Pasteuria penetrans was studied in three contrasted textured soils (a sandy, a sandy-clay and a clay soils), cultivated with tomato, inoculated with juveniles of Meloidogyne javanica and watered with 25 or 150 mm day⁻¹. One month after inoculation of the nematodes, 53% of the spores inoculated were leached by water flow in the sandy soil but only 14% in the sandy-clay soil and 0.1% in the clay soil. No nematodes survived in the clay soil, while the population was multiplied both in the sandy and in the sandy-clay soils. But juveniles of M. javanica were more infected by P. penetrans in the sandy-clay soil than in the sandy soil. Comparing different combinations of bare soils containing 1.1-57% of clay showed that the best spore percolation and retention balance occurred in soils amended with 10-30% clay. However, the spore recoveries decreased when the soil was enriched with more than 30% clay. The role of clay particles on the extractability of spores and on their availability to attach to the nematode cuticle in the soil is discussed.     

Response of soil microbial communities to compost amendments

Soil organic matter is considered as a major component of soil quality because it contributes directly or indirectly to many physical, chemical and biological properties. Thus, soil amendment with composts is an agricultural practice commonly used to improve soil quality and also to manage organic wastes. We evaluated in laboratory scale experiments the response of the soilborne microflora to the newly created soil environments resulting from the addition of three different composts in two different agricultural soils under controlled conditions. At a global level, total microbial densities were determined by classical plate count methods and global microbial activities were assessed by measuring basal respiration and substrate induced respiration (SIR). Soil suppressiveness to Rhizoctonia solani diseases was measured through bioassays performed in greenhouses. At a community level, the modifications of the metabolic and molecular structures of bacterial and fungal communities were assessed. Bacterial community level physiological profiles (CLPP) were determined using Biolog™ GN microtiter plates. Bacterial and fungal community structures were investigated using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Data sets were analyzed using analysis of variance and ordination methods of multivariate data. The impact of organic amendments on soil characteristics differed with the nature of the composts and the soil types. French and English spent mushroom composts altered all the biological parameters evaluated in the clayey soil and/or in the sandy silty clay soil, while green waste compost did not modify either bacterial and fungal densities, SIR values nor soil suppressiveness in any of the soils. The changes in bacterial T-RFLP fingerprints caused by compost amendments were not related to the changes in CLPP, suggesting the functional redundancy of soil microorganisms. Assessing the density, the activity and the structure of the soil microflora allowed us not only to detect the impact of compost amendment on soil microorganisms, but also to evaluate its effect at a functional level through the variation of soil disease suppressiveness. Differences in disease suppressiveness were related to differences in chemical composition, in availability of nutrients at short term and in microbial composition due to both incorporation and stimulation of microorganisms by the compost amendments.     

Soil feedback effects to the foredune grass Ammophila arenaria by endoparasitic root-feeding nematodes and whole soil communities

In coastal foredunes, the grass Ammophila arenaria develops a soil community that contributes to die-back and replacement by later successional plant species. Root-feeding nematodes and pathogenic soil microorganisms are involved in this negative feedback. Regular burial by wind-blown beach sand results in vigorous growth of A. arenaria, probably because of enabling a temporary escape from negative soil feedback. Here, we examine the role of root-feeding nematodes as compared to the whole soil community in causing negative feedback to A. arenaria. We performed a 3-year sand burial experiment in the field and every year we determined the feedback of different soil communities to plant growth in growth chamber bioassays.In the field, we established A. arenaria in tubes with beach sand, added three endoparasitic root-feeding nematode species (Meloidogyne maritima, Heterodera arenaria and Pratylenchus penetrans) or root zone soil to the plants, and created series of ceased and continued sand burial. During three subsequent years, plant biomass was measured and numbers of nematodes were counted. Every year, bioassays were performed with the field soils and biomass of seed-grown A. arenaria plants was measured to determine the strength of feedback of the established soil communities to the plant.In the field, addition of root zone soil had a negative effect on biomass of buried plants. In the bioassays, addition of root zone soil also reduced the biomass of newly planted seedlings, however, only in the case when the field plants had not been buried with beach sand. Addition of the three endoparasitic root-feeding nematodes did not influence plant biomass in the field and in the bioassays. Our results strongly suggest that the negative feedback to A. arenaria is not due to the combination of the three endoparasitic nematodes, but to other components in the soil community, or their interactions with the nematodes.