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The establishment of apple orchards as temperate forest garden systems and their impact on indigenous bacterial and fungal population abundance in Southern Ontario, Canada

  • P.C. Wartman (a1), K.E. Dunfield (a2), K. Khosla (a2), C. Loucks (a1), R.C. Van Acker (a1) and R.C. Martin (a1)...


This research investigated soil microbial abundances affected by different ground management systems in establishing apple (Malus domestica cv. Idared, M9) orchards in Ontario, Canada. Four treatments, including forest garden systems with and without compost (FGSC and FGS), and grass understory systems with and without compost (GC and G), were assessed over two establishment years for gene copy abundance of soil arbuscular mycorrhizal (AM) fungi, total fungi and total bacteria using quantitative real-time polymerase chain reactions. Time had a greater effect on all three soil microbial abundances, with total bacterial and AM fungi decreasing and total fungal abundance increasing from spring 2013 to fall 2014. The changes were greatest between the sampling dates of fall 2013 and spring 2014, which is 1 yr after the establishment of the experimental apple plots. There were no significant differences in soil microbial abundances between treatments at any specific sampling date. Apple tree trunk circumference was greatest for FGSC and FGS after 2 yr, but no significant differences in GC and G treatments. In the last sampling period, fall 2014, FGSC plots had significantly greater trunk circumferences compared with G plots. Soil chemical properties neither changed over the 2 yr, nor did they differ between treatments at any one sampling time. We conclude that the apple-based FGS treatments can benefit apple tree growth and there is a basis for future research to explore specific plant–plant, plant–microbe and microbe–microbe relations in FGSs.

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This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (, which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Allen, M.F., Swenson, W., Querejeta, J.I., Egerton-Warburton, L.M., and Treseder, K.K. 2003. Ecology of mycorrhizae: A conceptual framework for complex interactions among plants and fungi. Annual Review of Phytopathology 41:271303.
Askegaard, M. and Eriksen, J. 2007. Growth of legume and nonlegume catch crops and residual-N effects in spring barley on coarse sand. Journal of Plant Nutrition and Soil Science 170:773780.
Bainard, L.D., Klironomos, J.N., and Gordon, A.M. 2011. Arbuscular mycorrhizal fungi in tree-based intercropping systems: A review of their abundance and diversity. Pedobiologia 54:5761.
Bonfante, P. and Anca, I. 2009. Plants, mycorrhizal fungi, and bacteria: A network of interactions. Annual Review of Microbiology 63:6383.
Brown, W. 2012. Roles of biodiversity in integrated fruit production in Eastern North American orchards. Agriculture and Forest Entomology 14:8999.
Butt, S., Ramprasad, P., and Fenech, A. 2012. Changes in the Landscape of Southern Ontario, Canada since 1750: Impacts of European Colonization. Available at Web site (verified 3 February 2015).
Carter, M.R. and Gregorich, E.G. 2006. Soil Sampling and Methods of Analysis. 2nd ed. Taylor & Francis Group, Florida.
Cheng, F., Peng, X., Zhao, P., Yuan, J., Zhong, C., Cheng, Y., Cui, C., and Zhang, S. 2013. Soil microbial biomass basal respiration and enzyme activity of main forest types in the Qinling Mountains. PLoS ONE 8(6):e67353. doi: 10.1371/journal.pone.0067353
Chifflot, V.C., Rivest, D., Olivier, A., Cogliastro, A., and Khasa, D. 2009. Molecular analysis of arbuscular mycorrhizal community structure and spores distribution in tree-based intercropping and forest systems. Agriculture Ecosystems and the Environment 131:3239.
Crawford, M. 2012. Creating a Forest Garden: Working with Nature to Grow Edible Crops. UIT Cambridge Ltd, Cambridge.
Ferguson, R.S. and Lovell, S.T. 2014. Permaculture for agroecology: Design, movement, practice and worldview. A review. Agronomy for Sustainable Development 34:251274.
Fierer, N., Jackson, J.A., Vilgalys, R., and Jackson, R.B. 2005. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Applied Environmental Microbiology 71:41174120.
FliBbach, A., Oberholzer, H., Gunst, L., and Mäder, P. 2007. Soil organic matter and biological soil quality indicators after 21 years of organic and conventional farming. Agriculture Ecosystems and the Environment 1118:273284.
Gardes, M. and Bruns, T.D. 1993. ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Molecular Ecology 2:113118.
Gardes, M., White, T.J., Fortin, J.A., Bruns, T.D., and Taylor, J.W. 1990. Identification of indigenous and introduced symbiotic fungi in ectomycorrhizae by amplification of nuclear and mitochondrial ribosomal DNA. Canadian Journal of Botany 69:180190.
Government of Canada 2015. Canadian Climate Normal: 1981–2010 Climate Normal & Averages. Available at Web site (verified 20 February 2015).
Granatstein, D. and Sanchez, E. 2009. Research knowledge and needs for orchard floor management in organic tree fruit systems. International Journal of Fruit Science 7:257281.
Handson, D., Kotuby-Amacher, J., and Miller, R.O. 1997. Soil analysis: Western states proficiency testing program for 1996. Fresenius Journal of Analytical Chemistry 360:348350.
Hirsch, P.R., Mauchline, T.H., and Clark, I.M. 2010. Culture-independent molecular techniques for soil microbial ecology. Review of Soil Biology and Biochemistry 42:878887.
Hoagland, L, Carpenter-Boggs, L, Granatstein, D., Mazzola, M., Smith, J., Peryea, F., and Reganold, J.P. 2008. Orchard floor management effects on nitrogen fertility and soil biological activity in a newly established organic apple orchard. Biology and Fertility of Soils 45:1118.
Jacke, D. and Toensmeier, E. 2005. Edible Forest Gardens, Vol. 1. Chelsea Green, Vermont.
Jackson, W. 2002. Natural systems agriculture: A truly radical alternative. Agriculture Ecosystems Environment 88:111117.
Janick, J. 2003. Horticultural Reviews: Wild Apple and Fruit Trees of Central Asia. Vol. 29. Wiley & Sons, New York.
Jose, S. 2009. Agroforestry for ecosystem services and environmental benefits: An overview. Agroforestry Systems 76:110.
Kimmins, J.P. 2004. Forest Ecology: A foundation for Sustainable Forest Management and Environmental ethics in Forestry, 3rd ed. Upper Saddle River, New Jersey.
Lacombe, S., Bradley, R.L., Chantel, H., and Beaulieu, C. 2009. Do tree-based intercropping systems increase the diversity and stability of soil microbial communities? Agriculture Ecosystems and the Environment 131:2531.
Lee, J., Lee, S., and Young, P.W. 2008. Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi. FEMS Microbiology Ecology 65:339349.
Leinfelder, M.M. and Merwin, I.A. 2006. Management strategies for apple replant disease. New York Fruit Quarterly 14:3942.
Nair, A. and Ngouajio, M. 2012. Soil microbial biomass, functional microbial diversity and nematode community structure as affected by cover crops and compost in an organic vegetable production system. Applied Soil and Ecology, 58:4555.
Nemeth, D.D., Wagner-Riddle, C., and Dunfield, K.E. 2014. Abundance and gene expression in nitrifier and denitrifier communities associated with a field scale spring thaw N2O flux event. Soil Biology and Biochemistry 73:19.
Nerlich, K., Graeff-Honninger, S., and Claupeinm, W. 2013. Agroforestry in Europe: A review of the disappearance of traditional systems and development of modern agroforestry practices, with emphasis on experiences in Germany. Agroforestry Systems 87:475492.
Olsen, S.R., Cole, C.V., Watanabe, F.S., and Dean, L.A. 1954. Estimation of Available Phosphorus Soils by Extraction with Sodium Bicarbonate. US Department of Agriculture, Washington, DC, Circular 939.
Shortt, K.B. and Vamosi, S.M. 2012. A review of the biology of the weedy Siberian peashrub, Caragana arborescnes, with an emphasis on its potential effects in North America. Botanical Studies 53:18.
Smith, S.E. and Smith, F.A. 2011. Mycorrhizas in plant nutrition and growth: New paradigms from cellular to ecosystem scales. Annual Review of Plant Biology 62:227250.
Thevathasan, N.V. and Gordon, A.M. 2004. Ecology of tree intercropping systems in the north temperate region: Experiences from Southern Ontario. Agroforestry Systems 61:257268.
Tomich, T.P., Brodt, S., Ferris, H., Galt, R., Horwath, W.R., and Kebreab, E. 2011. Agroecology: A review from a global-change perspective. Annual Review of Environment and Resources 36:193222.
Unger, I.M., Goyne, K.W., Kremer, R.J., and Kennedy, A.C. 2013. Microbial community diversity in agroforestry and grass vegetative filter strips. Agroforestry Systems 87:395402.
Uprety, Y., Asselin, H., Dhakal, A., and Julien, N. 2012. Traditional use of medicinal plants in the boreal forest of Canada: A review and perspectives. Journal of Ethnobiology and Ethnomedicine 8:7.
Wang, D. and Anderson, D.W. 1998. Direct measurement of organic carbon content in soils by the Leco CR-12 carbon analyzer. Communications in Soil Science and Plant Analysis 29(1–2):1521.
Welbaum, G.E., Sturz, A.V., Dong, Z., and Nowak, J. 2004. Managing soil microorganisms to improve productivity of agro-ecosystems. Critical Review of Plant Science 23:175193.
Whiteside, M.D., Digman, M.A., Gratton, E., and Treseder, K.K. 2012. Organic nitrogen uptake by arbuscular mycorrhizal fungi in a boreal forest. Soil Biology and Biochemistry 55:713.
Wiersum, K.F. 2004. Forest gardens as an intermediate land-use system in the nature-culture continuum: Characteristics and future potential. Agroforestry Systems, 61:123134.
Wotherspoon, A. 2014. Quantification of Carbon Gains and Losses for Five Tree Species in a 25-year Old Tree-based Intercropping System in Southern Ontario, Canada. University of Guelph, Canada.
Wu, J. and Hobbs, R. 2002. Key issues and research priorities in landscape ecology: An idiosyncratic synthesis. Landscape Ecology 17:355365.
Yao, S., Merwin, I.A., Bird, G.W., Abawi, G.S., and Thies, J.E. 2005. Orchard floor management practices that maintain vegetative or biomass groundcover stimulate soil microbial activity and alter soil microbial community composition. Plant and Soil 271:377389.
Zak, D.R., Holmes, W.E., White, D.C., Peacock, A.D., and Tilman, D. 2003. Plant diversity, soil microbial communities, and ecosystem function: Are there any links? Ecology 84:20422050.
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