harnessing beneficial microbial communities: opportunities and challenges for enhancing crop...

Harnessing beneficial microbial communities: opportunities and challenges for enhancing crop productivity

Richard BroglieDuPont Pioneer

Key challenges to agricultural productivity and overall food security

Productivity improvements have reduced cropland expansion

World Maize Production

Mill

ion M

T

93% increase in output | only 31% due to land use

97 million virtual hectares

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Qrome®Qrome®

PG Economics, Ltd, 2010, 2013 & 2016

Insect protected corn has resulted in more than 10% increase in yield worldwide

Insect protected corn and cotton have increased farm income by >$56B between 1996 and 2001

Trait crop

Increase in

farm income

2011

(million US $)

Increase in farm

income 1996-

2011

(million US $)

Farm income

benefit as % of

total

production

Insect resistant

corn7,104.9 25,762.0 6.8

Insect resistant

cotton6,559.6 31,263.2 14.7

The tremendous benefit of insect control traits

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New corn genetics deliver improve yield

Source: 2015 Pioneer on-farm trial database. Customer comparisons based on 2015 yield results including data from weigh wagon and PKP trials for all Pioneer® brand hybrids against all competitors. Individual results may vary. All data weighted by comparisons within 4CRM and adjusted to 15% moisture. Product performance is variable and subject to any number of environmental, disease and pest pressures.

World Record of 532 bu/acre

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bullets please use the

Increase/Decrease Indent

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Microbials represent an underexploited component of integrated crop management

Increased offerings of beneficial

microbials that reduce use of

limited water, chemical pesticides

and fertilizers

Biologicals integrate with, or

complement, traits and/or

chemical inputs

Current products represent only a

fraction of total benefit that could

be realized with deeper knowledge

of microbiomes

Seed-applied technologies

Advanced genetics

Nutrient cycling

Biotech traits

Agronomy expertise

Crop / nitrogen models

Microbial consortia

Climate / weather

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Beneficial interactions in the rhizosphere

Increase nutrient uptakeSiderophore production

Phosphate solubilization

Lower soil pH

Protection from pests

Induce systemic resistance

Secondary metabolites

Barrier formation on roots

Stimulate plant growth

Plant hormone production

Plant hormone modulation

Roeland L. Berendsen, Corné M.J. Pieterse, Peter A.H.M. Bakker Trends in Plant Science 2012 17, 478-486DOI: (10.1016/j.tplants.2012.04.001)

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Microbiome discovery platform

ENVIRONMENTAL / MICROBIOME SAMPLES

SEQUENCING

16S or 18S rRNA genesCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTGGGATCCGGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGTGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCTATGATGCAGGTAACCACACTGCAATGGC

COMMUNITY ANALYSES

ProfilingCultivation

IDENTIFICATION OF IMPORTANT

CONSORTIA

TAXON STRAIN COLLECTION

Human Agriculture EnergyAnimal

MEDIA PANEL ENRICHMENTS

CONSTRUCT SYNTHETIC

CONSORTIUM

Yield, yield stability, nutrient use efficiency, early growth, vigor, biotic and abiotic stress tolerance, etc.

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Viewing communities through a 16S rRNA lens

v5v6 Profiling

PCR fusion primers with barcodes

DNA sequence

Trim at primer, anchor site

v5v6 sequence tag (barcode)

Making sense of a microbial community

Vibrant information content of

distribution profiles

Hierarchical order – consortia

Biochemical capabilities

PT14

1000 2000 3000 4000 5000 6000

PT

43

1000

2000

3000

PT174

0 1000 2000 3000

PT

78

0

1000

2000

3000

C12H26

Txc-168244

microbe:microbe microbe:microbe

microbe:metadata

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Bioinformatics interface tool

Displays frequency distribution of every microbe across all samples

Organizes the community based on 2D correlations

Microbes that perform a given process will associate with that process

Microbes that have relationships with one another will co-distribute

Mic

robia

l S

equ

en

ces

Consortium identification

Pre data mining and pattern recognition Post data mining and pattern recognition

Meta

data

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Identifying synthetic consortia for crop applications

New technologies

and innovations

Combine profiling and

metadataSort tags by correlation

with metadata of

interest

Identify tags based on significant

correlations Retrieve lead

isolates in culture

collection

Growth optimization

and production

Grow room and field

tests

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Seed-applied is a preferred delivery option

Product development challenges

Stable for use in commercial seed treatment handling practices

Compatible with high speed commercial planting equipment

Shelf-life to meet seed supply chain requirements

Deliver consistent performance across environments and genotypes

Compatible with other seed treatment components

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Efficacy &

Performance

Application

Compatibility

Seed Safety

Planting

Regulatory

Stewardship

Product Development

DuPontTM LumiviaTM

InsecticideDuPontTM LumisenaTM*

Fungicide

Untreated

• Excellent control of

cutworms, grubs,

wireworms on corn

• Uniform crop stands;

improved yields

• Novel technology to

manage seed and

seedling diseases

• Healthier crops,

better yield potential

Treated with LumiviaTM

Treated with Competitive Product

Treated with LumisenaTM

*Lumisena™ is pending regulatory approvals. No sale or offer for sale can be made until all applicable governmental approvals have been obtained

Pioneer Premium Seed Treatment

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Biological seed treatment delivers a unique mode-of-action for corn rootworm control

A rhizosphere competent entomopathogenic fungus

Excellent root protection as an integrated solution

Infects corn rootworm larvae through a complex process

New mode-of-action compared to insecticidal Bt proteins

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Summary comments

Increased understanding of crop microbiomes can unleash

additional yield potential

Proprietary computational tools to accelerate discovery of

important microbial consortia

Sustainable crop production can be achieved through integrated, data-driven management practices

New strategies for precision agriculture will optimize

management of seeds, nutrients, soil, water and

microbial communities

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Acknowledgements

Taxon Biosciences co-foundersMatt Ashby

Stewart Scherer

Jasper Rine

Tiburon, CA

Matthew Ashby, Philip Cavales,

Christine Clarke, Joe Derla, Gillie

Ish-Shalom, Tsotne Javahishvili,

Allison Johnston, Caroline

Kostecki, Matt Kuchta, Victor

Kunin, Rika Lidstrom,, Brian

Ruddy, and Jennifer Yip

Johnston, IA

Denny Bruck, Kent Wood, David

Hallahan, Steve Paszkiewicz and

Renee Lafitte