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Jeff Dangl, UNC Chapel HillPhil Hugenholtz, Susannah Tringe, JGI
Ruth Ley, Cornell
Rhizosphere Grand Challenge Pilot Project
Scott ClingenpeelProject Scientist, JGI
• Do plant roots assemble specific microbial rhizosphere and endophyte communities?
• Do different mutants or natural genotypes within a plant species assemble different microbial communities?
• Can the plant genes controlling these microbial communities be determined?
• What does the microbial community offer the plant, and how does the plant communicate with its microbiota?
Specific Questions
Approach to Answer the Questions• Grow multiple genotypes of Arabidopsis and corn (maize)
in natural soils.
• Characterize the rhizosphere and root endophyte microbial communities using pyrotags and iTAGs.
• Characterize the function of the microbial communities using metagenomics and metatranscriptomics.
• To focus on specific plant-microbe interactions by obtaining single cell genomes and plant transcriptomes.
Rhizosphere DNA isolationRemove soil to within 1mm radius from roots
Place roots in sterile phosphate buffer with Silwet
collection tube
Spin Collection Tube. Transfer pellet to 1.5mL tube
= rhizosphere
Shake 150 rpm, 30min; sonicate
Derek Lundberg, UNC
Obtaining Cells from Rhizosphere
Mason FarmNov. 2008
Mason FarmJan. 2009
ClaytonNov. 2008
Col-0 n=17MF Soil n=10
Col-0 n=8MF Soil n=3
Col-0 n=3C Soil n=3
Rank Abundance Curves, ranked by Mason Farm Nov. 2008 soil,showing the percent abundance of each major OTU in every sample
Though soils differ, Arabidopsis rhizospheres reliably assemble several OTUs
From Dangl lab, April 15, 2010 Pyrotagger run
The rhizosphere of Arabidopsis missing efr1 have OTUs with different abundances than wild type
There are a few OTUs that have different abundances in efr1fls2 plant.
From Dangl lab, April 15, 2010 Pyrotagger run
Bray Curtis similarity of samples from three experiments,using OTUs above 0.5% in any sample
Clayton Exp. 1Nov. 2008
1) Samples cluster by soil type or experiment date2) Bulk soil clearly differs from rhizospheres3) No separation of genotypes based on rhizospheres
Mason Farm Exp. 1 Nov. 2008
Mason Farm Exp. 2 Jan. 2009
From Dangl lab, April 15, 2010 Pyrotagger run
Single Cell Genomics• Provides context for interpreting metagenomes
and metatranscriptomes
• Provides insight into metabolic capability of particular organisms that are enriched by the plant
• This could begin to tell us what the plant is getting from the microbes and what they are getting from the plant
Methods
• Fluorescently Activated Cell Sorting (FACS)• Multiple Displacement Amplification (MDA) of
the single cell genome• Amplify 16S rRNA gene• Screen for organisms of interest• Sequence the MDA products of organisms of
interest• Analyze the genomic data
Fluorescently Activated Cell Sorting (FACS)
Photomultiplier tubes
Flow Nozzle
Laser Cell Forward ScatterCellLaser
Fluorescence
CellLaser
Side Scatter
Flow Nozzle
Sorted Cells
Multiple Displacement Amplification (MDA)
Bacterial Genome
Denature DNA Random Primers
+
Amplification
Lots of Copies!
Microbes to Focus On• 150 OTUs are enriched in the rhizosphere of wild
type Arabidopsis by at least 2 fold over bulk soilAcidobacteriaAlphaproteobacteriaBacteroidetesGammaproteobacteriaActinobacteriaFirmicutesBetaproteobacteriaGemmatimonadetesPlanctomycetesChloroflexiCyanobacteriaVerrucomicrobiaOP10SPAMNitrospiraeDeltaproteobacteriaChlamydiaeElusimicrobiaThaumarchaeota
AcidobacteriaAlphaproteobacteriaBacteroidetesGammaproteobacteriaActinobacteriaFirmicutesBetaproteobacteriaGemmatimonadetesPlanctomycetesChloroflexiCyanobacteriaVerrucomicrobiaOP10SPAMNitrospiraeDeltaproteobacteriaChlamydiaeElusimicrobiaThaumarchaeota
Chances of Getting What We Want• Getting a specific enriched OTU is unlikely without screening
lots of cells– Most abundances are less than 1% of the community
• Getting OTUs of interest is likely– Total abundance of rhizosphere-enriched OTUs where no genome
exists in the same family is 21%
• Variability means it can be useful to test multiple samples– Abundances between replicates can differ by several fold
• High throughput process– If we test enough cells, eventually we should get what we want