Skip to main content Accessibility help

In vitro elucidation of suppression effects of composts to soil-borne pathogen Phytophthora nicotianae on pepper plants using 16S amplicon sequencing and metaproteomics

  • Margarita Ros (a1), Josefa Blaya (a1), Petr Baldrian (a2), Felipe Bastida (a1), Hans H Richnow (a3), Nico Jehmlich (a4) and Jose Antonio Pascual (a1)...


Compost production is a critical component of organic waste management. One of the most important properties of compost is its ability to suppress soil-borne pathogens such as Phytophthora nicotianae in pepper plants. Both the physico-chemical and biological properties of composts can be responsible for the suppression of pathogens, although biological properties are the main driver. In this study, we analyzed composts with various levels of suppressiveness against P. nicotianae. We analyzed both physico-chemical properties like pH and electrical conductivity and biological properties like microbial activity, amplicon sequencing and metaproteomics. We believed that the link between community structures and proteins could provide deep insights into the mechanism of compost suppressiveness. Our results indicate that there are differences between suppressive and non-suppressive composts at the phylogenetic level (sequencing) and at the functional level (based on analysis of the cluster of orthologous groups, COGs). The proteins identified were assigned to the carbohydrate process, cell wall structure and inorganic ion transport and metabolism. Proteobacteria could also be new indicators of P. nicotianae suppression.


Corresponding author

Author for correspondence: Margarita Ros, E-mail:


Hide All

These authors contributed equally to this work.



Hide All
Adetumbi, MA and Lau, BHS (1983) Allium sativum (garlic): a natural antibiotic. Medical Hypotheses 12, 227237.
Aronesty, E (2013) Comparison of sequencing utility programs. Open Bioinformatics Journal 7, 18.
Bastida, F, Hernández, T and Garcia, C (2014) Metaproteomics of soils from semiarid environment: functional and phylogenetic information obtained with different protein extraction methods. Journal of Proteomics 101, 3142.
Bastida, F, Selevsek, N, Torres, IF, Hernandez, T and Garcia, C (2015) Soil restoration with organic amendments: linking cellular functionality and ecosystem processes. Scientific Reports 5, 15550.
Bastida, F, Torres, IF, Moreno, JL, Baldrian, P, Ondoño, S, Ruiz-Navarro, A, Hernandez, T, Richnow, HH, Starke, R, García, C and Jehmlich, N (2016) The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi-arid soils. Molecular Ecology 25, 46604673.
Blaya, J, Lloret, E, Ros, M and Pascual, J (2015) Identification of predictor parameters to determine agro-industrial compost suppressiveness against Fusarium oxysporum and Phytophthora capsici diseases in muskmelon and pepper seedlings. Journal of the Science of Food and Agriculture 95, 14821490.
Blaya, J, Marhuenda, F, Pascual, J and Ros, M (2016) Microbiota characterization of compost using omics approaches opens new perspectives for Phytophthora root rot control. PLoS ONE 11, e0158048.
Bonanomi, G, Antignani, V, Capodilupo, M and Scala, F (2010) Identifying the characteristics of organic soil amendments that suppress soilborne plant diseases. Soil Biology and Biochemistry 42, 136144.
Caporaso, JG, Lauber, CL, Walters, WA, Berg-Lyons, D, Huntley, J, Fierer, N, Owens, SM, Betley, J, Fraser, L, Bauer, M, Gormley, N, Gilbert, JA, Smith, G and Knight, R (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME Journal 6, 16211624.
Carini, P, Marsden, PJ, Leff, JW, Morgan, EE, Strickland, MS and Fierer, N (2016) Relic DNA is abundance in soil and obscures estimates of soil microbial diversity. Nature Microbiology 2, 16242.
Castaño, R, Borreo, C and Aviles, M (2011) Organic matter fractions by SP-MAS 13C NMR and microbial communities involved in the suppression of Fusarium wilting organic growth media. Biological Control 58, 286293.
Chourey, K, Jansson, J, VerBerkmoes, N, Shah, M, Chavarria, KL, Tom, LM, Brodie, EL and Hettich, RL (2010) Direct cellular lysis/protein extraction protocol for soil metaproteomics. Journal of Proteome Research 9, 66156622.
Cole, JR, Wang, Q, Fish, JA, Chai, B, McGarrell, DM, Sun, Y, Brown, CT, Porras-Alfaro, A, Kuske, CR and Tiedje, JM (2014) Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Research 42, D633D642.
Danon, M, Franke-Whittle, IH, Insam, H, Chen, Y and Hadar, Y (2008) Molecular analysis of bacterial community succession during prolonged compost curing. FEMS Microbiology Ecology 65, 133144.
de Gannes, V, Eudoxie, G and Hickey, WJ (2013) Prokaryotic successions and diversity in composts as revealed by 454-pyrosequencing. Bioresource Technology 133, 573580.
Edgar, RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics (Oxford, England) 26, 24602461.
Edgar, RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 10, 996998.
Garcia, C, Hernandez, T, Costa, F, Cecanti, B and Masciandaro, G (1993) Dehydrogenase activity of soil as an ecological marker in processes of perturbed system regeneration. In Gallardp-Lancho, J (ed.), Proceedings of the XI International Symposium of Environmental Biogeochemistry. Salamanca, España: CSIC, pp. 89100.
García, C, Roldán, A and Hernández, T (1997) Changes in microbial activity alter abandonment of cultivation in a semiarid Mediterranean environment. Journal of Environmental Quality 26, 285291.
Gonzalez-Sanchez, MA, Perez-Jimenez, RM, Pliego, C, Ramos, C, de Vicente, A and Cazorla, FM (2010) Biocontrol bacteria selected by a direct plant protection strategy against avocado white root rot show antagonism as a prevalent trait. Journal of Applied Microbiology 109, 6578.
Gopalakrishnan, S, Srinivas, V, Alekhya, G, Prakash, B, Kudapa, H, Rathore, A and Varshney, RK (2015) The extent of grain yield and plant growth enhancement by plant growth-promoting broad-spectrum Streptomyces sp. in chickpea. SpringerPlus 4, 31.
Hadar, Y and Papadopoulou, KK (2012) Suppressive composts: microbial ecology links between abiotic environments and healthy plants. Annual Review of Phytopathology 50, 133153.
Haug, RT (1993) The Practical Handbook of Compost Engineering. Boca Raton, FL: Lewis Publishers, 717 pages.
Hoitink, H and Boehm, M (1999) Biocontrol within the context of soil microbial communities: a substrate-dependent phenomenon. Annual Review of Phytopathology 37, 427446.
Hoitink, HAJ and Fahy, PC (1986) Basis for the control of soilborne plant-pathogens with composts. Annual Review of Phytopathology 24, 93114.
Hoitink, HAJ and Grebus, ME (1997) Composts and the control of plant disease. In Hayes, MHB and Wilson, WS (eds), Humic Substances in Soil, Peats and Waters: Health and Environmental Aspects. Cambridge, UK: Royal Society of Chemistry, pp. 359366.
Ihrmark, K, Bödeker, IT, Cruz-Martinez, K, Friberg, H, Kubartova, A, Schenck, J, Strid, Y, Stenlid, J, Brandström-Durling, M, Clemmensen, KE and Lindahl, BD (2012) New primers to amplify the fungal ITS2 region evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiology Ecology 82, 666677.
Ishii, K and Takii, S (2003) Comparison of microbial communities in four different composting processes as evaluated by denaturing gradient gel electrophoresis analysis. Journal of Applied Microbiology 95, 109119.
Jehmlich, N, Schmidt, F, Von Bergen, M, Richnow, HH and Vogt, C (2008) Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures. ISME Journal 2, 11221133.
Kersters, K, De Vos, P, Gillis, M, Swings, J, Vandamme, P and Stackebrandt, E (2006) Introduction to the Proteobacteria. In: Dwarkin, M, Falkow, S, Rosenberg, E, Schleifer, K-H, Stackebrandt, E (eds), The Prokaryotes, 3rd Edn. vol. 5. New York: Springer, pp. 337.
Koljalg, U, Nilsson, RH, Abarenkov, K, Tedersoo, L, Taylor, FS, Bahram, M, Bates, ST, Bruns, TD, Bengtsson-Palme, J, Callaghan, TM, Douglas, B, Drenkhan, T, Eberhardt, U, Dueñas, M, Grebenc, T, Griffith, GW, Hartmann, M, Kirk, PM, Kohout, P, Larsson, E, Lindahl, BD, Lücking, R, Martín, MP, Matheny, PB, Nguyen, NH, Niskanen, T, Oja, J, Peay, KG, Peintner, U, Peterson, M, Põldmaa, K, Saag, L, Saar, I, Schüßler, A, Scott, JA, Senés, C, Smith, ME, Suija, A, Taylor, DL, Telleria, MT and Weiss, M (2013) Towards a unified paradigm for sequence-based identification of fungi. Molecular Ecology 22, 52715277.
Kurtboke, DI (2012) Biodiscovery from rare actinomycetes: an ecotaxonomical perspective. Applied Microbiology and Biotechnology 93, 18431852.
Laemmli, BUK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680685.
Lemaire, F, Dartigues, A and Rivière, LM (1985) Properties of substrate made with spent mushroom compost. Acta Horticulturae 172, 1329.
Liu, D, Li, M and XI, B (2015) Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant. Microbial Biotechnology 8, 950960.
Martin, CCG and Brathwaite, RAI (2012) Compost and compost tea: principles and prospects as substrates and soil-borne disease management strategies in soil-less vegetable production. Biological Agriculture and Horticulture 28, 133.
Mehta, CM, Yu, D, Srivastava, R, Sinkkonen, A, Kurola, JM, Gupta, V, Jääskeläinen, H, Palni, U, Sharma, AK and Romantschuk, M (2016) Microbial diversity and bioactive substances in disease suppressive composts from India. Compost Science and Utilization 24, 105116.
Mengesha, WK, Gill, WM, Powell, SM, Evans, KJ and Bary, KM (2017) A study of selected factors affecting efficacy of compost tea against several fungal pathogens of potato. Journal of Applied Microbiology 123, 732747.
Morales, AB, Ros, M, Ayuso, LM, Bustamante, MA, Moral, R and Pascual, JA (2017) Agroindustrial composts to reduce the use of peat and fungicides in the cultivation of muskmelon seedlings. Journal of the Science of Food and Agriculture 97, 875881.
Neher, DA, Weicht, TR, Bates, ST, Leff, JW and Fierer, N (2013) Changes in bacterial and fungal communities across compost recipes, preparation and composting times. PLoS One 8, e79512.
Nilsson, RH, Veldre, V, Hartmann, M and Kristiansson, E (2010) An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology. Fungal Ecology 3, 284287.
Ntougias, S, Papadopoulou, KK and Zervakis, GI (2008) Suppression of soil-borne pathogens of tomato by composts derived from agro-industrial wastes abundant in Mediterranean regions. Biology and Fertility of Soils 44, 10811090.
Partanen, P, Hultman, J, Paulin, L, Auvinen, P and Romantschuk, M (2010) Bacterial diversity at different stages of the composting process. BMC Microbiology 10, 94.
Postma, J, Sheper, RWA and Schilder, MT (2010) Effect of successive cauliflower plantings and Rhizoctonia solani AG 2-1 inoculations on disease suppressiveness of a suppressive and conducive soil. Soil Biology and Biochemistry 42, 804812.
Rynk, R (1992) On-farm Composting Handbook (NRAES-54). Ithaca, NY: Northeast Regional Agricultural Engineering Service.
Schneider, T, Keblinger, KM, Schmid, E, Sterflinger-Gleixner, K, Ellersdorfer, G, Roschitzki, B, Richter, A, Eberl, L, Zechmeister-Boltenstern, S and Riedel, K (2012) Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions. ISME Journal 6, 17491762.
Stackebrandt, E and Ebers, J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiology Today 33, 152155.
Sullivan, DM and Miller, RO (2000) Compost, quality attributes measurements and variability. In Stoffella, PJ and Kahn, BA (eds), Compost Utilization in Horticultural Cropping Systems. Boca Raton, FL: CRC Press, pp. 95120.
Thinggaard, K and Andersen, H (1995) Influence of watering frequency and electrical conductivity of the nutrient solution on Phytophthora root rot in pot plants of Gerbera. Plant Disease 79, 259263.
Tian, B, Yang, J and Zhang, KQ (2007) Bacteria used in the biological control of plant-parasitic nematodes: populations, mechanisms of action, and future prospects. FEMS Microbiology Ecology 61, 197213.
Větrovský, T and Baldrian, P (2013) Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED. Biology and Fertility of Soils 49, 10271037.
Wilmes, P and Bond, PL (2006) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends in Microbiology 14, 9297.
Yu, D, Sinkkonen, A, Hui, N, Kurola, JM, Kukkonen, S, Parikka, P, Vestberg, M and Romantschuk, M (2015) Molecular profile of microbiota of Finnish commercial compost suppressive against Pythium disease on cucumber plants. Applied Soil Ecology 92, 4753.
Žifčáková, L, Větrovský, T, Howe, A and Baldrian, P (2016) Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter. Environmental Microbiology 18, 288301.


Type Description Title
Supplementary materials

Ros et al. supplementary material
Tables S1 and S2

 Word (98 KB)
98 KB


Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed