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Phylogenetic distribution of potential cellulases in bacteria

Phylogenetic distribution of potential cellulases in bacteria. R. Berlemont & A. Martiny. The cellulose degradation. ?. ?. ?. ?. ?. ?. ?. Project Goals. 4 main questions :. 1) How do microbial taxa respond to environmental changes?

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Phylogenetic distribution of potential cellulases in bacteria

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  1. Phylogenetic distribution of potential cellulases in bacteria R. Berlemont & A. Martiny

  2. The cellulose degradation ? ? ? ? ? ? ?

  3. Project Goals 4 main questions : 1) How do microbial taxa respond to environmental changes? 2) How are extracellular enzyme genes distributed among microbial taxa? 3) Can we predict enzyme function and litter decomposition rates by combining enzyme gene distributions with microbial taxa responses to environmental change? 4) Are microbial communities and their functions resilient to environmental change? Analyze the Gene Content in Available sequenced bacterial genomes

  4. CAZy classification • Endo/Exo-cellulases, -glucosidases • Glycoside Hydrolases, GH • >100 GH families (14 folds) • >100 activities • multifunctional enzymes contain catalytic domains that belong to different GH families

  5. Mining the CAZy - Endo/exo -

  6. Accessing the genomes • SEED environment • PATRIC database • GH : 1, 3, 5, 6, 8, 9, 12, 44, 45, 48

  7. CAZy Vs. us - Endo/exo - CAZY : all the NCBI genomes (including genome fragments) – 9,631 genes SEED : Only the sequenced genomes (3711) are considered - 22,523 genes

  8. Variations across phyla GH rich: Acidobacteria, Bacteroidetes, Digtyoglomi, Fibrobacteres, Thermotogae, Verrucomicrobia Lentisphaerae (Actinobacteria, Chloroflexi, Firmicutes)

  9. Variations across subphyla • Actinobacteria • 402 genomes • Niches (soil : Streptomycetales) • ‘GH-rich’

  10. Strain specific GH distribution 16S rRNA phylogeny 0 GH 1 GH >1 GH

  11. GH associations Synergistic model Spearman Correlation Glycoside Hydrolase abundance Redundancy Group IIIa Endocellulases Endo/exo - Group IIIb Exocellulases Complementarities - Group I Group II BcsZ -glucosidases

  12. GH associations • Nothing ! (can’t degrade cellulose) (21%) • No Group II – III : opportunists (Opp.) (44%) • 100% Gr.I and 0% Gr.II:Gr.III • putative Cellulose Degraders (pCD) (35%) • 100% GII/III and GI (94%) • pCD vs. Opp. ?

  13. GH associations

  14. Cellulose degraders and opportunists • Actinobacteria • + Bacteroidetes • + Proteobacteria • + Firmicutes = 86 % • Sequenced strains • putative Cell. Degr., • Opportunists, in all phyla •  35 % pCD [16-56%] • G1pCD = (1.7-4.4) G1Opp. Opportunists put. cell. degr.

  15. Poor strains … and their life styles • “Poor phyla, subphyla and strains” ? • e.g. : Cyanobacteria RuBisCO

  16. Life-style vs. GH content Autotrophs Intracellular Actinobacteria

  17. Phylogeny vs. GH content • Our first “delivrable” • 16s rRNA Phylogeny (Neighbor Joining) • Glycoside hydrolases based-clustering (Bray Curtis) • distance between the matrices, CADM (Mantel)

  18. Phylogeny vs. GH content 402 Actinobacteria ? 16s rRNA phylogeny GH – based clustering

  19. Conclusions • No information concerning the Activity of these enzymes • 3711 sequenced genomes ≠ natural population (pathogens) • Genomic perspectives • New “pipeline” for genes distribution/association • Tell me what is your GH content, I ‘ll tell you who you are! • Ecological perspectives • Functional redundancy in sequenced genomes (substrate, pH, …), • 44% opportunists, 35% putative cellulose degraders • Implications for ecosystems processes • -glucosidases reveal nothing about the cellulose degradation ! • More than 35% of the strains have endo/exo-cellulases ! • Cellulose degraders have multiple copies of these genes !

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