Didymella pinodella: An Important Pea Root Rot Pathogen in France to Watch Out For?

Root rot pathogens restrict pea and wheat production globally. In the EU, pea and pea-based cereal mixtures are being promoted; however, root rot pathogen dynamics in such mixtures are poorly understood. Winter pea and wheat were grown either in pure stands or in mixtures in the field in western France, and the severity of root rot in pea, wheat, and their mixtures, as well as the key pathogens associated with these crops, were assessed. Disease severity was moderate in pea and low in wheat, with no effect of sowing pattern. Didymella pinodella, a previously unreported pathogen in the pea-root rot complex in France, emerged as the most dominant pathogen in pea. It also occurred in low frequencies in wheat. Subsequent greenhouse aggressiveness tests showed that ten of the commonly grown pea cultivars in France lack resistance to D. pinodella. Among the Fusarium spp. isolated, F. avenaceum was the most frequent, occurring at similar frequencies in pea and wheat. In conclusion, D. pinodella may be an important pea root rot pathogen in France and there is a lack of resistance in the tested pea cultivars. In addition, F. avenaceum is a shared pathogen of wheat and pea.

Polydomus karssenii gen. nov. sp. nov. is a dark septate endophyte with a bifunctional lifestyle parasitising eggs of plant parasitic cyst nematodes (Heterodera spp.)

In this study fungal strains were investigated, which had been isolated from eggs of the cereal cyst nematode Heterodera filipjevi, and roots of Microthlaspi perfoliatum (Brassicaceae). The morphology, the interaction with nematodes and plants and the phylogenetic relationships of these strains originating from a broad geographic range covering Western Europe to Asia Minor were studied. Phylogenetic analyses using five genomic loci including ITSrDNA, LSUrDNA, SSUrDNA, rpb2 and tef1-α were carried out. The strains were found to represent a distinct phylogenetic lineage most closely related to Equiseticola and Ophiosphaerella, and Polydomus karssenii (Phaeosphaeriaceae, Pleosporales) is introduced here as a new species representing a monotypic genus. The pathogenicity tests against nematode eggs fulfilled Koch's postulates using in vitro nematode bioassays and showed that the fungus could parasitise its original nematode host H. filipjevi as well as the sugar beet cyst nematode H. schachtii, and colonise cysts and eggs of its hosts by forming highly melanised moniliform hyphae. Light microscopic observations on fungus-root interactions in an axenic system revealed the capacity of the same fungal strain to colonise the roots of wheat and produce melanised hyphae and microsclerotia-like structure typical for dark septate endophytes. Confocal laser scanning microscopy further demonstrated that the fungus colonised the root cells by predominant intercellular growth of hyphae, and frequent formation of appressorium-like as well as penetration peg-like structures through internal cell walls surrounded by callosic papilla-like structures. Different strains of the new fungus produced a nearly identical set of secondary metabolites with various biological activities including nematicidal effects irrespective of their origin from plants or nematodes.

Farming system effects on root rot pathogen complex and yield of faba bean (vicia faba) in Germany

A survey across Germany was undertaken from 2016-2019 to evaluate effects of management system (organic vs conventional), pedo-climatic conditions and crop rotation history on faba bean root health status, diversity of major root rot pathogens and yield. Root rot incidence was generally low and there was no effect of the management system on the spectrum of pathogens isolated. Among the most common fungal species identified, frequencies of Fusarium redolens and Didymella pinodella were significantly higher in roots from organic fields compared with conventional and lower was observed for F. avenaceum, F. tricinctum and F. culmorum. Faba bean roots were colonized at similar rates by F. equiseti and the members of the F. oxysporum (FOSC) and F. solani (FSSC) species complexes in both management systems. Almost no legumes had been grown in the 5-11 years preceding the conventional faba beans surveyed while legumes had almost always been present during this period in the organic fields. This difference in rotational histories between the farming systems led to apparent cropping systems effects on the isolation frequencies of several species. For example, D. pinodella was ubiquitous in organic fields with a high frequency of legumes in the rotations but much rarer and often absent in conventional fields. Pedo-climatic conditions, particularly cool conditions at sowing and plant emergence and/or during the vegetative season favored most of the most prevalent Fusarium species identified in this study. In organic systems, yields correlated negatively with D. pinodella and F. redolens frequencies whereas higher levels of F. tricintum in faba bean roots had a positive correlation with yield. In conventional systems, faba bean yields depended more on the total precipitation before sowing and during the main growing season but were also negatively correlated with the frequencies of FOSC and F. culmorum. Phylogenetic analysis based on the TEF1 alpha locus indicated that the FSSC isolates mainly belonged to the F. pisi lineage. In contrast, the FOSC isolates were placed in 9 different lineages, with a conspicuous dominance of F. libertatis that has until now not been associated with any leguminous host.

Increased Resilience of Peas Toward Root Rot Pathogens Can Be Predicted by the Nematode Metabolic Footprint

Legumes are important drivers of soil fertility, however, their frequent use in rotations fosters long-lived soil-borne pathogens that can seriously compromise legume root health and nitrogen fixation. To overcome this, the current study aims at improving the general soil suppressiveness toward pests and diseases by agroecosystem management that can be predicted by nematode-based bioindicators. Two long-term organically managed agroecosystems comparing plow and shallow non-inversion tillage were analyzed for free-living nematode communities. Soils out of these agroecosystems were evaluated further in a greenhouse assay for their ability to suppress pea root rot caused by Didymella pinodella, Fusarium avenaceum, and F. redolens. There was a general trend for higher levels of pea root rot disease severity following inoculations with single pathogens, however, this effect was heterogeneous among experiments and tillage systems. This was mainly due to an already very high resident population of D. pinodella in soil and the presence of seed-borne F. oxysporum determined by their high incidence in pea roots irrespective of the soil and inoculated pathogens. Additional inoculation with D. pinodella, for example, resulted in only 8.5% biomass reduction compared to the non-inoculated control, in both tillage systems. Similar biomass losses were recorded in non-inversion tilled soils inoculated with F. redolens. When analyzed across inoculation treatments, the pea root rot disease severity was only slightly reduced in non-inversion tilled soils when compared to the plough systems (11% in Exp 1 and, 9% in Exp 2), however in both experiments non-inversion tillage resulted in greater pea biomass (33 and 19% in Exp1 and 2, respectively). Furthermore, the metabolic, enrichment, and bacterivore carbon footprints of nematodes were 88, 81, and 97% higher, respectively, in the non-inversion tilled soils compared to the plough. The metabolic carbon footprint of nematodes correlated negatively with pea root rot disease severity (rho = −0.71, p = 0.047). Hence, non-inversion tillage was effective in controlling pea root rot. The use of nematode metabolic footprints for predicting soil health should be extended for various agroecosystems aiming for its general use in evaluating effects of agroecosystem management through researchers and potentially farm management advisors.

Mixture × Genotype Effects in Cereal/Legume Intercropping

Cropping system diversification through annual intercropping provides a pathway for agricultural production with reduced inputs of fertilizer and pesticides. While several studies have shown that intercrop performance depends on the genotypes used, the available evidence has not been synthesized in an overarching analysis. Here, we review the effects of genotypes in cereal/legume intercropping systems, showing how genotype choice affects mixture performance. Furthermore, we discuss the mechanisms underlying the interactions between genotype and cropping system (i.e., sole cropping vs. intercropping). Data from 69 articles fulfilling inclusion criteria were analyzed, out of which 35 articles reported land equivalent ratio (LER), yielding 262 LER data points to be extracted. The mean and median LER were 1.26 and 1.24, respectively. The extracted genotype × cropping system interaction effects on yield were reported in 71% out of 69 publications. Out of this, genotype × cropping system interaction effects were significant in 75%, of the studies, whereas 25% reported non-significant interactions. The remaining studies did not report the effects of genotype × cropping system. Phenological and morphological traits, such as differences in days to maturity, plant height, or growth habit, explained variations in the performance of mixtures with different genotypes. However, the relevant genotype traits were not described sufficiently in most of the studies to allow for a detailed analysis. A tendency toward higher intercropping performance with short cereal genotypes was observed. The results show the importance of genotype selection for better in cereal/legume intercropping. This study highlights the hitherto unrevealed aspects of genotype evaluation for intercropping systems that need to be tackled. Future research on genotype effects in intercropping should consider phenology, root growth, and soil nutrient and water acquisition timing, as well as the effects of weeds and diseases, to improve our understanding of how genotype combination and breeding may help to optimize intercropping systems.

Genome-wide association study reveals white lupin candidate gene involved in anthracnose resistance

GWAS identifies candidate gene controlling resistance to anthracnose disease in white lupin. White lupin (Lupinus albus L.) is a promising grain legume to meet the growing demand for plant-based protein. Its cultivation, however, is severely threatened by anthracnose disease caused by the fungal pathogen Colletotrichum lupini. To dissect the genetic architecture for anthracnose resistance, genotyping by sequencing was performed on white lupin accessions collected from the center of domestication and traditional cultivation regions. GBS resulted in 4611 high-quality single-nucleotide polymorphisms (SNPs) for 181 accessions, which were combined with resistance data observed under controlled conditions to perform a genome-wide association study (GWAS). Obtained disease phenotypes were shown to highly correlate with overall three-year disease assessments under Swiss field conditions (r > 0.8). GWAS results identified two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161 encoding a RING zinc-finger E3 ubiquitin ligase which is potentially involved in plant immunity. Population analysis showed a remarkably fast linkage disequilibrium decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarcity of modern breeding efforts in white lupin. Together with 15 highly resistant accessions identified in the resistance assay, our findings show promise for further crop improvement. This study provides the basis for marker-assisted selection, genomic prediction and studies aimed at understanding anthracnose resistance mechanisms in white lupin and contributes to improving breeding programs worldwide.

Supply Chain Perspectives on Breeding for Legume-Cereal Intercrops

Compared to sole crops, intercropping-especially of legumes and cereals-has great potential to improve crop yield and resource use efficiency, and can provide many other ecosystem services. However, the beneficial effects of intercrops are often greatly dependent on the end use as well as the specific species and genotypes being co-cultivated. In addition, intercropping imposes added complexity at different levels of the supply chain. While the need for developing crop genotypes for intercropping has long been recognized, most cultivars on the market are optimized for sole cropping and may not necessarily perform well in intercrops. This paper aims to place breeding targets for intercrop-adapted genotypes in a supply chain perspective. Three case studies of legumes and cereals intercropped for human consumption are used to identify desirable intercrop traits for actors across the supply chains, many of which are not targeted by traditional breeding for sole crops, including certain seed attributes, and some of which do not fit traditional breeding schemes, such as breeding for synchronized maturity and species synergies. Incorporating these traits into intercrop breeding could significantly reduce complexity along the supply chain. It is concluded that the widespread adoption and integration of intercrops will only be successful through the inclusion and collaboration of all supply chain actors, the application of breeding approaches that take into account the complexity of intercrop supply chains, and the implementation of diversification strategies in every process from field to fork.

Appropriate sampling methods and statistics can tell apart fraud from pesticide drift in organic farming

Pesticide residues are much lower in organic than in conventional food. The article summarizes the available residue data from the EU and the U.S. organic market. Differences between samples from several sources suggest that organic products are declared conventional, when they have residues—but the origin of the residues is not always investigated. A large number of samples are being tested by organic certifiers, but the sampling methods often do not allow to determine if such residues stem from prohibited pesticide use by organic farmers, from mixing organic with conventional products, from short-range spray-drift from neighbour farms, from the ubiquitous presence of such substances due to long-distance drift, or from other sources of contamination. Eight case studies from different crops and countries are used to demonstrate that sampling at different distances from possible sources of short-distance drift in most cases allows differentiating deliberate pesticide application by the organic farmer from drift. Datasets from 67 banana farms in Ecuador, where aerial fungicide spraying leads to a heavy drift problem, were subjected to statistical analysis. A linear discriminant function including four variables was identified for distinguishing under these conditions application from drift, with an accuracy of 93.3%.

A High-Throughput Phenotyping Tool to Identify Field-Relevant Anthracnose Resistance in White Lupin

The seed- and air-borne pathogen Colletotrichum lupini, the causal agent of lupin anthracnose, is the most important disease in white lupin (Lupinus albus) worldwide and can cause total yield loss. The aims of this study were to establish a reliable high-throughput phenotyping tool to identify anthracnose resistance in white lupin germplasm and to evaluate a genomic prediction model, accounting for previously reported resistance quantitative trait loci, on a set of independent lupin genotypes. Phenotyping under controlled conditions, performing stem inoculation on seedlings, showed to be applicable for high throughput, and its disease score strongly correlated with field plot disease assessments (r = 0.95, P < 0.0001) and yield (r = -0.64, P = 0.035). Traditional one-row field disease phenotyping showed no significant correlation with field plot disease assessments (r = 0.31, P = 0.34) and yield (r = -0.45, P = 0.17). Genomically predicted resistance values showed no correlation with values observed under controlled or field conditions, and the parental lines of the recombinant inbred line population used for constructing the prediction model exhibited a resistance pattern opposite to that displayed in the original (Australian) environment used for model construction. Differing environmental conditions, inoculation procedures, or population structure may account for this result. Phenotyping a diverse set of 40 white lupin accessions under controlled conditions revealed eight accessions with improved resistance to anthracnose. The standardized area under the disease progress curves (sAUDPC) ranged from 2.1 to 2.8, compared with the susceptible reference accession with a sAUDPC of 3.85. These accessions can be incorporated into white lupin breeding programs. In conclusion, our data support stem inoculation-based disease phenotyping under controlled conditions as a time-effective approach to identify field-relevant resistance, which can now be applied to further identify sources of resistance and their underlying genetics.

Biology, pathotype, and virulence of Globodera rostochiensis populations from Kenya

The potato cyst nematodes (PCN), Globodera rostochiensis (Woll.) and G. pallida (Stone), are important pests of potato globally. Due to their extensive damage potential and the challenge of managing them, these nematodes are under strict regulations in many countries; however, despite these regulations, PCN continue to spread into new areas and countries. In Kenya, G. rostochiensis was first reported in 2015 and G. pallida was reported three years later, both in Nyandarua County. Research was conducted to characterize the biology, pathotype, and virulence of G. rostochiensis populations from Kenya in glasshouse and laboratory studies. The development of G. rostochiensis was assessed in roots of susceptible potato ‘Désirée’ and resistant ‘Laura’ carrying the H1 resistance gene. The ‘HAR1’ population from Kenya and ‘Ecosse’ from Germany were not able to produce females in the roots of the resistant potato ‘Laura’. The rate of root penetration by G. rostochiensis juveniles did not differ (p > 0.05) between populations and cultivars. However, in the resistant cultivar, juveniles developed into males only. A total of 736 cumulative degree-days at 6°C base temperature (DD₆) were required by ‘HAR1’ to complete the life cycle on ‘Désirée’, whereas ‘Ecosse’ completed the life cycle within 645 DD₆. The Kenyan populations lacked obligatory diapause and high numbers of juveniles hatched immediately after maturity. Consequently, the Kenyan populations had the potential to complete up to three reproduction cycles in less than a year. On selected potato cultivars, the populations from Kenya failed to reproduce on 10 out of 13 commercial cultivars tested. The 10 cultivars carried the H1 resistance gene, which suggests that the G. rostochiensis populations tested belong to the Ro1/4 pathotype group. The virulence of the G. rostochiensis populations from Kenya did not differ from that of the standard reference population ‘Ecosse’ and therefore can be effectively managed with the commercially available potato cultivars carrying the H1 resistance gene.

Population dynamics and host range of Paratylenchus bukowinensis

The plant-parasitic nematode, Paratylenchus bukowinensis, occurs ubiquitously in arable fields. Economic damage has been reported from, among others, cabbage, parsley, and celery, but other crops might be affected as well. Management of P. bukowinensis is difficult. Resistant cultivars are not available and chemical control is prohibited in most European countries. In addition, sustainable management is often hindered by a lack of information regarding the biology and host range of P. bukowinensis. To improve the management of P. bukowinensis in the future, a good understanding of the life cycle and host plant-nematode interactions is required. We investigated the host range, life cycle and natural decline of P. bukowinensis in five glasshouse experiments. A total of 26 plant genotypes comprising 22 plant species from eight plant families were studied. Plant species within the families Brassicaceae and Apiaceae were confirmed as good hosts, while plant species within the families Fabaceae, Asteraceae, Amaryllidaceae, Solanaceae, Amaranthaceae and Poaceae can be considered non-hosts or poor hosts. In roots of good hosts, P. bukowinensis completed its life cycle within 3-4 weeks. In the absence of a host plant, P. bukowinensis declined by 40% within the first 4 weeks, but then remained at this level until the experiment was terminated after 14 weeks. Overall, the host range of P. bukowinensis seems to be smaller than for other species within the genus Paratylenchus, such as P. projectus or P. similis. Control of P. bukowinensis using crop rotation should be feasible by rotating good hosts belonging to the families Brassicaceae and Apiaceae with non-hosts or poor hosts.

Effects of ten years organic and conventional farming on early seedling traits of evolving winter wheat composite cross populations

Early vigour traits of wheat composite cross populations (CCPs) based on high yielding (Y) or high quality (Q) or Y*Q varietal intercross evolving under organic or conventional conditions in parallel populations were studied hydroponically. To eliminate storage and year effects, frozen F6, F10, F11 and F15 seeds were multiplied in one field, resulting in the respective Fx.1 generations. This eliminated generation and growing system effects on seed size for the F6.1 F10.1 and F15.1. Due to a severe winter kill affecting the F11, the generation effect persisted, leading to larger seeds and markedly different seedling traits in the F11.1 compared to the F10.1 and F15.1. Seedling traits were similar among parallel populations. Shoot length and weight increased in both systems until the F11.1 across farming systems and remained constant thereafter. Over time, seminal root length and root weight of organic CCPs increased and total- and specific- root length decreased significantly compared to the conventional CCPs. Rooting patterns under organic conditions suggests better ability to reach deeper soil nutrients. In both systems, Q and YQ CCPs were more vigorous than Y CCPs, confirming genetic differences among populations. Overall, heterogeneous populations appear very plastic and selection pressure was stronger in organic systems.

One Health - Cycling of diverse microbial communities as a connecting force for soil, plant, animal, human and ecosystem health

The One Health concept proposes that there is a connection between human, animal and environmental health. Plants and their health are not explicitly included. In this review, we broaden the One Health concept to include soil, plant, animal and ecosystem health. We argue that the health conditions of all organisms in an ecosystem are interconnected through the cycling of subsets of microbial communities from the environment (in particular the soil) to plants, animals and humans, and back into the environment. After an introduction on health concepts, we present examples of community stability and resilience, diversity and interconnectedness as affected by pollutants, and integrity of nutrient cycles and energy flows. Next, we explain our concept of microbial cycling in relation to ecosystem health, and end with examples of plant and animal disease outbreaks in relation to microbial community composition and diversity. We conclude that we need a better understanding of the role of interconnected microbiomes in promoting plant and animal health and possible ways to stimulate a healthy, diverse microbiome throughout human-dominated ecosystems. We suggest that it is essential to maintain ecosystem and soil health through diversification of plant communities and oligotrophication of managed ecosystems.

Cover crops and compost prevent weed seed bank buildup in herbicide-free wheat-potato rotations under conservation tillage

Weeds are a major constraint affecting crop yields in organic farming and weed seed bank analysis can be an important tool for predicting weed infestation and assessing farming system sustainability.We compared the weed seed banks two and four years after transition from conventional to reduced tillage in organically managed winter wheat-potato cropping sequences in two replicated field trials. Experimental factors were either conventional (CT) with moldboard (25 cm) or reduced tillage (RT) with chisel ploughing (5-15 cm). Dead mulch (8-10 cm), consisting of rye-pea or triticale-vetch mixtures, was additionally applied to potatoes in the RT system. In both systems, one-half of the plots received 5 t (ha/year) dry matter of a commercially sold yard waste compost as an organic amendment. Furthermore, subsidiary crops were grown in both systems, either as legume living mulches undersown in wheat or as cover crops sown after wheat. Prior to sowing the wheat and after potatoes, the soil seed bank from 0 to 12.5 and from 12.5 to 25 cm was sampled and assessed in an unheated glasshouse over nine months.The initial weed seed bank size in the topsoil was uniform (4,420 seedlings m-2). Two years later, wheat-associated weeds, such as Galium aparine, Lamium spp., and Myosotis arvensis, were 61% higher on average in RT than in CT. This was independent of subsidiary crops used. In contrast, Chenopodium album, a potato-associated weed that depends on intensive tillage, was reduced by 15% in the mulched RT system compared to CT. When RT was combined with cover crops and compost application, the seed bank did not differ significantly from the CT system.We conclude that subsidiary crops, mulches, and potentially compost are important management tools that contribute to the success of RT in herbicide-free cereal-based systems in temperate climates.

Reproduction of Globodera pallida on tissue culture-derived potato plants and their potential use in resistance screening process

Globodera pallida infestation on potato is responsible for huge yield losses globally. Screening of potato germplasm for resistance to the nematode at the early stages of a breeding programme can significantly enhance resistance-based management. This study assessed the suitability of tissue culture (TC)-derived potato plants as screening material for resistance to G. pallida. Reproduction of the nematode on TC plants was similar to the reproduction on tuber- and eye-plug-derived plants. The pot volume, inoculum density and inoculation time had a significant effect on the reproduction. A positive correlation was found between the mean number of white females on the root surface and the final number of nematode cysts after extraction. Resistance ranking using TC plants and the tubers yielded comparable results, thus justifying the use of TC in the screening process. Tissue culture plants have the potential of speeding up the screening process and reducing resource requirements, thus lowering breeding cost.

Advocating a need for suitable breeding approaches to boost integrated pest management: a European perspective

Currently, European farmers do not have access to sufficient numbers and diversity of crop species/varieties. This prevents them from designing cropping systems more resilient to abiotic and biotic stresses. Crop diversification is a key lever to reduce pest (pathogens, animal pests and weeds) pressures at all spatial levels from fields to landscapes. In this context, plant breeding should consist of: (1) increased efforts in the development of new or minor crop varieties to foster diversity in cropping systems, and (2) focus on more resilient varieties showing local adaptation. This new breeding paradigm, called here 'breeding for integrated pest management (IPM)', may boost IPM through the development of cultivars with tolerance or resistance to key pests, with the goal of reducing reliance on conventional pesticides. At the same time, this paradigm has legal and practical implications for future breeding programs, including those targeting sustainable agricultural systems. By putting these issues into the context, this article presents the key outcomes of a questionnaire survey and experts' views expressed during an EU workshop entitled 'Breeding for IPM in sustainable agricultural systems'. © 2017 Society of Chemical Industry.

Two new species of the Fusarium solani species complex isolated from compost and hibiscus (Hibiscus sp.)

Two new species in the Fusarium solani species complex (FSSC) are described and introduced. The new taxa are represented by German isolates CBS 142481 and CBS 142480 collected from commercial yard waste compost and vascular tissue of a wilting branch of hibiscus, respectively. The phylogenetic relationships of the collected strains to one another and within the FSSC were evaluated based on DNA sequences of 6 gene loci. Due to the limited sequence data available for reference strains in GenBank, however, a multi-gene phylogenetic analysis included partial sequences for the internal transcribed spacer region and intervening 5.8S nrRNA gene (ITS), translation elongation factor 1-alpha (tef1) and the RNA polymerase II second largest subunit (rpb2). Morphological and molecular phylogenetic data independently showed that these strains are distinct populations of the FSSC, nested within Clade 3. Thus, we introduce Fusarium stercicola and Fusarium witzenhausenense as novel species in the complex. In addition, 19 plant species of 7 legume genera were evaluated for their potential to host the newly described taxa. Eighteen plant species were successfully colonized, with 6 and 9 of these being symptomatic hosts for F. stercicola and F. witzenhausenense, respectively. As plants of the family Fabaceae are very distant to the originally sourced material from which the new taxa were recovered, our results suggest that F. stercicola and F. witzenhausenense are not host-specific and are ecologically fit to sustain stable populations in variety of habitats.

Environmental and health effects of the herbicide glyphosate

The herbicide glyphosate, N-(phosphonomethyl) glycine, has been used extensively in the past 40years, under the assumption that side effects were minimal. However, in recent years, concerns have increased worldwide about the potential wide ranging direct and indirect health effects of the large scale use of glyphosate. In 2015, the World Health Organization reclassified glyphosate as probably carcinogenic to humans. A detailed overview is given of the scientific literature on the movement and residues of glyphosate and its breakdown product aminomethyl phosphonic acid (AMPA) in soil and water, their toxicity to macro- and microorganisms, their effects on microbial compositions and potential indirect effects on plant, animal and human health. Although the acute toxic effects of glyphosate and AMPA on mammals are low, there are animal data raising the possibility of health effects associated with chronic, ultra-low doses related to accumulation of these compounds in the environment. Intensive glyphosate use has led to the selection of glyphosate-resistant weeds and microorganisms. Shifts in microbial compositions due to selective pressure by glyphosate may have contributed to the proliferation of plant and animal pathogens. Research on a link between glyphosate and antibiotic resistance is still scarce but we hypothesize that the selection pressure for glyphosate-resistance in bacteria could lead to shifts in microbiome composition and increases in antibiotic resistance to clinically important antimicrobial agents. We recommend interdisciplinary research on the associations between low level chronic glyphosate exposure, distortions in microbial communities, expansion of antibiotic resistance and the emergence of animal, human and plant diseases. Independent research is needed to revisit the tolerance thresholds for glyphosate residues in water, food and animal feed taking all possible health risks into account.

Roots of symptom-free leguminous cover crop and living mulch species harbor diverse Fusarium communities that show highly variable aggressiveness on pea (Pisum sativum)

Leguminous cover crop and living mulch species show not only great potential for providing multiple beneficial services to agro-ecosystems, but may also present pathological risks for other crops in rotations through shared pathogens, especially those of the genus Fusarium. Disease severity on roots of subterranean clover, white clover, winter and summer vetch grown as cover crop and living mulch species across five European sites as well as the frequency, distribution and aggressiveness to pea of Fusarium spp. recovered from the roots were assessed in 2013 and 2014. Disease symptoms were very low at all sites. Nevertheless, out of 1480 asymptomatic roots, 670 isolates of 14 Fusarium spp. were recovered. The most frequently isolated species in both years from all hosts were F. oxysporum and F. avenaceum accounting for 69% of total isolation percentage. They were common at the Swiss, Italian and German sites, whereas at the Swedish site F. oxysporum dominated and F. avenaceum occurred only rarely. The agressiveness and effect on pea biomass were tested in greenhouse assays for 72 isolates of six Fusarium species. Isolates of F. avenaceum caused severe root rot symptoms with mean severity index (DI) of 82 and 74% mean biomass reduction compared to the non-inoculated control. Fusarium oxysporum and F. solani isolates were higly variable in agressiveness and their impact on pea biomass. DI varied between 15 and 50 and biomass changes relative to the non-inoculated control -40% to +10%. Isolates of F. tricinctum, F. acuminatum and F. equiseti were non to weakly agressive often enhancing pea biomass. This study shows that some of the major pea pathogens are characterized by high ecological plasticity and have the ability to endophytically colonize the hosts studied that thus may serve as inoculum reservoir for susceptible main legume grain crops such as pea.

The 'forma specialis' issue in Fusarium: A case study in Fusarium solani f. sp. pisi

The Fusarium solani species complex (FSSC) has been studied intensively but its association with legumes, particularly under European agro-climatic conditions, is still poorly understood. In the present study, we investigated phylogenetic relationships and aggressiveness of 79 isolates of the FSSC collected from pea, subterranean clover, white clover and winter vetch grown under diverse agro-climatic and soil conditions within Temperate and Mediterranean Europe. The isolates were characterized by sequencing tef1 and rpb2 loci and by greenhouse aggressiveness assays. The majority of the isolates belonged to two lineages: the F. pisi comb. nov. lineage (formerly F. solani f. sp. pisi) mainly accommodating German and Swiss isolates, and the Fusisporium (Fusarium) solani lineage accommodating mainly Italian isolates. Based on the results of aggressiveness tests on pea, most of the isolates were classified as weakly to moderately aggressive. In addition, using one model strain, 62 accessions of 10 legume genera were evaluated for their potential to host F. pisi, the species known mainly as a pathogen of pea. A total of 58 accessions were colonized, with 25 of these being asymptomatic hosts. These results suggest a broad host range for F. pisi and challenge the forma specialis naming system in Fusarium.

Oilseed radish/black oat subsidiary crops can help regulate plant-parasitic nematodes under non-inversion tillage in an organic wheat-potato rotation

Soil conservation is one of the major challenges for agriculture in the 21st century. For this reason, non-inversion tillage systems including subsidiary crops have become popular over the last three decades in Europe. However, the adoption of new agricultural practices may change the diversity and abundance of certain pests and diseases. For example, plant-parasitic nematodes that are major threats towards cultivated plants may be promoted if good hosts, such as certain subsidiary crops and weeds, occur more frequently. The indigenous plant-parasitic nematode fauna under organic farming systems is already adapted to diverse crop rotations and usually dominated by nematodes with broad host ranges. These may be further enhanced in organic farming systems if non-inversion tillage is introduced, which generally increases the abundance and biomass of certain weeds. We evaluated the early effects of non-inversion tillage and subsidiary crops in an organic wheat-potato rotation on plant-parasitic nematodes in two field experiments in two successive years. The total densities of plant-parasitic nematodes increased from an initial 1260 nematodes (100 ml soil)−1 at the start of the experiment to 1850 and 1700 nematodes (100 ml soil)−1 after wheat under non-inversion and conventional tillage, respectively. Plant-parasitic nematode densities then decreased on average to 1100 and 560 nematodes (100 ml soil)−1 after subsidiary crops and potatoes, respectively. Parasitic nematode densities tended to be higher under non-inversion than conventional tillage, except where oilseed radish and black oats had been used as cover crops. For the latter, no differences between tillage treatments occurred. In the second experiment, about 1700 free-living nematodes (100 ml soil)−1 were found under conventional tillage without mulch while under reduced tillage with mulch their numbers were significantly higher at 3100 nematodes (100 ml soil)−1. We conclude that an appropriate choice of subsidiary crops can be an important management factor for the long term sustainability of non-inversion tillage systems.

Plant Diseases and Management Approaches in Organic Farming Systems

Organic agriculture has expanded worldwide. Numerous papers were published in the past 20 years comparing plant diseases in organic and conventional crops. Root diseases are generally less severe owing to greater soil health, whereas some foliar diseases can be problematic in organic agriculture. The soil microbial community and nitrogen availability play an important role in disease development and yield. Recently, the focus has shifted to optimizing organic crop production by improving plant nutrition, weed control, and plant health. Crop-loss assessment relating productivity to all yield-forming and -reducing factors would benefit organic production and sustainability evaluation.

Plant disease management in organic farming systems

Organic farming (OF) has significantly increased in importance in recent decades. Disease management in OF is largely based on the maintenance of biological diversity and soil health by balanced crop rotations, including nitrogen-fixing and cover crops, intercrops, additions of manure and compost and reductions in soil tillage. Most soil-borne diseases are naturally suppressed, while foliar diseases can sometimes be problematic. Only when a severe disease outbreak is expected are pesticides used that are approved for OF. A detailed overview is given of cultural and biological control measures. Attention is also given to regulated pesticides. We conclude that a systems approach to disease management is required, and that interdisciplinary research is needed to solve lingering disease problems, especially for OF in the tropics. Some of the organic regulations are in need of revision in close collaboration with various stakeholders.

Resilience as a universal criterion of health

To promote and maintain health in agricultural and food systems, appropriate criteria are needed for the description and assessment of the health of soils, plants, animals, humans and ecosystems. Here we identify the concept of resilience as a universally applicable and fundamentally important criterion of health in all relevant areas of agriculture. We discuss definitions of resilience for soils, plants, animals, humans and ecosystems, and explore ways in which resilience can be applied as a criterion of health in different agricultural contexts. We show how and why resilience can be seen as a key criterion of health. Based on this, we discuss how resilience can be used as a link between soil, plant, animal, human and ecosystem health. Finally, we highlight four key areas for future research on resilience in agriculture, namely spatial and temporal scaling of resilience; effects of diversity; the role of networks for resilience; and stakeholder involvement.

Pathogenic Variability of Pyricularia grisea from the High- and Mid-Elevation Zones of Bhutan

ABSTRACT Thirty isolates of P. griseacollected from rice during a blast epidemic in 1995 in the high (1,800 to 2,600 m) and middle (1,200 to 1,800 m) elevations of Bhutan and 80 isolates collected from one rice cultivar from two high- and two mid-elevation sites in 1996 were analyzed for virulence. Differential varieties were indica CO39, with five near-isogenic lines (NILs) for resistance genes in the genetic background of CO39, and japonica Lijiangxintuanheigu (LTH), with five NILs for LTH. Twelve selected Bhutanese landraces also were studied. In addition, 10 blast nurseries consisting of the NIL sets, important local landraces, and representatives of international differential groups were established in the 1996 and 1997 growing seasons in the mid- and high-elevation agroecological zones. The 110 isolates were differentiated into 53 pathotypes based on the 2 NIL sets. Thirteen isolates were avirulent on all of the NILs but were compatible with some landraces. Several isolates were able to attack one of the NILs of CO39 but not CO39. These results strongly suggest that both CO39 and LTH possess previously unidentified resistance. The landraces were not uniform in their reactions to the isolates. When a reaction index taking into account all individual plant reactions was used, isolates that had been assigned to the same pathotype could be further differentiated, indicating that the NIL sets could not completely discriminate virulences in Bhutanese P. grisea populations. In the trap nurseries, disease was always present in the middle elevations, but disease was very low during July 1996 in the high elevations and only present during August and September 1997. Almost all varietal groups were more frequently attacked in the middle than in the high elevations, indicating that the virulence spectrum is wider and the conduciveness of the environment is greater in the middle elevations. Landraces from the high elevations were most susceptible, followed by international differential groups 7 and 8. The results suggest that selection has yielded landraces with more complete and complex resistance in the more disease-conducive mid-elevation environment. At the same time, the pathogen population also possesses a wider virulence spectrum in that environment.

Primary disease gradients of bacterial blight of rice

ABSTRACT The dispersal potential of Xanthomonas oryzae pv. oryzae, causal agent of bacterial blight of rice (Oryzae sativa), was investigated through measurement of primary disease gradients. Plants within individual hills of rice were inoculated, and the number of new lesions in the primary generation of dispersal from these inoculated sources was counted. Two dispersal models that can describe the number of infections at the source (the Kiyosawa and Shiyomi and the modified Gregory) were fit to the lesion counts. Estimated gradient slopes were similar in the 2 years of the study for both gradient models. However, the Kiyosawa and Shiyomi model gave a better fit in both years, as indicated by higher coefficients of determination and significances of slopes and by a more random pattern of residuals. Primary disease gradients were very steep, with half-distances (distances over which lesion numbers are calculated to decrease by half) estimated from the Kiyosawa and Shiyomi model of 0.091 and 0.081 m in 1994 and 1995, respectively. Splash dispersal of X. oryzae pv. oryzae is the most likely explanation for both the steep slopes measured and the superior fit of the Kiyosawa and Shiyomi model over the modified Gregory model.

Epidemiological effect of gene deployment strategies on bacterial blight of rice

ABSTRACT Experiments were conducted in farmers' fields at two locations of the irrigated lowlands of Laguna province in southern Luzon island, Philippines, during the wet seasons of 1993 and 1994. Nine rice populations were studied including pure stands, two-component mixtures, two-gene combinations of backcrossed lines containing varying combinations of the bacterial blight resistance genes Xa-4, xa-5, and Xa-10, and a non-isogenic cultivar containing Xa-4 and partial resistance to bacterial blight. The area under the disease progress curve (AUDPC) of both gene combinations studied was significantly less than the single most effective gene of each combination deployed singly. A mixture of a susceptible and a resistant line expressed an AUDPC significantly less than the mean of its component pure stands, but two other mixtures did not. The cultivar IR20, which contains both Xa-4 and partial resistance, reduced the AUDPC by about two-thirds as compared with IR-BB4, which contains Xa-4 and little or no partial resistance.

Effects of stripe rust on the evolution of genetically diverse wheat populations

Eighteen populations, composed of four wheat (Triticum aestivum) varieties that were originally mixed together at equal frequencies, were grown for one-to-three generations at two locations. In addition, pure stands of the four varieties were grown in each year. Populations were either exposed to two stripe rust (Puccinia striiformis) races, protected from stripe rust, or exposed to alternating years of diseased and disease-free conditions. Regression of the logit of a variety's frequency versus generation number was used to calculate the relative fitness of each variety in each population. These analyses suggest that the relative fitnesses of the wheat varieties were affected by disease and geographic location and were constant over time. However, frequency-changes of varieties in the mixtures were negatively correlated with their planting frequencies (0.0001 < P < 0.085 in 14 out of 16 cases), suggesting that fitnesses were frequency-dependent in both the presence and absence of disease. We hypothesize that failure to detect frequency-dependence of fitness in the logit analyses was due to a limited number of generations and a limited range of initial variety frequencies. This is supported by data from longer-term studies in the literature that provide evidence for frequency-dependence of fitness in plant mixtures. Analyses of currently available field data suggest that stable equilibria may be a more likely outcome for mixtures of varieties that are more closely related and/or more uniformly adapted to the environment in which they are grown.