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Structure and Functions of the Bacterial Root Microbiota in Wild and Domesticated Barley

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Structure and Functions of the Bacterial Root Microbiota in Wild and Domesticated Barley Structure and functions of the bacterial root microbiota in wild and domesticated barley Ruben Garrido Oter Structure, Function and Dynamics in Microbial Communities 30 / 11 / 2014 Introduction Othersources Atmosphere ~101–105 m–3 endophytic rhizosphere microbiome microbiome Leafarea ~106–107cm–2 Soil ~106–109 g–1 Rootendosphere ~104–108 g–1 Rhizosphere ~106–109 g–1 Bacterialphyla Actinobacteria BacteroidetesandFirmicutes Proteobacteria Bulgarelli et al. Annu. Rev. Plant Biol. (2012) Hirsch, Mauchline, et al. Nature Biotech. (2012) Outline introduction part I structure of the barley root and rhizosphere bacterial communities effect of domestication in the barley root microbial diversity part II the barley rhizosphere metagenome: taxonomic characterization of the rhizosphere metagenome functions enriched in root-associated taxa w.r.t. the surrounding soil biota signatures of possitive selection and microevolution future work & conclusions Three different accessions represent three stages in the domestication process of barley Hv ssp. spontaneum Hv ssp. vulgare Landrace Hv ssp. vulgare Modern Three different accessions represent three stages in the domestication process of barley ~ 10.000 years ~ 60 years (advent of agriculture) (green revolution) Experimental setup (x 2 soil batches) unplanted soil controls (3 replicates) H. vulgare ssp. spontaneum H. vulgare ssp. vulgare Landrace H. vulgare ssp. vulgare Modern rhizosphere rhizosphere rhizosphere (3 replicates) (3 replicates) (3 replicates) 16S rRNA: - 42 samples - 691,822 reads root root root (3 replicates) (3 replicates) (3 replicates) metagenome: rhizosphere rhizosphere rhizosphere - 6 samples (shotgun metagenome) (shotgun metagenome) (shotgun metagenome) ~ 255 M paired-end reads Factors influencing the diversity of the barley root-associated bacterial communities Microhabitat Genotype 22% of variance; P < 0.005, CI = 17%, 30% 5.7% of variance; P < 0.005, CI = 5%, 6.4% Marked rhizosphere effect across barley accessions barley Arabidopsis Soil Soil 0.4 0.2 Root Rhizosphere Root Rhizosphere Root OTUs Rhizosphere OTUs Root and Rhizosphere OTUs Bulgarelli et al., Nature, 2012 Outline introduction part I structure of the barley root and rhizosphere bacterial communities effect of domestication in the barley root microbial diversity part II the barley rhizosphere metagenome: taxonomic characterization of the rhizosphere metagenome functions enriched in root-associated taxa w.r.t. the surrounding soil biota signatures of possitive selection and microevolution future work & conclusions Taxonomic abundances in the barley rhizosphere metagenome Acidobacteria Bacteroidetes Bacteroidetes #nc. sedis Firmicutes Haloplasmatales Elusimicrobiales Thermotogales Sphingobacteriales Cytophagales !oribacteria Fla%obacteriales Bacteroidales Ignavibacteriales Chlorobiales Mycoplasmatales AcholeplasmatalesNitrospirales Dictyoglomales Aquificales Fusobacteriales Fibrobacterales Holophagales Solibacterales Bdellovibrionales Acidobacteriales Desulfobacterales Lactobacillales Bacillales δ - proteobacteria Halanaerobiales Syntrophobacterales Thermoanaerobacterales Desulfarculales Clostridiales Erysipelotrichales Desulfovibrionales Selenomonadales Spirochaetales Synergistales DesulfuromonadalesMyxococcales Sulfolobales Desulfurococcales Thermoproteales Archaea CampylobacteralesNautiliales Thermoplasmatales Halobacteriales Sphingomonadales Thermococcales Magnetococcales Methanosarcinales Methanocellales Rhizobiales Methanomicrobiales α - proteobacteria Caulobacterales Methanobacteriales Methanococcales Rickettsiales Archaeoglobales Rhodospirillales Nitrosopumilales !arvularculales Cenarchaeales Rhodobacterales Armatimonadetes Thermales Legionellales Deinococcales !asteurellales Gemmatimonadales Spartobacteria Xanthomonadales ,errucomicrobiales Acidithiobacillales Methylacidiphilales Cardiobacteriales Puniceicoccales Lentisphaerales Alteromonadales Chlamydiales Enterobacteriales Dehalococcoidales Anaerolineales Pseudomonadales Ktedonobacterales OceanospirillalesVibrionales Thermomicrobiales Chlamydiales / Sphaerobacterales Chloroflexales Verrucomicrobia γ - proteobacteria Salinisphaerales Herpetosiphonales Chromatiales Caldilineales Thiotrichales Gloeobacterales Oscillatoriales Chroococcales Prochlorales Nostocales Methylococcales Stigonematales Acidimicrobiales Solirubrobacterales Rubrobacterales Gaiellales AeromonadalesGallionellales Bifidobacteriales Rhodocyclales Nitrosomonadales Neisseriales Chloroflexi Methylophilales Hydrogenophilales Burkholderiales Mariprofundales DeferribacteralesPhycisphaerales Coriobacteriales Actinomycetales Planctomycetales metagenome abundances β - proteobacteria Cyanobacteria 16S amplicon abundances Actinobacteria overlap Biases in abundance estimates 16S rRNA in shotgun metagenome reads ρ = 0.89 primer bias (P = 1.55E-14) 16S rRNA amplicon survey (excluding Cyanobacteria) primer bias rRNA operon ρ = 0.86 (P = 1.75E-12) copy number metagenome bins (excluding Eukaryotes, Archaea and Cyanobacteria) Functions enriched in root and rhizosphere-associated bacterial taxa with respect to the surrounding soil biota Soil 0.4 0.2 Root Rhizosphere Root OTUs Rhizosphere OTUs Root and Rhizosphere OTUs * Wilcoxon test, FDR correction Functions enriched in root and rhizosphere-associated bacterial taxa with respect to the surrounding soil biota Soil Functional Category P value* Protein secretion system Type III 0.0013 Adhesion 0.0014 Regulation of virulence 0.0016 Siderophores 0.0016 Secretion 0.0053 Transposable elements 0.0138 0.4 Periplasmic Stress 0.0152 Sugar Phosphotransferase Systems 0.0209 0.2 Bacteriophage integration excision lysogeny 0.0300 Invasion and intracellular resistance 0.0300 Root Rhizosphere Detoxification 0.0339 Protein secretion system Type VI 0.0339 Acid stress 0.0356 Root OTUs Rhizosphere OTUs Root and Rhizosphere OTUs * Wilcoxon test, FDR correction Outline introduction part I structure of the barley root and rhizosphere bacterial communities effect of domestication in the barley root microbial diversity part II the barley rhizosphere metagenome: taxonomic characterization of the rhizosphere metagenome functions enriched in root-associated taxa w.r.t. the surrounding soil biota signatures of possitive selection and microevolution future work & conclusions Protein families related to host-microbe AND microbe-microbe interactions exhibit strong signatures of positive selection 1.00 0.75 0.50 density 0.25 0.00 mean pathogenesis/ secretion ~dN/dS pathogenesis / secretion phages ~dN/dS Philipp Muench Microbial elicitors of plant immunity under positive selection in the barley rhizosphere TIGR00377: anti-anti-sigma factor Gap proportion 7.5 0.8 S /d , 5 0.6 ~d 0.4 2.5 0.2 0.0 0 5 TIGR01573: CRISPR-associated endoribonuclease Cas2 S /d , 2.5 0 10 TIGR02241: conserved hypothetical phage tail region protein 7.5 S /d , 5 ~d 2.5 0 Sequence Position (nt) clusters of residues with high dN / dS ratios in well conserved genes (putative epitopes) Philipp Muench Conclusions wild and cultivated barley accessions host a taxonomically coherent microbiota whose structure is determined by the host microhabitat and fine-tuned by the host genotype small but statistically significant effect of domestication in the assembly of root-associated microbiota manifested by combinations of bacterial taxa protein families and functional processes relating to pathogenicity, phages and secretion, are significantly enriched in root-associated bacterial taxa evidence that protein families related to the same traits are affected by co-evolutionary arms races with the host as well as with other microbes the combined effect of both, microbe-microbe and host-microbe interactions shapes the differentiation of root-associated microbiota from the surrounding soil Acknowledgements MPIPZ HHUD Paul Schulze-Lefert Alice McHardy PSL - root group Algorithmic bioinformatics group Yang Bai Marc André Daxer Davide Bulgarelli Johannes Dröge Nina Dombrowski Ivan Gregor Stéphane Hacquard Thorsten Klingen Haruhiko Inoue Andreas Klötgen Ryohei Thomas Nakano Sebastian Konietzny Girish Srinivas David Lähnemann Spaepen Stijn Philipp Münch Rafal Zgadzaj Yao Pan Barbara Kracher Aaron Weimann Thank you! Root-enriched bacterial taxa in barley Streptomycetaceae Barley root OTUs Actinomycetales Actinobacteria Arabidopsis root OTUs Microbacteriaceae Thermomonosporaceae relative abundance (log transformed) 0.1% 1% 10% Burkholderiales Comamonadaceae β Oxalobacteraceae γ Pseudomonadaceae Bacteria Xanthomonadaceae Proteobacteria α Rhizobiales δ Myxococcales Bacteroidetes Fla"obacteriaceae kingdom phylum class order family The genotype-effect is manifested by combinations of a large number of bacterial OTUs 0 6.0 ns 5.5 E−2 * 5.0 P−value % of variance E−4 ** 4.5 4.0 0 50 100 150 200 0 50 100 150 200 number of OTUs permutated number of OTUs permutated Permutation-based analysis of the significance of the observed genotype-effect in barley The barley root-inhabiting bacterial microbiota Rhizosphere Root Cholorflexi Soil Hv ssp. spontaneum Hv ssp. vulgare Landrace Firmicutes Hv ssp vulgare Modern Bacteroidetes Actinobacteria Proteobacteria 0 200 400 600 800 0 200 400 600 800 Phyllobacteriaceae Nocardioidaceae Hyphomicrobiaceae Alteromonadaceae Xanthomonadaceae Streptomycetaceae Oxalobacteraceae Rhizobiaceae Flavobacteriaceae Comamonadaceae 0 50 100 150 200 250 300 0 50 100 150 200 250 300 SnapShot: Plant Immune Response Pathways Ralph Panstruga, J ane E. Parker, and Paul Schulze-Lefert.
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