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Improving Crop Productivity Through a Comprehensive Understanding Of Improving crop productivity through a comprehensive understanding of the phytobiome Mejorando la productividad de cultivos a través del conocimiento comprensivo del fitobioma Jan E. Leach Colorado State University XIII IRCLAC Piura National University Piura, Peru May 2018 Phytobiomes are complex systems Phytobiome: • Interactions of the environment and living organisms that influence or are influenced by plants Plant Microbiome: Phytobiome • The dynamic community of microbes associated with plants Phytobiomes: A Roadmap for Research and translation, 2016. (St. Paul, MN: American Phytopathological Society), pp. 15 Phytobiome members in the soil In 1 g soil: *1 billion bacteria *100 million virus *100 thousand fungi & microalgae plpnemweb.ucdavis.edu *10’s of thousands of protozoa *hundreds of nematodes Embracing the complexity of the Phytoboime! It’s a SYSTEM!!! It’s bacteria! Gut bacteria could predict asthma in kids Sarah Williams, SCIENCE Sept 30, 2015 When Gut Bacteria Changes Brain Function ….the microbiome may play a role in regulating how people think and feel. David Kohn The Atlantic June 24, 2015 Wherever You Go, Your Personal Cloud Of Microbes Follows ROB STEIN, NPR SEPTEMBER 22, 2015 8:38 AM ET Grazers & predators: important phytobiome members e.g., Vermamoeba vermiformis attach to Rhizoctonia solani mycelia, consume mycelial contents, and encyst. • What is the net impact of predators & grazers onplpnemweb.ucdavis.edu the microbiome? • Can these be manipulated to enhance plant health, quality 10 µm and productivity? John Long et al. unpubl. Phytobiome members communicate! Leach et al. 2017 Cell How do they communicate? What are the outcomes? It’s complex! Interkingdom communications: Quorum sensing (QS) Leach et al. 2017 Cell • Bacteria induce plant roots to • Bacteria and plants communicateVirulence, through biofilms, stress responses, secrete rosmarinic acid, a motility, etc. mimic of a bacterial QS signal Early activation chemical signals of plant • Rosmarinic acid induces a defenses Bacterial ‘premature’ QS response in produced bacteria production of QS signal • virulenceCan factors, we manipulateetc. production of signals to • Rapidincrease activation of plantplant disease resistance? defense responses plant Plant produced protection QS mimics Premature production of virulence factors, biofilms, etc Corral-Lugo et al., 2016. Sci Signal Adapted from Curr Opin Plant Biol 2004 Plants control their microbiome composition/diversity • Plant signals attract/enrich specific microbes in the rhizosphere • Plants regulate the entry of microbes to fine-tune the internalized microbial communities Trivedi in Leach et al. 2017. Cell • Plants can transmit bacterial endophytes from generation to generation through seed • Geographically distinct soils contribute taxonomically similar sources of bacterial endophytes Exploiting knowledge of the phytobiome What guides plant microbiome composition and dynamics? • Can we exploit that information to improve crop health and productivity? • Can we breed for plants that select for ‘healthy’ or ‘useful’ microbomes? • Can we develop/engineer microbial mixes that establish/restore a ‘healthy’ microbiome? Environmental impacts on phytobiome interactions “Warming in the climate system is unequivocal…” International Panel on Climate Change 2007, Climate Change Synthesis Report Battisti and Naylor, 2009. Science “For the major crops (wheat, rice, and maize) in tropical and temperate regions, climate change without adaptation is projected to negatively impact production ….“ IPCC, 2014 (http://www.ipcc.ch/report/ar5/) Members of the phytobiome and their interactions are impacted by the environment Abiotic Stresses Biotic Stresses Temperature Stress Pathogen Attack Drought Pest Attack Salinity Competition Nutrient Stress Microbes confer heat tolerance to plants Inside Inside Virus Fungus Plant Thermotolerant Thermotolerant Heat-treated tomato plants + Fungus + virus Dead + Fungus Uninfected Alive + Fungus + Fungus Uninfected + virus Marquez 2007. Science 315:513 Abiotic and biotic stresses are usually simultaneous Heat Stress Heat Tolerance Disease Pathogen Attack Disease Resistance For many plant diseases, disease pressure increases with increasing temperature Xoo What is the influence ofPXO145 • Bacterial blight (BB) of rice: – disease is higherhigh in the temperatures hot/humid on season HTHT – much resistanceless disease occurs in theto BB disease in cool/dry season rice? LTLT 35°C day/29°C night = High 29°C day/21°C night = Low IR24 (no R gene) Most sources of resistance to bacterial blight disease are single R genes ~40 R genes identified Most rice bacterial blight resistance genes lose efficacy at high temperatures EXCEPT Xa7 3.5 a 35°C day/29°C night HIGH Why aare plants more susceptible to 2.5 29°C day/21°C night LOW diseaseb at high temperatures? 1.5 a Why are someb resistance genes more Lesion length (cm) length Lesion b b 0.5effective at high temperatures?a a a Xa3 Xa4 xa5 Xa7 Xa10 Cohen et al., 2017 Webb et al., 2010; Rice bacterial blight resistance gene Balidion et al., unpubl. ABA responsive genes are downregulated by high temperature during resistant interactions (Transcriptome Analysis) ABA responsive genes Why do we care? H1: During simultaneous Resistant Mock treated high temperature stress (Xa7-avrXa7 Susceptible •Identify/createinteraction) resistance sourcesand that pathogen are attack, rice interaction effective and durable at high temperaturesfavors abiotic stress •Facilitate planning/breeding for sustainableresponse pathways. crop kernel estimate density kernel • Plants show more production under conditions of increasingdisease global log2 fold change High Temp relative to Normal Temp temperatures H2: Xa7 suppresses the abiotic responses Cohen et al. 2017 Can we manage the phytobiome to control plant pests? • Do bacteria associated with Russian wheat aphids enhance aphid virulence to plants? Luna et al. submitted The Russian wheat aphid microbiome is diverse Dirty aphids Luna, Van Eck, Campillo et al., in prep Bacteria associated with Russian wheat aphid enhance aphid virulence to wheat Aphids treated with antibiotics (to kill bacteria) cause less damage to wheat Clean Dirty aphids aphids Luna, Van Eck, Campillo et al., submitted Managing the phytobiome to control plant pests Phytobiome knowledge can guide • H0 : Bacteriamanagementassociated with strategies • ShouldRussian breeding wheat programs aphid target the bacteria rather than the insect?manipulate plant defenses • Canto enhance the leaf microbiomes aphid virulence be altered to protect plants from aphid feeding? • Have some aphids evolved to rely on bacteria for virulence, and if so, can we identify novel resistances that detect/disrupt that process? Luna et al. submitted A future of ….Healthy and productive cropping systems • Plants that ‘select’ & foster beneficial microbiomes to: – Enhance plant growth/productivity – Control diseases and insect pests – Increase plant nutritional quality A future of: • Managed/engineered phytobiomes that: – rebuild Source: UNEP depleted/degraded soils *1.5 billion people depend on degraded lands for survival! – produce with less water, or in unfavorable environments Texasdroughtproject.org A future of….. Practices that promote healthy, productive soils A future of safer, healthier foods….. Phytobiome…. Achieve sustainable agricultural productivity through a systems-level understanding of the diverse interacting components INTERNATIONAL ALLIANCE FOR PHYTOBIOMES RESEARCH A nonprofit consortium of industry, academic, and governmental scientists ¡Gracias! Thank you! .
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