9.1 Plant-associated microbiomes and their impact on crop health

Plant microbiomes are vital for crop health, influencing nutrient uptake and disease resistance. These diverse communities of bacteria, fungi, and other microorganisms colonize plant tissues and surrounding soil, forming complex relationships with their host plants.

Understanding plant microbiomes can revolutionize agriculture. By manipulating these microbial communities, we can enhance crop productivity, reduce chemical inputs, and improve plant resilience to stress. This knowledge is crucial for developing sustainable farming practices in a changing climate.

Plant Microbiome Composition and Diversity

Microbial Community Structure

Top images from around the web for Microbial Community Structure

• 

  Frontiers | Revisiting Plant–Microbe Interactions and Microbial Consortia Application for ... View original

  Is this image relevant?

• 

  Frontiers | Engineering Host Microbiome for Crop Improvement and Sustainable Agriculture View original

  Is this image relevant?

• 

  Frontiers | Linking Plant Secondary Metabolites and Plant Microbiomes: A Review View original

  Is this image relevant?

• 

  Frontiers | Revisiting Plant–Microbe Interactions and Microbial Consortia Application for ... View original

  Is this image relevant?

• 

  Frontiers | Engineering Host Microbiome for Crop Improvement and Sustainable Agriculture View original

  Is this image relevant?

1 of 3

Top images from around the web for Microbial Community Structure

• 

  Frontiers | Revisiting Plant–Microbe Interactions and Microbial Consortia Application for ... View original

  Is this image relevant?

• 

  Frontiers | Engineering Host Microbiome for Crop Improvement and Sustainable Agriculture View original

  Is this image relevant?

• 

  Frontiers | Linking Plant Secondary Metabolites and Plant Microbiomes: A Review View original

  Is this image relevant?

• 

  Frontiers | Revisiting Plant–Microbe Interactions and Microbial Consortia Application for ... View original

  Is this image relevant?

• 

  Frontiers | Engineering Host Microbiome for Crop Improvement and Sustainable Agriculture View original

  Is this image relevant?

1 of 3

• Plant-associated microbiomes encompass diverse microbial communities colonizing different plant tissues and surrounding soil
  • Include bacteria, fungi, archaea, and viruses
• Rhizosphere harbors a distinct and highly diverse microbial community compared to bulk soil
  • Narrow zone of soil influenced by root secretions
• Endophytic microorganisms reside within plant tissues without causing apparent harm to the host
  • Found in roots, stems, leaves, and seeds
• Phyllosphere hosts unique microbial communities adapted to harsh conditions of leaf surfaces
  • Encompasses above-ground plant surfaces

Diversity and Core Microbiomes

• Plant microbiomes exhibit high taxonomic and functional diversity
• Core microbiomes consist of consistently present taxa across plant species or cultivars
• Next-generation sequencing technologies crucial for characterizing composition and diversity
  • 16S rRNA gene sequencing
  • Metagenomic approaches

Factors Influencing Microbiome Composition

• Plant genotype significantly influences composition and diversity
• Soil type affects microbial community structure
• Climate impacts microbiome composition
  • Temperature
  • Precipitation
• Agricultural practices shape microbial communities
  • Tillage
  • Fertilization
  • Crop rotation

Plant Microbiome Roles in Nutrient Acquisition and Disease Resistance

Nutrient Acquisition Enhancement

• Plant growth-promoting rhizobacteria (PGPR) enhance nutrient uptake
  • Solubilize phosphorus
  • Fix atmospheric nitrogen
  • Produce siderophores for iron acquisition
• Mycorrhizal fungi form symbiotic associations with plant roots
  • Expand root surface area
  • Improve nutrient and water uptake
• Certain microbiome members produce phytohormones
  • Auxins stimulate root growth
  • Cytokinins promote shoot development

Disease Resistance Mechanisms

• Beneficial microorganisms induce systemic resistance (ISR) in plants
  • Prime plant's immune system against pathogens
• Microbiome-mediated disease suppression occurs through various mechanisms
  • Competition for nutrients
  • Production of antimicrobial compounds (antibiotics, lytic enzymes)
  • Parasitism of pathogens
• Plant microbiome modulates plant hormone signaling pathways
  • Influences plant responses to biotic stresses (pathogen attacks)
  • Affects plant responses to abiotic stresses (drought, salinity)
• Specific microbial taxa directly antagonize pathogens
  • Produce volatile organic compounds
  • Secrete enzymes that degrade pathogen cell walls

Plant Microbiome Applications in Sustainable Agriculture

Microbial Inoculants and Engineered Microbiomes

• Microbial inoculants enhance crop productivity
  • Reduce reliance on chemical fertilizers
  • Decrease dependence on pesticides
• Engineering of synthetic plant microbiomes creates customized microbial communities
  • Tailored for specific crop species (maize, wheat, rice)
  • Adapted to particular environmental conditions (arid, tropical, temperate)

Microbiome Manipulation Strategies

• Manipulation of plant microbiome through breeding improves crop performance
  • Select for plants with enhanced beneficial microbial associations
• Genetic engineering of plants enhances beneficial plant-microbe interactions
  • Modify root exudate composition to attract beneficial microbes
• Microbiome-based biocontrol strategies manage plant pathogens and pests
  • Reduce need for chemical pesticides
• Harness plant microbiomes to improve crop tolerance to abiotic stresses
  • Drought resistance
  • Salinity tolerance
  • Heavy metal remediation

Integration into Agricultural Practices

• Integrate plant microbiome management into agricultural practices
  • Develop more sustainable cropping systems
  • Enhance resilience of agricultural ecosystems
• Inform design of crop rotation strategies using microbiome dynamics
  • Optimize soil health
  • Improve plant productivity
• Guide intercropping systems based on plant-microbe interactions
  • Enhance nutrient cycling
  • Promote natural pest control

Factors Influencing Plant Microbiome Structure and Function

Plant and Soil Factors

• Plant genotype shapes microbiome composition
  • Different plant species harbor distinct microbial communities
  • Cultivars within species show variations in associated microbiomes
• Soil physicochemical properties impact plant-associated microbiomes
  • pH affects microbial community structure
  • Soil texture influences microbial habitat
  • Nutrient availability shapes microbial functional diversity

Environmental and Management Factors

• Environmental factors influence microbiome structure and function
  • Temperature affects microbial growth rates
  • Precipitation alters soil moisture and microbial activity
  • Light intensity impacts phyllosphere microbiome
• Agricultural management practices alter microbiome composition and functionality
  • Tillage disrupts soil microbial networks
  • Fertilization changes nutrient availability for microbes
  • Pesticide use selects for resistant microbial populations

Biological and Temporal Factors

• Plant developmental stage determines microbiome structure
  • Seedling stage microbiome differs from mature plant microbiome
• Tissue type influences associated microbial communities
  • Root microbiome distinct from leaf microbiome
• Biotic interactions within plant microbiome shape community structure
  • Microbial competition for resources
  • Cooperative relationships between microbes
  • Predation by protozoa and nematodes
• Climate change alters plant-microbe interactions
  • Shifts in temperature and precipitation patterns affect microbial communities
  • Changes in atmospheric CO2 influence plant-microbe symbioses