Finding and optimizing soil microbes for enhancing agricultural productivity and sustainability

Transcription

1 Finding and optimizing soil microbes for enhancing agricultural productivity and sustainability Daniel Schachtman University of Nebraska, Lincoln June 30, 2015

2 Nebraska is a Living Laboratory for agricultural microbiome studies Scottsbluff Omaha Diversity in: Rainfall Soil fertility Soil types Stresses Lincoln BREBS locations

3 Specialized Infrastructure Drought research capabilities and field facilities NE a natural lab for stress biology Automated Phenotyping Crop Transformation

4 Our program at UNL - one year on How do host plants alter the root microbiome? Characterize the exudates that shape the rhizosphere and endosphere. How environmental stress alters the microbiome? Characterize diversity of microbes Prospecting for the good guys Nitrogen fixing endophytes Enhancer Fe availability

5 What s out there in the universe Shovels, microscopes, petri plates and sequencing

6 The program collaboration based Phase 1: Census and hypothesis building using Nextgen sequencing (Uni of Minnesota Genomics) Crop focused in different environments Corn, Sorghum, Soy Drought, low N, high CO 2 and O 2 Phase 2: Hypothesis testing and microbial discovery

7 Corn microbes and drought Corn ERA Hybrids and drought (Collaborators: Lorenz and Kruger) Are there any changes in microbial communities due to genetics? Are there changes in microbial communities due to drought

8 Brule, NE precision irrigation to generate water deficit

9 FACE experiments in Champaign, IL Changes in the bacterial and fungal communities in high CO 2 (soybean) and ozone (corn) Survey for changes in microbial communities Correlate with changes in root metabolites Collaborators: Lisa Ainsworth and Andrew Leaky

10 Sweet Sorghum Energy feedstock Sweet sorghum (Ismail Dweikat) How does low nitrogen effect microbial communities? Do sugar concentrations in sweet sorghum varieties correlate with microbe community composition? Do we find more N fixing endophytes under low N conditions?

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13 Discovery Microbial discovery has already revolutionized agricultural Gene variants and new pathways that enhance pest resistance and create herbicide tolerance Agrobacteria Gene transfer workhorse Resistant enzyme from Agrobacteria strain Pseudomonas - DMO gene Bacillus subtilis Bacillus firmus I-1582.

14 Microbial Discovery The Sandhills Largest sand dune complex in the northern hemisphere The Gem of the Great Plains 19,000 miles 2 A remnant of clash between the upheaval of the Rockies and the grinding of the glaciers. Dunes, lakes, meadows, fens with a buried water feature. Dunes are a giant sponge to refill aquifer. Prairie Fire June 2015

15 Building our culture collections Endophytes and soil microbes Prospecting in agricultural soils and the Sandhills and on drought, salinity, alkalinity, low fertility grasses Multiple types of culture conditions Ashby nitrogen free media R2A Reasoner's 2A Yeast Mannitol Agar Medium (YMA) YPD - Yeast Extract Peptone Dextrose Medium TSA - Tryptic Soy Agar/Medium

16 Root of Sweet Sorghum N109 endophytic growth 12/15/14

17 ichip - more innovative approaches

18 Establishment of culture collection Isolated microorganisms from soil and roots of various genotypes very late in 2014 season Sweet sorghum, switch grass and millet in NE Extracted DNA and amplified 16S gene 16S sequencing with 27F primer Isolates from 20 out of 36 soils samples were unique 6 out of 68 unique from root samples Distance matrices used to determine similarity < 97% considered unique in distance matrix

19 Soil Bacteria Plate Sphingomonas sp. CC-E-3 Growth Example Uncultured bacterium clone 7.C Uncultured bacterium clone MA54_2003T7B_G08 Arthrobacter sp. ES1-12 Uncultured Bacteriodetes bacterium clone MA193T1-3r2_G03 Uncultured Sphingobacteria bacterium clone GASP- WC1S2_H04

20 Soil bacteria plate growth example

21 Endophyte: R2A(+) Sweet sorghum roots Pseudomonas frederiksbergensis strain BDR1P1B1 Pseudomonas sp. RBBP4 Pseudomonas sp.

22 Our current favorite purple bacteria Janthinobacterium lividum

23 Discover, culture and utilize for agriculture Multiple culturing techniques and improve current methods Microbes from different environments Re-inoculate roots and soils to determine which microbes successfully colonize roots. Use automated phenotyping facilities in greenhouse and eventually test in field Function - genome sequence unique isolate, annotate, determine how microbes contribute to plant growth

24 How far have we come with microbiome studies in for agriculture? 10 20% of the way so far Largely descriptive, but more descriptions are vital Spatial, temporal More discovery Correlative stage -> must move to function Genetics, natural variation, genetic engineering Holistic Monitor plants, roots and soils

25 Taxonomic resolution Past - There are differences Prior to 2010 lower resolution methods not able to provide much insight into microbe species Present - Differences in the community structure at phylum or family level. Technical leap to get to high throughput species level resolution. Future - X species causes increased yields due the secretion of y metabolite or due to improved nutrition.

26 Important questions to answer for agriculture How do we efficiently find the best microbes for enhancing growth and development? How do we engineer stable relationships between plant roots and specific microbes?

27 Thanks to my lab: Ellen Marsh Morgan McPherson Yen-Ning Chai Daniel Clutter Collaborators Aaron Lorenz and Greg Kruger Lisa Ainsworth and Andrew Leaky Ismail Dweikat Daryl Gohl and Kenny Beckmann University of Minn - Genomics