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

Understanding the root of the problem for tackling pea root rot disease

Pea (Pisum sativum), a crop historically significant in the field of genetics, is regaining momentum in sustainable agriculture due to its high protein content and environmental benefits. However, its cultivation faces significant challenges from root rot, a complex disease caused by multiple soil-borne pathogens prevalent across most pea growing regions. This disease leads to substantial yield losses, further complicated by the dynamic interactions among pathogens, soil conditions, weather, and agricultural practices. Recent advancements in molecular diagnostics provide promising tools for the early and precise detection of these pathogens, which is critical for implementing effective disease management strategies. In this review, we explore how the availability of latest pea genomic resources and emerging technologies, such as CRISPR and cell-specific transcriptomics, will enable a deeper understanding of the molecular basis underlying host-pathogen interactions. We emphasize the need for a comprehensive approach that integrates genetic resistance, advanced diagnostics, cultural practices and the role of the soil microbiome in root rot. By leveraging these strategies, it is possible to develop pea varieties that can withstand root rot, ensuring the crop's resilience and its continued importance in global agriculture.

Exploring the temporal dynamics of a disease suppressive rhizo-microbiome in eggplants

The rhizosphere microbiome is important for plant health, yet their contributions to disease resistance and assembly dynamics remain unclear. This study employed rhizosphere microbiome transplantation (RMT) to delineate the impact of the rhizosphere microbiome and the immune response of eggplant (Solanum melongena) on resistance to bacterial wilt caused by Ralstonia solanacearum. We first identified disease-suppressive and disease-conducive rhizosphere microbiome in a susceptible tomato recipient. Using a non-destructive rhizobox and 16S rRNA amplicon sequencing, we monitored the dynamics of both microbiome types during the eggplant development. Most differences were observed at the early stage and then diminished over time. The suppressive microbiome maintained a higher proportion of initial community members throughout eggplant development and exhibited stronger deterministic processes in the early stage, underscoring the importance of plant selection in recruiting protective microbes for rhizosphere immunity. Our study sheds light on the development of microbiome-based strategies for plant disease management and resistance breeding.

Engineering the Crop Microbiota Through Host Genetics

The microbiota populating the plant-soil continuum defines an untapped resource for sustainable crop production. The host plant is a driver for the taxonomic composition and function of these microbial communities. In this review, we illustrate how the host genetic determinants of the microbiota have been shaped by plant domestication and crop diversification. We discuss how the heritable component of microbiota recruitment may represent, at least partially, a selection for microbial functions underpinning the growth, development, and health of their host plants and how the magnitude of this heritability is influenced by the environment. We illustrate how host-microbiota interactions can be treated as an external quantitative trait and review recent studies associating crop genetics with microbiota-based quantitative traits. We also explore the results of reductionist approaches, including synthetic microbial communities, to establish causal relationships between microbiota and plant phenotypes. Lastly, we propose strategies to integrate microbiota manipulation into crop selection programs. Although a detailed understanding of when and how heritability for microbiota composition can be deployed for breeding purposes is still lacking, we argue that advances in crop genomics are likely to accelerate wider applications of plant-microbiota interactions in agriculture.

Effect of Trichoderma viride on rhizosphere microbial communities and biocontrol of soybean root rot

Biological seed dressing is a cost-effective means to protect plant roots from pathogens. Trichoderma is generally considered as one of the most common biological seed dressings. However, there is still a dearth of information on the effects of Trichoderma on microbial community of rhizosphere soil. High-throughput sequencing was used to analyze the effects of Trichoderma viride and a chemical fungicide on microbial community of soybean rhizosphere soil. The results showed that both T. viride and chemical fungicide could significantly reduce the disease index of soybean (15.11% for Trichoderma and 17.33% for Chemical), while no significant difference was observed between them. Both T. viride and chemical fungicide could affect the structure of rhizosphere microbial community, they increased the β-diversity of microbial community and significantly reduce the relative abundance of Saprotroph-Symbiotroph. Chemical fungicide could reduce the complexity and stability of co-occurrence network. However, T. viride is beneficial for maintaining network stability and increasing network complexity. There were 31 bacterial genera and 21 fungal genera significantly correlated with the disease index. Furthermore, several potential plant pathogenic microorganisms were also positively correlated with disease index, such as Fusarium, Aspergillus, Conocybe, Naganishia, and Monocillium. From this work, T. viride may be used as a substitute for chemical fungicide to control soybean root rot and be more friendly to soil microecology.

A fine-tuned defense at the pea root caps: Involvement of border cells and arabinogalactan proteins against soilborne diseases

Plants have to cope with a myriad of soilborne pathogens that affect crop production and food security. The complex interactions between the root system and microorganisms are determinant for the whole plant health. However, the knowledge regarding root defense responses is limited as compared to the aerial parts of the plant. Immune responses in roots appear to be tissue-specific suggesting a compartmentalization of defense mechanisms in these organs. The root cap releases cells termed root "associated cap-derived cells" (AC-DCs) or "border cells" embedded in a thick mucilage layer forming the root extracellular trap (RET) dedicated to root protection against soilborne pathogens. Pea (Pisum sativum) is the plant model used to characterize the composition of the RET and to unravel its function in root defense. The objective of this paper is to review modes of action of the RET from pea against diverse pathogens with a special focus on root rot disease caused by Aphanomyces euteiches, one of the most widely occurring and large-scale pea crop diseases. The RET, at the interface between the soil and the root, is enriched in antimicrobial compounds including defense-related proteins, secondary metabolites, and glycan-containing molecules. More especially arabinogalactan proteins (AGPs), a family of plant extracellular proteoglycans belonging to the hydroxyproline-rich glycoproteins were found to be particularly present in pea border cells and mucilage. Herein, we discuss the role of RET and AGPs in the interaction between roots and microorganisms and future potential developments for pea crop protection.

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.

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.