The Phytobiomes Initiative proposes a systems-level approach to studying the entire microbial community associated with plants, including bacteria, viruses, and eukaryotes in the rhizosphere, phyllosphere, and within plants. Recent advances in metagenomic technologies now allow comprehensive analysis of both culturable and non-culturable microbes. Two recent studies using these methods revealed that root microbial communities are non-random and depend on host genotype and environment. The initiative aims to establish a foundation for understanding how phytobiomes influence plant health and productivity, with the goal of developing strategies to improve crop yields, reduce disease and environmental impacts, and enhance food safety and security.

1. A proposal from the American Phytopathological Society (APS)
Phytobiomes Initiative
Presenter: Jan E. Leach, APS Public Policy Board Chair Moderator: Kellye Eversole, Eversole Associates

2. What is the Phytobiome?
•The entire microbial community in, on, and adjacent to plants
–rhizosphere, phyllosphere and endophytic compartments
•Includes virus, prokaryotes and eukaryotes
–Plant pathogens, beneficial microbes, plant-associated human pathogens
–Culturable and non-culturable members
•The Phytobiomes Initiative targets an understanding of how the associated microbial community influences or is influenced by the plant and how that information can be used to improve crop productivity

3. Where are we starting: knowledge of plant-microbe associations?
–What microbes are in and on plant surfaces (usually leaf)?
–What factors are important for their survival, colonization, and distribution on the surface? their ability to cause disease or induce resistance?
–How do they communicate with each other and with the plants?

4. •Microbial composition
•How microbes finding and communicate with roots
–e.g., Agrobacterium and Ti plasmid ‘colonization’ of the rhizosphere
What is known about rhizosphere microbes?
Arabidopsis root colonized by the beneficial bacterium, Bacillus subtilis
Quorum sensing and Ti plasmid colonization of soils by Agrobacterium

5. •non-culturable microbes?
–All microbes studied were culturable
•communities?
–Only one or a few microbes at a time
•system?
–Interaction of plant with one microbe
–No integration of biotic and abiotic stresses
But, what about the:

6. Why the Phytobiomes Initiative now?
•Advances in metagenomics-enabling technologies:
–high-throughput sequencing,
–computational biology,
–other ‘omics’ technologies
•These advances enable the metagenomic analyses needed to assess the community composition, function, and activity of both culturable and non- culturable organisms in the phytobiome

7. Enter: METAGENOMICS!
•Genomic study of all organisms
–Sequencing 16S rRNA, DNA, or mRNA from environmental samples
•Address questions on:
–community composition (“Who is there?”)
–function (“What can they do?”)
–activity (“What are they doing?”)

8. Two Recent Root Metagenomic Studies
•DNA fractionated from microbes in the soil, rhizosphere, & endophytic compartments for metagenomic sequencing
Nature Biotech 2012 30:961
Nature 2012 488: 86
Nature 2012 488:91

9. What did they find?
•Many microbes abundant in the soil are NOT found in the endophytic communities
•Endophytic communities from soils from different parts of the world were surprisingly similar
•Host genotype –dependent selection within the root corpus fine- tunes community profiles.
•Bottom line: communities are not a product of random assembly, but rather, they may be predicted based on knowledge of the processes driving their development
Nature Biotech 2012 30:961
Nature 2012 488: 86
Nature 2012 488:91

10. •Eukaryotes? Virus?
–Focus so far on prokaryotes
•The system?
–Field crop studies
–No integration of biotic and abiotic stresses
•Application?
A good start, but what is lacking?

11. What’s new about the Phytobiomes Initiative?
•Systems approach
•Foundational to applied science
•Builds on our current understanding of plant-microbe- environmental interactions and networks
•Collaborative: inter- and multi-disciplinary
•Global research and advocacy partners in the private and public sector
•Focus on downstream application
–Doubling production of safe and nutritious food, feed, and fiber

12. Example Phytobiomes Questions:
•How do phytobiomes influence plant responses to pathogens and affect plant productivity?
•How is the composition of phytobiomes influenced by the environment and human inputs?
•What useful organisms, genes, or products can be discovered by study of phytobiomes?
•Can phytobiomes be tailored to:
– improve food composition and safety?
–improve animal and human microbiomes?
–increase agricultural production in an environmentally sound, sustainable manner?

13. Phytobiomes Initiative Opportunities: 2025
Foundation to:
–Assess climatic impacts on crop-related phytobiomes
–Understand relationships with nutrient uptake and utilization
–Relate the phytobiome to its impacts on animal and human health and safety
–Safely and sustainably intensify production of food, feed and fiber
–Change the discovery paradigms for plant disease control and crop improvement
– etc.…..

14. The Phytobiomes Initiative: An opportunity to partner -across agencies, industry, scientific societies -globally
Vision
Comprehensive knowledge of phytobiomes
Outcomes
New strategies for reduced plant disease, improved yields, reduced environmental degradation, safer food, healthier soils, improved response to weather extremes, managing microbial communities, improved human health, reduced resistance to antimicrobials, reduced non-renewable inputs. Increased and more robust human, genetic and technological infrastructure
Impact More safe and healthy food, feed, and fiber

15. So, why this webinar? To start conversations for a new agricultural science paradigm……
•Science across disciplines that creates a foundation to understand and manipulate phytobiomes

16. •Partnerships with and among scientific societies to advocate for support of needed research and resources
–co-sponsorship of a workshop to refine goals for the initiative
So, why this webinar? To start conversations for a new agricultural science paradigm……

17. Thank you! Questions? Contact: Jan.Leach@colostate.edu eversole@eversoleassociates.com Visit www.phytobiomes.org