Exploiting root exudates to manage soil-borne disease complexes in a changing climate.

Ongoing climate change will both profoundly impact land-use (e.g., changes in crop species or cultivar and cropping practices) and abiotic factors (e.g., moisture and temperature), which will in turn alter plant-microorganism interactions in soils, including soil-borne pathogens (i.e., plant pathogenic bacteria, fungi, oomycetes, viruses, and nematodes). These pathogens often cause soil-borne disease complexes, which, due to their complexity, frequently remain undiagnosed and unmanaged, leading to chronic yield and quality losses. Root exudates are a complex group of organic substances released in the rhizosphere with potential to recruit, repel, stimulate, inhibit, or kill other organisms, including the detrimental ones. An improved understanding of how root exudates affect interspecies and/or interkingdom interactions in the rhizosphere under ongoing climate change is a prerequisite to effectively manage plant-associated microbes, including those causing diseases.

Seedling emergence and biomass production of soybean cultivars under wheat-soybean relay cropping.

Diversification and intensification of cropping systems can ensure farm profitability while reducing negative environmental impacts of agriculture. Wheat-soybean relay cropping (RC), which consists in planting soybean into standing wheat prior to its harvest, may have this potential although it is poorly adopted by French and European farmers. One of the reasons underlying this lack of adoption could be poor emergence rates and biomass production of soybean, due to a severe competition from the already established primary crop for water, light and nutrients during the co-growth or intercrop phase. All these constraints during the early plant growth could finally affect soybean grain yield and thus farm profitability. Here, we performed a laboratory experiment followed by a 2-year field trial (2021-2022) to investigate potential differences among seven soybean cultivars belonging to different maturity groups (from very early to late) in terms of early growth traits viz. seed germination, seedling emergence vigor and final rates, and early biomass production in wheat-soybean RC. A reference soybean variety belonging to late maturity group (cv. ES Pallador) was also sown under conventional cropping system as control treatment (hereafter referred to as CC). Under laboratory conditions, the base water potential for germination ranged from -0.65 to -0.45 MPa with significant differences (p<0.001) among the tested cultivars indicating their differential tolerance to water stress. Under field conditions, seedling emergence vigor, an index explaining the speed of emergence, ranged from 0.23 to 0.41 and from 0.24 to 0.33 while final emergence rates ranged from 69% to 93% and from 65 to 90% in 2021 and 2022, respectively. We found significant effect of cultivar, year and cultivar x year interaction on emergence vigor (p<0.001) and final emergence rates (p<0.01, p<0.05 and p<0.01, respectively) of soybean cultivars. Significantly higher emergence vigor of the referent cv. ES Pallador was observed in RC compared to CC cropping system in 2021 (0.40 and 0.34, respectively) but not in 2022 (0.29 and 0.31, respectively). Water stress in the seedbed was higher in RC compared to the CC and was the main cause affecting seed germination and seedling emergence vigor especially in 2022. We found a positive correlation between seedling emergence vigor and seedling final emergence rates indicating that a lower speed of seedling emergence, due to seedbed stress factors, affects final emergence rates of soybean. Post-emergence losses due to pigeons were significantly higher (p<0.001) in CC compared to RC (30% and 2% in 2021, and 29% and 2% in 2022 in CC and RC, respectively). Significantly higher biomass production was observed in CC compared to that in RC both in 2021 (162 vs 33 g/m2 of dry matter; p<0.001) and 2022 (252 vs 60 g/m2 of dry matter; p<0.001). Overall, pre-/post-emergence water stress in the seedbed and post-emergence damage due to pigeons are the most important factors affecting a uniform and robust soybean establishment under RC and CC, respectively under southern French conditions.

Ecosystem services of cover crops: a research roadmap.

Crops that provide ecosystem services (ESs) beyond crop production are gaining interest from farmers, policymakers, and society at large. Cover crops (CCs), grown either as the sole crop or mixture, provide multiple ESs that contribute to achieving the sustainable development goals (SDGs) of the United Nations. Little is known to date as to whether and to what extent ESs provided by CCs are affected by genotype × environment × management (G×E×M) interactions. Understanding these interactions could help to maximize the ESs of CCs while minimizing their ecosystem disservices. To this end, we highlight existing research gaps in CC research and then propose key research strategies, including the need for a paradigm shift in defining, managing, and utilizing CCs.

Effect of cropping systems and climate on soil physical characteristics, field crop emergence and yield: A dataset from a 19-year field experiment.

A long-term field experiment was conducted from 1989 to 2007 in northern France in a loamy soil to assess the cumulative effects of cropping systems (CSs) on soil compaction, soil porosity, soil structure, crop emergence and yield. Three CSs, including different crop rotations and cultivations (early or late sowing and harvesting), were compared. CS I was the succession of spring pea/winter wheat/oilseed rape (flax from 2001)/winter wheat while CSs II and III were the succession of sugar beet/winter wheat/maize/winter wheat. The latter two CSs consisted of different sowing dates, based on two distinct decision rules aimed at minimizing the risk of soil compaction in the CS II or maximizing the duration of the crop in the CS III. The tillage system was only mouldboard ploughing up to 2000 while a new treatment with superficial tillage (i.e. at 6 cm depth) was integrated since then into the experiment to compare the effects of annual ploughing and reduced tillage on changes in soil structure over time. Soil water content was measured for each field operation by taking samples every 0.05 m up to a depth of 0.30 m in the topsoil. Soil compaction and soil structure was evaluated after each sowing using a morphological approach and soil bulk density measurements. The ''profil cultural'' method was used to map soil structure variations in the topsoil below the seedbed. Dry bulk density was measured with a gamma-ray transmission probe. Seedling emergence rates and crop yield were also measured in relation to CSs. This dataset represents an important description of the changes in the soil compaction level, crop emergence rates and yield, in relation to CSs and climate, and the overall impact on seedbed structure variations for major field crops under northern France conditions. This information can be used as input variables of several soil-crop models aiming at evaluating the impact of CSs and climate on soil compaction and seedbed structures.

Post-emergence seedling damage due to vertebrate pests and its impact on soybean establishment.

The quality of field crop establishment is an indicator of the productivity and yield quality of a given crop. Several biotic and abiotic factors, as well as cropping practices, affect the quality of field crop establishment. More specifically to soybean, recent studies quantified pre-emergence seedling losses and identified the associated causes of non-emergence. However, little is known about post-emergence seedling damage, mainly due to vertebrate pests, which represent an important problem for growers. A 2-year field observation was conducted to quantify near- and post-emergence seedling damage due to vertebrate pests. The common wood pigeon (Columba palumbus) and the European hare (Lepus europaeus) were associated with this kind of damage. The characteristic damage due to the common wood pigeon consisted of either partially-damaged cotyledons during emergence or completely uprooted seedlings at emergence. In contrast, damage due to the European hare consisted of chewed seedling or seedling parts. There was significant effect of year (p < 0.001) on the final rates of post-emergence seedling damage due to the wood pigeon but not on those due to the European hare. The final rates of post-emergence damage due to the wood pigeon were higher (32% for 2018 and 22% for 2020) compared with those owing to the European hare (18% for 2018 and 17% for 2020). The severity of damage due to vertebrate pests was related to the type of seedling damage that, in turn, affected the capacity of soybean to compensate for post-emergence seedling damage.

Challenges With Managing Disease Complexes During Application of Different Measures Against Foliar Diseases of Field Pea.

Studies were undertaken across five field locations in Western Australia to determine the relative changes in disease severity and subsequent field pea yield from up to four foliar pathogens associated with a field pea foliar disease complex (viz. genera Didymella, Phoma, Peronospora, and Septoria) across four different pea varieties sown at three different times and at three different densities. Delaying sowing of field pea significantly (P < 0.05) reduced the severity of Ascochyta blight (all five locations) and Septoria blight (one location), increased the severity of downy mildew (four locations), but had no effect on seed yield. In relation to Ascochyta blight severity at 80 days after sowing, at all locations the early time of sowing had significantly (P < 0.05) more severe Ascochyta blight than the mid and late times of sowing. Increasing actual plant density from 20 to 25 plants m-2 to 58 to 78 plants m-2 significantly (P < 0.05) increased the severity of the Ascochyta blight (four locations) and downy mildew (one location), and it increased seed yield at four locations irrespective of sowing date and three locations irrespective of variety. Compared with varieties Dundale, Wirrega, and Pennant, variety Alma showed significantly (P < 0.05) less severe Ascochyta blight, downy mildew, and Septoria blight (one location each). Grain yield was highest for the early time of sowing at three locations. Varieties Alma, Dundale, and Wirrega significantly (P < 0.05) outyielded Pennant at four locations. The percentage of isolations of individual Ascochyta blight pathogens at 80 days after the first time of sowing varied greatly, with genus Didymella ranging from 25 to 93% and genus Phoma ranging from 6 to 23% across the five field locations. This fluctuating nature of individual pathogen types and proportions within the Ascochyta blight complex, along with variation in the occurrence of pathogens Peronospora and Septoria, highlights the challenges to understand and manage the complexities of co-occurring different foliar pathogens of field pea. While the search for more effective host resistance continues, there is a need for and opportunities from further exploring and exploiting cultural management approaches focusing on crop sequence diversification, intercropping, manipulating time of sowing and stand density, and application of improved seed sanitation and residue/inoculum management practices. We discuss the constraints and opportunities toward overcoming the challenges associated with managing foliar disease complexes in field pea.

Parsimonious Use of Pesticide-Treated Seeds: An Integrated Pest Management Framework.

Pesticide-treated seeds are usually supplied in 'default' packages that leave farmers little choice for tailor-made management of soil-borne pests and pathogens. This has led to a socioeconomic impasse thereby questioning the sustainability of planting pesticide-treated seeds. Here the author proposes an integrated pest management framework to overcome the current impasse.

Combining Experimental and Modeling Approaches to Understand Genotype x Sowing Date x Environment Interaction Effects on Emergence Rates and Grain Yield of Soybean.

Soybean emergence and yield may be affected by many factors. A better understanding of the cultivar x sowing date x environment interactions could shed light into the competitiveness of soybean with other crops, notably, to help manage major biotic and abiotic factors that limit soybean production. We conducted a 2-year field experiments to measure emergence dynamics and final rates of three soybean cultivars from different maturity groups, with early and conventional sowing dates and across three locations. We also measured germination parameter values of the three soybean cultivars from different maturity groups under controlled experiments to parametrize the SIMPLE crop emergence model. This allowed us to assess the prediction quality of the model for emergence rates and to perform simulations. Final emergence rates under field conditions ranged from 62% to 92% and from 51% to 94% for early and conventional sowing, respectively. The model finely predicted emergence courses and final rates (root mean square error of prediction (RMSEP), efficiency (EF), and mean deviation (MD) ranging between 2% to 18%, 0.46% to 0.99%, and -10% to 15%, respectively) across a wide range of the sowing conditions tested. Differences in the final emergence rates were found, not only among cultivars but also among locations for the same cultivar, although no clear trend or consistent ranking was found in this regard. Modeling suggests that seedling mortality rates were dependent on the soil type with up to 35% and 14% of mortality in the silty loam soil, due to a soil surface crust and soil aggregates, respectively. Non-germination was the least important cause of seedling mortality in all soil types (up to 3% of emergence losses), while no seedling mortality due to drought was observed. The average grain yield ranged from 3.1 to 4.0 t ha-1, and it was significantly affected by the irrigation regime (p < 0.001) and year (p < 0.001) but not by locations, sowing date or cultivars. We conclude that early sowing is unlikely to affect soybean emergence in South-West of France and therefore may represent an important agronomic lever to escape summer drought that markedly limit soybean yield in this region.

Revisiting Sustainability of Fungicide Seed Treatments for Field Crops.

The use of fungicide seed treatment (FST) is a very common practice worldwide. The purported effectiveness of many fungicides in providing broad-spectrum and systemic control of important diseases and the perception that FST reduces overall pesticide use, hence lowering environmental impacts, have greatly promoted the use of FST in the last five decades. Since there have been rapid advancements in the types, formulations, and application methods for seed treatments, there is a need to re-evaluate the benefits versus the risks of FST as a practice. While the use of seeds treated with neonicotinoid insecticides has come under scrutiny due to concern over potential nontarget effects, there are knowledge gaps on potential negative impacts of FST on operators' (those who apply, handle, and use treated seeds) health and nontarget soil organisms (both macro- and microorganisms). Here we review existing knowledge on key fungicides used for seed treatments, benefits and risks related to FST, and propose recommendations to increase benefits and limit risks related to the use of FST. We found FST is applied to almost 100% of sown seeds for the most important arable crops worldwide. Fungicides belonging to 10 chemical families and with one or several types of mobility (contact, locally systemic, and xylem mobile) are used for seed treatment, although the majority are xylem mobile. Seed treatments are applied by the seed distributor, the seed company, and the farmer, although the proportion of seed lots treated by these three groups vary from one crop to another. The average quantity of fungicide active ingredient (a.i.) applied via seed treatment depends on the crop species, environment(s) into which seed is planted, and regional or local regulations. Cost-effectiveness, protection of the seed and seedlings from pathogens up to 4-5 weeks from sowing, user friendliness, and lower impact on human health and nontarget soil organisms compared with foliar spray and broadcast application techniques, are among the most claimed benefits attributed to FST. In contrast, inconsistent economic benefits, development of resistance by soilborne pathogens to many fungicides, exposure risks to operators, and negative impacts on nontarget soil organisms are the key identified risks related to FST. We propose eight recommendations to reduce risks related to FST and to increase their benefits.

Understanding Why Effective Fungicides Against Individual Soilborne Pathogens Are Ineffective with Soilborne Pathogen Complexes.

Annual forage legumes across southern Australia continue to be devastated by soilborne diseases. Nine fungicide seed treatments (thiram, metalaxyl, iprodione, phosphonic acid, propamocarb, fluquinconazole, difenoconazole + metalaxyl, ipconazole + metalaxyl, sedaxane + difenoconazole + metalaxyl) and four foliar fungicide treatments (phosphonic acid, metalaxyl, propamocarb, iprodione) were tested on four subterranean clover cultivars against individual oomycete soilborne pathogens Pythium irregulare, Aphanomyces trifolii, and Phytophthora clandestina and the fungal pathogen Rhizoctonia solani. Best treatments were then further tested across southern Australia in 2 years of field experiments. Under controlled conditions, seed treatment with thiram was best against damping-off caused by P. irregulare across the four cultivars (Woogenellup, Riverina, Seaton Park, Meteora), while metalaxyl was the most effective for maximizing root and shoot weights. Against A. trifolii, metalaxyl, iprodione, difenoconazole + metalaxyl, ipconazole + metalaxyl, and sedaxane + difenoconazole + metalaxyl, all reduced damping-off; sedaxane + difenoconazole + metalaxyl, fluquinconazole, and ipconazole + metalaxyl all reduced lateral root disease across two or more cultivars; while iprodione, thiram, and sedaxane + difenoconazole + metalaxyl increased shoot dry weight. Against P. clandestina, metalaxyl was the most effective in reducing tap and lateral root rot followed by ipconazole + metalaxyl or phosphonic acid for tap and lateral rot, respectively. Against R. solani, there were no effects of fungicides. For P. irregulare and P. clandestina, there were strong seed fungicide × cultivar interactions (P < 0.001). Under controlled conditions for foliar fungicide spray treatments, phosphonic acid was best at preventing productivity losses from A. trifolii, but was ineffective against P. clandestina, P. irregulare, or R. solani. Overall, controlled environment studies highlighted strong potential for utilizing seed treatments against individual pathogens to ensure seedling emergence and early survival, with seed and foliar sprays enhancing productivity by reducing seedling damping-off and root disease from individual pathogens. However, in field experiments over 2 years across southern Australia against naturally occurring soilborne pathogen complexes involving these same pathogens, only rarely did fungicide seed treatments or foliar sprays tested show any benefit. It is evident that currently available fungicide seed and/or foliar spray treatment options do not offer effective field mitigation of damping-off and root disease on annual forage legumes that underpin livestock production across southern Australia. The main reason for this failure relates to the unpredictable and ever-changing soilborne pathogen complexes involved, highlighting a need to now refocus away from fungicide options, particularly toward developing and deploying new host tolerances, but also in deploying appropriate cultural control options.

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.

Integrated weed management systems with herbicide-tolerant crops in the European Union: lessons learnt from home and abroad.

Conventionally bred (CHT) and genetically modified herbicide-tolerant (GMHT) crops have changed weed management practices and made an important contribution to the global production of some commodity crops. However, a concern is that farm management practices associated with the cultivation of herbicide-tolerant (HT) crops further deplete farmland biodiversity and accelerate the evolution of herbicide-resistant (HR) weeds. Diversification in crop systems and weed management practices can enhance farmland biodiversity, and reduce the risk of weeds evolving herbicide resistance. Therefore, HT crops are most effective and sustainable as a component of an integrated weed management (IWM) system. IWM advocates the use of multiple effective strategies or tactics to manage weed populations in a manner that is economically and environmentally sound. In practice, however, the potential benefits of IWM with HT crops are seldom realized because a wide range of technical and socio-economic factors hamper the transition to IWM. Here, we discuss the major factors that limit the integration of HT crops and their associated farm management practices in IWM systems. Based on the experience gained in countries where CHT or GMHT crops are widely grown and the increased familiarity with their management, we propose five actions to facilitate the integration of HT crops in IWM systems within the European Union.

Identifying obstacles and ranking common biological control research priorities for Europe to manage most economically important pests in arable, vegetable and perennial crops.

EU agriculture is currently in transition from conventional crop protection to integrated pest management (IPM). Because biocontrol is a key component of IPM, many European countries recently have intensified their national efforts on biocontrol research and innovation (R&I), although such initiatives are often fragmented. The operational outputs of national efforts would benefit from closer collaboration among stakeholders via transnationally coordinated approaches, as most economically important pests are similar across Europe. This paper proposes a common European framework on biocontrol R&I. It identifies generic R&I bottlenecks and needs as well as priorities for three crop types (arable, vegetable and perennial crops). The existing gap between the market offers of biocontrol solutions and the demand of growers, the lengthy and expensive registration process for biocontrol solutions and their varying effectiveness due to variable climatic conditions and site-specific factors across Europe are key obstacles hindering the development and adoption of biocontrol solutions in Europe. Considering arable, vegetable and perennial crops, a dozen common target pests are identified for each type of crop and ranked by order of importance at European level. Such a ranked list indicates numerous topics on which future joint transnational efforts would be justified. © 2016 Society of Chemical Industry.

Extensive Field Survey, Laboratory and Greenhouse Studies Reveal Complex Nature of Pseudomonas syringae-Associated Hazelnut Decline in Central Italy.

Pseudomonas avellanae (Pav) has been reported as the causal agent of bacterial decline and bacterial canker of hazelnut in Italy and Greece, respectively. Both hazelnut diseases were reported to be similar in terms of symptoms, severity and persistence. In this study, we found that both symptomatic and asymptomatic trees in the field were colonized by Pav. Multilocus Sequence Typing (MLST) analysis showed that Pav strains isolated during this study in Italy belong to the P. syringae phylogroup 1 and they are closely related to Pav strains previously isolated in Greece from hazelnut bacterial canker. On the other hand, strains isolated in earlier studies from hazelnut decline in Italy belong to both phylogroup 1 and 2 of P. syringae. Both phylogroup 1 strains of P. syringae from Greece and Italy are different than strains isolated in this study in terms of their capacity to excrete fluorescent pigments on different media. Despite the same plant genotype and cropping practices adopted, the incidence of hazelnut decline ranged from nearly 0 to 91% across our study sites. No disease developed on plants inoculated with Pav through wounding while leaf scar inoculations produced only mild disease symptoms. Based on our results and the previously reported correlation between pedo-climatic conditions and hazelnut decline, we conclude that hazelnut decline in central Italy could be incited by a combination of predisposing (adverse pedo-climatic conditions) and contributing factors (Pav). Because this is a true decline different from "bacterial canker" described in Greece, we refer to it as hazelnut decline (HD).

Molecular mechanisms underlying the emergence of bacterial pathogens: an ecological perspective.

The rapid emergence of new bacterial diseases negatively affects both human health and agricultural productivity. Although the molecular mechanisms underlying these disease emergences are shared between human- and plant-pathogenic bacteria, not much effort has been made to date to understand disease emergences caused by plant-pathogenic bacteria. In particular, there is a paucity of information in the literature on the role of environmental habitats in which plant-pathogenic bacteria evolve and on the stress factors to which these microbes are unceasingly exposed. In this microreview, we focus on three molecular mechanisms underlying pathogenicity in bacteria, namely mutations, genomic rearrangements and the acquisition of new DNA sequences through horizontal gene transfer (HGT). We briefly discuss the role of these mechanisms in bacterial disease emergence and elucidate how the environment can influence the occurrence and regulation of these molecular mechanisms by directly impacting disease emergence. The understanding of such molecular evolutionary mechanisms and their environmental drivers will represent an important step towards predicting bacterial disease emergence and developing sustainable management strategies for crops.

Toward a Reduced Reliance on Conventional Pesticides in European Agriculture.

Whether modern agriculture without conventional pesticides will be possible or not is a matter of debate. The debate is meaningful within the context of rising health and environmental awareness on one hand, and the global challenge of feeding a steadily growing human population on the other. Conventional pesticide use has come under pressure in many countries, and some European Union (EU) Member States have adopted policies for risk reduction following Directive 2009/128/EC, the sustainable use of pesticides. Highly diverse crop production systems across Europe, having varied geographic and climatic conditions, increase the complexity of European crop protection. The economic competitiveness of European agriculture is challenged by the current legislation, which banned the use of many previously authorized pesticides that are still available and applied in other parts of the world. This challenge could place EU agricultural production at a disadvantage, so EU farmers are seeking help from the research community to foster and support integrated pest management (IPM). Ensuring stable crop yields and quality while reducing the reliance on pesticides is a challenge facing the farming community is today. Considering this, we focus on several diverse situations in European agriculture in general and in European crop protection in particular. We emphasize that the marked biophysical and socio-economic differences across Europe have led to a situation where a meaningful reduction in pesticide use can hardly be achieved. Nevertheless, improvements and/or adoption of the knowledge and technologies of IPM can still achieve large gains in pesticide reduction. In this overview, the current pest problems and their integrated management are discussed in the context of specific geographic regions of Europe, with a particular emphasis on reduced pesticide use. We conclude that there are opportunities for reduction in many parts of Europe without significant losses in crop yields.