Conditioning the soil microbiome through plant-soil feedbacks suppresses an aboveground insect pest

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.

Improving crop salt tolerance through soil legacy effects

Soil salinization poses a critical problem, adversely affecting plant development and sustainable agriculture. Plants can produce soil legacy effects through interactions with the soil environments. Salt tolerance of plants in saline soils is not only determined by their own stress tolerance but is also closely related to soil legacy effects. Creating positive soil legacy effects for crops, thereby alleviating crop salt stress, presents a new perspective for improving soil conditions and increasing productivity in saline farmlands. Firstly, the formation and role of soil legacy effects in natural ecosystems are summarized. Then, the processes by which plants and soil microbial assistance respond to salt stress are outlined, as well as the potential soil legacy effects they may produce. Using this as a foundation, proposed the application of salt tolerance mechanisms related to soil legacy effects in natural ecosystems to saline farmlands production. One aspect involves leveraging the soil legacy effects created by plants to cope with salt stress, including the direct use of halophytes and salt-tolerant crops and the design of cropping patterns with the specific crop functional groups. Another aspect focuses on the utilization of soil legacy effects created synergistically by soil microorganisms. This includes the inoculation of specific strains, functional microbiota, entire soil which legacy with beneficial microorganisms and tolerant substances, as well as the application of novel technologies such as direct use of rhizosphere secretions or microbial transmission mechanisms. These approaches capitalize on the characteristics of beneficial microorganisms to help crops against salinity. Consequently, we concluded that by the screening suitable salt-tolerant crops, the development rational cropping patterns, and the inoculation of safe functional soils, positive soil legacy effects could be created to enhance crop salt tolerance. It could also improve the practical significance of soil legacy effects in the application of saline farmlands.

Drought induces moderate, diverse changes in the odour of grassland species

Plants react to drought stress with numerous changes including altered emissions of volatile organic compounds (VOC) from leaves, which provide protection against oxidative tissue damage and mediate numerous biotic interactions. Despite the share of grasslands in the terrestrial biosphere, their importance as carbon sinks and their contribution to global biodiversity, little is known about the influence of drought on VOC profiles of grassland species. Using coupled gas chromatography-mass spectrometry, we analysed the odorants emitted by 22 European grassland species exposed to an eight-week-lasting drought treatment (DT; 30% water holding capacity, WHC). We focused on the odorants emitted during the light phase from whole plant shoots in their vegetative stage. Emission rates were standardised to the dry weight of each shoot. Well-watered (WW) plants (70% WHC) served as control. Drought-induced significant changes included an increase in total emission rates of plant VOC in six and a decrease in three species. Diverging effects on the number of emitted VOC (chemical richness) or on the Shannon diversity of the VOC profiles were detected in 13 species. Biosynthetic pathways-targeted analyses revealed 13 species showing drought-induced higher emission rates of VOC from one, two, three, or four major biosynthetic pathways (lipoxygenase, shikimate, mevalonate and methylerythritol phosphate pathway), while six species exhibited reduced emission rates from one or two of these pathways. Similarity trees of odorant profiles and their drought-induced changes based on a biosynthetically informed distance metric did not match species phylogeny. However, a phylogenetic signal was detected for the amount of terpenoids released by the studied species under WW and DT conditions. A comparative analysis of emission rates of single compounds released by WW and DT plants revealed significant VOC profile dissimilarities in four species only. The moderate drought-induced changes in the odorant emissions of grassland species are discussed with respect to their impact on trophic interactions across the food web. (294 words).

Partner or perish: tree microbiomes and climate change

Understanding the complex relationships between plants, their microbiomes, and environmental changes is crucial for improving growth and survival, especially for long-lived tree species. Trees, like other plants, maintain close associations with a multitude of microorganisms on and within their tissues, forming a 'holobiont'. However, a comprehensive framework for detailed tree-microbiome dynamics, and the implications for climate adaptation, is currently lacking. This review identifies gaps in the existing literature, emphasizing the need for more research to explore the coevolution of the holobiont and the full extent of climate change impact on tree growth and survival. Advancing our knowledge of plant-microbial interactions presents opportunities to enhance tree adaptability and mitigate adverse impacts of climate changes on trees.

Customized plant microbiome engineering for food security

Plant microbiomes play a vital role in promoting plant growth and resilience to cope with environmental stresses. Plant microbiome engineering holds significant promise to increase crop yields, but there is uncertainty about how this can best be achieved. We propose a step-by-step approach involving customized direct and indirect methods to condition soils and to match plants and microbiomes. Although three approaches, namely the development of (i) 'plant- and microbe-friendly' soils, (ii) 'microbe-friendly' plants, and (iii) 'plant-friendly' microbiomes, have been successfully tested in isolation, we propose that the combination of all three may lead to a step-change towards higher and more stable crop yields. This review aims to provide knowledge, future directions, and practical guidance to achieve this goal via customized plant microbiome engineering.

Plants recruit insecticidal bacteria to defend against herbivore attacks

Pest feeding affects the rhizobacteria community. The rhizomicrobiota activates salicylic acid and jasmonic acid signaling pathways to help plants deal with pest infestation. However, whether plants can recruit special pesticidal microorganisms to deal with attack from herbivores is unclear. A system composed of peanuts and first-instar larvae of Holotrichia parallela were used to analyze whether peanuts truly enrich the insecticidal bacteria after feeding by larvae, and whether inoculation of the enriched bacteria promotes the resistance of plants to herbivore. In this study, high-throughput sequencing of 16 S rRNA gene amplicons was used to demonstrate that infestation of the subterranean pest H. parallela quickly changed the rhizosphere bacterial community structure within 24 h, and the abundance of Enterobacteriaceae, especially Enterobacter, was manifestly enriched. Root feeding induced rhizobacteria to form a more complex co-occurrence network than the control. Rhizosphere bacteria were isolated, and 4 isolates with high toxicity against H. parallela larvae were obtained by random forest analysis. In a back-inoculation experiment using a split-root system, green fluorescent protein (GFP)-labeled Enterobacter sp. IPPBiotE33 was observed to be enriched in uneaten peanut roots. Additionally, supplementation with IPPBiotE33 alleviated the adverse effects of H. parallela on peanuts. Our findings indicated that herbivore infestation could induce plants to assemble bacteria with specific larvicidal activity to address threats.

A trait-based framework linking the soil metabolome to plant-soil feedbacks

By modifying the biotic and abiotic properties of the soil, plants create soil legacies that can affect vegetation dynamics through plant-soil feedbacks (PSF). PSF are generally attributed to reciprocal effects of plants and soil biota, but these interactions can also drive changes in the identity, diversity and abundance of soil metabolites, leading to more or less persistent soil chemical legacies whose role in mediating PSF has rarely been considered. These chemical legacies may interact with microbial or nutrient legacies to affect species coexistence. Given the ecological importance of chemical interactions between plants and other organisms, a better understanding of soil chemical legacies is needed in community ecology. In this Viewpoint, we aim to: highlight the importance of belowground chemical interactions for PSF; define and integrate soil chemical legacies into PSF research by clarifying how the soil metabolome can contribute to PSF; discuss how functional traits can help predict these plant-soil interactions; propose an experimental approach to quantify plant responses to the soil solution metabolome; and describe a testable framework relying on root economics and seed dispersal traits to predict how plant species affect the soil metabolome and how they could respond to soil chemical legacies.

Active soil microbial composition and proliferation are directly affected by the presence of biocides from building materials

Combinations of biocides are commonly added to building materials to prevent microbial growth and thereby cause degradation of the façades. These biocides reach the environment by leaching from façades posing an environmental risk. Although ecotoxicity to the aquatic habitat is well established, there is hardly any data on the ecotoxicological effects of biocides on the soil habitat. This study aimed to characterize the effect of the biocides terbutryn, isoproturon, octhilinone, and combinations thereof on the total and metabolically active soil microbial community composition and functions. Total soil microbial community was retrieved directly from the nucleic acid extracts, while the DNA of the active soil microbial community was separated after bromodeoxyuridine labeling. Bacterial 16S rRNA gene and fungal internal transcribed spacer region gene-based amplicon sequencing was carried out for both active and total, while gene copy numbers were quantified only for the total soil microbial community. Additionally, soil respiration and physico-chemical parameters were analyzed to investigate overall soil microbial activity. The bacterial and fungal gene copy numbers were significantly affected by single biocides and combined biocide soil treatment but not soil respiration and physico-chemical parameters. While the total soil microbiome experienced only minor effects from single and combined biocide treatment, the active soil microbiome was significantly impacted in its diversity, richness, composition, and functional patterns. The active bacterial richness was more sensitive than fungal richness. However, the adverse effects of the biocide combination treatments on soil bacterial richness were highly dependent on the identities of the biocide combination. Our results demonstrate that the presence of biocides frequently used in building materials affects the active soil microbiome. Thereby, the approach described herein can be used as an ecotoxicological measure for the effect on complex soil environments in future studies.

Impact of bacterial and fungal inoculants on the resident rhizosphere microbiome and the volatilome of tomato plants under leaf herbivory stress

Various studies have addressed the impact of microbial inoculants on the composition of the resident microbiome. How microbial inoculants impact plant metabolism and interact with the resident rhizobiota under herbivory stress remains elusive. Here, we investigated the impact of two bacterial and two fungal inoculants, inoculated as single species and as a synthetic community, on the rhizosphere microbiome and volatilome of tomato plants (Solanum lycopersicum) comparing nonstress conditions to exposed to leaf herbivory by Spodoptera exigua. Based on amplicon sequencing analysis, rhizobacterial community composition was significantly affected by all four inoculants and the magnitude of this effect was dependent on herbivory stress. Fungal community composition was altered by the microbial inoculants but independent of herbivory stress. The rhizosphere volatilome was impacted by the microbial inoculation and differences between treatments were evened under herbivory stress. Each microbial inoculant caused unique changes in the volatilome of stressed plants but also shared similar responses, in particular the enhanced production of dimethyl disulfide and benzothiazole. In conclusion, the introduction of microbial inoculants in the tomato rhizosphere caused unique as well as common changes in the rhizosphere microbiome and volatilome, but these changes were minor compared to the microbiome changes induced by herbivory stress.

Warm Temperature Increments Strengthen the Crosstalk between Roots and Soil in the Rhizosphere of Soybean Seedlings

The plant rhizosphere underlies the crosstalk between plant and soil and has a crucial role in plant growth and development under various environments. We examined the effect of temperature rise on the rhizosphere environment of soybean roots to clarify the rhizosphere crosstalk between roots and soil in response to warm temperature rises in a global warming background. The in situ results of root enzyme activity revealed that soybean roots secrete β-glucosidase, and enzyme spectrum imaging demonstrated different enzymatic activities under different temperature environments. The soil enzyme kinetics results showed that soil enzymatic activity increased with increasing temperature, and soybean rhizosphere soil enzymatic activity was higher than that of non-rhizosphere soil. Rhizosphere soil and non-rhizosphere soil showed that the dominant bacterial phylum in soybean rhizosphere soil was Acidobacteria, and the dominant bacterial genus was JG30-KF-AS9. Compared with non-rhizosphere soil, rhizosphere soil was more nutrient-rich, and root secretions provided abundant carbon sources and other nutrients for soil microorganisms in the rhizosphere. Rhizosphere microorganisms affect plant growth by influencing the decomposition of soil organic carbon. The organic carbon content of rhizosphere soil was higher than that of non-rhizosphere soil under high temperatures.

More persistent weather causes a pronounced soil microbial legacy but does not impact subsequent plant communities

A soil history of exposure to extreme weather may impact future plant growth and microbial community assembly. Currently, little is known about whether and how previous precipitation regime (PR)-induced changes in soil microbial communities influence plant and soil microbial community responses to a subsequent PR. We exposed grassland mesocosms to either an ambient PR (1 day wet-dry alternation) or a persistent PR (30 days consecutive wet-dry alternation) for one year. This conditioned soil was then inoculated as a 10 % fraction into 90 % sterilized "native" soil, after which new plant communities were established and subjected to either the ambient or persistent PR for 60 days. We assessed whether past persistent weather-induced changes in soil microbial community composition affect soil microbial and plant community responses to subsequent weather persistence. The historical regimes caused enduring effects on fungal communities and only temporary effects on bacterial communities, but did not trigger soil microbial legacy effects on plant productivity when exposed to either current PR. This study provides experimental evidence for soil legacy of climate persistence on grassland ecosystems in response to subsequent climate persistence, helping to understand and predict the influences of future climate change on soil biota.

Plant secondary metabolite-dependent plant-soil feedbacks can improve crop yield in the field

Plant secondary metabolites that are released into the rhizosphere alter biotic and abiotic soil properties, which in turn affect the performance of other plants. How this type of plant-soil feedback affects agricultural productivity and food quality in the field in the context of crop rotations is unknown. Here, we assessed the performance, yield and food quality of three winter wheat varieties growing in field plots whose soils had been conditioned by either wild type or benzoxazinoid-deficient bx1 maize mutant plants. Following maize cultivation, we detected benzoxazinoid-dependent chemical and microbial fingerprints in the soil. The benzoxazinoid fingerprint was still visible during wheat growth, but the microbial fingerprint was no longer detected. Wheat emergence, tillering, growth, and biomass increased in wild type conditioned soils compared to bx1 mutant conditioned soils. Weed cover was similar between soil conditioning treatments, but insect herbivore abundance decreased in benzoxazinoid-conditioned soils. Wheat yield was increased by over 4% without a reduction in grain quality in benzoxazinoid-conditioned soils. This improvement was directly associated with increased germination and tillering. Taken together, our experiments provide evidence that soil conditioning by plant secondary metabolite producing plants can increase yield via plant-soil feedbacks under agronomically realistic conditions. If this phenomenon holds true across different soils and environments, optimizing root exudation chemistry could be a powerful, genetically tractable strategy to enhance crop yields without additional inputs.

Effects of tomato inoculation with the entomopathogenic fungus Metarhizium brunneum on spider mite resistance and the rhizosphere microbial community

Entomopathogenic fungi have been well exploited as biocontrol agents that can kill insects through direct contact. However, recent research has shown that they can also play an important role as plant endophytes, stimulating plant growth, and indirectly suppressing pest populations. In this study, we examined the indirect, plant-mediated, effects of a strain of entomopathogenic fungus, Metarhizium brunneum on plant growth and population growth of two-spotted spider mites (Tetranychus urticae) in tomato, using different inoculation methods (seed treatment, soil drenching and a combination of both). Furthermore, we investigated changes in tomato leaf metabolites (sugars and phenolics), and rhizosphere microbial communities in response to M. brunneum inoculation and spider mite feeding. A significant reduction in spider mite population growth was observed in response to M. brunneum inoculation. The reduction was strongest when the inoculum was supplied both as seed treatment and soil drench. This combination treatment also yielded the highest shoot and root biomass in both spider mite-infested and non-infested plants, while spider mite infestation increased shoot but reduced root biomass. Fungal treatments did not consistently affect leaf chlorogenic acid and rutin concentrations, but M. brunneum inoculation via a combination of seed treatment and soil drenching reinforced chlorogenic acid (CGA) induction in response to spider mites and under these conditions the strongest spider mite resistance was observed. However, it is unclear whether the M. brunneum-induced increase in CGA contributed to the observed spider mite resistance, as no general association between CGA levels and spider mite resistance was observed. Spider mite infestation resulted in up to two-fold increase in leaf sucrose concentrations and a three to five-fold increase in glucose and fructose concentrations, but these concentrations were not affected by fungal inoculation. Metarhizium, especially when applied as soil drench, impacted the fungal community composition but not the bacterial community composition which was only affected by the presence of spider mites. Our results suggest that in addition to directly killing spider mites, M. brunneum can indirectly suppress spider mite populations on tomato, although the underlying mechanism has not yet been resolved, and can also affect the composition of the soil microbial community.

Engineering plant microbiomes by integrating eco-evolutionary principles into current strategies

Engineering plant microbiomes has the potential to improve plant health in a rapid and sustainable way. Rapidly changing climates and relatively long timelines for plant breeding make microbiome engineering an appealing approach to improving food security. However, approaches that have shown promise in the lab have not resulted in wide-scale implementation in the field. Here, we suggest the use of an integrated approach, combining mechanistic molecular and genetic knowledge, with ecological and evolutionary theory, to target knowledge gaps in plant microbiome engineering that may facilitate translatability of approaches into the field. We highlight examples where understanding microbial community ecology is essential for a holistic understanding of the efficacy and consequences of microbiome engineering. We also review examples where understanding plant-microbe evolution could facilitate the design of plants able to recruit specific microbial communities. Finally, we discuss possible trade-offs in plant-microbiome interactions that should be considered during microbiome engineering efforts so as not to introduce off-target negative effects. We include classic and emergent approaches, ranging from microbial inoculants to plant breeding to host-driven microbiome engineering, and address areas that would benefit from multidisciplinary approaches.

Correlation of microbiomes in "plant-insect-soil" ecosystem

Introduction

Traditional chemical control methods pose a damaging effect on farmland ecology, and their long-term use has led to the development of pest resistance.

Methods

Here, we analyzed the correlations and differences in the microbiome present in the plant and soil of sugarcane cultivars exhibiting different insect resistance to investigate the role played by microbiome in crop insect resistance. We evaluated the microbiome of stems, topsoil, rhizosphere soil, and striped borers obtained from infested stems, as well as soil chemical parameters.

Results and Discussion

Results showed that microbiome diversity was higher in stems of insect-resistant plants, and contrast, lower in the soil of resistant plants, with fungi being more pronounced than bacteria. The microbiome in plant stems was almost entirely derived from the soil. The microbiome of insect-susceptible plants and surrounding soil tended to change towards that of insect-resistant plants after insect damage. Insects' microbiome was mainly derived from plant stems and partly from the soil. Available potassium showed an extremely significant correlation with soil microbiome. This study validated the role played by the microbiome ecology of plant-soil-insect system in insect resistance and provided a pre-theoretical basis for crop resistance control.

Gut microbiota composition in the sympatric and diet-sharing Drosophila simulans and Dicranocephalus wallichii bowringi shaped largely by community assembly processes rather than regional species pool

Clarifying the mechanisms underlying microbial community assembly from regional microbial pools is a central issue of microbial ecology, but remains largely unexplored. Here, we investigated the gut bacterial and fungal microbiome assembly processes and potential sources in Drosophila simulans and Dicranocephalus wallichii bowringi, two wild, sympatric insect species that share a common diet of waxberry. While some convergence was observed, the diversity, composition, and network structure of the gut microbiota significantly differed between these two host species. Null model analyses revealed that stochastic processes (e.g., drift, dispersal limitation) play a principal role in determining gut microbiota from both hosts. However, the strength of each ecological process varied with the host species. Furthermore, the source-tracking analysis showed that only a minority of gut microbiota within D. simulans and D. wallichii bowringi are drawn from a regional microbial pool from waxberries, leaves, or soil. Results from function prediction implied that host species-specific gut microbiota might arise partly through host functional requirement and specific selection across host-microbiota coevolution. In conclusion, our findings uncover the importance of community assembly processes over regional microbial pools in shaping sympatric insect gut microbiome structure and function.

Tritrophic defenses as a central pivot of low-emission, pest-suppressive farming systems

The ongoing COVID-19 pandemic has spotlighted the intricate connections between human and planetary health. Given that pesticide-centered crop protection degrades ecological resilience and (in-)directly harms human health, the adoption of ecologically sound, biodiversity-driven alternatives is imperative. In this Synthesis paper, we illuminate how ecological forces can be manipulated to bolster 'tritrophic defenses' against crop pests, pathogens, and weeds. Three distinct, yet mutually compatible approaches (habitat-mediated, breeding-dependent, and epigenetic tactics) can be deployed at different organizational levels, that is, from an individual seed to entire farming landscapes. Biodiversity can be harnessed for crop protection through ecological infrastructures, diversification tactics, and reconstituted soil health. Crop diversification is ideally guided by interorganismal interplay and plant-soil feedbacks, entailing resistant cultivars, rotation schemes, or multicrop arrangements. Rewarding opportunities also exist to prime plants for enhanced immunity or indirect defenses. As tritrophic defenses spawn multiple societal cobenefits, they could become core features of healthy, climate-resilient, and low-carbon food systems.

Biodiversity-based cropping systems: A long-term perspective is necessary

Biodiversity-based cropping systems are an interesting option to address the many challenges that agriculture faces. However, benefits of these systems should not obscure the fact that creating biodiversity-based cropping systems represents a major change for farmers. To address this challenge, we argue that designing biodiversity-based cropping systems requires transforming ecological concepts into technical opportunities. Indeed, integrating ecological concepts such as plant-soil feedback and plant functional traits more strongly into cropping system design offers promising opportunities for the provision of ecosystem services, such as pest and disease control, crop production (including crop yield stability), climate regulation and regulation of soil quality. Accordingly, we demonstrate that designing biodiversity-based cropping systems requires considering not only the short term but also the long term. This would ensure that the expected ecosystem services have enough time to build up and provide their full effects, that the cropping systems are resilient and that they avoid the limitations of short-term assessments, which do not sufficiently consider multi-year effects. Considering long-term consequences of system change - induced by biodiversity - is essential to identify potential trade-offs between ecosystem services, as well as agricultural obstacles to and mechanisms of change. Including farmers and other food-chain actors in cropping system design would help find acceptable compromises that consider not only the provision of ecosystem services, but also other dimensions related to economic viability, workload or the technical feasibility of crops, which are identified as major obstacles to crop diversification. This strategy represents an exciting research front for the development of agroecological cropping systems.

Legacies at work: plant-soil-microbiome interactions underpinning agricultural sustainability

Agricultural intensification has had long-lasting negative legacies largely because of excessive inputs of agrochemicals (e.g., fertilizers) and simplification of cropping systems (e.g., continuous monocropping). Conventional agricultural management focuses on suppressing these negative legacies. However, there is now increasing attention for creating positive above- and belowground legacies through selecting crop species/genotypes, optimizing temporal and spatial crop combinations, improving nutrient inputs, developing intelligent fertilizers, and applying soil or microbiome inoculations. This can lead to enhanced yields and reduced pest and disease pressure in cropping systems, and can also mitigate greenhouse gas emissions and enhance carbon sequestration in soils. Strengthening positive legacies requires a deeper understanding of plant-soil-microbiome interactions and innovative crop, input, and soil management which can help to achieve agricultural sustainability.

Barley Rhizosphere Microbiome Transplantation – A Strategy to Decrease Susceptibility of Barley Grown in Soils With Low Microbial Diversity to Powdery Mildew

Beneficial bacteria in the rhizosphere are known to trigger faster and stronger plant immune responses to biotic and abiotic stressors. In the present study, we aimed to test the hypothesis that a rhizosphere microbiome transplant (RMT) may improve the immune response and reduce the disease rates of barley (Hordeum vulgare). This hypothesis was tested in a greenhouse system with the powdery mildew-causing fungus Blumeria graminis f. sp. hordei (Bgh). Detached rhizosphere microbiome from barley grown in a field soil was transplanted to barley seedlings grown in potting soil with reduced microbial diversity. Saline-treated plants served as control. At the three-leaf stage, barley was infected with Bgh. Decreased susceptibility to Bgh was observed for barley treated with the RMT as displayed by lower Bgh pustule counts in a detached leaf assay. A trend toward enhanced relative transcript abundances of the defense-related genes PR1b and PR17b was observed in leaves, 24 h after the Bgh challenge, when compared to the control. Moreover, 10 days after the Bgh challenge, the barley rhizosphere microbiome was harvested and analyzed by sequencing of 16S rRNA gene amplicons. The microbial community composition was significantly influenced by the RMT and displayed higher microbial diversity compared to the control. Furthermore, microbial beta-diversity and predicted functional profiles revealed a treatment-dependent clustering. Bacterial isolates from the RMT showed in vitro plant beneficial traits related to induced resistance. Our results showed that transplantation of a rhizosphere microbiome could be a sustainable strategy to improve the health of plants grown in potting soil with low microbial diversity under greenhouse conditions.

Optimisation of root traits to provide enhanced ecosystem services in agricultural systems: A focus on cover crops

Roots are the interface between the plant and the soil and play a central role in multiple ecosystem processes. With intensification of agricultural practices, rhizosphere processes are being disrupted and are causing degradation of the physical, chemical and biotic properties of soil. However, cover crops, a group of plants that provide ecosystem services, can be utilised during fallow periods or used as an intercrop to restore soil health. The effectiveness of ecosystem services provided by cover crops varies widely as very little breeding has occurred in these species. Improvement of ecosystem service performance is rarely considered as a breeding trait due to the complexities and challenges of belowground evaluation. Advancements in root phenotyping and genetic tools are critical in accelerating ecosystem service improvement in cover crops. In this study, we provide an overview of the range of belowground ecosystem services provided by cover crop roots: (1) soil structural remediation, (2) capture of soil resources and (3) maintenance of the rhizosphere and building of organic matter content. Based on the ecosystem services described, we outline current and promising phenotyping technologies and breeding strategies in cover crops that can enhance agricultural sustainability through improvement of root traits.

Tea Plants With Gray Blight Have Altered Root Exudates That Recruit a Beneficial Rhizosphere Microbiome to Prime Immunity Against Aboveground Pathogen Infection

Tea gray blight disease and its existing control measures have had a negative impact on the sustainable development of tea gardens. However, our knowledge of safe and effective biological control measures is limited. It is critical to explore beneficial microbial communities in the tea rhizosphere for the control of tea gray blight. In this study, we prepared conditioned soil by inoculating Pseudopestalotiopsis camelliae-sinensis on tea seedling leaves. Thereafter, we examined the growth performance and disease resistance of fresh tea seedlings grown in conditioned and control soils. Next, the rhizosphere microbial community and root exudates of tea seedlings infected by the pathogen were analyzed. In addition, we also evaluated the effects of the rhizosphere microbial community and root exudates induced by pathogens on the performance of tea seedlings. The results showed that tea seedlings grown in conditioned soil had lower disease index values and higher growth vigor. Soil microbiome analysis revealed that the fungal and bacterial communities of the rhizosphere were altered upon infection with Ps. camelliae-sinensis. Genus-level analysis showed that the abundance of the fungi Trichoderma, Penicillium, and Gliocladiopsis and the bacteria Pseudomonas, Streptomyces, Bacillus, and Burkholderia were significantly (p < 0.05) increased in the conditioned soil. Through isolation, culture, and inoculation tests, we found that most isolates from the induced microbial genera could inhibit the infection of tea gray blight pathogen and promote tea seedling growth. The results of root exudate analysis showed that infected tea seedlings exhibited significantly higher exudate levels of phenolic acids and flavonoids and lower exudate levels of amino acids and organic acids. Exogenously applied phenolic acids and flavonoids suppressed gray blight disease by regulating the rhizosphere microbial community. In summary, our findings suggest that tea plants with gray blight can recruit beneficial rhizosphere microorganisms by altering their root exudates, thereby improving the disease resistance of tea plants growing in the same soil.

Soil composition and plant genotype determine benzoxazinoid-mediated plant-soil feedbacks in cereals

Plant-soil feedbacks refer to effects on plants that are mediated by soil modifications caused by the previous plant generation. Maize conditions the surrounding soil by secretion of root exudates including benzoxazinoids (BXs), a class of bioactive secondary metabolites. Previous work found that a BX-conditioned soil microbiota enhances insect resistance while reducing biomass in the next generation of maize plants. Whether these BX-mediated and microbially driven feedbacks are conserved across different soils and response species is unknown. We found the BX-feedbacks on maize growth and insect resistance conserved between two arable soils, but absent in a more fertile grassland soil, suggesting a soil-type dependence of BX feedbacks. We demonstrated that wheat also responded to BX-feedbacks. While the negative growth response to BX-conditioning was conserved in both cereals, insect resistance showed opposite patterns, with an increase in maize and a decrease in wheat. Wheat pathogen resistance was not affected. Finally and consistent with maize, we found the BX-feedbacks to be cultivar-specific. Taken together, BX-feedbacks affected cereal growth and resistance in a soil and genotype-dependent manner. Cultivar-specificity of BX-feedbacks is a key finding, as it hides the potential to optimize crops that avoid negative plant-soil feedbacks in rotations.

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.

Novel chemicals engender myriad invasion mechanisms

Non-native invasive species (NIS) release chemicals into the environment that are unique to the invaded communities, defined as novel chemicals. Novel chemicals impact competitors, soil microbial communities, mutualists, plant enemies, and soil nutrients differently than in the species' native range. Ecological functions of novel chemicals and differences in functions between the native and non-native ranges of NIS are of immense interest to ecologists. Novel chemicals can mediate different ecological, physiological, and evolutionary mechanisms underlying invasion hypotheses. Interactions amongst the NIS and resident species including competitors, soil microbes, and plant enemies, as well as abiotic factors in the invaded community are linked to novel chemicals. However, we poorly understand how these interactions might enhance NIS performance. New empirical data and analyses of how novel chemicals act in the invaded community will fill major gaps in our understanding of the chemistry of biological invasions. A novel chemical-invasion mechanism framework shows how novel chemicals engender invasion mechanisms beyond plant-plant or plant-microorganism interactions.

Conditioned soils reveal plant-selected microbial communities that impact plant drought response

Rhizobacterial communities can contribute to plant trait expression and performance, including plant tolerance against abiotic stresses such as drought. The conditioning of microbial communities related to disease resistance over generations has been shown to develop suppressive soils which aid in plant defense responses. Here, we applied this concept for the development of drought resistant soils. We hypothesized that soils conditioned under severe drought stress and tomato cultivation over two generations, will allow for plant selection of rhizobacterial communities that provide plants with improved drought resistant traits. Surprisingly, the plants treated with a drought-conditioned microbial inoculant showed significantly decreased plant biomass in two generations of growth. Microbial community composition was significantly different between the inoculated and control soils within each generation (i.e., microbial history effect) and for the inoculated soils between generations (i.e., conditioning effect). These findings indicate a substantial effect of conditioning soils on the abiotic stress response and microbial recruitment of tomato plants undergoing drought stress.

Microbial Biocontrol Strategies for Ambrosia Beetles and Their Associated Phytopathogenic Fungi

Ambrosia beetles and their symbiotic fungi are causing severe damage in natural and agro-ecosystems worldwide, threatening the productivity of several important tree crops such as avocado. Strategies aiming at mitigating their impact include the application of broad-spectrum agrochemicals and the incineration of diseased trees, but the increasing demand for environment-friendly strategies call for exploring biological control for the management of ambrosia beetles and their phytopathogenic fungal symbionts. The aim of this review is to examine the existing knowledge on biocontrol approaches using beneficial microorganisms and microbial natural products with entomopathogenic and antifungal activity against ambrosia beetles and fungi. We show that biocontrol has been mainly focused on the insect, using entomopathogenic fungi (EPF) such as Beauveria spp. or Metarhizium spp. However, recent studies have been integrating EPF with mycoparasitic fungi such as Trichoderma spp. to simultaneously challenge the vector and its fungal symbionts. Novel approaches also include the use of microbial natural products as insect lures or antifungal agents. Contrastingly, the potential of bacteria, including actinobacteria (actinomycetes), as biocontrol agents of ambrosia fungi has been little investigated. We thus suggest that future research should further examine the antifungal activity of bacterial strains, with an emphasis on harsh environments. We also suggest pursuing the isolation of more effective microbial strains with dual biocontrol effect, i.e., exhibiting fungicidal/insecticidal activities. Moreover, additional efforts should aim at determining the best application methods of biocontrol agents in the field to ensure that the positive effects detected in vitro are sustained. Finally, we propose the integration of microbiome studies in pest and disease management strategies as they could provide us with tools to steer the beneficial host plant microbiome and to manipulate the beetle microbiome in order to reduce insect fitness.

Microbiota-root-shoot-environment axis and stress tolerance in plants

Reminiscent to the microbiota-gut-brain axis described in animals, recent advances indicate that plants can take advantage of belowground microbial commensals to orchestrate aboveground stress responses. Integration of plant responses to microbial cues belowground and environmental cues aboveground emerges as a mechanism that promotes stress tolerance in plants. Using recent examples obtained from reductionist and community-level approaches, we discuss the extent to which perception of aboveground biotic and abiotic stresses can cascade along the shoot-root axis to sculpt root microbiota assembly and modulate the growth of root commensals that bolster aboveground stress tolerance. We propose that host modulation of microbiota-root-shoot circuits contributes to phenotypic plasticity and decision-making in plants, thereby promoting adaptation to rapidly changing environmental conditions.

Enabling sustainable agriculture through understanding and enhancement of microbiomes

Harnessing plant-associated microbiomes offers an invaluable strategy to help agricultural production become more sustainable while also meeting growing demands for food, feed and fiber. A plethora of interconnected interactions among the host, environment and microbes, occurring both above and below ground, drive recognition, recruitment and colonization of plant-associated microbes, resulting in activation of downstream host responses and functionality. Dissecting these complex interactions by integrating multiomic approaches, high-throughput culturing, and computational and synthetic biology advances is providing deeper understanding of the structure and function of native microbial communities. Such insights are paving the way towards development of microbial products as well as microbiomes engineered with synthetic microbial communities capable of delivering agronomic solutions. While there is a growing market for microbial-based solutions to improve crop productivity, challenges with commercialization of these products remain. The continued translation of plant-associated microbiome knowledge into real-world scenarios will require concerted transdisciplinary research, cross-training of a next generation of scientists, and targeted educational efforts to prime growers and the general public for successful adoption of these innovative technologies.

Host plant resistance to thrips (Thysanoptera: Thripidae) - current state of art and future research avenues

Integrated Pest Management (IPM) is endorsed as the future standard for crop protection worldwide. This holistic concept integrates preventative and curative measures amongst which host plant resistance (HPR) plays an essential role. Up to now HPR has been a somewhat under-utilized tool in pest management due to widespread use of pesticides and technological hindrance. Thrips are key pests in agriculture and horticulture worldwide. Here we provide an overview on the current status of research on constitutive and induced HPR including thrips-host relationships and thrips as virus vectors. We stress modulation of plant defense responses by abiotic and biotic elicitors to increase HPR and provide an outlook on the increasing potential of HPR inspired by the fast advancement of -omics techniques.

Shift of Dominant Species in Plant Community and Soil Chemical Properties Shape Soil Bacterial Community Characteristics and Putative Functions: A Case Study on Topographic Variation in a Mountain Pasture

Reducing management intensity according to the topography of pastures can change the dominant plant species from sown forages to weeds. It is unclear how changes in species dominance in plant community drive spatial variation in soil bacterial community characteristics and functions in association with edaphic condition. Analysing separately the effects of both plant communities and soil chemical properties on bacterial community is crucial for understanding the biogeographic process at a small scale. In this paper, we investigated soil bacterial responses in five plant communities (two forage and three weed), where >65% of the coverage was by one or two species. The structure and composition of the bacterial communities in the different microbiome were analysed using sequencing and their characteristics were assessed using the Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Firmicutes and Planctomycetes responded only to one specific plant community, and each plant community harboured unique operational taxonomic units (OTUs) at the species level. There were a large percentage of uniquely absent OTUs for specific plant communities, suggesting that a negative effect is critical in the relationship between plants and bacteria. Bacterial diversity indices were influenced more by soil chemical properties than by plant communities. Some putative functions related to C and N recycling including nitrogen fixation were correlated with pH, electrical conductivity (EC) and nutrient levels, and this also implied that some biological functions, such as ureolysis and carbon metabolism, may decline when fertilisation intensity is reduced. Taken together, these results suggest that a shift of dominant species in plant community exerts individual effects on the bacterial community composition, which is different from the effect of soil chemical properties.

Foliar Aphid Herbivory Alters the Tomato Rhizosphere Microbiome, but Initial Soil Community Determines the Legacy Effects

Aboveground herbivory can impact the root-associated microbiome, while simultaneously different soil microbial communities influence herbivore performance. It is currently unclear how these reciprocal top-down and bottom-up interactions between plants, insects and microbes vary across different soils and over successive plant generations. In this study, we examined top-down impacts of above-ground herbivory on the rhizosphere microbiome across different soils, assessed bottom-up impacts of soil microbial community variation on herbivore performance, and evaluated their respective contributions to soil legacy effects on herbivore performance. We used Macrosiphum euphorbiae (potato aphid) and Solanum pimpinellifolium (wild tomato) to capture pre-domestication microbiome interactions with a specialist pest. First, using 16S rRNA sequencing we compared bacterial communities associated with rhizospheres of aphid-infested and uninfested control plants grown in three different soils over three time points. High aphid infestation impacted rhizosphere bacterial diversity in a soil-dependent manner, ranging from a 22% decrease to a 21% increase relative to uninfested plants and explained 6–7% of community composition differences in two of three soils. We next investigated bottom-up and soil legacy effects of aphid herbivory by growing wild tomatoes in each of the three soils and a sterilized “no microbiome” soil, infesting with aphids (phase one), then planting a second generation (phase two) of plants in the soil conditioned with aphid-infested or uninfested control plants. In the first phase, aphid performance varied across plants grown in different soil sources, ranging from a 20 to 50% increase in aphid performance compared to the “no microbiome” control soil, demonstrating a bottom-up role for soil microbial community. In the second phase, initial soil community, but not previous aphid infestation, impacted aphid performance on plants. Thus, while herbivory altered the rhizosphere microbiome in a soil community-dependent manner, the bottom-up interaction between the microbial community and the plant, not top-down effects of prior herbivore infestation, affected herbivore performance in the following plant generation. These findings suggest that the bottom-up effects of the soil microbial community play an overriding role in herbivore performance in both current and future plant generations and thus are an important target for sustainable control of herbivory in agroecosystems.

Embracing the complexity of plant-microbe-insect interactions under a changing climate for sustainable agriculture

Using beneficial soil bacteria to promote plant growth and reduce pests is a promising direction for sustainable agriculture. However, we need to understand the ecological basis of these interactions in order to identify those with the greatest potential to have an impact in the field. To do this, we need to embrace the complexity of multifactorial experiments to observe the strength of benefits across variable environments. I briefly review the recent literature on plant-microbe-insect interactions across changing environments, focusing on those using multiple factors. I finish by exploring ecological research approaches and multifactorial experimental designs that can be used to simplify the study of plant-microbe-insect interactions.

Untapping the potential of plant mycobiomes for applications in agriculture

Plant-fungal interactions are widespread in nature, and their multiple benefits for plant growth and health have been amply demonstrated. Endophytic and epiphytic fungi can significantly increase plant resilience, improving plant nutrition, stress tolerance and defence. Although some of these interactions have been known for decades, the relevance of the plant mycobiome within the plant microbiome has been largely underestimated. Our limited knowledge of fungal biology and their interactions with plants in the broader phytobiome context has hampered the development of optimal biotechnological applications in agrosystems and natural ecosystems. Exciting recent technical and knowledge advances in the context of molecular and systems biology open a plethora of opportunities for developing this field of research.

Emerging strategies for precision microbiome management in diverse agroecosystems

Substantial efforts to characterize the structural and functional diversity of soil, plant and insect-associated microbial communities have illuminated the complex interacting domains of crop-associated microbiomes that contribute to agroecosystem health. As a result, plant-associated microorganisms have emerged as an untapped resource for combating challenges to agricultural sustainability. However, despite growing interest in maximizing microbial functions for crop production, resource efficiency and stress resistance, research has struggled to harness the beneficial properties of agricultural microbiomes to improve crop performance. Here, we introduce the historical arc of agricultural microbiome research, highlighting current progress and emerging strategies for intentional microbiome manipulation to enhance crop performance and sustainability. We synthesize current practices and limitations to managing agricultural microbiomes and identify key knowledge gaps in our understanding of microbe-assisted crop production. Finally, we propose research priorities that embrace a holistic view of crop microbiomes for achieving precision microbiome management that is tailored, predictive and integrative in diverse agricultural systems.

Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches

Plants recruit specific microorganisms to live inside and outside their roots that provide essential functions for plant growth and health. The study of the microbial communities living in close association with plants helps in understanding the mechanisms involved in these beneficial interactions. Currently, most of the research in this field has been focusing on the description of the taxonomic composition of the microbiome. Therefore, a focus on the plant-associated microbiome functions is pivotal for the development of novel agricultural practices which, in turn, will increase plant fitness. Recent advances in microbiome research using model plant species started to shed light on the functions of specific microorganisms and the underlying mechanisms of plant–microbial interaction. Here, we review (1) microbiome-mediated functions associated with plant growth and protection, (2) insights from native and agricultural habitats that can be used to improve soil health and crop productivity, (3) current -omics and new approaches for studying the plant microbiome, and (4) challenges and future perspectives for exploiting the plant microbiome for beneficial outcomes. We posit that integrated approaches will help in translating fundamental knowledge into agricultural practices.

Soil Microbiomes From Fallow Fields Have Species-Specific Effects on Crop Growth and Pest Resistance

Communities of microorganisms in the soil can affect plants' growth and interactions with aboveground herbivores. Thus, there is growing interest in utilizing soil microbiomes to improve plant performance in agriculture (e.g., for pest control), but little is known about the phenotypic responses of various crop species to different microbiomes. In this study, we inoculated four crop species from different botanical families, maize (Zea mays, Poaceae), cucumber (Cucumis sativus, Cucurbitaceae), tomato (Solanum lycopersicum, Solanaceae), and lettuce (Lactuca sativa, Asteraceae), with diverse soil microbiomes originating from actively-managed agricultural fields or fallow fields under varying stages of succession (1, 3, and 16-years post-agriculture) sourced from a large-scale field experiment. We compared the crops' responses to these different microbiomes by assessing their growth and resistance to two generalist insect pests, cabbage looper (Trichoplusia ni) and fall armyworm (Spodoptera frugiperda). These different microbiomes affected both plant growth and resistance, but the effects were species-specific. For instance, lettuce produced the largest leaves when inoculated with a 3-year fallow microbiome, the microbiome in which cucumber performed worst. Plants were generally more resistant to T. ni when inoculated with the later succession microbiomes, particularly in contrast to those treated with agricultural microbiomes. However, for tomato plants, the opposite pattern was observed with regard to S. frugiperda resistance. Collectively, these results indicate that plant responses to microbiomes are species-specific and emphasize the need to characterize the responses of taxonomically diverse plant species to different microbiomes.