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Advanced Microbial Selection: Evolving Plant Microbiomes To Improve Crop Traits
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Transcript of Advanced Microbial Selection: Evolving Plant Microbiomes To Improve Crop Traits
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