Impact of organic and conventional peach and apple production practices on soil microbial populations and plant nutrients

Abstract

This work expects to supplement information on soil biological processes, particularly for fruit production systems in a semiarid region, by comparing soil microbial diversity and density, and nutrient concentration in soil as well as plant tissues in organic and conventional production systems for different varieties of apple and peach. Organic and conventional practices were compared by taking soil samples and analyzing soil microbial populations and plant and soil nutrients using several laboratory procedures. Significantly higher active and total fungal biomass, flagellate, and Actinobacteria populations and plant nutrients, P and Cu in plant tissues and OM, P, and S in soils were observed in organic compared to the conventional practices, irrespective of crops and varieties. In peach, protozoa and nematode populations were significantly higher in organic than in conventional soils, but not in apple. Organic fruit production practices harbored both greater microbial activity and higher concentrations of some plant and soil nutrients and are anticipated to promote better soil health and productivity than conventional practices. However, introduction and/or enhancement of certain microbes, especially mycorrhizae in both production systems, expected to increase soil health and productivity, are suggested. Use of ranges of microbial population to estimate soil health and management strategy is proposed.

This is a preview of subscription content, access via your institution.

References

  1. Alphei J, Bonkowski M, Scheu S (1996) Protozoa, Nematoda and Lumbricidae in the rhizosphere of Hordelymuseuropaeus (Poaceae): faunal interactions, response of microorganisms and effects on plant growth. Oecologia 106:111–126

    Article  Google Scholar 

  2. Angers DA, Bolinder MA, Carter MR, Gregorich EG, Drury CF, Liang BC, Voroney RP, Simard RR, Donald RG, Beyaert RP, Martel J (1997) Impact of tillage practices on organic carbon and nitrogen storage in cool, humid soils of eastern Canada. Soil Tillage Res 41:191–201

    Article  Google Scholar 

  3. Appropriate Technology Transfer for Rural Area (ATTRA) (1999) Sustainable Soil Management. Soil System Guide http://www.soilandhealth.org/01aglibrary/010117attrasoilmanual/010117attra.html

  4. Barker KR (1985) Nematode extraction and bioassays. In: Barker KR, Carter CC, Sasser JN (eds) An advanced treatise on Meloidogyne, 2nd edn, Methodology. North Carolina State University, Graphics, Raleigh, pp 19–35

    Google Scholar 

  5. Bender FS, van der Heijden MGA (2014) Soil biota enhance agricultural sustainability by improving crop yield, nutrient uptake and reducing nitrogen leaching losses. J Appl Ecol. doi:10.1111/1365-2664.12351

    Google Scholar 

  6. Bongers T (1990) The maturity index: an ecological measure of environmental disturbance based on nematode species composition. Oecologia 83:14–19

    Article  Google Scholar 

  7. Bulluck LR, Brosius M, Evanylo GK, Ristaino JB (2002) Organic and synthetic amendments influence soil microbial, physical and chemical properties on organic and conventional farms. Appl Soil Ecol 19:147–160

    Article  Google Scholar 

  8. Bünemann EK, Schwenke GD, Van Zwieten L (2006) Impact of agricultural inputs on soil organisms—a review. Aust J Soil Res 44:379–406

    Article  Google Scholar 

  9. Clarholm C (1985) Interaction of bacteria, protozoa and plant leading to mineralization of soil nitrogen soil. Biochemistry 17(2):181–187

    CAS  Google Scholar 

  10. Clark MS, Horwarth WR, Shennan C, Scow MR (1998) Change in soil chemical properties resulting from organic and low-input farming. Agron J 3:357–374

    Google Scholar 

  11. Cleary AJ (2012) Organic or not? Is organic produce healthier body balance. http://www.medfusion.net/templates/groups/3655/5438/6100_Newsletter022010.pdf

  12. Coleman DC, Odum EP, Crossley DA Jr (1992) Soil biology, soil ecology and global change. Biol Fert Soils 14:104–111

    Article  Google Scholar 

  13. Combs SM, Denning JL, Frank D (1998) In: Brown JR (ed) Recommended chemical soil test procedures for the North Central Region. North Central Publication No. 221 (Revised). University of Missouri Ag Exp Station, Columbia, pp 35–40

    Google Scholar 

  14. de Vries FT, Thébault E, Liiri M, Birkhofer K, Tsiafouli MA, Bjørnlund L, Jørgensen HB, Brady MV, Christensen S, de Ruiter PC, Hertefeldt TD, Frouz J, Hedlund K, Hemerik L, Hol WHG, Hotes S, Mortimer SR, Setälä H, Sgardelis SP, Uteseny K, van der Putten SP, Wolters V, Bardgett RD (2013) Soil food web properties explain ecosystem services across European land use system. PANAS 110(35):14296–14301. doi:10.1073/pnas.1305198110

    Article  Google Scholar 

  15. Del Val C, Barea JM, Azcón-Aguilar C (1999) Diversity of arbuscular Mycorrizal fungus populations in heavy metal contaminated soils. Appl Environ Microbiol 65(2):718–723

    PubMed Central  CAS  PubMed  Google Scholar 

  16. Ekelund F (1998) Enumeration and abundance of mycophagous protozoa in soil, with special emphasis on heterotrophic flagellates. Soil Biol Biochem 30:1343–1347

    Article  CAS  Google Scholar 

  17. Ekelund F, Rønn R (1994) Notes on protozoa in agricultural soil with emphasis on heterotrophic 396 flagellates and naked amoebae and their ecology. FEMS Microbiol Rev 15:321–353

    Article  CAS  PubMed  Google Scholar 

  18. Forge TA, Hogue EJ, Neilsen G, Neilsen D (2008) Organic mulches alter nematode communities, root growth and fluxes of phosphorus in the root zone of apple. Appl Soil Ecol 39:15–22

    Article  Google Scholar 

  19. Frampton GK (1997) The potential of Collembola as indicators of pesticide usage evidence and methods from the UK arable ecosystem. Pedobiologia 41:179–184

    Google Scholar 

  20. Frank K, Beegle D, Denning J (1998) Phosphorus. In Brown JR (ed.) Recommended chemical soil test procedures for the North Central Region. North Central Regional Publication No. 221 (revised). University of Missouri Ag Exp Station, Columbia, MO 65211, pp. 21–29

  21. Gabriel D, Sait SM, Hodgson JA, Schmutz U, Kunin WE, Benton TG (2010) Scale matters: the impact of organic farming on biodiversity at different spatial scales. Ecol Lett 13(7):858–869

    Article  PubMed  Google Scholar 

  22. Geldeman RH, Beegle D (1998) Nitrate-Nitrogen. In Brown JR (ed) Recommended chemical soil test procedures for the North Central Region. North Central Publication No. 221 (Revised). University of Missouri Ag. Exp. Station, Columbia, MO 65211, pp. 17–20

  23. Glover JD, Reganold JP, Andrews PK (2000) Systematic method for rating soil quality of conventional, organic, and integrated apple orchards in Washington State. Agric Ecosyst Environ 80:29–45

    Article  Google Scholar 

  24. Gupta VVSR, Yeates GW (1997) Soil microfauna as bio-indicators of soil health. In: Pankhurst C, Doube BM, Gupta VVSR (eds) Biological indicators of soil health. CAB International, Oxon, United Kingdom, Pp, pp 201–233

    Google Scholar 

  25. Haby VA, Russelle MP, Skoley EO (1990) Testing Soils for potassium, calcium, and magnesium. In: Westerman RL (ed) Soil testing and plant analysis (third edition). Soil Sci Soc of Am, Madison, pp 181–227

    Google Scholar 

  26. Heilmann B, Lebuhn M, Beese F (1995) Methods for investigation of metabolic activity and shifts in the microbial community in soil treated with a fungicide. Biol Fertil Soils 19:186–192

    Article  CAS  Google Scholar 

  27. Ingham ER (1994) Soil organisms and forest health. In: Headwaters Journal, Spring, pp 12–15

  28. Ingham RE, Trofymow JA, Coleman DC (1985) Interactions of bacteria, fungi, and their nematode grazers: effects on nutrient cycling and plant growth. Ecol Monogr 55:119–140

    Article  Google Scholar 

  29. Ingham ER, Doyle JD, Hendricks CW (1995) Assessing interactions between soil food web and a strain of Pseudomonas putida genetically engineered to degrade 2,4-D. Appl Soil Ecol 2:263–274

    Article  Google Scholar 

  30. Jentschke G, Bonkowski M, Godbold DL, Scheu S (1995) Soil protozoa and forest tree growth: non-nutritional effects and interactions with mycorrhizae. Biol Fertil Soils 20:263–269

    Article  Google Scholar 

  31. Johnson CM, Ulrich A (1959) Analytical methods for use in plant analysis. California Agr Exp Station, Bull 766. Elemental analysis performed by ThermoElectron 6500 Inductively Coupled Argon Plasma

  32. Kirby E, Granatstein D (2012) Organic tree fruit in Washington State. Washington State University Extension, EM046E

  33. Kleineidam K, Sharma S, Kotzerke A, Heuer H, Thiele-Bruhn S, Smalla K, Wilke BM, Schloter M (2010) Effect of sulfadiazine on abundance and diversity of denitrifying bacteria by determining nirK and nirS genes in two arable soils. Microb Ecol 60:703–707

    Article  CAS  PubMed  Google Scholar 

  34. Koorem K, Gazol A, Pik MO, Moora M, lle Saks U, Uibopuu U, Sober U, Zobel M (2014) Soil nutrient content influences the abundance of soil microbes but not plant biomass at the small-scale. PLOS ONE | www.ploson 14(3) 1:8

  35. Kukreja R, Meredith S (2011) Resource efficiency and organic farming: facing up to the challenge. International Federation of organic agriculture movements EU Group Rue du Commerce 124, 1000 Brussels, Belgium. http://www.ifoam-eu.org/sites/default/files/page/files/ifoameu_policy_resource_efficiency_handbook_201112.pdf

  36. Laurent AS, Merwin IA, Thies JE (2008) Long-term orchard groundcover management systems affect soil microbial communities and apple replant disease severity. Plant Soil 304:209–225

    Article  Google Scholar 

  37. Lindsay WL, Norvell WA (1978) Development of a DTPA test for zinc, iron, manganese, and copper. Soil Sci Soc Am J 42:421–428

    Article  CAS  Google Scholar 

  38. Maloney PE, Van Bruggen AHC, Hu S (1997) Bacterial community structure in relation to the carbon environments in lettuce and tomato rhizospheres and in bulk soil. Microb Ecol 34(2):109–117

    Article  CAS  PubMed  Google Scholar 

  39. Manici LM, Ciavatta C, Kelderer M, Erschbaumer G (2003) Replant problems in South Tyrol: role of fungal pathogens and microbial population in conventional and organic apple orchards. Plant Soil 256:315–324

    Article  CAS  Google Scholar 

  40. Martens DA, Johanson JB, Frankenberger WT Jr (1992) Production and persistence of soil enzymes with repeatedadditions of organic residues. Soil Sci 153:53–61

    Article  CAS  Google Scholar 

  41. McGraw AC, Schenck NC (1980) Growth stimulation of fungi. Proc Fla State Hortic Soc 93:201–205

    Google Scholar 

  42. Minoshima H, Jackson LE, Cavagnaro TR, Sánchez-Moreno S, Ferris H, Temple SR, Goyal S, Mitchell JP (2007) Soil food webs and carbon dynamics in response to conservation tillage in California. Soil Biol Biochem. doi:10.2136/sssaj2006.0174

    Google Scholar 

  43. Nannipieri P, Grego S, Ceccanti B (1990) Ecological significance of the biological activity in soil. Soil Biochem 6:293–355

    CAS  Google Scholar 

  44. Neher DA, Peck SL, Rawlings JO, Campbell CL (1995) Measures of nematode community structure and sources of variability among and within agricultural fields. Plant Soil 170:167–181

    Article  CAS  Google Scholar 

  45. Niggli U (2010) Organic agriculture and biodiversity—a review from literature. In: IFOAM EU Group. Organic Farming and Biodiversity in Europe: Examples from the Polar Circle to Mediterranean Regions, Brussels, 5–9. Available at: http://www.ifoam.org/about_ifoam/around_world/eu_group-new/positions/Papers/ pdf/Biodiversity_manual_web_18112010.pdf. Last accessed: 27.10.2011

  46. Nopamornbodi O, Thamsurakul S, Charoensook P (1987) Selection of efficient VA mycorrhizal species for increasing soybean mungbean and peanut growth. Annual Report 1987. Soil Sci Div, Bangkok,16 pp

  47. North Central Agriculture Experiment stations (1998) Recommended chemical soil test procedures for the North Central Region, North Central Regional Research Publication No. 221 (revised)

  48. Oka Y (2009) Mechanisms of nematode suppression by organic amendments—a review. Appl Soil Ecol 44:101–115

    Article  Google Scholar 

  49. Padmore JM (1990) Protein (Crude) in animal feed—Dumas Method, Method No. 968.06. In: Herlich K (ed) Official methods of analysis of the association of official analytical chemists, 15th edn. AOAC, Inc, Arlington, pp 71–72

    Google Scholar 

  50. Parham JA, Deng SP, Da HN, Sun HY, Raun WR (2003) Long-term cattle manure application in soil. II. Effect on soil microbial populations and community structure. Biol Fertil Soils 38:209–215

    Article  Google Scholar 

  51. Penton CR, Gupta VVS, Tiedje JM, Neate SM, Ophel-Keller K, Gillings M, Harvey P, Pham A, Roget DK (2014) Fungal community structure in disease suppressive soils assessed by 28S lsu gene sequencing. doi:10.1371/journal.pone.0093893

  52. Pokharel R, Reich D, Reighard G (2014) Deficit irrigation for iron chlorosis did not affect fruit production and quality in peach. ActHort (accepted)

  53. Pratt RG, Tewolde H (2009) Soil fungal population levels in cotton fields fertilized with poultry litter and their relationships to soil nutrient concentrations and plant growth parameters. App Soil Ecol 41(1):41–49

    Article  Google Scholar 

  54. Reganold JP, Glover JD, Andrew PK, Hinman HR (2001) Sustainability of three apple production systems. Nature 410:926–929

    Article  CAS  PubMed  Google Scholar 

  55. Ruf A (1998) A maturity index for predatory soil mites (Mesostigmata: Gamasina) as an indicator of environmental impacts of pollution on forest soils. Appl Soil Ecol 9:447–452

    Article  Google Scholar 

  56. Schenck NC, Perez Y (1990) Isolation and culture of VA mycorrhizal fungi. In: Labeda DP (ed) Isolation of biotechnological organisms from nature. McGraw-Hill Book Co., New York, pp 237–258

    Google Scholar 

  57. Scow KM, Somasco O, Gunapala N, Lau S, Venette R, Ferris H, Miller R, Shennan C (1994) Transition from conventional to low-input agriculture changes soil fertility and biology. Calif Agric 48(5):20–26. doi:10.3733/ca.v048n05p20

    Google Scholar 

  58. Stamatiadis S, Doran JW, Ingham ER (1990) Use of staining inhibitors to separate fungal and bacterial 450 activity in soil. Soil Biol Biochem 22:81–88

    Article  CAS  Google Scholar 

  59. Strauss EA, Dodds WK (1997) Influence of protozoa and nutrient availability on nitrification rates in subsurface sediments. Microb Ecol 34:155–165

    Article  CAS  PubMed  Google Scholar 

  60. Sylvia DM, Williams SE (1992) Vesicular-arbuscular mycorrhizae and environmental stress. In: Mycorrhizae in sustainable agriculture. As a special publication no. 54. AS A, CSSA, SSSA, Madison, pp 101–124

    Google Scholar 

  61. Valentine AJ, Osborne BA, Mitchell DT (2001) Interactions between phosphorus supply and total nutrient availability on mycorrhizal colonization, growth and photosynthesis of cucumber. Sci Hortic 88:177–189

    Article  CAS  Google Scholar 

  62. Vig AC, Singh NT (1983) Yield and P uptake by wheat as affected by P fertilization and soil moisture regime. Fertil Res 4(1):21–29

    Article  Google Scholar 

  63. Wang XY, Miao Y, Yu S, Chen XY, Schmid B (2014) Genotypic diversity of an invasive plant species promotes litter decomposition and associated processes. Oecologia 174:993–1005. doi:10.1007/s00442-013-2816-3

    Article  PubMed  Google Scholar 

  64. Whitford WG (1996) The importance of the biodiversity of soil biota in arid ecosystems. Biodivers Conserv 5:185–195

    Article  Google Scholar 

  65. Wolf B (1974) Improvements in the azomethine-H method for the determination of boron. Commun Soil Sci Plant Anal 5:39–44

    Article  CAS  Google Scholar 

  66. Yeates GW, King KL (1997) Soil nematodes as indicators of the effect of management in grasslands in the New England Tablelands (NSW): comparison of native and improved grasslands. Pedobiology 41:526–536

    Google Scholar 

  67. Yeates GW, Newton PCD, Ross DJ (2003) Significant changes in soil microfauna in grazed pasture under elevated carbon dioxide. Biol Fertil Soils 38:319–326

    Article  Google Scholar 

Download references

Acknowledgments

The author appreciates the financial support from the Western Colorado Research Center for study, previous researchers for the establishment of these orchard blocks, and Gaye Williams for the initial review of the article.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Ramesh R. Pokharel.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Pokharel, R.R., Zimmerman, R. Impact of organic and conventional peach and apple production practices on soil microbial populations and plant nutrients. Org. Agr. 6, 19–30 (2016). https://doi.org/10.1007/s13165-015-0106-6

Download citation

Keywords

  • Nematodes
  • Bacteria
  • Fungi
  • Flagellates
  • Actinobacteria
  • Plant nutrients