Advanced Microbial Selection (AMS):Evolving plant microbiomes to improve crop traits

Global Biocontrol & Biostimulants Congress12th – 13th September, 2016

Marcus Meadows-Smith

Founded in New Zealand in 1994• Microbe library contains more than 34k isolates screened for

bioactivity / active metabolites, including 6k+ endophytes

Breakthrough in R&D – AMS in 2009• Focused on perfecting revolutionary discovery platform,

Advanced Microbial Selection

Established in Davis, California in 2014• Raised $15 million from Khosla Ventures and Otter Capital

Strong R&D Expertise• 30 highly experienced experts from industry and

academia, including 12 PhDs

Research Collaboration• Participating in projects and testing with a number of

multinational companies

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Transfer microbiome of best performing plants onto new seeds

Plants scored on a range of traits that indicate improved future yield, stress resistance, growth promotion etc.

Naturally occurring microbes colonize the growing plant in controlled

environment conditions

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Evolving the Microbiome

Plant-Microbe Selection

Phenotype Selection

Microbiome Analysis

Reinoculation

100+ soil samples for microbial genetic diversity & chemically treated seeds

Each AMS selection round evolves the microbiome to deliver higher performing

plants

Proprietary, BioConsortia patented process

Iterative Process

Directed Selection

-10 0 10

SuperiorAverageInferior

Phenotype distribution

Driving an improvement in trait performanceResults in an accumulation of microbes responsible for enhanced targeted traits.

Selecting the superior phenotype & associated microbiomeSelection in both ideal & stressed environments.

Changing the microbial communityAdvancement of the most beneficial microbes through iterative selection rounds.

The AMS Process

Proprietary, BioConsortia patented process

G x E x M = P

Normal Distribution(prior to selection)

After Directed Selection

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Advanced Microbial Selection (AMS)

Proprietary, BioConsortia patented process

Plant-Microbe Selection

Phenotype Selection

Microbiome Analysis

Reinoculation

Microbe isolationFinal selectionDirected selectionMicrobe captureDiverse soil microbes

We select the crop trait -- the plant selects the microbes

Process and selection informed by DNA and microbiome analysis

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A

BC

D

E

Microbes

AB, AC, AD, AE, BC,BD, BE, DE, ABC, ABD,ABE, ACD, ACE, ADE,BCD, BCE, CDE, ABCD,ABCE, A B C D E

Microbe Evaluations including a range of:• Soils• Hybrids/varieties• Base seed-applied chemistries

Isolate & identify microbes

Prepare combinations(key microbial consortia)

Final screens(determine best consortia)

Informed by high-throughput DNA sequencing of plant microbiome

Identify Effective Consortia

Eliminate:• Pathogenic (plants, humans, etc.)• Hard to produced or deliver

To replicate or improve past performance

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Underpinning Technology Platform

• Plant Growth & Phenotyping

• Microbiome Analysis

• DNA sequencing

• Microbial Phenotyping

• Plant Gene Expression

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Saccharomonospora

Thermobifida

[Chthoniobacteraceae] DA101

[Chloracidobacteria] RB41

Acidobacteria-6 iii1-15

Cyanobacteria 4C0d-2 SM1D11

Cellvibrio

Arthrobacter 2

Pseudomonas 2

Pedobacter cryoconitis

Pedobacter 2

Pseudomonadaceae 2

Hydrogenophaga

Enterobacteriaceae 1

Pseudomonas stutzeri

Pseudomonas 1

Pseudomonas nitroreducens

Verrucomicrobiaceae

Fluviicola

Rhodanobacter

Agrobacterium 2

Sphingopyxis 2

Devosia

Burkholderia 1

Acidobacteriaceae

Bradyrhizobiaceae 2

Rhodoplanes 2

Oxalobacteraceae 1

Asticcacaulis biprosthecium

Xanthomonadaceae 2

Chitinophagaceae 2

Sphingobacteriaceae 2

Chitinophaga 2

Limnobacter

Comamonadaceae 1

Comamonadaceae 2

Arthrobacter 1

Sphingomonas 2

Kaistobacter

Cytophagaceae 2

Deltaproteobacteria Myxococcales

Erwinia 1

Deltaproteobacteria Spirobacillales

Kiloniellales

Thermogemmatisporaceae

Burkholderia 2

Burkholderia andropogonis

Acetobacteraceae 2

Erwinia 2

Stenotrophomonas 1

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100

200 AMS RoundSoil

MC

R1

R2

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High-Throughput Microbial Screening

60 microbial strains

150 soil samples> 1013 microbes

> 105 different strains> Multiple seed chemistries

11 microbial consortia

Selection

Pot trial

Field trial

Lab & Growth Chamber Trials

One AMS example

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Unique Discovery Platform

True Teams• Microbes selected as a team• Complementary functions & effects• Effective plant colonizers: endophytes,

epiphytes, rhizospheric microbes

Selection for compatibility• Plant - Microbe: selected by the plant from soil• Microbe – Microbe• Microbe - Chemistry: seeds pre-treated

Rapid, Low Cost• Expedited development taking ~9 months rather than years• Compared to GM & conventional plant breeding, and

conventional microbial R&D model• Allows for research into minor crops and almost any trait

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Yield & Productivity

Std. Agronomic Practice / Yield

Nitrogen Use Efficiency

Phosphate Use Efficiency

Early Vigor & Yield

Abiotic Stress Tolerance

Drought Tolerance

Salt Tolerance

Cold & Wet Tolerance

Biotic Stress Tolerance

Nematode Control

Insecticides

Soil & Early Season Fungicides

Metabolite Expression

Increased Sugar Content

Proof of concept

AMS / Identify leads

Growth chamber / Greenhouse evaluation

Field trials Product launch

Registration & Development

Corn Soybean Wheat Tomato Leafy Veg Pasture

Corn, Soybean, Wheat

Corn, Soybean Wheat

Corn, Wheat

R&D Pipeline: seed treatment, in-furrow, drench

Soybean

Corn rootworm

Wheat, Leafy Veg Tomato

Sorghum, Lettuce Tomato

Sorghum, Soybean, Spring Wheat Corn

Wheat, Soybean Corn

Corn, Wheat

Vegetative tissue in model crop

Plus R&D collaborations with multinational companies on additional crops and combination products

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Thank You