Pythium Species Associated with Damping-off of Pea in Certified Organic Fields in the Columbia Basin of Central Washington

Polyyne-producing Burkholderia suppress Globisporangium ultimum damping-off disease of Pisum sativum (pea)

Extensive crop losses are caused by oomycete and fungal damping-off diseases. Agriculture relies heavily on chemical pesticides to control disease, but due to safety concerns multiple agents have been withdrawn. Burkholderia were successfully used as commercial biopesticides because of their fungicidal activity and plant protective traits. However, their potential for opportunistic pathogenicity led to a moratorium on their registration as biopesticides. Subsequently, Burkholderia were shown to produce multiple specialised metabolites including potent antimicrobial polyynes. Cepacin A, a polyyne produced by Burkholderia ambifaria biopesticide strains was shown to be an important metabolite for the protection of germinating peas against Globisporangium ultimum (formerly Pythium) damping-off disease. Recently, there has been an expansion in bacterial polyyne discovery, with the metabolites and their biosynthetic gene pathways found in several bacterial genera including Burkholderia, Collimonas, Trinickia, and Pseudomonas. To define the efficacy of these bacterial polyyne producers as biopesticidal agents, we systematically evaluated metabolite production, in vitro microbial antagonism, and G. ultimum biocontrol across a panel of 30 strains representing four bacterial genera. In vitro polyyne production and antimicrobial activity was demonstrated for most strains, but only Burkholderia polyyne producers were protective within the in vivo G. ultimum damping-off pea protection model. B. ambifaria was the most effective cepacin-expressing biopesticide, and despite their known potential for plant pathogenicity Burkholderia gladioli and Burkholderia plantarii were uniquely shown to be protective as caryoynencin-producing biopesticides. In summary, Burkholderia are effective biopesticides due to their suite of antimicrobials, but the ability to deploy polyyne metabolites, caryoynencin and cepacin, is strain and species dependent. Graphical Abstract.

Nanotechnological approaches for management of soil-borne plant pathogens

Soil borne pathogens are significant contributor of plant yield loss globally. The constraints in early diagnosis, wide host range, longer persistence in soil makes their management cumbersome and difficult. Therefore, it is crucial to devise innovative and effective management strategy to combat the losses caused by soil borne diseases. The use of chemical pesticides is the mainstay of current plant disease management practices that potentially cause ecological imbalance. Nanotechnology presents a suitable alternative to overcome the challenges associated with diagnosis and management of soil-borne plant pathogens. This review explores the use of nanotechnology for the management of soil-borne diseases using a variety of strategies, such as nanoparticles acting as a protectant, as carriers of actives like pesticides, fertilizers, antimicrobials, and microbes or by promoting plant growth and development. Nanotechnology can also be used for precise and accurate detection of soil-borne pathogens for devising efficient management strategy. The unique physico-chemical properties of nanoparticles allow greater penetration and interaction with biological membrane thereby increasing its efficacy and releasability. However, the nanoscience specifically agricultural nanotechnology is still in its toddler stage and to realize its full potential, extensive field trials, utilization of pest crop host system and toxicological studies are essential to tackle the fundamental queries associated with development of commercial nano-formulations.

Pea Breeding for Resistance to Rhizospheric Pathogens

Pea (Pisum sativum L.) is a grain legume widely cultivated in temperate climates. It is important in the race for food security owing to its multipurpose low-input requirement and environmental promoting traits. Pea is key in nitrogen fixation, biodiversity preservation, and nutritional functions as food and feed. Unfortunately, like most crops, pea production is constrained by several pests and diseases, of which rhizosphere disease dwellers are the most critical due to their long-term persistence in the soil and difficulty to manage. Understanding the rhizosphere environment can improve host plant root microbial association to increase yield stability and facilitate improved crop performance through breeding. Thus, the use of various germplasm and genomic resources combined with scientific collaborative efforts has contributed to improving pea resistance/cultivation against rhizospheric diseases. This improvement has been achieved through robust phenotyping, genotyping, agronomic practices, and resistance breeding. Nonetheless, resistance to rhizospheric diseases is still limited, while biological and chemical-based control strategies are unrealistic and unfavourable to the environment, respectively. Hence, there is a need to consistently scout for host plant resistance to resolve these bottlenecks. Herein, in view of these challenges, we reflect on pea breeding for resistance to diseases caused by rhizospheric pathogens, including fusarium wilt, root rots, nematode complex, and parasitic broomrape. Here, we will attempt to appraise and harmonise historical and contemporary knowledge that contributes to pea resistance breeding for soilborne disease management and discuss the way forward.

Untangling the Pea Root Rot Complex Reveals Microbial Markers for Plant Health

Plant health is recognised as a key element to ensure global food security. While plant breeding has substantially improved crop resistance against individual pathogens, it showed limited success for diseases caused by the interaction of multiple pathogens such as root rot in pea (Pisum sativum L.). To untangle the causal agents of the pea root rot complex and determine the role of the plant genotype in shaping its own detrimental or beneficial microbiome, fungal and oomycete root rot pathogens, as well as previously identified beneficials, i.e., arbuscular mycorrhizal fungi (AMF) and Clonostachys rosea, were qPCR quantified in diseased roots of eight differently resistant pea genotypes grown in four agricultural soils under controlled conditions. We found that soil and pea genotype significantly determined the microbial compositions in diseased pea roots. Despite significant genotype x soil interactions and distinct soil-dependent pathogen complexes, our data revealed key microbial taxa that were associated with plant fitness. Our study indicates the potential of fungal and oomycete markers for plant health and serves as a precedent for other complex plant pathosystems. Such microbial markers can be used to complement plant phenotype- and genotype-based selection strategies to improve disease resistance in one of the world's most important pulse crops of the world.

First report of Pythium aristosporum causing corn stalk rot in China

Corn (Zea mays L.) stalk rot, caused by various pathogens, is one of the most prevalent corn diseases worldwide. In October 2019, a survey was carried out to determine pathogenic fungi causing corn stalk rot in 3 fields (~120 ha) in Harbin city (44.04°N 125.42°E), Heilongjiang Province, China. In each field, 100 plants at 5 sampling points were assessed at the milk stage (R3) of development. Disease incidence was 12%. Symptomatic plants showed rapid death of the upper leaves, drooping ears and stalks were soft, hollow, watersoaked with white hyphae present on teh outside of the stalk. Pieces of tissue (0.25 cm2) from 15 individual diseased stalks (5 plants/field) were surface disinfested in 0.5% NaOCl for 5 min, rinsed three times in sterile distilled water and cultured on potato dextrose agar (PDA) containing streptomycin (50 μg/mL). After three days of incubation, a total of twelve fungal cultures with uniform characteristics were isolated and subcultured by transferring hyphal tips onto V8. Colonies on V8 selective medium were creamy white and floccus, with a growth rate of 20 mm/day at 26°C in darkness. Oospores were mostly plerotic, and oogonia walls were 1.3 to 2.7 μm thick (n = 50); globose oogonia, 23.9 to 30.5 μm in diameter (n = 50), and had 1 to 8 antheridia. Based on these characteristics, the isolates were identified as Pythium sp. (van der Plaats-Niterink 1981). Genomic DNA was extracted from single conidial cultures of representative isolates (MZYJF1, MZYJF3 and MZYJF7), and the internal transcribed spacer (ITS) region and cytochrome coxidase subunit II (CoxII) gene were amplified and sequenced using the primers ITS1/ITS4 (Yin et al. 2012) and COX2f/COX2r (Hudspeth et al. 2000), respectively. Partial nucleotide sequences of 796 bp and 573 bp for the ITS and COX11 amplicons, respectively, were obtained and deposited in GenBank (accession no. MW447501 for ITS, and MW471006 for COXII). MegaBLAST analysis of the ITS and CoxII sequences of MZYJF1 isolate showed 100% similarity with sequences from P. aristosporum strain ATCC 11101. The isolates were identified as P. aristosporum based on the fact that P. aristosporum has aplerotic oospores and less antheridia per oogonium than P. arrhenomanes (van der Plaats-Niterink 1981). A pathogenicity test was performed on corn cv. Xianyu 335 at tasseling stage (VT) in the field. An oospore suspension, obtained from isolate MZYJF1 grown on V8 agar media for 4 weeks (Green and Jensen, 2000) and diluted to 1×104 oospores/mL using blood cell counting method, was injected into the base of the maize stems of 6 healthy plants (1.5 ml/plant ) using a syringe. Control plants were injected with distilled sterile water. All inoculated plants showed symptoms 25 days after inoculation that were similar to those observed in the field. The oomycete of P. aristosporum was reisolated from symptomatic plants on V8 agar media and identified according to morphological and molecular characteristics. No symptoms were observed on the control plants. P. aristosporum has previously been reported on causing damping-off of pea in the Columbia basin of Central Washington (Alcala et al. 2016) and on soybean in North Dakota (Zitnick-Anderson and Nelson 2015). To our knowledge, this is the first report of P. aristosporum causing corn stalk rot in China. Corn stalk rot caused by P. aristosporum poses a threat to significantly reduce the quality of corn. Thus, its distribution needs to be investigated and effective disease management strategies developed.

Heritable Variation in Pea for Resistance Against a Root Rot Complex and Its Characterization by Amplicon Sequencing

Soil-borne pathogens cause severe root rot of pea (Pisum sativum L.) and are a major constraint to pea cultivation worldwide. Resistance against individual pathogen species is often ineffective in the field where multiple pathogens form a pea root rot complex (PRRC) and conjointly infect pea plants. On the other hand, various beneficial plant-microbe interactions are known that offer opportunities to strengthen plant health. To account for the whole rhizosphere microbiome in the assessment of root rot resistance in pea, an infested soil-based resistance screening assay was established. The infested soil originated from a field that showed severe pea root rot in the past. Initially, amplicon sequencing was employed to characterize the fungal microbiome of diseased pea roots grown in the infested soil. The amplicon sequencing evidenced a diverse fungal community in the roots including pea pathogens Fusarium oxysporum, F. solani, Didymella sp., and Rhizoctonia solani and antagonists such as Clonostachys rosea and several mycorrhizal species. The screening system allowed for a reproducible assessment of disease parameters among 261 pea cultivars, breeding lines, and landraces grown for 21 days under controlled conditions. A sterile soil control treatment was used to calculate relative shoot and root biomass in order to compare growth performance of pea lines with highly different growth morphologies. Broad sense heritability was calculated from linear mixed model estimated variance components for all traits. Emergence on the infested soil showed high (H 2 = 0.89), root rot index (H 2 = 0.43), and relative shoot dry weight (H 2 = 0.51) medium heritability. The resistance screening allowed for a reproducible distinction between PRRC susceptible and resistant pea lines. The combined assessment of root rot index and relative shoot dry weight allowed to identify resistant (low root rot index) and tolerant pea lines (low relative shoot dry weight at moderate to high root rot index). We conclude that relative shoot dry weight is a valuable trait to select disease tolerant pea lines. Subsequently, the resistance ranking was verified in an on-farm experiment with a subset of pea lines. We found a significant correlation (r s = 0.73, p = 0.03) between the controlled conditions and the resistance ranking in a field with high PRRC infestation. The screening system allows to predict PRRC resistance for a given field site and offers a tool for selection at the seedling stage in breeding nurseries. Using the complexity of the infested field soil, the screening system provides opportunities to study plant resistance in the light of diverse plant-microbe interactions occurring in the rhizosphere.

Phytopythium litorale: A Novel Killer Pathogen of Plane (Platanus orientalis) Causing Canker Stain and Root and Collar Rot

Decline symptoms associated with lethal stem and branch canker stain along with root and collar rots were observed on 5- to 7-year-old roadside oriental plane trees (Platanus orientalis) in Diyarbakır, Turkey. Above-ground symptoms included leaf necrosis, leaf curling, extensive bluish or blackish staining of shoots, branches, stem bark, and wood surfaces, as well as stem cankers and exfoliation of branch bark scales. A general decline of the trees was distinctly visible from a distance. A Phytophthora/Pythium-like oomycete species with globose to ovoid, often papillate and internally proliferating sporangia was consistently isolated from the fine and coarse roots and stained branch parts and shoots. The pathogen was identified as Phytopythium litorale based on several morphological features. Partial DNA sequences of three loci, including nuclear rDNA internal transcribed spacer (ITS) and the large ribosomal subunit (LSU), and mitochondrial cytochrome c oxidase subunit II (coxII) confirmed the morphological identification. All P. litorale isolates were homothallic, developing gametangia, ornamented oogonia with elongate to lobate antheridia. Pathogenicity of P. litorale was tested by inoculation on excised shoots and by root inoculation on seedlings. P. litorale produced large lesions and blights on shoots in just 5 days and killed 100% of the seedlings in a month. This paper presents the first confirmed report of P. litorale as an important pathogen on a plant species causing branch and stem cankers, and root and collar rot, in and on P. orientalis, resulting in a rapid decline of trees and suggesting a threat to plane.

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.

Detection and Quantification of Pythium tracheiphilum in Soil by Multiplex Real-Time qPCR

In Canada, head lettuce (Lactuca sativa capitata) is extensively produced in the muck soils of southwestern Québec. However, yields are increasingly affected by various soilborne pathogens, including Pythium spp., which cause wilt and damping off. In a survey conducted in Québec muck soils in 2010 and 2011, Pythium tracheiphilum Matta was identified as the predominant Pythium sp. in the root of head lettuce showing Pythium stunt symptoms. Therefore, to improve risk assessment and help further understanding of disease epidemiology, a specific and sensitive real-time quantitative polymerase chain reaction (qPCR) assay based on TaqMan-minor groove binder (MGB) technology was developed for P. tracheiphilum. The PCR primers along with a TaqMan-MGB probe were designed from the ribosomal internal transcribed spacer 2 region. A 100-bp product was amplified by PCR from all P. tracheiphilum isolates tested while no PCR product was obtained from 38 other Pythium spp. or from a selection of additional lettuce pathogens tested. In addition to P. tracheiphilum, the assay was multiplexed with an internal control allowing for the individual validation of each PCR. In artificially infested soils, the sensitivity of the qPCR assay was established as 10 oospores/g of dry soil. P. tracheiphilum was not detected in soils in which lettuce has never been grown; however, inoculum ranged from 0 to more than 200,000 oospores/g of dry soil in commercial lettuce fields. Also, disease incidence was positively correlated with inoculum concentration (r = 0.764). The results suggest that inoculum concentration should be considered when making Pythium stunt management decisions. The developed qPCR assay will facilitate reliable detection and quantification of P. tracheiphilum from field soil.

Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes

Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant-microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant-associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant-microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil-borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere-related traits, (c) the role of root exudation in microbe-mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.