Composts to control plant diseases Techniques to link compost characteristics to manage soil-borne plant pathogens

Transcription

1 Composts to control plant diseases Techniques to link compost characteristics to manage soil-borne plant pathogens Josefa Blaya Fernandez CEBAS-CSIC, Spain

2 Soil-borne pathogens Kamoun et al. 2012

3 Control of soil-borne plant diseases PUBLIC CONCERN LEGISLATIVE PRESSURES FAILED TREATMENTS Biological Control Agents (BCA) C ompost 3

4 Why composts?

5 Disease suppression (%) Disease suppression (%) Compost and plant disease control Plant host Pathogen Microorganisms composts 3 pathosystems Suppressiveness (Hadar & Papadopoulou, 2012) Environment in which plant disease development is reduced, even when the 10 pathogen is favored by the presence of a susceptible host 0 STUDY A: Scheuerell et al., 2005 STUDY B: Termorshuizen et al., Starting materials 18 composts 7 pathosystems 5

6 Compost and plant disease control Fertilizing value Waste recovery Low cost Limited environmental effects Growing media 6

7 BIOLOGICAL FACTOR Suppressiveness (Hadar & Papadopoulou, 2012) GENERAL SUPPRESSION Sum of activities of the overall microbial biomass SPECIFIC SUPPRESSION Activities of one of a few microorganisms - Antibiosis (Howell, 2003) Directs - Competence for nutrients and space (Hjeljord & Tronsmo, 1998) - Mycoparasitism (Rincón et al., 2008) Indirects - Stimulation of plant growth (Bailey & Lumsden, 1998) - Induction of systemic resistance (Shoresh et al., 2010)

8 Some examples Phytophthora spp. Fusarium oxysporum General microbial activity Specific microorganisms

9 STARTING MATERIALS Colonization of microbial communities Scheuerell & Mahaffee 2005

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11 Why Is so important TO PREDICT Compost suppresiveness?

12 1 Not all composts are suppressive 2 Suppressiveness is pathogen-related 3 Long storage is related to loss in suppressiveness

13 Disease incidence (%) Prolonged compost storage affects negatively the disease levels month old 10-month old

14 Which TECHNIQUES are available?

15 Disease incidence (%) µg INTF g-1 h-1 General suppression model PREDICTIVE PARAMETERS GENERAL MICROBIAL ACTIVITY Fluorescein diceatate hydrolysis (FDA) Basal respiration Dehydrogenase activity 90 Phytophthora Disease incidence (%) 45 Dehydrogenase activity High levels of recalcitrant compounds may define the longevity of the suppressive effect C2 C7 C11 COM Peat 0 C2 C7 C11 COM Peat Blaya et al unpublished

16 Disease incidence (%) General suppression model PREDICTIVE PARAMETERS GENERAL MICROBIAL ACTIVITY Fluorescein diceatate hydrolysis (FDA) Basal respiration Dehydrogenase activity Phytophthora Disease incidence (%) c b b a g NTF g -1 h b Dehydrogenase activity d c a 0 C1 C2 C3 Peat 0 C1 C2 C3 Peat Blaya et al. 2014

17 Specific antagonistics PREDICTIVE PARAMETERS CHITINASE PRODUCING BACTERIA Β-glucosidase activity NAGase activity Chitinase activity μmol PNP g -1 h Glucosidase activity C1 C2 C3 Peat μmol PNP g -1 h NAGase activity C1 C2 C3 Peat g N-acetylglucosamine g -1 h Chitinase activity C1 C2 C3 Peat Quebec

18 Which TECHNIQUES are available to study the microbial community structure?

19 TECHNIQUES Culturebased Cultivationindependent Culture media Biolog-based methods Partial community Whole community Postgenomic

20 TECHNIQUES Culturebased Cultivationindependent Culture media Biolog-based methods Partial community Whole community Postgenomic

21 TECHNIQUES Culturebased Cultivationindependent Culture media Biolog-based methods Partial community Whole community Postgenomic

22 TECHNIQUES Culture-based Cultivationindependent Culture media Biolog-based methods Partial community Whole community Post-genomic Clone library Genetic fingerprinting Stable isotope probing DNA microarrays qpcr FISH

23 TECHNIQUES Culture-based Cultivationindependent Culture media Biolog-based methods Partial community Whole community Post-genomic Clone library Genetic fingerprinting Stable isotope probing DNA microarrays qpcr FISH N ational Compost Conference, September Gatineau, Quebec

24 TECHNIQUES Culture-based Cultivationindependent Culture media Biolog-based methods Partial community Whole community Post-genomic Clone library Genetic fingerprinting Stable isotope probing DNA microarrays qpcr FISH DGGE/TGGE ARDRA T-RLFA SSCP RISA PLFAS

25 TECHNIQUES Culture-based Cultivationindependent Culture media Biolog-based methods Partial community Whole community Post-genomic Clone library Genetic fingerprinting Stable isotope probing DNA microarrays qpcr FISH DGGE/TGGE ARDRA T-RLFA SSCP RISA PLFAS N ational Compost Conference, September Gatineau, Quebec

26 Phospholipid fatty acids (PLFAs) Broad-range biochemical approach Fingerprint of the microbial community composition Viable (living) biomass concentrations

27 PLFA analysis Parameter C1 C2 C3 Peat Disease incidence (%) F. oxysporum Bacteria Gram + (mol g -1 ) 1.0 a 0.92 a 1.1 a 0.00 b Bacteria Gram - (mol g -1 ) 2.4 a 3.1 a 2.0 a 0.21 b Total saturated PLFA (mol g -1 ) 9.0 a 10.4 a 9.4 a 2.2 b Total monounsaturated PLFA (mol g -1 ) 1.4 a 2.2 a 1.9 a 0.29 b Gram + /Gram - ratio 0.43 b 0.31 c 0.5 a 0.00 d Monounsaturated/Saturated ratio 0.15 b 0.22 a 0.20 ab 0.13 b (Ntougias et al., 2008) Preferential development of Gram + (Ntougias et al., 2008) Enriched actinomycete community (Patel et al., 2010) 27 N ational Compost Conference, September Gatineau, Quebec

28 PLFA analysis PLFA profiles Microbial community changes (Kindo et al., 2012) Composition starting materials (Hoitink & Boehm, 1999) C3 Dry olive cake High % lignin 28

29 TECHNIQUES Culture-based Cultivationindependent Culture media Biolog-based methods Partial community Whole community Post-genomic DNA-DNA hybridization Guanina+Citosina content fractination Whole-microbialgenome sequencing Metagenomics

30 TECHNIQUES Culture-based Cultivationindependent Culture media Biolog-based methods Partial community Whole community Post-genomic DNA-DNA hybridization Guanina+Citosina content fractination Whole-microbialgenome sequencing Metagenomics

31 Metagenomics Based on the analysis of DNA Investigation of collective microbial communities No need for isolation and lab cultivation of individual species

32 COM COM COM COM -A Pepper -B Artichoke -C Pepper -D Artichoke sludge waste sludge sludge Pepper waste Pepper waste Carrot waste Artichoke waste Vineyard prunning waste Vineyard pruning waste Pepper waste Vineyard pruning waste Vineyard pruning waste N ational Compost Conference, September Gatineau, Quebec

33 Disease incidence Bacterial community Fungal communities (Hardy & Sivasithampram, 1995) 16S rrna Ascomycota phylum Fungal community Negative correlation ITS region ION TORRENT (Life technologies) Jeffries & Young

34 Fungal communities Bacterial communities Genus PA PAC AC CC PEAT Zopfiella Fusarium Pseudallescheria Haematonectria Doratomyces Galactomyces Myriococcum Geomyces Penicillium Aspergillus Hypocrea Genus PA PAC AC CC PEAT Agrococcus Microbacterium Mycobacterium Streptomyces Bacillus Devosia Pedomicrobium Rhodoplanes Mesorhizobium Agrobacterium Streptomyces spp. Bacillus spp. Fusarium spp. Zopfiella spp. Penicillium spp. (Bonanomi et al., 2010) (Susi et al., 2011) 34

35 Clone libraries Based on the analysis of DNA Gold Standard for preliminary microbial diversity surveys Accurate phylogenetic identification of cloned sequences N ational Compost Conference, September Gatineau, Quebec

36 16S rrna gene Chitinase gene (Hoster et al., 2005) Shannon-Wiener Index (H') Simpsons Index (1-D) GCTh GC GCTh GC 16S rrna gene sequences Chitinase gene sequences (Kawase et al., 2006) (Susi et al., 2011) 36

37 TECHNIQUES Culture-based Cultivationindependent Culture media Biolog-based methods Partial community Whole community Post-genomic Metaproteomics Metatranscriptomics Metabolomics

38 Postgenomic approaches Genetic potential Metatranscriptomics Metaproteomics Metabolomics Functionality N ational Compost Conference, September Gatineau, Quebec

39 Metabolome analysis PEAT CC AC PAC PC Phytophtora Disease incidence (%) Streptomyces spp. (Fushimi et al., 1989; Hwang et al., 1994) Bacillus cereus (Milner et al., 1996; Shekkar et al., 2006) Tuberdicidin Zwittermicin A Phosphalactomycin Kanosamine suppressive Nonsuppressive Conducive Candicidin 39

40 THANKS FOR YOUR ATTENTION