Large, well-characterized datasets of plant genotype, yield and health â Greater power to associate phytobiomes and plant health outcomes. â« Crop ...
UNDERSTANDING THE PHYTOBIOMES FOR IMPROVED CROP PRODUCTIVITY Jan E. Leach, Gwyn Beattie, Kellye Eversole American Phytopathological Society Public Policy Board
The Phytobiome is a system: All organisms living in, on and around plants microbes (the plant & soil microbiomes) virus animals (insects, nematodes, etc) other plants
the Environment
An interdisciplinary, systems approach is required to understand the dynamic and multitrophic interactions in Phytobiomes
Enabling Technological Advances • Advances in metagenomics-enabling technologies – high-throughput sequencing – computational biology & modeling – other ‘omics’ technologies
• Advances in systems-level approaches • Human Microbiome discoveries – lessons learned – paradigm shifts – applications
These advances are enabling assessment of the (1) community composition, function, and activity of living organisms in the phytobiome, and (2) environmental influences on those interactions
Phytobiome studies present distinct opportunities from human microbiome studies Can inoculate experimental subjects and control compliance with trts Greater opportunities to establish causal relationships Germplasm collections and breeding/engineering of plants Greater power to identify host genotype effects Large, well-characterized datasets of plant genotype, yield and health Greater power to associate phytobiomes and plant health outcomes Crop management systems associated with modern agriculture Enable rapid application of knowledge of phytobiomes to improving crops and production practices
Phytobiomes present distinct challenges from the dominant human microbiome: the gut GI tract is a static structure Gut microbiomes exhibit homeostasis and dysbiosis (disrupted homeostasis) The gut is a hostdominated
Plants grow continuously Do phytobiomes attain homeostasis? Is dysbiosis an appropriate concept for phytobiomes? Phytobiomes are influenced by plants, soils, animals (insects), and fluctuating environmental conditions
Systems-levels approaches encompass more system components for phytobiomes
Sample collection Community DNA extraction
Community RNA, protein, metabolite extraction
PCR amplify
(16S-18S rRNA, ITS, cpn60)
Amplicon sequencing
Metagenome Meta- Metaproteome Metabolome sequencing transcriptome analysis analysis sequencing
Species (taxa) number, abundance, composition Community function “Who is there?”
“What can they do?”
Community activity “What are they doing?”
Sample collection Community DNA extraction
Community RNA, protein, metabolite extraction
PCR amplify
(16S-18S rRNA, ITS, cpn60)
Amplicon sequencing
Metagenome Meta- Metaproteome Metabolome sequencing transcriptome analysis analysis sequencing
• Need Species (taxa)standardized protocols: number,– abundance, diversity and lack of standards in microbiome composition Community function Community activity
research (everything from sample collection and “Who is there?” candeposition they do?” are they doing?” storage “What to data and“What file format) make it very difficult to reconcile data from different Huttenhower et al., 2014. Cell studies. Goodrich et al, 2014. Cell
Phenotypic data are diverse & often illdefined: – Plant health/disease status – Physiological states – Biomass – Soil health – 3-D structure – Metabolome, metatranscriptome, metaproteome – Etc.
Phenotyping needs: – Capability to scale
• Single cell vs organ vs plant vs population?
– High throughput
• Continuous or multiple times • Across environments
– Ability to integrate & store diverse data • Novel & improved algorithms • Increased personnel trained in analysis of microbiome data • Access to sufficient computing power
– Reduced costs
Application of Phytobiomes Research: • Increase agricultural productivity/reduce needs for inputs • Improve food quality and safety • Remediate environmental perturbations & restore soil • Breed or engineer plants that select health for & maintain beneficial • Discover useful organisms or products phytobiomes • Provide precise insights into the mechanisms and consequences of plant disease (andaresistance) • Assemble or engineer beneficial • Elucidate the evolution/co-evolution of phytobiomes phytobiome • Promote animal and human microbiomes that favor health and well-being
Phytobiomes 2015: Designing a New Paradigm for Crop Improvement:
A Summit, Summer 2015, Washington, D.C.
Bring together a broad community of scientists to establish current and future priorities in phytobiomes research Forge interdisciplinary, interagency, international, and public-private collaborations Discuss how to translate phytobiomes knowledge to safe and sustainable crop production practices
