Healthy Soil Starts with Active Microbes
When we think of healthy soil, we often imagine rich, dark earth that holds moisture and supports growth of healthy crops. But underneath the surface, something much more complex is happening. Soil is home to an enormous living community of microorganisms — bacteria, fungi, and more — working silently and constantly. These tiny creatures are capable of:
- breaking down plant residues,
- unlocking nutrients,
- storing carbon,
- and forming symbiotic relationships with roots.
In short, they act as nature’s engineers, recycling plant material, supporting fertility and defending plants from disease.
We might not see these microbes with the naked eye, but their impact is visible in every field. Just as a well-functioning machine requires all its parts, no matter how small – an active and diverse microbial community is essential for healthy, fertile soil.
So how do we monitor the condition of something we cannot see? How do we evaluate if our soil’s microbial team is thriving, underperforming, or struggling to adapt to change?
This is where a scientific approach known as CLPP – Community-Level Physiological Profiling – comes in.
CLPP: A Simple Way to Measure What Microbes Can Do
CLPP is a scientific method used to measure the function and functional diversity of microbial communities — that is, not just who is there, but what they are capable of doing.
The method works a bit like offering a buffet to the microbes in the soil. Here in BIOTREX, we use Biolog EcoPlates™, which contain 31 wells, each filled with a different carbon source — sugars, amino acids, organic acids and other compounds that microbes might encounter in real soil environments. These carbon sources serve as food options.
Here’s how it works in practice:
- A small amount of soil is collected and mixed with a sterile solution to extract microbes.
- This solution — containing a sample of the microbial community — is added to the EcoPlate.
- The plate is then incubated to observe how the microbes respond to each “meal” in the buffet.
If the microbes can consume a particular carbon source, they begin to transform it into other compounds. Eventually, this chain of reactions produces formazan, a compound that causes a visible colour change in the well. The stronger and faster the colour change, the more active the microbial community. At the end of the analysis, a colourful pattern appears on the plate — it’s like a metabolic fingerprint of the soil.
Want to know how it works in practice?
Watch our short video to see how BIOTREX Soil Microbial Analysis works, and how we turn microbes into meaningful allies in agriculture.
Functional Diversity: Why It Matters for Your Farm
So why is this metabolic fingerprint important?
Because it tells us more than just how many microbes are in the soil — it tells us how adaptable and diverse their metabolic capabilities are. This is what we mean by functional diversity.
Let’s use an analogy. Imagine your soil’s microbial community as a team of workers. If every worker has the same skill, the team is limited in what it can do. But if the team includes builders, electricians, mechanics, and planners — it can adapt to many different jobs. Similarly, a microbially diverse soil can handle a wider range of environmental changes, plant needs, and stressors.
High functional diversity means your soil’s microbial community can perform a wider range of tasks — and adapt when conditions change. In practice, this has been linked to:
- Improved nutrient cycling – soils with diverse microbial functions release nutrients more efficiently, reducing the need for synthetic fertilisers and supporting steady crop growth throughout the season.
- Stronger plant-microbe relationships – such as enhanced root development and natural disease suppression, often observed after introducing compost or microbial inoculants.
- Greater resilience to stress – a diverse microbial community can shift its metabolism and adjust to maintain its function under pressure.
- Faster recovery after disturbance – soils with high microbial functional diversity tend to bounce back more quickly and maintain productivity.
Measuring What Soil Microbes Actually Do
There are many ways to study soil microbiology — from DNA sequencing to microscopy — but the Biolog EcoPlate method used in CLPP offers a unique advantage: it focuses on what microbes can do, not just who they are. It reveals their ability to metabolise different carbon sources — in other words, how active and adaptable your soil’s microbial workforce really is.
Think of it this way: DNA-based methods give you a list of everyone in the house — bacteria, fungi, archaea — even if they’re asleep on the couch. CLPP tells you who’s actually up and cooking, cleaning, or fixing the roof. It reflects the expressed metabolic activity, making it especially valuable when you need to assess how soil biology responds to changes like cover cropping, tillage, or biological inputs.
How BIOTREX Makes CLPP Good Fit for Agriculture
While CLPP offers unique insight into how soil microbial communities function, it has traditionally been used in research settings — often with inconsistent procedures that make results hard to compare or apply in practice. Some limitations remain: the method favours fast-growing bacteria, certain fungi may be underrepresented, and results depend on proper handling of plates and samples. However, when done right, CLPP provides one of the most actionable tools available for assessing microbial activity and diversity.
At BIOTREX, we’ve taken this powerful method and transformed it into a fully standardised, field-ready service designed specifically for agriculture. We’ve optimised every step — from sample collection to plate incubation and data analysis — to ensure that results are reliable, repeatable, and easy to interpret.
In short, BIOTREX takes CLPP out of the lab and puts it to work — turning complex microbial data into clear, actionable insights that support better decisions in the field. Our service is designed for real-world use, making it easy to track changes, compare treatments, and understand how your soil biology is performing.
Whether you’re a:
- Farmer exploring biological inputs and looking to improve soil performance
- Agronomist monitoring the impact of soil management strategies
- Input producer testing the effects of microbial or biostimulant products
- Regenerative agriculture consultant looking for measurable proof of change
BIOTREX is a ready-to-use solution to monitor microbial activity and functional diversity in agricultural soils.
From Research to the Field: Applying CLPP in Real-World Agriculture
CLPP and Biolog EcoPlates have been widely used by scientists to study how different land management strategies affect soil microbial communities. Researchers have applied the method to compare land-use types, assess the impact of long-term organic farming, and evaluate how chemical fertilisation influences microbial activity. These studies have consistently shown that practices such as organic cultivation or reduced chemical inputs can enhance microbial functional diversity — a key indicator of soil quality and resilience.
At BIOTREX, we build on this foundation by applying CLPP in practice with our customers. We’ve worked with farmers, advisors, and organisations across Europe to track how regenerative practices affect soil microbial function — including in collaborative projects with EIT Food and NABU. Our clients have used the method to monitor changes during the transition to regenerative systems, test the biological effects of organic inputs like compost and manure, and evaluate the performance of microbial inoculants and biostimulants.
Ready to Understand What Microbes Are Telling About Your Soil?
Understanding how your soil’s microbial community functions is key to building healthier, more resilient systems. With a method like CLPP — and a field-ready service like BIOTREX — you don’t need to guess what’s happening underground. You can measure it, monitor it, and respond with confidence. Whether you’re improving your soil, developing new products, or supporting the transition to regenerative farming, BIOTREX helps you bring microbial insight into everyday agricultural decision-making.
If you’re looking for a practical, science-based way to monitor soil life and evaluate the impact of your practices, we’re here to help — get in touch to explore how BIOTREX can support your work.
Sources and further reading:
Xu, W., Ge, Z., & Poudel, D. R. (2015). Application and Optimization of Biolog EcoPlates in Functional Diversity Studies of Soil Microbial Communities. MATEC Web of Conferences, 22, 04015.
https://doi.org/10.1051/matecconf/20152204015Preston-Mafham, J., Boddy, L., & Randerson, P. F. (2002). Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles – a critique. FEMS Microbiology Ecology, 42(1), 1–14.
https://doi.org/10.1016/S0168-6496(02)00324-0Nautiyal, C. S., Chauhan, P. S., & Bhatia, C. R. (2010). Changes in soil physicochemical properties and microbial functional diversity due to 14 years of conversion of grassland to organic agriculture in a semi-arid agroecosystem. Soil and Tillage Research, 109(2), 55–60.
https://doi.org/10.1016/j.still.2010.04.008Wang, G., Liu, J., Qi, X., Jin, J., Wang, Y., & Liu, X. (2008). Effects of fertilization on bacterial community structure and function in a black soil of Dehui region estimated by Biolog and PCR-DGGE methods. Acta Ecologica Sinica, 28(1), 220–226.
https://doi.org/10.1016/S1872-2032(08)60023-2
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