Soil microbiota and herbivory drive the assembly of tomato plant-associated microbial communities through different mechanisms

Plant-associated microbial communities are key to shaping many aspects of plant biology. In this study, we tested whether soil microbial communities and herbivory influence the bacterial community of tomato plants and whether their influence in different plant compartments is driven by microbial spillover between compartments or whether plants are involved in mediating this effect. We grew our plants in soils hosting three different microbial communities and covered (or not) the soil surface to prevent (or allow) passive microbial spillover between compartments, and we exposed them (or not) to herbivory by Manduca sexta. Here we show that the soil-driven effect on aboveground compartments is consistently detected regardless of soil coverage, whereas soil cover influences the herbivore-driven effect on belowground microbiota. Together, our results suggest that the soil microbiota influences aboveground plant and insect microbial communities via changes in plant metabolism and physiology or by sharing microorganisms via xylem sap. In contrast, herbivores influence the belowground plant microbiota via a combination of microbial spillover and changes in plant metabolism. These results demonstrate the important role of plants in linking aboveground and belowground microbiota, and can foster further research on soil microbiota manipulation for sustainable pest management.

Biotic stress-induced changes in root exudation confer plant stress tolerance by altering rhizospheric microbial community

Every organism on the earth maintains some kind of interaction with its neighbours. As plants are sessile, they sense the varied above-ground and below-ground environmental stimuli and decipher these dialogues to the below-ground microbes and neighbouring plants via root exudates as chemical signals resulting in the modulation of the rhizospheric microbial community. The composition of root exudates depends upon the host genotype, environmental cues, and interaction of plants with other biotic factors. Crosstalk of plants with biotic agents such as herbivores, microbes, and neighbouring plants can change host plant root exudate composition, which may permit either positive or negative interactions to generate a battlefield in the rhizosphere. Compatible microbes utilize the plant carbon sources as their organic nutrients and show robust co-evolutionary changes in changing circumstances. In this review, we have mainly focused on the different biotic factors responsible for the synthesis of alternative root exudate composition leading to the modulation of rhizosphere microbiota. Understanding the stress-induced root exudate composition and resulting change in microbial community can help us to devise strategies in engineering plant microbiomes to enhance plant adaptive capabilities in a stressful environment.

Characterizing rhizosphere microbial communities associated with tolerance to aboveground herbivory in wild and domesticated tomatoes

Root-associated microbial communities are well known for their ability to prime and augment plant defenses that reduce herbivore survival or alter behavior (i.e., resistance). In contrast, the role root microbes play in plant tolerance to herbivory, an evolutionarily sustainable alternative to resistance, is overlooked. In this study, we aimed to expand our limited understanding of what role rhizosphere microbial communities play in supporting tolerance to insect damage. Using domesticated tomatoes and their wild ancestors (Solanum spp.), we first documented how tobacco hornworm (Manduca sexta) herbivory impacted tomato fruit production in order to quantify plant tolerance. We then characterized the bacterial and fungal rhizosphere communities harbored by high and low tolerance plants. Wild tomatoes excelled at tolerating hornworm herbivory, experiencing no significant yield loss despite 50% leaf area removal. Their domesticated counterparts, on the other hand, suffered 26% yield losses under hornworm herbivory, indicating low tolerance. Ontogeny (i.e., mid- vs. late-season sampling) explained the most variation in rhizosphere community structure, with tomato line, tolerance, and domestication status also shaping rhizosphere communities. Fungal and bacterial community traits that associated with the high tolerance line include (1) high species richness, (2) relatively stable community composition under herbivory, and (3) the relative abundance of taxa belonging to Stenotrophomonas, Sphingobacterium, and Sphingomonas. Characterizing tolerance-associating microbiomes may open new avenues through which plant defenses are amended in pest management, such as plant breeding efforts that enhance crop recruitment of beneficial microbiomes.

Shoot and root insect herbivory change the plant rhizosphere microbiome and affects cabbage-insect interactions through plant-soil feedback

Plant-soil feedback (PSF) may influence plant-insect interactions. Although plant defense differs between shoot and root tissues, few studies have examined root-feeding insect herbivores in a PSF context. We examined here how plant growth and resistance against root-feeding Delia radicum larvae was influenced by PSF. We conditioned soil with cabbage plants that were infested with herbivores that affect D. radicum through plant-mediated effects: leaf-feeding Plutella xylostella caterpillars and Brevicoryne brassicae aphids, root-feeding D. radicum larvae, and/or added rhizobacterium Pseudomonas simiae WCS417r. We analyzed the rhizosphere microbial community, and in a second set of conspecific plants exposed to conditioned soil, we assessed growth, expression of defense-related genes, and D. radicum performance. The rhizosphere microbiome differed mainly between shoot and root herbivory treatments. Addition of Pseudomonas simiae did not influence rhizosphere microbiome composition. Plant shoot biomass, gene expression, and plant resistance against D. radicum larvae was affected by PSF in a treatment-specific manner. Soil conditioning overall reduced plant shoot biomass, Pseudomonas simiae-amended soil causing the largest growth reduction. In conclusion, shoot and root insect herbivores alter the rhizosphere microbiome differently, with consequences for growth and resistance of plants subsequently exposed to conditioned soil.

Effects of Glucosinolate-Derived Isothiocyanates on Fungi: A Comprehensive Review on Direct Effects, Mechanisms, Structure-Activity Relationship Data and Possible Agricultural Applications

Plants heavily rely on chemical defense systems against a variety of stressors. The glucosinolates in the Brassicaceae and some allies are the core molecules of one of the most researched such pathways. These natural products are enzymatically converted into isothiocyanates (ITCs) and occasionally other defensive volatile organic constituents (VOCs) upon fungal challenge or tissue disruption to protect the host against the stressor. The current review provides a comprehensive insight on the effects of the isothiocyanates on fungi, including, but not limited to mycorrhizal fungi and pathogens of Brassicaceae. In the review, our current knowledge on the following topics are summarized: direct antifungal activity and the proposed mechanisms of antifungal action, QSAR (quantitative structure-activity relationships), synergistic activity of ITCs with other agents, effects of ITCs on soil microbial composition and allelopathic activity. A detailed insight into the possible applications is also provided: the literature of biofumigation studies, inhibition of post-harvest pathogenesis and protection of various products including grains and fruits is also reviewed herein.

Understanding Plant Social Networking System: Avoiding Deleterious Microbiota but Calling Beneficials

Plant association with microorganisms elicits dramatic effects on the local phytobiome and often causes systemic and transgenerational modulation on plant immunity against insect pests and microbial pathogens. Previously, we introduced the concept of the plant social networking system (pSNS) to highlight the active involvement of plants in the recruitment of potentially beneficial microbiota upon exposure to insects and pathogens. Microbial association stimulates the physiological responses of plants and induces the development of their immune mechanisms while interacting with multiple enemies. Thus, beneficial microbes serve as important mediators of interactions among multiple members of the multitrophic, microscopic and macroscopic communities. In this review, we classify the steps of pSNS such as elicitation, signaling, secreting root exudates, and plant protection; summarize, with evidence, how plants and beneficial microbes communicate with each other; and also discuss how the molecular mechanisms underlying this communication are induced in plants exposed to natural enemies. Collectively, the pSNS modulates robustness of plant physiology and immunity and promotes survival potential by helping plants to overcome the environmental and biological challenges.

Rhizosphere Microbiome Cooperations: Strategies for Sustainable Crop Production

Interactions between microorganisms and host plants determine the growth and development as well as the health of the host plant. Various microbial groups inhabit the rhizosphere, each with its peculiar function. The survival of each microbial group depends to a large extent on its ability to colonize the plant root and outcompete the native organisms. The role of the rhizospheric microbiome in enhancing plant growth has not been fully maximized. An understanding of the complexities of microbial interactions and factors affecting their assembly in the community is necessary to benefit maximally from the cooperations of various microbial communities for sustainable crop production. In this review, we outline the various organisms associated with the plant rhizosphere with emphasis on their interactions and mechanisms used in plant growth promotion.

Climate change alters plant-herbivore interactions

Plant-herbivore interactions have evolved in response to coevolutionary dynamics, along with selection driven by abiotic conditions. We examine how abiotic factors influence trait expression in both plants and herbivores to evaluate how climate change will alter this long-standing interaction. The paleontological record documents increased herbivory during periods of global warming in the deep past. In phylogenetically corrected meta-analyses, we find that elevated temperatures, CO₂ concentrations, drought stress and nutrient conditions directly and indirectly induce greater food consumption by herbivores. Additionally, elevated CO₂ delays herbivore development, but increased temperatures accelerate development. For annual plants, higher temperatures, CO₂ and drought stress increase foliar herbivory. Our meta-analysis also suggests that greater temperatures and drought may heighten florivory in perennials. Human actions are causing concurrent shifts in CO₂ , temperature, precipitation regimes and nitrogen deposition, yet few studies evaluate interactions among these changing conditions. We call for additional multifactorial studies that simultaneously manipulate multiple climatic factors, which will enable us to generate more robust predictions of how climate change could disrupt plant-herbivore interactions. Finally, we consider how shifts in insect and plant phenology and distribution patterns could lead to ecological mismatches, and how these changes may drive future adaptation and coevolution between interacting species.

Hatching of Globodera pallida Induced by Root Exudates Is Not Influenced by Soil Microbiota Composition

Plant-parasitic nematodes are among the most harmful pests of cultivated crops causing important economic losses. The ban of chemical nematicides requires the development of alternative agroecological approaches to protect crops against nematodes. For cyst nematodes, egg hatching is stimulated by host plant root exudates. Inducing "suicide hatching" of nematode second-stage juveniles (J2), using root exudates in the absence of the host plant, may constitute an effective and innovative biocontrol method to control cyst nematodes. However, before considering the development of this approach, understanding the effect of soil biotic component on cyst nematode hatching by root exudates is a major issue. The effectiveness of this approach could be modulated by other soil organisms consuming root exudates for growth as soil microbiota, and this must be evaluated. To do that, four different native agricultural soils were selected based on their physicochemical properties and their microbiota composition were characterized by rDNA metabarcoding. To disentangle the effect of microbiota from that of soil on hatching, four recolonized artificial soils were obtained by inoculating a common sterile soil matrix with the microbiota proceeding from each agricultural soil. Each soil was then inoculated with cysts of the potato cyst nematode, Globodera pallida, and low or high doses of potato root exudates (PREs) were applied. After 40 days, viable J2 remaining in cysts were counted to determine the efficiency of root exudates to stimulate hatching in different soils. Results showed that (i) when physicochemical and microbiota compositions varied among native soils, the hatching rates remained very high albeit small differences were measured and no dose effect was detected and (ii) when only microbiota composition varied among recolonized soils, the hatching rates were also high at the highest dose of PREs, but a strong dose effect was highlighted. This study shows that abiotic and biotic factors may not compromise the development of methods based on suicide hatching of cyst nematodes, using root exudates, molecules inducing J2 hatch, or trap crops.

Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes

The contribution of surrounding plant microbiota to disease development has led to the 'pathobiome' concept, which represents the interaction between the pathogen, the host plant and the associated biotic microbial community, resulting or not in plant disease. The aim herein is to understand how the soil microbial environment may influence the functions of a pathogen and its pathogenesis, and the molecular response of the plant to the infection, with a dual-RNAseq transcriptomics approach. We address this question using Brassica napus and Plasmodiophora brassicae, the pathogen responsible for clubroot. A time-course experiment was conducted to study interactions between P. brassicae, two B. napus genotypes and three soils harbouring high, medium or low microbiota diversities and levels of richness. The soil microbial diversity levels had an impact on disease development (symptom levels and pathogen quantity). The P. brassicae and B. napus transcriptional patterns were modulated by these microbial diversities, these modulations being dependent on the host genotype plant and the kinetic time. The functional analysis of gene expressions allowed the identification of pathogen and plant host functions potentially involved in the change of plant disease level, such as pathogenicity-related genes (NUDIX effector) in P. brassicae and plant defence-related genes (glucosinolate metabolism) in B. napus.

Soil Microarthropods and Soil Health: Intersection of Decomposition and Pest Suppression in Agroecosystems

Two desirable functions of healthy soil are nutrient cycling and pest suppression. We review relevant literature on the contributions of soil microarthropods to soil health through their intersecting roles in decomposition and nutrient cycling and direct and indirect suppression of plant pests. Microarthropods can impact soil and plant health directly by feeding on pest organisms or serving as alternate prey for larger predatory arthropods. Indirectly, microarthropods mediate the ability of crop plants to resist or tolerate insect pests and diseases by triggering induced resistance and/or contributing to optimal nutritional balance of plants. Soil fauna, including microarthropods, are key regulators of decomposition at local scales but their role at larger scales is unresolved. Future research priorities include incorporating multi-channel omnivory into food web modeling and understanding the vulnerability of soil carbon through global climate change models.