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Beneficial and Pathogenic Microbes in Agriculture. Chapter 18 Text. Soil Environments. Surface and subsurface soils are typically nutrient-poor environments for microbes Rhizosphere is enriched in nutrients as a result of nearby plant activities. Rhizosphere. Rhizoplane

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soil environments
Soil Environments
  • Surface and subsurface soils are typically nutrient-poor environments for microbes
  • Rhizosphere is enriched in nutrients as a result of nearby plant activities
  • Rhizoplane
    • soil in direct contact with plant root
  • Endophytes
    • microbes attached to root surface

Decreasing moisture

Increasing organic C

organic material in rhizosphere
Organic material in rhizosphere
  • Exudates
    • low molecular weight compounds released from plant cells in a non-metabolic manner (leakage)
  • Secretions
    • compounds metabolically released from plant cells
  • Lysates
    • compounds released from moribund cells during autolysis
  • Plant mucilage
    • plant polysacchrides
densities of microorganisms in rhizosphere
Densities of microorganisms in rhizosphere




beneficial root microbe interactions
Beneficial root-microbe interactions
  • Atmosphere contains 1015 tons N2 gas
    • Biological nitrogen fixation
    • Minimum of 70 million tons N fixed/year
  • Symbiotic Relationships
    • Both host and parasite benefit
    • Ex. Rhizobia (Symbiont) and Legumes (Host)
    • Rhizobia: sugars, proteins, and oxygen
    • Plant: usable nitrogen
  • Legumes
    • Preserve the nitrogen balance in the soil
    • Two Types
      • Legumes
      • Non-Legume
    • Release flavonoids

Importance of



beneficial root microbe interactions12
Beneficial root-microbe interactions
  • Biological nitrogen fixation

N2 + 3H2 2NH3

root nodule initiation
Root NoduleInitiation
  • Two types of Nodule
    • Effective
    • Ineffective
  • Two groups of Genes Necessary
    • Common Nodulation Genes (nodABCD)
      • nodD only gene expressed in absence of a suitable host
    • Host Specific Nodulation Genes
  • Legumes release flavonoids
  • Triggers production of Nod Factors (Lipochitooligosaccharide) by bacteria
  • Flavenoids interact with nodD product
  • Expression of nodABC genes
plant rhizobia genetic interactions
Plant-rhizobia genetic interactions


root nodule development
Root NoduleDevelopment
  • Nod factor sensed by root
  • Cell division occurs
  • Rhizobia attach within minutes
  • Root hair curling begins
  • Rhizobia travel along an infection thread
  • As infection thread penetrates the root cortex, Rhizobia are released
root nodule function
Root NoduleFunction
  • Nodule forms 1 to 2 weeks after infection
  • Two types of Nodules
    • Determinate
    • Indeterminate
  • Rhizobia enlarge approx. 5 times
  • Change physiologically to form bacteroids
root nodule fixation
Root NoduleFixation
  • Nodulins produced during maturation include:Leghemoglobin (protects nitrogenase enzyme) and also nitrogenase and gluatmine synthetase
  • Fixation usually occurs after about 15 days
  • Indeterminate
      • Fixation: ammonia Exported: asparagine
  • Determinate
      • Fixation: ammonia Exported: purine
enhancing the symbiosis
Enhancing the Symbiosis
  • Natural symbiosis is reasonably effective
    • Free-living nitrogen fixation gives 25kg/hectare/year
    • Symbiotic nitrogen fixation gives 100kg/hectare/crop
  • Current enhancements
    • Application of rhizobial inoculants
      • Peat-based carrier with 109 rhizobia/gram of peat
        • Application directly to seeds, then planting
      • Application to seed furrow
      • Crop rotation/breeding

Crop Production

Land Remediation

  • Symbiotic N2-fixation in leguminous plants is a complex interaction between plant and bacterium
  • Understanding the interactions is one of the most significant triumphs of environmental microbiology of the modern age.
  • Environmental microbiology has enabled better management of agricultural soils and crop productivity
ice minus bacteria
Ice-minus bacteria
  • Frost causes over $1 billion damage to crops in the U.S. each year
  • University of California scientists genetically engineered a plant leaf bacterium Pseudomonas syringae to reduce frost damage to plants
ice minus bacteria23
Ice-minus bacteria
  • A gene encoding a protein that promotes ice nucleation on the surface of the bacterium colonizing a plant leaf was deleted
  • This reduced the temperature at which ice crystals formed on the plant leaf by 1-2oC
ice minus bacteria24
Ice-minus bacteria
  • Ice-minus bacteria are cultivated in laboratory and sprayed on plants
  • The EPA classified the genetically modified bacterium as a “pesticide” since the naturally-occurring ice-plus bacterium is considered a “pest”
ice minus bacteria25
Ice-minus bacteria
  • There was a huge movement against introducing these genetically engineered bacteria to the environment
    • Why?
  • At the same time the environmentalists were trying to get ice-minus bacteria banned for agricultural use, ski areas were spraying the naturally-occurring ice-plus bacteria in snow-making equipment to make artificial snow

Ice nucleation active microorganism

United States Patent 5972686

The present invention relates to a novel ice nucleation active Xanthomonas strain and a bacterial ice nucleator comprising the ice nucleation active microorganism which can be applied for food processing and artificial snow making. The present inventors have screened ice nucleation active microorganisms from leaves of crops and plants, and investigated their ice-nucleation activities. As a result, the inventors discovered that a novel microorganism belonging to Xanthomonas campestris has a superior ice-nucleation activity than those of the conventional ice nucleation active microorganisms. Accordingly, the ice nucleation active microorganism of the invention can be used as a potent bacterial ice nucleator for food processing and artificial snow making.

  • Genetic engineering of plant epilithic microbial populations has expanded the boundaries of agricultural land for raising strawberries, potatos, and citrus crops.
  • To date there is no evidence that removal of a gene from a naturally-occurring bacterium exerts a deleterious impact on the plant or soil microbial community