Want to know which microbes are living in your soil and if it contains enough beneficial microbes?

My Soil Biology Microscopy Assessments, i.e., soil testing, will give you a starting point and help you track progress in your soil regeneration.

I help Farmers, Growers, Landscapers and Compost makers implement soil regeneration practices with a focus on soil biology. I also produce and sell biologically rich Thermo-Compost and Vermicompost soil amendments.

Give me a Call 1-256-665-7500 Email: doug.ayers@sapbwconsulting.com

What is the Soil Food Web

The Soil Food Web refers to all living things within our soils. The microbes within our soils affect plant health the most. Microbes are responsible for feeding and protecting all surfaces of the plant and it's local environment. The composition of soil microbes can vary greatly from one spot to the next.

A healthy Soil Food Web (SFW) provides plants with all the nutrients they need. Healthy plants are further protected from problems, pests and diseases. The SFW is responsible for sequestering carbon in the soil. A healthy Soil Food Web builds soil structure, increases water holding capacity and further suppressing diseases through soil aeration.

A healthy Soil Food Web results in healthier plants that produce more flavorful, nutrient dense foods without the need for fertilizers, sprays, chemicals or other types of inputs.

A healthy Soil Food Web can reverse the effects of climate change.

The Soil Food Web is easily killed off by modern farming practices. Most all farm soils today are classified as "bacterial dominant" dirt lacking in most all the micro-organism components of the Soil Food Web.

 

What are the Best Practices for assessing soil microbiology

Assessing soil microbiology involves evaluating the abundance, diversity, and activity of soil microorganisms, which are critical for nutrient cycling, plant health, and ecosystem sustainability. Best practices require a combination of consistent, representative sampling with a "polyphasic approach"—using both culture-dependent and culture-independent methods to overcome the limitations of any single technique.

 

1. Representative Soil Sampling

Proper sampling is the most critical step for reliable results. 

• Consistency: Sample from the same location (e.g., using GPS) and at the same time of year (seasonal changes affect microbial life).
• Depth: For most microbial studies, collect samples at a depth of 0–15 cm or 0–20 cm. For studies in mountain areas or to examine vertical distribution, stratified sampling down to 35–40 cm is recommended.
• Method: Use a soil probe or auger to take 3–12 core samples, then combine them to create a composite sample representative of the field, particularly if soil type or management is uniform (e.g., 1–2 acres).
• Timing: Avoid sampling immediately after extreme events like floods or intense droughts, or immediately after a tillage event which causes a temporary spike in respiration. 

2. Handling, Storage, and Transport

Soil microbial communities are highly sensitive to handling. 

• Temperature: Keep samples cool (but not frozen, ~4°C) immediately after sampling to reduce the potential for rapid change in community structure.
• Time: Ship samples overnight to the lab to arrive within 72 hours.
• Sterility: Sterilize sampling equipment with 70% ethanol between samples to prevent cross-contamination, especially if performing DNA analyses.
• Storage: If not immediate, samples for DNA analysis can be stored at -20°C, while samples for microbial biomass should be kept at 4°C. 

3. Recommended Analytical Techniques

 

A range of indicators is necessary, as no single method provides a complete picture. 

• Molecular Techniques (DNA-based): Metagenomics and next-generation sequencing can identify the types of microorganisms present by targeting 16S rRNA (bacteria/archaea) or ITS (fungi).
• Phospholipid Fatty Acid Analysis (PLFA): Used to measure living microbial biomass and the ratio of fungi-to-bacteria, which is a good indicator of the soil food web structure.
• Soil Respiration (CO2 Burst): Measures how actively the soil microbial community is breathing (e.g., Solvita test), which indicates the rate of organic matter decomposition and nutrient cycling.
• Enzyme Activity Tests: Measure the activity of specific enzymes (e.g., Beta-glucosidase) to assess the soil's capacity to break down organic matter.
• Microscopy: Used to directly count and measure the biomass of bacteria, fungi, protozoa, and nematodes, popularized for the Soil Food Web. 

4. Interpretation and Long-Term Trends

• Establish a Baseline: Perform testing to establish a baseline before changing management practices.
• Focus on Trends: Look for changes in microbial activity over 2–4 years, rather than relying on a single snapshot report.
• Compare Management: Compare sites with similar soil types and conditions (e.g., comparing no-till vs. tilled areas).
• Contextualize with Soil Health Data: Interpret microbial data alongside physical (compaction) and chemical (pH, organic carbon) data. 

5. Best Practices Checklist

• Use clean tools (sterilized with 70% ethanol).
• Sample 0–15cm (or 0–20cm).
• Create composite samples (8–15 cores).
• Store in a cool box (ice pack) during transport.
• Use a lab with ISO standardization for microbial analysis.
• Test at the same time each year.