Advertisement

Australasian Plant Pathology

, Volume 40, Issue 3, pp 207–214 | Cite as

Understanding soil processes: one of the last frontiers in biological and ecological research

  • D. C. ColemanEmail author
Article

Abstract

Soils are one of the great unknown realms on earth, despite decades of extensive research. We still see soils “through a ped darkly”. This opacity in milieu and understanding rewards innovative study, however, as soils are indeed “complex adaptive systems”, and show very sophisticated levels of self-organization. Viewed historically, soil ecological studies have progressed from what major groups of biota are present, what is their biomass, and what major processes occur. More recent studies have delineated multi-trophic interactions, extending both above- and below-ground, as well as specifically-targeted studies of substrates and organisms that are involved in the development and function of suppressive soils. One of the great unknowns in soil ecology is a fuller understanding of the complete array of predatory biota. Soils are teeming with organisms in all three Domains, but are also rife with many viruses infecting Archaea, Bacteria and Eukarya, meaning that they need more study in soil processes. Pursuing a more holistic approach including viral biology and ecology may enable us to more capably manage our soils that have supported the biosphere so much over the millennia. Looking into the future, the opportunity to exploit soil biodiversity in the context of ecosystem development should pay considerable dividends. Using chronosequence analysis, the relationships between soil biodiversity and ecosystem function are beginning to be understood. The interplays of aboveground and belowground herbivores on plant function and feedbacks on the attraction of the herbivores’ natural enemies. Finally, management of the plant-soil–microbial-faunal system via varied organic amendments shows possibilities in the study and management of suppressive soils.

Keywords

Domains detrital food webs suppressive soils 

Notes

Acknowledgments

This review paper has benefited from discussions with my colleagues Dr. Vadakattu Gupta, CSIRO Sustainable Ecosystems, Glen Osmond, South Australia, and Professor William B. Whitman, Dept. of Microbiology, University of Georgia, Athens, GA, USA. It is dedicated to the memory of Dr. Ken Lee, a pioneering Australasian soil ecologist in the CSIRO. Travel support was provided, in part, by Dr. Graham Stirling and the co-organizers of the 6th Australasian Soil Disease Society meeting, August 9–11, 2010.

References

  1. Adl MS, Coleman DC, Reed F (2006) Slow recovery of biodiversity in sandy loam soils of Georgia after 25 years of no-tillage management. Agric Ecosyst Environ 114:323–334CrossRefGoogle Scholar
  2. Andersson AF, Banfield JF (2008) Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320:1047–1050PubMedCrossRefGoogle Scholar
  3. Bardgett RD, Cook R, Yeates GW, Denton CS (1999) The influence of nematodes on below-ground processes in grassland systems. Plant Soil 212:23–33CrossRefGoogle Scholar
  4. Beare MH, Parmelee RW, Hendrix PF, Cheng W, Coleman DC, Crossley DA Jr (1992) Microbial and faunal interactions and effects on litter nitrogen and decomposition in agroecosystems. Ecol Monogr 62:569–591CrossRefGoogle Scholar
  5. Beare MH, Coleman DC, Crossley DA Jr, Hendrix PF, Odum EP (1995) A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling. Plant Soil 170:5–22CrossRefGoogle Scholar
  6. Boyer M, Yutin N, Pagnier I, Barrassi L, Fournous G, Espinosa L, Robert C, Azza S, Sun S, Rossmann MG, Suzan-Monti M, La Scola B, Koonin EV, Raoult D (2009) Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms. Proc Natl Acad Sci 106:21848–21853PubMedCrossRefGoogle Scholar
  7. Brussaard L, Bouwman LA, Geurs M, Hassink J, Zwart KB (1990) Biomass, composition and temporal dynamics of soil organisms of a silt loam soil under conventional and integrated management. Neth J Agric Sci 38:283–302Google Scholar
  8. Buée M, de Boer W, Martin F, van Overbeek L, Jurkevitch E (2009a) The rhizosphere zoo: an overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and some of their structural factors. Plant Soil 321:189–212CrossRefGoogle Scholar
  9. Buée M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F (2009b) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184:449–456PubMedCrossRefGoogle Scholar
  10. Coleman DC (1985) Through a ped darkly—an ecological assessment of root soil–microbial-faunal interactions. In: Fitter AH, Atkinson D, Read DJ, Usher MB (eds) Ecological interactions in the soil: plants, microbes and animals. British Ecological Society Special Publ. 4 Blackwells, Oxford, pp 1–21Google Scholar
  11. Coleman DC (2008) From Peds to Paradoxes: linkages between soil biota and their influences on ecological processes. Soil Biol Biochem 40:271–289CrossRefGoogle Scholar
  12. Coleman DC, Whitman WB (2005) Linking species richness, biodiversity and ecosystem function in soil systems. Pedobiologia 49:479–497CrossRefGoogle Scholar
  13. Coleman DC, Hendrix PF, Odum EP (1998) Ecosystem health: an overview. In: Wang PH (ed) Soil chemistry and ecosystem health. Soil Science Society of America Special Publication No. 52, Madison, Wisconsin, pp 1–20Google Scholar
  14. Coleman DC, Crossley DA Jr, Hendrix PF (2004) Fundamentals of soil ecology, 2nd edn. Elsevier Academic, San DiegoGoogle Scholar
  15. Coleman DC, Hunter MD, Hendrix PF, Crossley DA Jr, Simmons B, Wickings K (2006) Long-term consequences of biochemical and biogeochemical changes in the horseshoe bend agroecosystem, Athens, GA. Eur J Soil Biol 42:S79–S84CrossRefGoogle Scholar
  16. Cook RJ (2007) Management of resident plant growth-promoting rhizobacteria with the cropping system: a review of experience in the US Pacific Northwest. Eur J Plant Pathol 119:255–264CrossRefGoogle Scholar
  17. Crawford JW, Harris JA, Ritz K, Young IM (2005) Towards an evolutionary ecology of life in soil. Trends Ecol Evol 20:81–87PubMedCrossRefGoogle Scholar
  18. Elliott ET, Coleman DC (1988) Let the soil work for us. Ecol Bull (Copenhagen) 39:23–32Google Scholar
  19. Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73:7059–7066PubMedCrossRefGoogle Scholar
  20. Forterre P, Prangishvili D (2009) The origin of viruses. Res Microbiol 160:466–472PubMedCrossRefGoogle Scholar
  21. Fu S, Kisselle KW, Coleman DC, Hendrix PF, Crossley DA Jr (2001) Short-term impacts of aboveground herbivory (grasshopper) on the abundance and 14C activity of soil nematodes in conventional tillage and no-till agroecosystems. Soil Biol Biochem 33:1253–1258CrossRefGoogle Scholar
  22. Gessner MO, Swan CM, Dang CK, KcKie BG, Bardgett RD, Wall DH, Hättenschwiler S (2010) Diversity meets decomposition. Trends Ecol Evol 25:372–380PubMedCrossRefGoogle Scholar
  23. Ghorbani R, Wilcockson S, Koocheki A, Leifert C (2008) Soil management for sustainable crop disease control. Environ Chem Lett 6:149–162CrossRefGoogle Scholar
  24. Gupta VVSR, van Vliet PCJ, Abbott LK, Leonard E (1999). Farming system and soil biota in Western Australia, CRCSLM/CTT/2/99, Adelaide, South Australia (ISBN-1 876162 31 7), pp 4Google Scholar
  25. Hamilton AJ, Basset Y, Benke KK, Grimbacher PS, Miller SE, Novotný V, Samuelson GA, Stork NE, Weiblen GD, Yen JDL (2010) Quantifying uncertainty in estimation of tropical arthropod species richness. Am Nat 176:90–95PubMedCrossRefGoogle Scholar
  26. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–684PubMedCrossRefGoogle Scholar
  27. Harris J (2009) Soil microbial communities and Restoration ecology: facilitators or followers? Science 325:573–574PubMedCrossRefGoogle Scholar
  28. Holland JN, Cheng W, Crossley DA Jr (1996) Herbivory-induced changes in plant carbon allocation: assessment of below-ground C fluxes using carbon-14. Oecologia 107:87–94CrossRefGoogle Scholar
  29. Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167–170PubMedCrossRefGoogle Scholar
  30. Ingham RE, Trofymow JA, Ingham ER, Coleman DC (1985) Interactions of bacteria, fungi, and their nematode grazers: effects on nutrient cycling and plant growth. Ecol Monogr 55:119–140CrossRefGoogle Scholar
  31. Jones JB, Jackson LE, Balogh B, Obradovic A, Iriarte FB, Momol MT (2007) Bacteriophages for plant disease control. Annu Rev Phytopathol 45:245–262PubMedCrossRefGoogle Scholar
  32. Kimura M, Jia Z-J, Nakayama N, Asakawa S (2008) Review—ecology of viruses in soils: past, present and future perspectives. Soil Sci Plant Nutr 54:1–32CrossRefGoogle Scholar
  33. Lapierre P, Gogarten JP (2009) Estimating the size of the bacterial pan-genome. Trends Genet 25:107–110PubMedCrossRefGoogle Scholar
  34. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R (2005) The microbial pan- genome. Curr Opin Genet Dev 15:589–594PubMedCrossRefGoogle Scholar
  35. Moran MA (2009) Metatranscriptomics: eavesdropping on complex microbial communities. Microbe 4:1–7Google Scholar
  36. Moran NA, Degnan PH, Santos SR, Dunbar HE, Ochman H (2005) The players in a mutualistic symbiosis: insects, bacteria, viruses, and virulence genes. Proc Natl Acad Sci 102:16919–16926PubMedCrossRefGoogle Scholar
  37. Pace NR (2009) Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 73:565–576PubMedCrossRefGoogle Scholar
  38. Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, Moran MA (2009) Comparative day/night metatranscriptomics analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol 11:1358–1375PubMedCrossRefGoogle Scholar
  39. Sánchez-Moreno A, Ferris H (2007) Suppressive service of the soil food web: effects of environmental management. Agric Ecosyst Environ 119:75–87CrossRefGoogle Scholar
  40. Scheu S, Setälä H (2002) Multitrophic interactions in decomposer food-webs. In: Tscharntke B, Hawkins BA (eds) Multitrophic level interactions. Cambridge University Press, Cambridge, pp 223–264CrossRefGoogle Scholar
  41. Simmons BL, Coleman DC (2008) Microbial community response to transition from conventional to conservation tillage in cotton fields. Appl Soil Ecol 40:518–528CrossRefGoogle Scholar
  42. Srivastava DS, Cardinale BJ, Downing AL, Duffy JE, Jouseau C, Sankaran M, Wright JP (2009) Diversity has stronger top–down than bottom–up effects on decomposition. Ecology 90:1073–1083PubMedCrossRefGoogle Scholar
  43. Stirling GR, Wilson EJ, Stirling AM, Pankhurst CE, Moody PW, Bell AJ, Halpin N (2005) Amendments of sugarcane trash induce suppressiveness to plant-parasitic nematodes in a sugarcane soil. Australas Plant Pathol 34:203–211CrossRefGoogle Scholar
  44. Tyson GW, Banfield JF (2008) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol 10:200–207PubMedGoogle Scholar
  45. Upchurch RA, Chiu C-Y, Everett K, Dyszynski G, Coleman DC, Whitman WB (2008) Differences in the composition and diversity of bacterial communities from agricultural and forest soils. Soil Biol Biochem 40:1294–1305CrossRefGoogle Scholar
  46. Van der Putten WH, Bardgett RD, de Ruiter PC, Hol WHG, Meyer KM, Bezemer TM, Bradford MA, Christensen S, Eppinga MB, Fukami T, Hemerik L, Molofsky J, Schädler M, Scherber C, Strauss SY, Vos M, Wardle DA (2009) Empirical and theoretical challenges in aboveground–belowground ecology. Oecologia 161:1–14PubMedCrossRefGoogle Scholar
  47. Van Elsas JD, Speksnijder AJ, van Overbeek LS (2008) A procedure for the metagenomics exploration of disease-suppressive soils. J Microbiol Meth 75:515–522CrossRefGoogle Scholar
  48. Vossbrinck CR, Coleman DC, Woolley TA (1979) Abiotic and biotic factors in litter decomposition in a semiarid grassland. Ecology 60:265–271CrossRefGoogle Scholar
  49. Wakelin SA, Anstis ST, Warren RA, Ryder MH (2006) The role of pathogen suppression on the growth promotion of wheat by Penicillium radicum. Australas Plant Pathol 35:253–258CrossRefGoogle Scholar
  50. Wardle DA (2002) Communities and Ecosystems: linking the aboveground and belowground components. Princeton University Press, PrincetonGoogle Scholar
  51. Weinbauer MG (2004) Ecology of prokaryotic viruses. FEMS Microbiol Rev 28:127–181PubMedCrossRefGoogle Scholar
  52. Westphal A (2005) Detection and description of soils with specific nematode suppressiveness. J Nematol 37:121–130PubMedGoogle Scholar
  53. Whitman WB, Coleman DC, Wiebe WJ (1998) Perspective. Prokaryotes: The unseen majority. Proc Natl Acad Sci 95:6578–6583PubMedCrossRefGoogle Scholar
  54. Yeates GW (2010) Nematodes in ecological webs. In: Encyclopedia of life sciences (ELS). Wiley, Chichester. doi: 10.1002/9780470015902.a0021913
  55. Young IM, Crawford JW (2004) Interactions and self-organization in the soil-microbe complex. Science 304:1634–1637PubMedCrossRefGoogle Scholar

Copyright information

© Australasian Plant Pathology Society Inc. 2011

Authors and Affiliations

  1. 1.Odum School of EcologyUniversity of GeorgiaAthensUSA

Personalised recommendations