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Performance evaluation of locally available composts to reduce replant disease in apple orchards of central Europe

  • Ingrid H. Franke-Whittle (a1), Marina Fernández-Delgado Juárez (a1), Heribert Insam (a1), Simon Schweizer (a2), Andreas Naef (a2), Anne-Rosemarie Topp (a3), Markus Kelderer (a3), Thomas Rühmer (a4), Gerhard Baab (a5), Joana Henfrey (a5) and Luisa M. Manici (a6)...


A study on locally available composts in Austria, Germany, Italy and Switzerland was conducted to investigate the potential of these non-chemical based tools to increase soil health in orchards afflicted by apple replant disease (ARD). A total of 26 different composts (six to seven per country) were chosen for the study. Composts were divided into ten types according to the waste materials used as substrates in the composting process. Growth reduction is the main symptom associated with replant disease; therefore compost performance was evaluated based on the growth responses of apple rootstock plantlets in compost-amended soils in pots. These greenhouse trials were performed in one research station per country, located in an intensive apple-growing area, and soil was taken from an apple orchard affected by replanting disease. Plant growth response was measured as shoot elongation at the end of each greenhouse trial, and results showed increases in growth compared with the respective controls of 2–26% in 20 out of 26 composts evaluated. The heterogeneous nature of the composts most likely attributed to the finding that similar compost types originating from the different countries had varying effects on plant growth. Overall, no significant changes in chemical and biological properties were observed in amended soils as compared with non-amended controls. The high soil resilience was in part expected given the good organic matter content in the original soils (>2%). The bacterial communities of the composts were investigated using the COMPOCHIP microarray, and analyses showed that differences in plant growth response were mainly attributed to the microbial changes introduced into the soil through composts rather than to changes in soil chemical and biological parameters. However, the bacterial communities of composts appeared to be more influenced by geographical origin than by compost type. The results have shown that soil amendment with composts generated from locally produced wastes have the potential to reduce the effects of ARD, although the effects appear to be both compost and soil specific.


Corresponding author

Author for correspondence: Luisa M. Manici, E-mail:


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Akhter, A, Hage-Ahmed, K, Soja, G and Steinkellner, S (2015) Compost and biochar alter mycorrhization, tomato root exudation, and development of Fusarium oxysporum f. sp. lycopersici . Frontiers in Plant Science 6, 529.
Anderson, JPE and Domsch, KH (1978) A physiological method for the quantitative measurement of microbial biomass in soils. Soil Biology and Biochemistry 10, 215221.
Bonilla, N, Gutiérrez-Barranquero, JA, de Vicente, A and Cazorla, FM (2012) Enhancing soil quality and plant health through suppressive organic amendments. Diversity 4, 475491.
Braun, GP, Fuller, KD, McRae, K and Fillmore, SAE (2010) Response of ‘Honeycrisp®’ apple trees to combinations of pre-plant fumigation, deep ripping, and hog manure compost incorporation in a soil with replant disease. HortScience 45, 17021707.
Cayuela, ML, Mondini, C, Insam, H, Sinicco, T and Franke-Whittle, I (2009) Plant and animal wastes composting: effects of the N source on process performance. Bioresource Technology 100, 30973106.
Chaoui, HE, Brickner, CA, Lee, SS and Arancon, NQ (2002) Suppression of the plant diseases, Pythium (damping-off), Rhizoctonia (root rot) and Verticillium (wilt) by vermicomposts, In The BCPC Conference: Pests and Diseases, Brighton, UK, pp. 711716.
Chen, M-H and Nelson, EB (2008) Seed-colonizing microbes from municipal biosolids compost suppress Pythium ultimum damping-off on different plant species. Phytopathology 98, 10121018.
Compant, S, Duffy, B, Nowak, J, Clément, C and Barka, EA (2005) Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Applied Environmental Microbiology 71, 49514959.
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 Bertoldi, M (2010) Production and utilization of suppressive compost: environmental, food and health benefits. In Insam, H, Franke-whittle, I and Goberna, M (eds) Microbes at Work: From Wastes to Resources. Heidelberg: Springer, pp. 153170.
Dees, PM and Ghiorse, WC (2001) Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiology Ecology 35, 207216.
Erhart, E, Burian, K, Hartl, W and Stich, K (1999) Suppression of Pythium ultimum by biowaste composts in relation to compost microbial biomass, activity and content of phenolic compounds. Journal of Phytopathology 147, 299305.
Farrell, M and Jones, DL (2009) Critical evaluation of municipal solid waste composting and potential compost markets Critical evaluation of municipal solid waste composting and potential compost markets. Bioresource Technology 100, 43014310.
Franke-Whittle, IH, Klammer, SH and Insam, H (2005) Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. Journal of Microbial Methods 62, 3756.
Franke-Whittle, IH, Knapp, BA, Fuchs, J, Kaufmann, R and Insam, H (2009) Application of COMPOCHIP microarray to investigate the bacterial communities of different composts. Microbial Ecology 57, 510521.
Franke-Whittle, IH, Confalonieri, A, Insam, H, Schlegelmilch, M and Korner, I (2014) Changes in the microbial communities during co-composting of digestates. Waste Management 34, 632641.
Franke-Whittle, IH, Manici, LM, Insam, H and Stres, B (2015) Rhizosphere bacteria and fungi associated with plant growth in soils of three replanted apple orchards. Plant and Soil 395, 317333.
Githinji, L (2014) Effect of biochar application rate on soil physical and hydraulic properties of a sandy loam. Archives of Agronomy and Soil Science 60, 457470.
Hammer, Ø, Harper, DAT and Ryan, PD (2001) Past: paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4, 9.
Hargreaves, JC, Adl, MS and Warman, PR (2008) A review of the use of composted municipal solid waste in agriculture. Agronomy Ecosystems and Environment 123, 114.
Haygarth, PM, Bartgett, RD and Candron, LM (2013) Nitrogen and phosphorus cycles and their management. Chapt 5. In Gregory, PJ and Northcliff, S (eds). Soil Condition and Plant Growth. Ames, Iowa, USA: Wiley-Blackwell, pp. 132155.
Heinemeyer, O, Insam, H, Kaiser, EA and Walenzik, G (1989) Soil microbial biomass and respiration measurements: An automated technique based on infra-red gas analysis. Plant and Soil 116, 191196.
Hoitink, H and Boehm, M (1999) Biocontrol within the contect of soil microbial communities: A substrate-dependent phenomenon. Annual Review of Phytopathology 37, 427446.
Hoitink, H, Stone, A and Han, D (1997) Suppression of plant diseases by composts. HortScience 32, 184187.
Hunter, PJ, Petch, GM, Calvo-Bado, LA, Pettitt, TR, Parsons, NR, Morgan, JAW and Whipps, JM (2006) Differences in microbial activity and microbial populations of peat associated with suppression of damping-off disease caused by Pythium sylvaticum . Applied and Environmental Microbiology 72, 64526460.
Insam, H and Öhlinger, R (1996) Ecophysiological parameters. In Schinner, F, Öhlinger, R, Kandeler, E and Margesin, R (eds). Methods in Soil Biology. Germany: Springer, pp. 306309.
Insam, H, Franke-Whittle, I and Goberna, M (2010) Microbes in aerobic and anaerobic treatment. In Insam, H (ed.) Microbes at Work: From Waste to Resources. Heidelberg: Springer-Verlag Berlin, pp. 134.
Kampstra, P (2008) Beanplot: A Boxplot Alternative for Visual Comparison of Distributions. Journal of Statistical Software 28, Cod Snip 1. (verified 5 January 2018).
Kannangara, T, Utkhede, RS, Paul, JW and Punja, ZK (2000) Effects of mesophilic and thermophilic composts on suppression of Fusarium root and stem rot of greenhouse cucumber. Canadian Journal of Microbiology 46, 10211028.
Kelderer, M, Manici, LM, Caputo, F and Thalheimer, M (2012) Planting in the ‘inter-row’ to overcome replant disease in apple orchards: A study on the effectiveness of the practice based on microbial indicators. Plant and Soil 357, 381393.
LaMondia, JA, Gent, MPN, Ferrandino, FJ, Elmer, WH and Stoner, KA (1999) Effect of compost amendment or straw mulch on potato early dying disease. Plant Disease 83, 361366.
Lazarovits, G (2001) Management of soil-borne plant pathogens with organic soil amendments: a disease control strategy salvaged from the past. Canadian Journal of Plant Pathology 23, 17.
Leinfelder, MM and Merwin, IA (2006) Rootstock selection, preplant soil treatments, and tree planting positions as factors in managing apple replant disease. HortScience 41, 394401.
Loveland, PWJ (2003) Is there a critical level of organic matter in the agricultural soils of temperate regions: A review. Soil and Tillage Research 70, 118.
Manici, LM, Ciavatta, C, Kelderer, M and Erschbaumer, G (2003) Replant problems in South Tyrol: role of fungal pathogens and microbial population in conventional and organic apple orchards. Plant and Soil 256, 315324.
Manici, LM, Caputo, F and Babini, V (2004) Effect of green manure on Pythium spp. population and microbial communities in intensive cropping systems. Plant and Soil 63, 133142.
Manici, LM, Kelderer, M, Franke-Whittle, IH, Rühmer, T, Baab, G, Nicoletti, F, Caputo, F, Topp, A, Insam, H and Naef, A (2013) Relationship between root-endophytic microbial communities and replant disease in specialized apple growing areas in Europe. Applied Soil Ecology 72, 207214.
Mansoori, M, Heydari, A, Hassanzadeh, N, Rezaee, S and Naraghi, L (2013) Evaluation of Pseudomonas and Bacillus bacterial antagonists for biological control of cotton Verticillium wilt disease. Journal of Plant Protection Research 53, 54157.
Mazzola, M (1998) Elucidation of the microbial complex having a causal role in the development of apple replant disease in Washington. Phytopathology 88, 930938.
Mazzola, M (2010) Management of Resident Soil Microbial Community Structure and Function to Suppress Soilborne Disease Development. In Reynolds, M (ed.). UK: CABI Publishing, pp. 200218.
Mazzola, M and Gu, Y-H (2002) Wheat genotype-specific induction of soil microbial communities suppressive to disease incited by rhizoctonia solani anastomosis group (AG)-5 and AG-8. Phytopathology 92, 3001307.
Mazzola, M and Manici, LM (2012) Apple replant disease: role of microbial ecology in cause and control. Annual Review of Phytopathology 50, 4565.
MBTOC (2011) Montreal Protocol on Substances That Deplete the Ozone Layer. 2010 Report of the Methyl Bromide Technical Options Committee, 2010 Assessment. United Nations Environment Programme (UNEP). Ozone Secretariat, Nairobi, Kenya March 2011 Available at (verified 15 September 2017).
Mehta, CM, Palni, U, Franke-Whittle, IH and Sharma, AK (2014) Compost: Its role, mechanism and impact on reducing soil-borne plant diseases. Waste Management 34, 607622.
Moran, RE and Schupp, JR (2003) Preplant monoammonium phosphate fertilizer and compost affects the growth of newly planted ‘Macoun’ apple trees. HortScience 38, 3235.
Noble, R and Coventry, E (2005) Suppression of soil-borne plant diseases with composts: A review. Biocontrol Science and Technology 15, 320.
Ntougias, S, Papadopoulou, K, Zervakis, G, Kavroulakis, N and Ehaliotis, C (2008) Suppression of soil-borne pathogens of tomato by composts derived from agro-industrial wastes abundant in Mediterranean regions. Biology Fertility of Soils 44, 10811090.
Pascual, JA, Garcia, C, Hernandez, T, Lerma, S and Lynch, JM (2002) Effectiveness of municipal waste compost and its humic fraction in suppressing Pythium ultimum . Microbial Ecology 5, 968.
Peck, GM, Merwin, IA, Thies, JE, Shindelbeck, RR and Brown, MG (2011) Soil properties change during the transition to integrated and organic apple production in a New York orchard. Applied Soil Ecology 48, 1830.
Pérez-Piqueres, A, Edel-Hermann, V, Alabouvette, C and Steinberg, C (2006) Response of soil microbial communities to compost amendments. Soil Biology and Biochemistry 38, 460470.
Postma, J, Willemsen-De Klein, MJEIM and Van Elsas, JD (2000) Effect of the indigenous microflora on the development of root and crown rot caused by Pythium aphanidermatum in cucumber grown on rockwool. Phytopathology 90, 125133.
Postma, L, Geraats, BPJ, Pastoor, R and van Elsas, JD (2005) Characterization of the microbial community involved in the suppression of Pythium aphanidermatum in cucumber grown on rockwool. Phytopathology 95, 808818.
Rivera, M and Wright, E (2009) Research on Vermicompost as Plant Growth Promoter and Disease Suppressive Substrate in Latin America, Dynamic Soil. Middlesex, UK: Global Science Books, Ltd.
Rumberger, A, Yao, SR, Merwin, IA, Nelson, EB and Thies, JE (2004) Rootstock genotype and orchard replant position rather than soil fumigation or compost amendment determine tree growth and rhizosphere bacterial community composition in an apple replant soil. Plant and Soil 264, 247260.
Shemekite, F, Gomez-Brandon, M, Franke-Whittle, IH, Praehauser, B, Insam, H and Assefa, F (2014) Coffee husk composting: an investigation of the process using molecular and non-molecular tools. Waste Management 34, 642652.
Spath, M, Insam, H, Peintner, U, Kelderer, M, Kuhnert, R and Franke-Whittle, IH (2015) Linking soil biotic and abiotic factors to apple Replant disease: a greenhouse approach. Journal of Phytopathology 163, 287299.
Szczech, MM (1999) Suppressiveness of vermicompost against Fusarium wilt of tomato. Journal of Phytopathology 147, 155161.
ter Braak, C and Smilauer, P (2002) CANOCO reference manual and CanoDraw for Windows user's guide: software for canonical community ordination (version 4.5). Itaca: Microcomputer Power.
Termorshuizen, AJ, van Rijn, E, van der Gaag, DJ, Alabouvette, C, Chen, Y, Lagerlöf, J, Malandrakis, AA, Paplomatas, EJ, Rämert, B, Ryckeboer, J, Steinberg, C and Zmora-Nahum, S (2006) Suppressiveness of 18 composts against 7 pathosystems: variability in pathogen response. Soil Biology and Biochemistry 38, 24612477.
Uzun, I (2004) Use of spent mushroom compost in sustainable fruit production. Journal of Fruit and Ornamental Plant Research. Special ed. Special management of sustainable fruit production 12, 157165.
van Schoor, L, Denman, S and Cook, NC (2009) Characterisation of apple replant disease under South African conditions and potential biological management strategies. Scientiae Horticulturae 119, 153162.
Wilson, S, Andrews, P and Nair, TS (2004) Non-fumigant management of apple replant disease. Scientiae Horticolturae 102, 221231.
Yao, S, Merwin, IA, Abawi, GS and Thies, JE (2006) Soil fumigation and compost amendment alter soil microbial community composition but do not improve tree growth or yield in an apple replant site. Soil Biology and Biochemistry 38, 587599.
Zhang, X, Huang, Y, Harvey, PR, Ren, Y, Zhang, G, Zhou, H and Yang, H (2012) Enhancing plant disease suppression by Burkholderia vietnamiensis through chromosomal integration of Bacillus subtilis chitinase gene chi113. Biotechnology Letters 34, 287293.
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