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Science and management of soil biology

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This is a slightly modified version of a presentation that I shared at the VA No-till Alliance meeting in Harrisonburg, VA on 2/7/2012

This is a slightly modified version of a presentation that I shared at the VA No-till Alliance meeting in Harrisonburg, VA on 2/7/2012


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  • 1. The science and management of soil biology Joel Gruver WIU Agriculture j-gruver@wiu.edu The Furrow
  • 2. Is conventionally managed soil a biological ghost town?
  • 3. Microherd Even soils receiving intensive tillageand chemical inputs contain billions of bacteria per gram of soil Phil Brookes
  • 4. The soil beneath our feet may be teeming with a hundred times more species of bacteria than previously thought, according to biologists in New Mexico, US. Measuring the bacterial biodiversity of soil is difficultbecause only a few species can be cultured, according to Jason Gans of the Los Alamos National Lab. Fortunately, biologists can also estimate biodiversityusing a technique called DNA reassociation. This involves chemically unzipping the two strands of all the bacterial DNA in a sample, mixing them up and seeing how long they take to join up again with matching partners.
  • 5. Their results reveal that there are a fewvery common species in soil but lots of rare SSSA species. "There is a very large number of low abundance species," says Gans. Somany rare species, in fact, that the estimate of bacterial biodiversity rises to ~ 1 million species per gram of soil.
  • 6. How much of the C in these corn stalkswill return to the atmosphere within 1 year? > 75% This is not possible without an active microbial community
  • 7. Which trajectory for SOM is most common C in the US? B A150 b/a How is it possible for residue levels to Corn yield increase > 3x without building SOM?30 b/a 1950
  • 8. Broadbalk continuous wheat experiment Data modelled by RothC-26.3 (solid lines) 100 Organic C in soil NPK systems are both producing > 100 bu/a wheat The manure and (t C ha-1) Farmyard manure annually 80Soil C (tons/ha) 60 Why has the NPK program resulted in so little increase in 40 SOM? NPK 20 unfertilized Unmanured 0 1820 1840 1860 1880 1900 1920 1940 1960 1980 2000 2020 Year
  • 9. The current OM level in a soil is a result of the long-term balancebetween organic inputs and outputs
  • 10. The current OM level in a soil is a result of the long-term balancebetween organic inputs and outputs Organic outputs Yield enhancing practices will not build SOM if OM outputs increase at a comparable rate to OM inputs
  • 11. Drainage + Tillage + Lime + N + harvest = Accelerated loss of SOM ”But with the removal of water through furrows, ditches, and tiles, and the aeration of the soil by cultivation, what the pioneers did in effect was to fan the former simmering fires… into a blaze of bacterial oxidation and more complete combustion. The combustion of the accumulated organic matter began to take place at a rate far greater than its annual accumulation. Along with the increased rate of destruction of the supply accumulated from the past, the removal of cropslessened the chance for annual additions. The age-old processwas reversed and the supply of organic matter in the soil began to decrease instead of accumulating.” William Albrecht – 1938 Yearbook of Agriculture
  • 12. How do these soils differ ?? manure cover crops crop residues crop residues20 years of similar tillage and total organicinput but different types of organic inputs Rodale Institute Farming Systems Trial
  • 13. Granular crumb structure Poor structure The development of crumb structure is a key step in retaining SOM http://www.grdc.com.au/growers/gc/gc48/conference1.htm
  • 14. We are well aware that a poorly balanced diet for humans results in heart disease, tooth decay, obesity… what are the consequences of feeding soil a “white bread” diet?White bread diet for soil = very little diversity of organic inputs
  • 15. Unfortunately this is the norm in agriculture today :-< Acute root VS.disease Chronic root malfunction
  • 16. Dramatic effect of steamsterilization and compost on growth of pepper plants
  • 17. The digestive capacity of soilmicroorganismsgreatly exceedsorganic inputs to soils. http://picturethis.pnl.gov/im2/8208417-5cn0/8208417-5cn.jpg
  • 18. So why does organic matteraccumulate at all in soil?
  • 19. In the long run
  • 20. Nature, October 2011 …it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily… Recent analytical and experimental advances have demonstrated that molecular structure alone does notcontrol SOM stability: in fact, environmental and biological controls predominate…
  • 21. Mined humate products mayhave value but are not thesame as old soil organic matter The traditional concept of large stable humus molecules has been rejected by most scientists
  • 22. Organic matter accumulates under anaerobic conditions Blackland soils of North Carolina Lily (1981) > 1 million acres
  • 23. Impact of temperature on SOM accumulation Organic matter accumulates in climates that support high biomass production but limit Organic matter dynamics decomposition TemperatureBrady and Weil (2002)
  • 24. Organic matter production Impact of temperature on plant growth TemperatureBrady and Weil (2002)
  • 25. Organic matter consumption Impact of temperature on decomposition TemperatureBrady and Weil (2002)
  • 26. Visualizing soilhabitat at biologically relevant scales
  • 27. Worm’s eye view?
  • 28. Nematode’s eye view?
  • 29. Bacteria occupy< 5 % of soil surfaces and < 0.1% of soil porosity Visualizing soil habitat at relevant scales
  • 30. Most of the pores where soilmicroorganisms reside are eitherenvironmentally suppressive or lacking in suitable substrates.
  • 31. Microorganisms have very limited ability to move within the soil matrix.
  • 32. As a result, soil is a very sleepy place !osmobiosis anhydrobiosis thermobiosis anoxybiosis cryobiosis
  • 33. Most soil microorganisms are in a dormant state waiting…
  • 34. For their prince charmings to arrive !
  • 35. Roots Rain There are many types of prince charmings ! TillageOrganic Amendments
  • 36. Dormant earthworm SSSAJ 69(3) cover
  • 37. Earthworm cocoonsoffer much more protectionhttp://soils.usda.gov/sqi/soil_quality/soil_biology/images/CE8a-cocoon_LR_small.jpg
  • 38. Most plants in yoursoils are in a state of dormancy
  • 39. Seed dormancy thanis much better microbialunderstood dormancy
  • 40. Who lives in the soil?  Bacteria Body size  Fungi Microfloraincreasing  Algae  Protozoa Microfauna  Nematodes  Microarthropods Mesofauna  Enchytraeids  Earthworms Macrofauna  Ants, termites, spiders  Mollusks Megafauna  Others: rodents, snakes, voles, amphibians, etc.
  • 41. Most soil organisms widely in size Soil organisms vary are tiny !!!  Bacteria  Fungi Microflora aka microbes  Algae  Protozoa Microfauna  Nematodes  Microarthropods Mesofauna  Enchytraeids  Earthworms  Ants, termites, spiders Macrofauna  Mollusks  Others: rodents, snakes, MegafaunaAbundance voles, amphibians, etc.
  • 42. Soil microbes carry out > 90% of alldecomposition
  • 43. Soil animals have a disproportionate impact onnutrient cycling, energy fluxes and plant growth
  • 44. Soil animals are mobile but have limited digestive abilitySoil microbes are relatively immobile but have almost unlimited digestive ability fungi bacteria
  • 45. 3 main types of digestive interactionsoccur between soil animals and microbes
  • 46. Microbivory + NH4+ NH4 NH4+ NH4+ NH4+ NH4+ I want some bacteria for lunch ! Microfauna (e.g. protozoa and nematodes)harness the microbes’s digestive abilities by grazing on them
  • 47. External rumen digestionWhen mesofauna feed on fresh litter, their fecalpellets contain shredded, moistened and mixed but largely undigested residuesReingestion of fecal pellets after a few days ofmicrobial activity greatly increases assimilation
  • 48. Manymicroarthropods use this digestive strategy
  • 49. Leaf cutter ants are a more well known example of external rumen digestion
  • 50. Internal rumen digestiongreatly enhances utilization of complex substrates by soil macrofauna
  • 51. Macrofauna are alsoecosystem engineers
  • 52. Do roots andmacrofauna playsimilar ecological roles?
  • 53. Microbial activation Structural modification bacteria root hair rhizoplane Structural modification Microbial activation
  • 54. Navigating the rhizosphere Rhizoplane End of the rhizosphere Endo- Root free soilRhizosphere Ecto-Rhizosphere > 100 X microbial activity (Lavelle and Spain, 2001)
  • 55. Why do roots have a priming effect? Aggregate Release of protected Disruption organic matterGrowing Priming Root Effect Exudation Activation of microorganisms (Lavelle and Spain, 2001)
  • 56. Soil in organisms are HOTconcentrated SPOTS ! drilosphere porosphere detritusphere aggregatusphere rhizosphere Adapted from Coleman et al. (19??)
  • 57. casts middens Drilosphere Zone of earthworm influence
  • 58. Detritusphere fungisurface residue zone
  • 59. Clean tillageeliminates thedetritusphere Many soil organisms prefer to feed at the surface
  • 60. 3 main strategies forConservation managing soil Augmentation biology Activation
  • 61. Not all earthworms are sensitive to tillage…but the ones that make vertical burrowsthat connect the topsoil and subsoil are…
  • 62. Earthworm functional continuumEpigeic  Anecic  Endogeic worms worms worms
  • 63. Myco = fungus Mycorrhizal diversityRhiza = root Ectomycorrhizae Most woody plants AM endomycorrhizae Most herbaceous Arbutoid plants including mycorrhizae corn and soybeans Ericoid endomycorrhizae Orchid endomycorrhizae Lavelle and Spain (2001)
  • 64. Mycorrhizal Networks: Connecting plants intra- and interspecifically •Many plants are connected underground by mycorrhizal hyphal interconnections. •Mycorrhizal fungi are not very host specific. Illustration by Mark Brundrett Mycorrhizal inoculants are availablebut conservation of established networks is more important
  • 65. Increase nutrient uptake suppress pathogens (especially P) MycorrhizaeMediate plant competition Improve soil structure Glomalin Superglue of the soil ??
  • 66. Are you conserving the beneficial fungi on your crop foliage?
  • 67. Frogeye leafspot fungus resistance to strobilurinchemistry a concern for Mid-South soybean growersHembree Brandon - Mar. 2, 2011 5:36amAdd another to the growing list of weeds, insects, and diseases that havedeveloped resistance to the chemicals that farmers rely on to control pests andprotect yields — strobilurin-resistant Cercospora sojina, the fungus that causesfrogeye leafspot in soybeans.The strobilurin chemistry has been widely used as a first line of defense inpreventing yield loss from Frogeye leafspot.―There was documentation in 2010 of strobilurin-resistant Cercospora in Illinois,Kentucky, and Tennessee,‖ Tom Allen said at the annual conference of theMississippi Agricultural Consultants Association.
  • 68. Roots Rain Irrigation Biological activation strategies TillageOrganic Amendments
  • 69. Innovative cover cropping is a great way to activate your soil biology!!
  • 70. Bio-strip tillattempt #1September 2008
  • 71. Attempt #3Radish planted on 30” rows using milo plates in mid-August 2010
  • 72. Corn following cover crop experiment in 2011 at the WIU Organic Research Farm Relative Cover crop system corn yield Volunteer oats 79%Radishes planted on 30‖ 99%Radishes drilled on 7.5‖ 91% Corn planted on radish rows
  • 73. Wheat + radish trial at the Allison farm November 2010 3 lb/a = 2 lb/a = 1 lb/a > 0 lb/c ~ 2.5 bu/a yield boost Is this an activation effect?
  • 74. Have you tried any biological seed treatments?Augmenting soil biology
  • 75. Old school inoculation
  • 76. http://www.beckerunderwood.com/en/pages/scienceofinoculation
  • 77. VOTiVO contains a naturally occurring soil bacteria, or rhizobacteria, that live and grow with the plant’s root system. The bacteria creating a biofilm that becomes a living barrier limiting the number of receptor sites which could otherwise be occupied by plant pathogens such as nematodes. Nematodes use gaseous and solid exudates from the root as means to detect a root’s proximity, so reduced levels of exudates can decrease the ability of the nematodes to locate the receptor sites on the roots. The bacteria further reduce viable nematode populations by consuming exudates, depriving nematodes of an additional source of energy and nutrients.
  • 78. competition parasitism Ask vendors to explain specifically how their product works!antibiosis induced resistance
  • 79. Do recognize this scene? If you build it, they will come…The most important biological management strategy

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