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Biological Indicators for Soil Health: Potential for Development and Use of On-Farm Tests

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Modern Tools and Techniques to Understand Microbes

Abstract

Agricultural sustainability can be supported by monitoring soil quality. Laboratory soil tests are available to assess a range of soil chemical, physical, and biological characteristics. Farmers can also monitor the state of their soil according to its general appearance and response to disturbance. Soil organisms have significant roles that contribute to the sustainability of agricultural systems. While on-farm tests for assessing the abundance and diversity of larger soil fauna (e.g., earthworms and other macrofauna) are available, on-farm tests for soil mesofauna, microfauna, and microorganisms are not commonly used. Adaptation of laboratory methods for quantifying soil mesofauna and arbuscular mycorrhizal (AM) fungi have potential for on-farm assessment by farmers. This chapter focuses on these two groups of soil organisms because of their multifunctional contributions to physical, chemical, and biological components of soil fertility. Soil processes in which soil mesofauna and AM fungi are involved include stabilization of aggregates. Several laboratory-based methods are available for quantifying soil mesofauna and AM fungi which can be adapted for use on-farm by farmers. Farmer motivation for investigation of soil health could lead to more sustainable land use if contributions of soil organisms are optimized. Existing farmer knowledge of soil chemical and physical characteristics based on off-farm soil tests and their use could be complemented by local knowledge of soil biological characteristics, especially those that involve soil mesofauna and AM fungi.

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References

  • Abbott LK, Gazey C (1994) An ecological view of the formation of VA mycorrhizas. Plant Soil 159:69–78

    Article  Google Scholar 

  • Abbott LK, Lumley S (2014) Assessing economic benefits of arbyscular mycorrhizal fungi as a potential indicator of soil health. In: Solaiman ZM, Abbott LK, Varma A (eds) Mycorrhizal fungi: use in sustainable agriculture and land restoration. Springer, Heidelberg, pp 17–31

    Google Scholar 

  • Abbott LK, Manning DAC (2015) Soil health and related ecosystem services in organic agriculture. Sustain Agric Res 4:116–125

    Article  Google Scholar 

  • Abbott LK, Murphy DV (2003) What is soil biological fertility? In: Abbott LK, Murphy DV (eds) Soil biological fertility—a key to sustainable land use in agriculture. Kluwer Academic, Dordrecht, pp 1–15

    Google Scholar 

  • Abbott LK, Robson AD (1991) Factors influencing the occurrence of vesicular-arbuscular mycorrhizas. Agric Ecosyst Environ 35:121–150

    Article  Google Scholar 

  • Allen DE, Singh BP, Dalal RC (2011) Soil health indicators under climate change: a review of current knowledge. In: Singh BP, Cowie AL, Chan KY (eds) Soil health and climate change, Soil biology, vol 29. Springer, Berlin, pp 25–45

    Chapter  Google Scholar 

  • Altieri MA, Nicholls CI (2003) Soil fertility management and insect pests: harmonizing soil and plant health in agroecosystems. Soil Tillage Res 72:203–211

    Article  Google Scholar 

  • Ananyeva ND, Susyan EA, Gavrilenko EG (2011) Determination of the soil microbial biomass carbon using the method of substrate induced respiration. Eurasian Soil Sci 44:1215–1221

    Article  CAS  Google Scholar 

  • Bardgett RD, Chan KF (1999) Experimental evidence that soil fauna enhance nutrient mineralization and plant nutrient uptake in montane grassland ecosystems. Soil Biol Biochem 31:1007–1014

    Article  CAS  Google Scholar 

  • Bardgett RD, McAlister E (1999) The measurement of soil fungal:bacterial biomass ratios as an indicator of ecosystem self-regulation in temperate meadow grasslands. Biol Fertil Soils 29:282–290

    Article  Google Scholar 

  • Bhardwaj AK, Jasrotia P, Hamilton SK, Robertson GP (2011) Ecological management of intensively cropped agro-ecosystems improves soil quality with sustained productivity. Agric Ecosyst Environ 140:419–429

    Article  Google Scholar 

  • Briones MJI (2014) Soil fauna and soil functions: a jigsaw puzzle. Front Environ Sci 2:Article 7. doi:10.3389/fenvs.2014.00007

    Article  Google Scholar 

  • Brito I, Goss MJ, De Carvalho M (2012) Effect of tillage and crop on arbuscular mycorrhiza colonization of winter wheat and triticale under Mediterranean conditions. Soil Use Manag 28:202–208

    Article  Google Scholar 

  • Brookes PC, Landman A, Pruden G, Jenkinson DS (1985) Chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biol Biochem 17:837–842

    Article  CAS  Google Scholar 

  • Brundrett MC, Piché Y, Peterson RL (1984) A new method for observing the morphology of vesicular-arbuscular mycorrhizae. Can J Bot 62:2128–2134

    Article  Google Scholar 

  • Chandanie WA, Kubota M, Hyakumachi M (2006) Interactions between plant growth promoting fungi and arbuscular mycorrhizal fungus Glomus mosseae and induction of systemic resistance to anthracnose disease in cucumber. Plant Soil 286:209–217

    Article  CAS  Google Scholar 

  • Chiang K-S, Liu S-C, Bock CH, Cottwald TR (2014) What interval characteristics make a good categorical disease assessment scale? Phytopathology 104:575–585

    Article  PubMed  Google Scholar 

  • Desbiez A, Matthews R, Tripathi B, Ellis-Jones J (2004) Perceptions and assessment of soil fertility by farmers in the mid-hills of Nepal. Agric Ecosyst Environ 103:191–206

    Article  Google Scholar 

  • Doran WJ, Zeiss RM (2000) Soil health and sustainability: managing the biotic component of soil quality. Appl Soil Ecol 15:3–11

    Article  Google Scholar 

  • Fang X, You M, Barbetti M (2012) Reduced severity and impact of Fusarium wilt on strawberry by manipulation of soil pH, soil organic amendments and crop rotation. Eur J Plant Pathol 134:619–629

    Article  Google Scholar 

  • Gazey C, Abbott LK, Robson AD (2004) Indigenous and introduced arbuscular mycorrhizal fungi contribute to plant growth in two agricultural soils from south-western Australia. Mycorrhiza 14:355–362

    Article  CAS  PubMed  Google Scholar 

  • George E, Marschner H, Jakobsen I (1995) Role of arbuscular mycorrhizal fungi in uptake of phosphorus and nitrogen from soil. Crit Rev Biotechnol 15:257–270

    Article  Google Scholar 

  • Gollan JR, Lobry de Bruyn L, Reid N, Wilkie L (2013) Monitoring the ecosystem service provided by dung beetles offers benefits over commonly used biodiversity metrics and traditional trapping method. J Nat Conservat 21:183–188

    Article  Google Scholar 

  • Gregorich GE, Carter RM, Doran WJ, Pankhurst CE, Dwyer ML (1997) Biological attributes of soil quality. Dev Soil Sci 25:81–113

    Article  Google Scholar 

  • Handa T, Aerts R, Berendse F, Berg MP, Bruder A, Butenschoen O, Chauvet E, Gessner MO, Jabiol J, Makkonen M, McKie BG, Malmqvist B, Peeters ETHM, Scheu S, Schmid B, van Ruijven J, Vos VCA, Hattenschwiler S (2014) Consequences of biodiversity loss for litter decomposition across biomes. Nature 509:218–221

    Article  CAS  PubMed  Google Scholar 

  • Hildebrandt U, Regvar M, Bothe H (2007) Arbuscular mycorrhiza and heavy metal tolerance. Phytochemistry 68:139–146

    Article  CAS  PubMed  Google Scholar 

  • Idowu OJ, van Es HM, Abawi GS, Wolfe DW, Ball JI, Gugino BK, Moebius BN, Schindelbeck RR, Bilgili AV (2008) Farmer-oriented assessment of soil quality using field, laboratory and VNIR spectroscopy methods. Plant Soil 307:243–253

    Article  CAS  Google Scholar 

  • Juarez S, Nunan N, Duda AC, Pouteau V, Chenu C (2013) Soil carbon mineralization responses to alterations of microbial diversity and soil structure. Biol Fertil Soils 49:939–948

    Article  CAS  Google Scholar 

  • Juniper S, Abbott LK (1993) Vesicular-arbuscular mycorrhizas and soil salinity. Mycorrhiza 4:45–57

    Article  Google Scholar 

  • Karlen LI, Ditzlerb AC, Andrews SS (2003) Soil quality: why and how? Geoderma 114:145–156

    Article  CAS  Google Scholar 

  • Kilpatrick S, Johns S, Prior MR and Hart D (1999) Managing farming: how farmers learn. RIRDC publication no. 99/74

    Google Scholar 

  • Kobae Y, Ohtomo R (2015) An improved method for bright-field imaging of arbuscular mycorrhizal fungi in plant roots. Soil Sci Plant Nutr 62:1–4

    Google Scholar 

  • Lee KE, Pankhurst CE (1992) Soil organisms and sustainable productivity. Aust J Soil Res 30:855–892

    Article  Google Scholar 

  • Leinaas HP (1978) Seasonal variation in sampling efficiency of Collembola and Protura. Oikos 31:307–312

    Article  Google Scholar 

  • Lima RCA, Hoogmoed WB, Brussaard L, Sacco dos Anjos F (2011) Farmers’ assessment of soil quality in rice production systems. NJAS Wageningen J Life Sci 58:31–38

    Article  Google Scholar 

  • Lobry de Bruyn LA (1997) The status of soil macrofauna as indicators of soil health to monitor the sustainability of Australian agricultural soils. Ecol Econ 23:167–178

    Article  Google Scholar 

  • Lobry de Bruyn LA (1999) Ants as bioindicators of soil function in rural environments. Agric Ecosyst Environ 74:425–441

    Article  Google Scholar 

  • Lobry de Bruyn LA, Abbey AL (2003) Characterisation of farmers’ soil sense and the implications for on-farm monitoring of soil health. Aust J Exp Agric 43:285–305

    Article  Google Scholar 

  • Macfadyen A (1953) Notes on methods for the extraction of small soil arthropods. J Anim Ecol 22:65–77

    Article  Google Scholar 

  • Marshall VG (1972) Comparison of two methods of estimating efficiency of funnel extractors for soil microarthropods. Soil Biol Biochem 4:417–426

    Article  Google Scholar 

  • Mickan B (2014) Mechanisms for alleviation of plant water stress involving arbuscular mycorrhizas. In: Solaiman ZM, Abbott LK, Varma A (eds) Mycorrhizal fungi: use in sustainable agriculture and land restoration, Soil biology series, vol 41. Springer, Berlin, pp 225–239

    Google Scholar 

  • Milton N, Murphy D, Braimbridge M, Osler G, Jasper D, Abbott L (2002) Using power analysis to identify soil quality indicators. In: 17th world congress of soil science symposium no 32, paper 557, pp 1–8

    Google Scholar 

  • Neher AD (1999) Soil community composition and ecosystem processes Comparing. agricultural ecosystems with natural ecosystems. Agroforestry Syst 45:159–185

    Article  Google Scholar 

  • Olsson PA (1999) Signature fatty acids provide tools for determination of thedistribution and interactions of mycorrhizal fungi in soil. FEMS Microbiol Ecol 29:303–310

    Article  CAS  Google Scholar 

  • Paz-Ferreiro J, Fu S (2016) Biological indices for soil quality evaluation: perspectives and limitations. Land Degrad Dev 27:14–25

    Article  Google Scholar 

  • Phillips JM, Hayman DS (1970) Improved procedures for clearing and staining vesicular-arbuscular mycorrhizal fungi for rapid assessment of infection. Trans Br Mycol Soc 55:158–161

    Article  Google Scholar 

  • Pimentel D, Harvey C, Resosudarmo R, Sinclair K, Kurz K, McNair M, Crist S, Shpritz L, Fitton L, Saffouri R, Blair R (1995) Environmental and economic costs of soil erosion and conservation benefits. Science 267:1117–1123

    Article  CAS  PubMed  Google Scholar 

  • Pinton R, Varanini Z, Nanniperi P (2007) The rhizosphere biochemistry and organic substances at the soil-plant interface, 2 edn. CRC Press, Boca Raton, FL

    Book  Google Scholar 

  • Podolich O, Ardanov P, Zeats I, Pirttila AM, Kozyrovska N (2015) Reviving of the endophytic bacterial community as a putative mechanism of plant resistance. Plant Soil 388:367–377

    Article  CAS  Google Scholar 

  • Poole GJ, Harries M, Huberli D, Miyan S, Macleod WJ, Lawes R, Makay A (2015) Predicting cereal root disease in Western Australia using soil DNA and environmental parameters. Phytopathology 105:1069–1079

    Article  CAS  PubMed  Google Scholar 

  • Pretty J, Hine R (2011) Reducing food poverty with sustainable agriculture: a summary of new evidence. Final report from the “SAFE-World”

    Google Scholar 

  • Reen RA, Thompson JP, Clewett TG, Sheedy JG, Bell KL (2014) Yield response in chickpea cultivars and wheat following crop rotations affecting population densities of Pratylenchus thornei and arbuscular mycorrhizal fungi. Crop Pasture Sci 65:428–441

    Article  Google Scholar 

  • Rillig MC, Aguilar-Trigueros CA, Bergmann J, Verbruggen E, Veresoglou SD, Lehmann A (2015) Plant root and mycorrhizal fungal traits for understanding soil aggregation. New Phytol 205:1385–1388

    Article  CAS  PubMed  Google Scholar 

  • Romig DE, Garylynd MJ, Harris RF, McSweeney K (1995) How farmers assess soil health and quality. J Soil Water Conservat 50:229–236

    Google Scholar 

  • Sackett TE, Classen AT, Sanders NJ (2010) Linking soil food web structure to above- and belowground ecosystem processes: a meta-analysis. Oikos 119:1984–1992

    Article  Google Scholar 

  • Satchell JE (1971) Earthworms. In: Phillipson J (ed) Methods of study in quantitative soil ecology, IBP handbook no. 18. Blackwell, Oxford, pp 107–127

    Google Scholar 

  • Schwartz MW, Hoeksema JD, Gehring CA, Johnson NC, Klironomos JN, Abbott LK, Pringle A (2006) The promise and the potential consequences of the global transport of mycorrhizal fungal inoculum. Ecol Lett 9:501–515

    Article  PubMed  Google Scholar 

  • Siddiky MRK, Kolher J, Cosme M, MC R (2012) Soil biota effects on soil structure: interactions between arbuscular mycorrhizal fungal mycelium and collembola. Soil Biol Biochem 50:33–39

    Article  CAS  Google Scholar 

  • Six J, Bossuyt H, Degryze S, Denef K (2004) A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics. Soil Tillage Res 79:7–31

    Article  Google Scholar 

  • Smith SE, Read DJ (2008) Mycorrhizal symbiosis. Academic, London

    Google Scholar 

  • Smith FA, Smith SE (2011) What is the significance of the arbuscular mycorrhizal colonisation of many economically important crop plants? Plant Soil 348:63–79

    Article  CAS  Google Scholar 

  • Solaiman ZM (2014) Contribution of arbuscular mycorrhizal fungi to soil carbon sequestration. In: Solaiman ZM, Abbott LK, Varma A (eds) Mycorrhizal fungi: use in sustainable agriculture and land restoration, Soil biology series, vol 41. Springer, Berlin, pp 287–296

    Google Scholar 

  • Spurgeon DJ, Keith AM, Schmidt O, Lammertsma DR, Faber JH (2013) Land-use and land-management change: relationships with earthworm and fungi communities and soil structural properties. BMC Ecol 13:46. doi:10.1186/1472-6785-13-46

    Article  PubMed  PubMed Central  Google Scholar 

  • Stirling G, Smith M, Smith J, Stirling A, Hamill S (2012) organic inputs, tillage and rotation practices influence soil health and suppressiveness to soilborne pests and pathogens of ginger. Australas Plant Pathol 41:99–112

    Article  Google Scholar 

  • Sylvain ZA, Wall DH (2011) Linking soil biodiversity and vegetation: implications for a changing planet. Am J Bot 98:517–527

    Article  PubMed  Google Scholar 

  • van Bruggen A, Francis I, Krag R (2015) The vicious cycle of lettuce corky root disease: effects of farming system, nitrogen fertilizer and herbicide. Plant Soil 388:110–132

    Article  Google Scholar 

  • Vance ED, Brookes PC, Jenkinson DS (1987) An extraction method for measuring soil microbial biomass. Soil Biol Biochem 19:703–707

    Article  CAS  Google Scholar 

  • van Groenigen JW, Lubbers IM, Vos HMJ, Brown GG, De Deyn GB, van Groenigen KJ (2014) Earthworms increase plant production: a meta-analysis. Sci Rep 4:6365. doi:10.1038/srep06365

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vierheilig H, Coughlan PA, Wyss U, Pice Y (1998) Ink and vinegar, a simple staining technique for arbuscular-mycorrhizal fungi. Appl Environ Microbiol 64:5004–5007

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wood TG (1967) Acari and Collembola of moorland soils from Yorkshire, England. III. The micro-arthropod communities. Oikos 18:277–292

    Article  Google Scholar 

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Correspondence to Lynette K. Abbott .

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Mahdi, J.E., Abbott, L.K., Pauli, N., Solaiman, Z.M. (2017). Biological Indicators for Soil Health: Potential for Development and Use of On-Farm Tests. In: Varma, A., Sharma, A. (eds) Modern Tools and Techniques to Understand Microbes. Springer, Cham. https://doi.org/10.1007/978-3-319-49197-4_8

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