A. Multi-omics tools to explore phytobiome composition, dynamics and function
High throughput sequencing has been a powerful tool for profiling the composition of microbial communities in phytobiomes and characterizing the total genetic content of communities (metagenomics) and expression of genes in target organisms and communities (metatranscriptomics). Community profiling usually involves extracting the identity and abundance of organisms based on target sequences.
  • We need to improve the phylogenetic resolution, sensitivity, and representativeness of high throughput sequencing techniques for viral, bacterial, fungal, nematode, and insect community profiling, including high throughput methods that differentiate at the strain level for microbes.
  • We need methods for high throughput analysis of secondary metabolites in situ in phytobiome-relevant environments.
  • We need an interdisciplinary effort to identify the metadata that should accompany microbiome studies, including relevant plant physiology (e.g., root type and developmental stage), soil properties (e.g., soil classification), and climate data.
  • We need an interdisciplinary effort to identify best practices and standardize protocols for phytobiome studies.
  • Can we comprehensively sequence the genomes of phytobiome constituents, including both cultivated and uncultivated microbes?

B. High throughput, cost-effective plant phenotyping
Non-destructive, image-based phenotyping of plants is allowing for high-throughput plant characterization, which is greatly enhancing the association of genes and phenotypes. The strong impact of the environment on plant phenotypes, including the interactions between plants and other components of phytobiomes, indicates that studies need to be performed under field conditions.
  • Can we design high-throughput phenotyping in the field that is non-destructive? What traits/components need to be measured?
  • Can we improve root phenotyping techniques, especially for the field, and also tools to monitor the microbial colonization of root systems?
  • How can drones be adapted for real-time, high-throughput phenotyping?
  • How can sensor technologies be optimally deployed for real-time, high-throughput phenotyping?
  • What breakthroughs will be needed in high-throughput phenotyping of above- and belowground plant traits to enable connections to be made with the presence or activity of microbiome members?

C. Relevant model systems for phytobiome research
Model plant systems enable the coordination and integration of efforts across research groups and disciplines. Which plant, climate, and management systems, including native ecosystems, would enable the greatest progress in understanding phytobiomes if used as models?
  • Should the scientific community select model systems for advancing phytobiome studies, and if so, what criteria and decision process should be used for their selection?

D. Analytical limitations
The complexity of the phytobiome components, and particularly the microbial component, present challenges to their analyses. Extensive statistical and computational tools need to be further developed that enable streamlined analytical approaches for widespread use.
  • We need statistical tools that identify taxa differences among microbial communities in multifactorial experiments.
  • We need bioinformatics and computational tools for big data processing and manipulation in preparation for data analysis.
  • We need tools to better account for nonlinear interactions rather than just linear interactions.
  • We need to identify best practices and standardize protocols for analyzing data from phytobiome studies.
  • How can computational tools be developed to better characterize, analyze, and model species (genomic, phenotypic) interactions within complex communities?
  • How can we build predictive and prescriptive models of phytobiomes?