Appendix B: Knowledge Gaps

A. Phytobiome composition
Phytobiomes, and in particular plant and soil microbiomes, are complex in their diversity, with the bacteria alone often comprising hundreds of species, their distribution, with organisms numbering from 1 to billions of individuals, and their dynamics, with residents and transients each in constant flux. Despite this overwhelming complexity, some seemingly universal and environment-specific trends and commonalities emerge. By defining the components that are critical, dispensable, and interchangeable, including how they are altered by other phytobiome components such as climate, crop, soil type and disease, we can better predict phytobiome resilience and adaptability. Specific knowledge gaps include:
  • What species are keystone species for the establishment of microbial communities on plants and to what extent do different plant species share keystone microbial colonists? Are there true keystone species?
  • How much genetic diversity is present within taxa and what are the functional impacts of this diversity?
  • How interchangeable or dispensable are components of plant, soil, and insect microbiomes?
  • In looking for unifying principles underlying the composition of microbiomes, how do we deal with the infinitely high number of factors that may have an influence, particularly given that these factors are interacting within the entire phytobiome?
  • What are the unifying principles underlying the composition of phytobiomes? Is there evidence of parallel evolution of microbiomes?
  • Given the complexity of microbiomes, in what time-frame will we have the ability to be comprehensive in our understanding of all organisms in the phytobiome?
  • Are there significant differences between the functions of microbes, insects, and other phytobiome components in organic versus conventional plant production systems?
B. Processes driving phytobiome composition and dynamics
Knowledge of the principles underlying the development, stability, and resilience of phytobiomes is key to prescribing strategies for improved crop health and productivity. For example, our understanding of the general principles of microbial community assembly in distinct plant tissues and environs is currently limited, although it is clear that there must be niche partitioning to allow a diverse community to develop, and the order in which they assemble plays a part in how effectively the phytobiome functions. Critical knowledge for plant breeding and improvement strategies should include an evaluation of germplasm diversity for phenotypes that influence the development of microbial communities favorable to plant health and productivity. Generating this knowledge requires large-scale studies associating plant traits with plant microbiome members as well as community genetic approaches that recognize the interplay between plants, other components of the phytobiome, and the interspecies interactions among those members.
  • What are the principles underlying the development and compositional changes in phytobiomes in response to the environment? Are there general principles of assembly of phytobiome constituents that are operative over all agricultural systems?
  • How idiosyncratic are the drivers of the assembly of phytobiome constitutents for a given plant species or environment?
  • To what extent do plants live in an "open" environment from which the microbiome is locally selected?
  • To what extent is the assembly of microbial constituents subject to (i) a "legacy effect" where the order of assembly influences final community composition, or (ii) "mass effects" of dispersal from the surrounding environment that overwhelm the managed community?
  • What genetic linkages connect phytobiome components? For example, what plant genes or phenotypes are linked to particular microbial or animal taxa associated with those plants?
  • How do genetic loci in hosts shape the function and composition of the associated animal and microbial flora? What are the mechanisms by which plants recruit beneficial phytobiomes?
  • Are the phenological states of plants strongly associated with the impacts of microbial constituents?
  • How does an initial microbiome inoculum affect the target plant phenotype regardless of final community composition?
  • Are there differences in the relative magnitude or qualitative differences in the effects of associations of phytobiome constituents on perennial versus annual plants?
  • What are the roles of secondary metabolites and other small molecules in the establishment and function of phytobiomes?
C. Predictive modles and networks that integrate phytobiomes data
A comprehensive understanding of phytobiome requires knowledge at all scales, from molecular interactions and the sharing of chemical signals to long-range dispersal mechanisms that reach across continents. Identifying the dynamics and interactions among individual components of phytobiomes across a range of spatial and temporal scales will provide data that may be integrated using conceptual and predictive models.
  • How do we successfully integrate data to capture the complex beneficial, synergistic, antagonistic, exploitative, parasitic, and pathogenic associations that cascade through complex, real-world phytobiomes?
  • How do we relate an explicit body of understanding, predictions, and principles in phytobiome ecology, evolutionary biology, and function to plant productivity?
  • Can we exploit predictive and prescriptive analytics to design seeds, management practices, and ecosystems adapted to future environmental challenges?
D. Comprehensive impacts of phytobiomes on plant health and plant productivity
Plant health and productivity is influenced by pests, pathogens and pollinators, nutrient availability, and environmental stress, but also by more complex phenomena that are still being discovered. For example, root-associated microbes can positively and negatively influence insect herbivores, leaf infestations by insects can induce defenses against root pathogens, and nematode-vectored microbes can colonize plants and produce toxins that sicken livestock. The full impacts of such multitrophic interactions on the health of plants, plant ecosystems, and the consumers of plants and plant products are not yet known, but are certainly much broader than is currently recognized. Conversely, plant invasiveness and agronomic practices such as tilling impact the health of phytobiomes, but we know very little about resilience and responsiveness to such perturbations. Characterization of this multidirectional feedback through network analysis and model generation will be required to distill the massive quantities of data into tangible, actionable outcomes.
  • How do phytobiomes affect plant performance?
  • Are there universal plant symbionts that can colonize most or all plants?
  • What are the functional capacities of diverse strains within taxa, individual taxa, and simple communities to alter plant productivity?
  • Are the net effects of the microbial communities on a plant different from the effects of individual microbes?
  • Will rare members of the microbiome have large effects on plant productivity and how can they be studied and manipulated?
  • What is the extent and predictability of interaction of various taxa in the phytobiome and how might they influence plant health and productivity?
  • Do existing ecological models of interaction outcomes (e.g., competition models, predator-prey models, niche models) adequately predict these effects or do we need new approaches that scale to simultaneous multivariate interactions?
  • What are universal metrics that identify soil as "healthy"?
  • Are the effects of microbiome constituents on plant responses greater for foliar or subterranean plant parts?
  • Within phytobiomes, how are soil, plant, and ecosystem health influenced by interactions amongst and between individual components, such as plant-soil feedbacks in which plants change the biological, chemical and/or physical properties of the soil, which then change the fitness of neighboring plants or subsequent generations of plants?
  • How do multitrophic interactions, such as viruses in insects or microbes on plants, modulate host phenotypes and trophic interactions?
  • What are the mechanisms by which commensals evolve into pathogens, pests, or mutualists?
  • How do preharvest phytobiomes influence postharvest food storage and processing, feed digestibility and host nutrition, fermentation into biofuels, and other uses for plants and plant products?
E. Translation of phytobiome knowledge into strategies to enhance sustainable production of food, feed and fiber
Sustainable cropping systems and practices that promote phytobiome management with plant breeding efforts and sound agronomic practices are needed to support a new Green Revolution that ensures food security for future generations. We now have the technological capabilities to develop site-specific agronomic practices, that is, management practices tailored to specific plant genotypes in specific environments (Genotype x Environment x Management).
  • What can we learn from past and current efforts to modify phytobiomes to achieve disease control, increase plant productivity, and improve disease forecasting?
  • How can we design novel approaches for effectively and reproducibly managing phytobiomes to optimize plant productivity and the uses of plants and plant products?
  • In what contexts is it useful (and cost effective) to modify the phytobiome?
  • How do common cultural practices used in agriculture alter the phytobiome? Can they be used for directed modification?
  • Are "founder effects" of initial colonists of plants sufficiently robust that permanent shifts of microbiome constituents can be achieved from simple manipulations of early colonists?
  • Are there particular phenological stages of plants for which the phytobiome is most easily manipulated and/or to which the plant is most responsive?
  • To what extent are the microbiome constituents subject to vertical transmission, and hence amenable to manipulation by seed treatment?
  • Can we influence the microbiomes of a target group of plants by using a distinct set of plants, such as the non-crop plants used in cover crop rotations, relay-cropping and intercropping?
  • What is the most efficient way to engage growers in identifying and prioritizing their needs and challenges?
  • How can early science findings be more efficiently implemented to see outcomes in the field?
  • How can the phytobiomes of crops be modified to increase agricultural production in an environmentally sound manner?
  • How can we build a knowledge base that will empower the development of crop varieties, management practices, and nutrient inputs that are adapted to the environmental conditions and organismal composition of a specific site? How can we best disseminate this knowledge base?
  • How can the extensive infrastructure for breeding and crop management that has evolved with the development of modern agriculture facilitate the translation of knowledge of phytobiomes for agricultural improvements?

E1. Strategies that target cultural practices (crop or soil management, water, inputs, tillage, etc.)

    • How can we predict how specific management practices will affect the phytobiome?

E2. Strategies that target microbial management (inoculants, selection of indigenous mecrobes, etc.)

    • How can exogenous microbial signaling molecules or secondary metabolites be used to induce predictable shifts in microbial communities?
    • How can mixtures of microbes or microbial products be fermented and formulated, alone or in combinations with chemicals, to generate microbial consortia or communities as inoculants?

E3. Strategies that target plant selection/plant genetics

    • How can collaborations between plant breeders and microbiologists shift plant breeding practices to better incorporate the contributions of microbiomes, such as to maximize the impact of beneficial microbes?  
    • Are plant traits to optimize microbial composition readily selectable? Can readily selectable microbial traits help optimize plants for crop production?
F. Broader impacts of phytobiome knowledge
  • What useful organisms, genes, and products can be mined from phytobiomes?
  • How can we exploit knowledge of crop phytobiomes to double overall crop production in a sustainable manner?