Once isolated, high-value unknowns can then be synthesized to determine their direct biological activities and mobility. Additionally, they can be more finely monitored to discern their spatial distributions. There will be several translational opportunities stemming from these efforts. Biosynthetic pathways could be engineered to produce new bioactive metabolites into plants or other organisms; these could be useful beyond plant health applications. Furthermore, for pathogen/pest-derived chemicals, a next step will be to develop strategies such as HIGS to abrogate pest/microbe chemical effectors. As noted above, chemical immunomodulators could be applied in the field or plants with altered chemistry could be bred/engineered as part of a disease control strategy. Knowledge of the chemical repertoires of plants and their associated microbes/pests could allow the design of sensitive metabolite biosensors that would act as sentinels for perturbations.Diverse pathogens, pests, parasites, and symbionts deploy large repertoires of secreted proteins known as effectors to modify host processes for their benefit. Effector activities range from the suppression of plant immunity to the manipulation of host biochemical and developmental processes. In addition to these virulence activities, effectors can trigger immunity following recognition by cognate receptors, often NLR proteins . Effectors are thus central in dictating the outcomes of plant immunity and disease development. Comprehensive characterization of effector repertoires and determination of their modes of action should therefore be a high priority. Understanding effector biology offers several opportunities for disease control, pipp horticulture as well as tools for manipulating plant biochemistry and development in the absence of disease. Effectors that trigger immunity can expedite the discovery of R genes .
Selection of breeding material with individual effectors is an informative alternative to marker-assisted selection that can facilitate pyramiding multiple R genes, each of which confers resistance to most or all strains of a pathogen by allowing selection of each R gene individually. Effectors have been effectively used in resistance breeding to control diseases caused by diverse classes of pathogen . Effector directed breeding also provides the possibility of identifying and prioritizing R genes that recognize core effectors that are broadly conserved within the species and play important roles in virulence. R genes that recognize core effectors are potentially more durable to pathogen co-evolution, because deletion or silencing of the effector would impose a fitness penalty on the pathogen; however, the caveats regarding possible second site compensating mutations and redundancy in effector function need to be considered . In addition, effector-based screens can be used to identify sources of resistance in plants that are non-hosts for the pathogen of interest. Effectors are also needed for comparative functional studies of the biophysical/biochemical basis of immune-receptor activation . This will address how many ways there are to activate NLRs and how receptor complexes are impacted biochemically and biophysically by immune modulating effectors. Having this information will provide opportunities to re-wire activation mechanisms to facilitate resistance.Diverse pathogens, pests, parasites, and symbionts deploy large repertoires of secreted proteins known as effectors to modify host processes for their benefit. Effector activities range from the suppression of plant immunity to the manipulation of host biochemical and developmental processes.
In addition to these virulence activities, effectors can trigger immunity following recognition by cognate receptors, often NLR proteins . Effectors are thus central in dictating the outcomes of plant immunity and disease development. Comprehensive characterization of effector repertoires and determination of their modes of action should therefore be a high priority. Understanding effector biology offers several opportunities for disease control, as well as tools for manipulating plant biochemistry and development in the absence of disease. Effectors that trigger immunity can expedite the discovery of R genes . Selection of breeding material with individual effectors is an informative alternative to marker-assisted selection that can facilitate pyramiding multiple R genes, each of which confers resistance to most or all strains of a pathogen by allowing selection of each R gene individually. Effectors have been effectively used in resistance breeding to control diseases caused by diverse classes of pathogen . Effector directed breeding also provides the possibility of identifying and prioritizing R genes that recognize core effectors that are broadly conserved within the species and play important roles in virulence. R genes that recognize core effectors are potentially more durable to pathogen co-evolution, because deletion or silencing of the effector would impose a fitness penalty on the pathogen; however, the caveats regarding possible second site compensating mutations and redundancy in effector function need to be considered . In addition, effector-based screens can be used to identify sources of resistance in plants that are non-hosts for the pathogen of interest. Effectors are also needed for comparative functional studies of the biophysical/biochemical basis of immune-receptor activation .
This will address how many ways there are to activate NLRs and how receptor complexes are impacted biochemically and biophysically by immune modulating effectors. Having this information will provide opportunities to re-wire activation mechanisms to facilitate resistance.In addition to improving genetics of a crop itself to enhance resistance against deleterious organisms, there are multiple opportunities to use beneficial plant-associated organisms as allies . These include many types of microbes, arthropod predators and 12 / Molecular Plant-Microbe Interactionsparasitoids, companion crops, and other organisms. Beneficial microorganisms play a central role in maintaining plant health in terms of both nutrition and defense. For example, arbuscular mycorrhizal fungi and plant growth-promoting rhizobacteria not only enhance plant nutrient capture but also can directly modulate plant defenses . The advent of high throughput DNA and RNA sequencing technologies and increased capacity for characterizing small molecules from soil samples have driven a rapid expansion in environmental genomics directly germane to plant productivity . However, virtually nothing is known of the principles of evolution and biochemistries that determine the composition of plant-associated microbiota above and below ground. Robust experimental systems are crucially needed to investigate principles of microbiota structure and function, from reductionist settings, through increasingly complex ecological settings, to deployment. Most crops have been bred independently of many of their rhizosphere- and phyllosphere associated organisms, potentially due to loss of microbe diversity and intensity in agricultural ecosystems as a result of tillage and chemical inputs . Traditional breeding programs may have inadvertently selected against beneficial microbial associations due to their use of high nutrient conditions and pesticides, which decrease opportunities for microbial benefits. For example, under ample soil nutrient conditions, the carbon drain of AMF can present a fitness cost, potentially selecting against traits favoring mycorrhizal associations. Research is required to evaluate the performance of different crop genotypes under low input conditions, including their ability to attract and sustain beneficial microorganisms. There is a dearth of knowledge as to how intra- or inter-specific plant genetic variation impacts the plant-associated microbiota. Current results support the existence of a core microbiome that may be tuned by specific plant genotype x microbiome and genotype x environment interactions . For example, plant root exudates contain signaling chemicals that influence the species composition of the rhizosphere but little is known of natural genetic variation influencing the support of beneficial rhizosphere microbes. Harnessing beneficial microbes will be increasingly important as low-till, low-input agricultural systems are adopted . Foundational research is also needed to identify appropriate combinations of beneficial organisms that can be used to develop cocktails of plant growth promoting or bio-control organisms. Addressing this difficult challenge is dependent on deriving associations of microbes that provide diverse benefits to plants and are also able to invade and persist as complex microbial communities in the target environment, vertical growing weed potentially in a co-dependent manner. Research is needed to investigate trade-offs involved in hosting potentially beneficial microorganisms. Priming is a long-lasting memory that provides potentiation of faster and stronger defense responses . Beneficial microorganisms have been demonstrated to induce defense; well-studied examples include root-colonizing bacteria that promote plant growth and provide enhanced broad spectrum resistance to several types of pathogens . Pathogens can also activate resistance distant from the site of infection . Some signaling components are involved in both of these long-distance responses. The challenge is to ensure that plants have the capacity to be well-colonized with ISR-promoting microbes and also capable of adequately activating these signaling pathways for resistance.
Priming or induction of plant defenses, particularly SAR, may incur a yield penalty, which is yet to be fully understood. Germplasm should therefore be screened to find genotypes amenable to beneficial colonization. Plant genes that regulate responses to different microbial populations should also be characterized to identify input genotypes for breeding programs to enhance beneficial associations. Progress towards implementing these strategies will require extensive sequencing for microbial characterization, high resolution metabolomics, the ability to culture and maintain promising organisms, and the ability to assess many plants rapidly for a variety of responses. It is important to develop interventions for improving plant health that go beyond altering crop genetics. Small molecule signals generated in response to beneficial microorganisms could be commercialized for external application, in a similar manner to chemicals inducing SAR. Both biological control and bio-pesticides have much scope for development. There are multiple approaches to improving biological control by boosting populations of natural enemies of pests, pathogens, and weeds. Classical bio-control involves recruiting biological control agents from the areas of origin of invasive pests and weeds and introducing them to the areas where they have invaded. This approach has had several impressive successes as well as some inconsistent results. It requires long-term research efforts to find candidates, determine likely effectiveness, and verify safety. Conservation bio-control involves exploiting resident populations of natural enemies of pests, weeds and pathogens as an ecosystem service; interventions to improve the effectiveness of conservation bio-control are required to support natural populations. Again, the new tools for determining microbial community structure and identifying insect pest population structure help to build mechanistic understanding of the ecosystems, leading to more reliable predictions. This requires food resources and suitable habitat. Considerable progress has been made with field margins to support populations of natural enemies of insect pests; however, there is often insufficient movement of beneficials into the crop where they are needed. Lure and reward strategies to attract beneficials with semiochemicals coupled with food rewards that enhance their fitness and performance are required . A greater foundational understanding of the ecology of tritrophic interactions and signaling is needed to enable better recruitment of natural enemies of pests , perhaps by breeding. Companion cropping can both repel pests and attract their natural enemies; a successful example of this is the push-pull system in Kenya . The development of biopesticides involves formulation of living organisms, for example an entomopathogenic fungus or a virus that affects insects, can kill the pest target and can be sprayed or applied like a pesticide. Research priorities include discovery of new agents, development of new biopesticide delivery methods, and approaches in which a killing agent is formulated with an attractant semiochemical.Because viruses are obligate intra-cellular pathogens with small genomes, they are completely dependent on cellular host factors to complete their life cycle and on vectors such as insects, nematodes, or plasmodiophorids for dissemination. Plant viruses are comprised of either RNA or DNA genomes, which typically encode only four to ten proteins and differ in replication strategies . Several aspects of viral biology remain insufficiently characterized. The last decade has seen major advances in characterization of host factors involved in replication and movement and virus manipulation of host gene regulation . Viruses also modify host and insect vector behaviors . However, the knowledge of the underlying mechanisms is still lacking. In addition, virus-plant and virus-vector interactions as well as regulatory host small RNAs are affected by environmental factors such as temperature and light . The basis of virus specificity for certain cell types and tissues and why some viruses have wide or narrow host ranges are also not understood. It is known that hormone and defense pathways are affected by viruses, but information on spatial and temporal restriction of viruses at the cellular level is lacking. Discovery of the underlying reasons may enable the development of novel strategies that restrict virus infection. The drivers of virus evolution and the mechanisms by which vector population complexity influences viral population composition and transmission remain incompletely known. Multiple studies are needed to address these gaps in our knowledge. Single-cell genomics and transcriptional profiling may reveal molecular details of viral restriction, cell autonomous and nonautonomous virus responses, basis of seed transmission, and the influence of environmental factors and host developmental stage on virus infection. Development of anti-viral peptides targeting key components is needed to determine the basis of host and tissue specificity.