Structure, function and host control of rhizosphere microbiome
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1 Structure, function and host control of rhizosphere microbiome Davide Bulgarelli PhD, Microbiome AgBioTech Europe London, September 21st, 2017
2 Outline The rhizosphere microbiome Barley as a model to study host-microbiome interactions in crop plants What s next?
3 Plants wear their guts on the outside Novel insights into rhizosphere interactions: unlocking the full potential of crop production The rhizosphere: the interface where nutrient acquisition takes place The microbial communities inhabiting the rhizosphere: The rhizosphere microbiome
4 Determinants of the rhizosphere microbiome Alegria Terrazas et al., (2016) Adv Appl Microbiol. 95:1 Robertson-Albertyn et al., (2017) Front. Plant Sci. 8:1094 Can we manipulate plant-microbiome interactions to boost sustainable crop production?
5 The host as a driver of the microbiome Microbiome Root Shared Toothpick s Bulgarelli et al. (2012), Nature 488:91
6 Barley as a model to study crop-microbiome interactions Gobal Crop: world 4 th most cultivated cereal Diploid genome Large germplasm collections: accessions & mutants -omics resources Genome sequence available Wild relatives
7 A cultivation-independent protocol to study barley-microbiome interactions Modified fromhirsch and Maulchline (2012), Nat. Biotech. 30:961 16S rrna gene profiles Who is there? Data Analysis Shotgun metagenomics What can they do?
8 Barley shapes the root and rhizosphere microbiome Barley microbiota Bulgarelli et al. (2015) Cell Host Microbe 17:392 Arabidopsis microbiota Bulgarelli et al. (2012) Nature 488:91 Community composition Bacteria significantly enriched in root samples Bacteria not enriched/not significantly enriched Bacteria significantly enriched in rhizosphere samples Bacteria significantly enriched in root and rhizosphere samples
9 Shotgun metagenomics of the barley rhizosphere Golm soil #1 Golm soil #2 Wild Traditional Modern Rhizosphere DNA 2x soils; 3x reps Pooling 2x100bp, ~75M PE reads x genotype X soil Microbiota taxa & functions QC, assembly, binning, annotation
10 Bacteria dominate the annotated barley metagenome Archaea=0.054% Eukaryotes=5.90% metagenomics reads
11 Plant-microbe & microbe-microbe interactions shape the barley microbiome Ruben Garrido Oter Bulgarelli et al. (2015), Cell Host Microbe 17:392
12 A walk on the wild side B1K collection North Coast Desert modified from Hübner et al. (2009) Mol Eco, 18 Ecologically referenced populations Phenotypic and genetic diversity Adaptive niche of modern barley s ancestor Rodrigo Alegria Terrazas
13 Actinobacteria, Bacteroidetes and Proteobacteria are enriched in the barley microbiome Quarryfield soil: organic matter 5% Tayport soil: organic matter 2.9%
14 Soil type & microhabitat drive the barley microbiome Elite Desert Coast North Tayport Soil OTU OTU Bray -Curtis dissimilarity Quarryfield soil Unplanted permanova (significant variation explained) Soil effect 20% Rhizosphere effect 16% Ecotype effect 6.7%
15 From description Structure and functions of the barley rhizosphere microbiome Wild and cultivated barley accessions Defined soil conditions State-of-the art sequencing to causality Bacterial collection & recolonization experiments Sequencing-driven bacteria isolation Synthetic communities (SynCom) Host genetics
16 Towards next generation agriculture Schlaeppi and Bulgarelli (2014), MPMI 28:212
17 Bulgarelli Lab Senga Robertson Rodrigo Alegria Terrazas Credits Katharin Balbirnie, now at St Andrews Manuel Blank, now at Victoria U (NZ) Ridhdhi Rathore (visiting) IT Carlow Laura Pietrangelo (visiting) U Molise Fedrico Concas (ERASMUS) U Cagliari Collaborators A. Janiak & I. Szarejko (U Katowice) Kieran Germaine (IT Carlow) Tim George (JHI Dundee) Eric Paterson (JHI Aberdeen) Elizabeth Baggs (U Aberdeen) Eyal Fridman (ARO Volcani) Tanja Mimmo & Youry Pii (U Bolzano) Gino Naclerio (U Molise) Rodrigo Mendes (EMBRAPA Campinas) Funding:
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