Lesson Structure:   Soil Microbiome Management  BSC310

There are 9 lessons:

1. Scope and Nature of the Soil Microbiome
   • Nature of soil
   • Soil Structure & Texture
   • Soil Structure and Porosity
   • Soil Structure Research
   • Topsoil Thickness
   • Nutrient Components
   • Carbon and Nutrient Content
   • Carbon Retention
   • Nitrogen
   • Phosphorus
   • Sulphur
   • Other Important Indicators of Soil Health
   • Acidity (pH)
   • Salinity
   • Environmental Factors Affecting Soil Health
   • Drought
   • Frost
   • Erosion
   • Water Retention
   • Nature of soil Microbes
   • Bacteria
   • Archaea
   • Viruses
   • Fungi
   • Protozoa
   • Scope of the Soil Microbiome
   • Plant-Microbe Relationships
   • Microbe Interrelationships
   • Changes to the Soil Microbiome
   • Key Definitions and Concepts for Understanding Soil

2. Evaluating the Soil Microbiome Status

• • Measurement vs. Monitoring in Soil Biology
  • Things the Soil Microbiome can Help Measure or Monitor
  • Types of Soil Biological Testing and Analysis
  • Deciding on the Right Type of Test
  • Overview of Different Testing Types
  • Cotton Strip Assay
  • Microbial Activity Using Basal Carbon Dioxide Respiration
  • Microbial Biomass
  • Identification Through Culturing
  • Potentially Mineralisable Nitrogen
  • Biolog Plates
  • Microarrays
  • Community Profiling
  • More Advanced Approaches to the Microbiome: Omics
  • Transcriptomics
  • 16S rRNA
  • PCR
  • PCR-ELISA
  • Bioinformatics

3. Man’s impact on Microbiome

• • Human Impact on Microbiomes
  • Land Development and Urbanisation
  • Changes in Land Use and Microbial Communities
  • Problems with land development on soils
  • Climate Change
  • Pollution
  • Air Pollution
  • Deposition
  • Precipitation
  • Erosion
  • Microplastics
  • Anti-microbials
  • Antibiotic Resistance
  • Monocultures

4. Soil Substrates and Additives

• • Soil Substrates
  • Inorganic Substrate Materials
  • Perlite
  • Vermiculite
  • Sand
  • Rockwool
  • Organic Substrate Materials
  • Peat
  • Coir
  • Bark
  • Soilless Substrates and Microbes
  • Substrate Technology
  • Substrate Engineering
  • Substrate Evaluation
  • Novel Technologies used in Substrate Management
  • Tomography
  • Rhizometrics
  • Mini- Horhizotron
  • Rheometer
  • INORGANIC ADDITIVES
  • Organic Additives
  • Manures
  • Compost
  • Fungal Additives

5.  Conventional vs Organic soil management

• • Conventional vs Organic Soil Management practices
  • Conventional Practices
  • Soil Carbon Modelling
  • Organic Practices
  • Composting
  • Crop Rotations
  • Cover Crops
  • No Tillage Farming
  • Organic Pest & Disease Control
  • Weed Control
  • Rotational Grazing
  • Livestock Management
  • Biodynamics
  • Biodynamic preparations/sprays

6. Soil Fertility Management

• • Soil Management Strategies
  • Soil Organic Matter
  • Cover Crops
  • Cocktail Cover Crop
  • Legume Crops
  • Longer Crop Rotations
  • Reduced Tillage
  • Planting Trees
  • ORGANIC Additives
  • Soil Humus
  • Building Soil Humus
  • Humates
  • Composting
  • Animal Manures
  • Microbial Inoculants & MICROORGANISMS
  • Use of Arbuscular Mycorrhizal Fungi (AMF) Inoculants
  • Specific Inoculums
  • Protozoa Tea
  • Earthworms
  • INORGANIC ADDITIVES
  • Gypsum
  • Lime

7.  Plant Interactions with the Soil Microbiome

• • Soil Organisms
  • Function of Plant Microbiome
  • Effect of Non-native Species
  • Soil Microbiome and Plants
  • Plant-Soil Feedback
  • Plant-Microbe Associations
  • Examples of Plant-Microbe Associations with Plant Families & Species
  • Effects of Different Microbes
  • Other Associations
  • Cover Crops & Grapevines
  • Crop Rotations & Microbiomes
  • Types of Cover Crops & Microbiomes

8. Pest & Disease Interaction with Soil Microbiome

• • Biopesticides
  • Advantages of Biopesticides
  • Biological Control Agents
  • Microbial Pesticides
  • Advantages of Microbial Insecticides
  • Entomopathogenic Fungi
  • Protozoa
  • Bacteria
  • Engineering Microbial Inoculants to Suppress Disease

9.  Soil Regeneration Practices

• • Restoring the Soil Microbiome
  • Practical Methods Which Benefit the Soil Microbiome
  • Reducing soil disturbance
  • No tillage (Zero Tillage)
  • Advantages of no till farming
  • Controlled Traffic Farming
  • Advantages of Controlled Traffic Farming
  • Increasing crop diversity & organic matter
  • Alley Farming
  • Cover Crops
  • Mulching & Composting
  • Biochar
  • Increasing soil microbes
  • Microbial Inoculation
  • Plant Breeding and Microbiome Engineering

Please Note:  At the end of each lesson, there is an assignment to be completed and forwarded to your tutor for grading and marking.  This is then returned to you with relevant suggestions, comments, and if necessary, additional reading.

Learning Goals – Level 3 Certificate in Soil Microbiome Management – BSC310

• Describe different ways of identifying and monitoring components of a soil microbiome.
• Explain a range of human impacts on soil microbiomes.
• Compare different soil substrates and additives in different soil environments.
• Compare conventional soil management with organic soil management methods.
• Describe methods of managing soil fertility with consideration to the soil microbiome.
• Describe how plants interact with their microbiome in a variety of different situations.
• Explain different ways that pathogens and pest organisms interact with the soil microbiome.
• Determine appropriate soil regeneration strategies to boost the soil microbiome.

How to Analyse the Soil Microbiome Status

Working with a soil microbiome begins with understanding what each unique soil microbiome looks like. To do this, we need to explore ways to identify the organisms living in the microbiome, then work out how we can monitor these different organisms and keep them in balance for optimal soil health.

There are different ways to do this depending on the desired outcome and budget. Some ways of assessing the soil microbiome can be carried out relatively easily at home, though they won’t give as much detail as higher budget, more specialist methods that may require soil samples for analysis.

There is a whole spectrum of analysis types available, and it is worth understanding something about each of them as the cost of even the most expensive tests will come down over time as technology improves, and cheaper test kits slowly become available.

MEASUREMENT VS. MONITORING IN SOIL BIOLOGY

Measuring is where we take measurements from the soil, we take samples and test and use those to make decisions in the moment, or in the short-term. Monitoring is part of a long-term strategy, where we collect measurements over time then look for patterns and account for things like changes in climate and deliberate changes, such as applications of fertiliser or pesticide, both of which affect soil chemistry.

Things the Soil Microbiome can Help Measure or Monitor

Different soil microbes have different functions in the soil. Many of these functions are the result of traits exhibited by the specific type of microbe but provide us with information about our soils.

Some things, like soil temperature and pH, are easy and cheap to test. Other things, like oxygen levels, require more expensive testing. Looking at soil microbiome can give us useful information at a lower cost.

Some microbes can give us consistent indications of:

• Oxygen
• Nitrogen/phosphate availability
• The amount of movable (labile) carbon
• Overall (gross) nitrogen/phosphate mineralisation rates
• Concentrations of some pollutants

Let’s look at oxygen as an example. Testing oxygen levels is expensive. Yet if we know that certain types of bacteria usually found in our geographic region can only thrive in soils with a certain oxygen range, we can use the number of these bacteria in our soil to assess its oxygen status.

Microbes can also help us identify potential hotspots within the soil; areas where some processes such as denitrification, nitrification, and methane production may be happening at higher rates.

Such hot spots are usually found in the rhizosphere, mycosphere (part of the soil especially rich in fungi), drillosphere (area of the soil affected by earthworm tunnelling), and/or detritusphere (areas where organic matter is decaying/decomposing).

Finding anti-pathogen compounds in the soil can indicate the presence of microbes that are:

• Helping protect against pathogens
• Encouraging plant growth through the production of anti-pathogenic compounds

We can also look at some plant reactions. For instance, changes in the amount of ethylene may be traced back to ACC deaminase, which some bacteria in the rhizosphere produce.

ACC deaminase encourages plant growth because it’s an enzyme which breaks down or sequesters plant-produced ACC, the precursor to the plant stress hormone ethylene. In other words, plants can’t make as much ethylene, which lowers stress levels, and so growth can continue.

The products of the different microbes in soil communities can give us all kinds of information. Some of the microbes we see that are beneficial to plants include:

• Azospirilli (nitrogen fixation)
• Paenibacilli (nitrogen fixation)
• Pseudomonads (pathogen suppression)
• Bacilli (pathogen suppression)

Remember, there is no single ideal soil microbiome. Soil microbiomes differ according to many factors, and what’s healthy in a soil may be different in a different soil or location.

Don’t focus too much on what’s working for other people; instead, look at the characteristics of the soil and work to improve it from a functional perspective based on what is to be achieved.

Biosensors

The use of biosensors is revolutionising our understanding of the soil microbiome, by offering real-time, in-situ monitoring of soil conditions and microbial activity. These devices combine a biological component, like enzymes or microorganisms, with a transducer to detect specific substances or changes, such as contaminants, nutrient levels, or microbial presence.

This allows for early detection of problems, cost-effective long-term monitoring, and a deeper understanding of complex soil processes.

While challenges remain in improving selectivity, sensitivity, and durability, biosensors hold immense potential for advancing soil health management and the ability to effectively monitor outcomes.

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