#soil microbes

Healthy soil is the foundation of productive agriculture. While many growers focus on nutrients, irrigation, and crop protection, the biological life within the soil often determines long-term success. Soil microorganisms such as bacteria and fungi play a critical role in nutrient cycling, water retention, disease suppression, and plant resilience. Research increasingly shows that microbial biomass is one of the strongest indicators of soil health.

Traditionally, measuring soil biology required expensive laboratory testing and lengthy turnaround times. This made it difficult for farmers to monitor changes throughout the growing season. Modern innovations such as microBIOMETER provide growers with an affordable on-site method for measuring microbial biomass and fungal-to-bacterial ratios using smartphone technology. Results can be obtained in approximately 20 minutes, allowing farmers to make timely management decisions.

Why Soil Microbes Matter

Soil microbes perform countless functions that directly impact crop performance. They help convert organic matter into plant-available nutrients, improve soil structure, and enhance water infiltration. Healthy microbial communities also support root development and can increase a plant's ability to withstand environmental stress.

When microbial populations decline due to excessive tillage, synthetic inputs, or poor soil management, growers may experience reduced productivity and higher input costs. Monitoring microbial activity helps identify whether soil health practices are delivering measurable improvements.

The Value of Real-Time Soil Biology Data

One of the biggest advantages of on-site microbial testing is the ability to track soil health over time. Farmers can establish a baseline measurement and then evaluate the effects of cover crops, compost applications, reduced tillage, or biological amendments.

Real-time testing allows growers to:

Measure the effectiveness of soil management practices.

Compare different fields or treatment areas.

Monitor seasonal changes in microbial activity.

Make data-driven decisions that support regenerative agriculture.

Supporting Regenerative Agriculture

Regenerative farming focuses on rebuilding soil biology and increasing carbon sequestration. However, many producers struggle to quantify progress. Microbial testing offers a practical way to measure changes in soil life and verify whether management strategies are improving biological activity.

Frequent testing can reveal trends that may otherwise go unnoticed, helping growers optimize practices that contribute to healthier soils and more sustainable production systems.

Looking Ahead

As agriculture continues to evolve, biological indicators will become increasingly important alongside traditional soil chemistry tests. Understanding what is happening beneath the soil surface allows growers to maximize productivity while reducing unnecessary inputs.

The Europe Organic Fertilizers Market recorded a sale of 745,833 tons in 2024 and is estimated to reach a volume of 1.34 million tons by 2030 with a CAGR of 10.8% during the forecast period. One of the most exciting developments in the industry is the marriage of organic inputs with high-tech precision farming tools. Historically, organic fertilizers were seen as difficult to calibrate due to their varying nutrient densities. However, modern manufacturing processes are now producing highly uniform pellets and liquid concentrates that are perfectly compatible with GPS-guided spreaders and variable-rate application technology. This allows farmers to apply organic nutrients with the same level of accuracy as synthetic ones.

Analysis of the Europe Organic Fertilizers Market shows that the use of digital soil mapping is allowing for the "surgical" application of organic matter. Instead of blanketing a whole field, farmers can target areas that are low in organic carbon or microbial activity, maximizing the impact of every ton applied. This efficiency is crucial for the industry's volume growth, as it proves that organic fertilizers can be used effectively on large, high-tech farms. The 10.8% CAGR is partly driven by this technological "de-risking," making organic options more attractive to a wider demographic of professional agronomists and farm managers.

The role of "Bio-stimulants" within the organic fertilizer category is also expanding. These products contain natural substances or microorganisms that enhance a plant’s nutrient uptake and tolerance to abiotic stress. When combined with traditional organic fertilizers, bio-stimulants can significantly increase the "efficiency" of the applied nutrients. This means farmers can achieve the same yields with less total input, which is a major selling point in a market focused on environmental sustainability and cost control. As researchers identify more specific microbial strains that target certain crops, the market for these "active" organic fertilizers is expected to grow rapidly.

Furthermore, the data generated by precision farming equipment is helping manufacturers refine their formulations. By analyzing yield maps in relation to fertilizer applications, companies can see exactly how their products perform across different soil types and climates. this feedback loop is leading to the development of region-specific organic blends that are optimized for the unique conditions of the Mediterranean, the Atlantic, or the Central European plains. This localization of products is essential for the market to reach the 1.34 million ton target, as it ensures that farmers see a clear return on investment regardless of their location.

Real things a crop scientist said to me

I would be DELIGHTED to tell you about my soil microbes.

So, there are a ton of different kinds and they have all kinds of different metabolic needs. Most consume organic matter, but where we need oxygen and exhale CO2 and create water as a byproduct, that's not always the case for microbes. Some of them do that, meanwhile others need nitrate, certain manganese or iron ions, sulfate, or CO2. And instead of water as the byproduct, they produce nitrogen gas, ammonium, manganese and iron in different ionic forms, sulfur, or methane.

This big scary looking chart is essentially that. It's called the redox ladder because all those metabolic processes are oxidation-reduction reactions. And, crucially, they happen more or less in order as soil runs out of oxygen.

That's because the different types of microbes are competing with each other for space, food, etc. and one type will predominate most of the time.

Of course, well-aerated soil has a constant supply of oxygen and will never move on to those other reactions. But if soil is, say, waterlogged, it can run out of oxygen. Sure, some oxygen will diffuse through the water (that's how fish breathe), but it does so very slowly compared to the rate of diffusion in air. In waterlogged soil, there's no way it'll keep up with the consumption rate, so you wind up with an environment devoid of oxygen - anerobic is the technical term.

That means other microbes and other metabolic processes become a big deal. Including my favorite, methanogenesis! That just means methane production, and it happens, theoretically, when oxygen and all those other analogous chemicals run out, and only CO2 is left.

I spent three years trying to confirm that theory, and the data I got was supportive but incomplete. I was especially interested in soil that gets flooded, unflooded, and flooded again, going back and forth repeatedly between aerobic and anerobic.

New research reveals how a powerful blend of microbes can naturally enhance hemp growth, improve soil health, and boost plant resilience. Could this be the future of sustainable hemp farming? Read more to find out!

A recent study has uncovered how a carefully selected mixture of microbes can significantly enhance hemp growth, offering a promising natural solution for farmers and cultivators. As the demand for hemp continues to rise for its industrial, medicinal, and wellness applications, researchers are exploring innovative ways to improve its cultivation without relying on synthetic fertilizers or…

There was a reminder in a recent edition of Nature (Dance, vol 632, 494) that pointed out that the current crisis with antibiotics leads to the requirement familiar to those who follow Lewis Carol – we have to run increasingly fast just to stay in the same place. There is plenty of blame to go around for why we are in this predicament, but that is pointless. We are here: live with it. It is…

Re: your tags, PLEASE tell me about soil microbes. I only know them as funky l’il guys who break down dead matter and some of them can make you sick.

I would be happy to talk about soil microbes! They ARE funky little guys who break down dead stuff, or at least some of them are, and they're basically the foundation of nutrient cycling. Which gets very complicated very quickly, because there are ALL KINDS of nutrients and ALL KINDS of microbes that deal with them. I mostly know about carbon cycling, and a bit about nitrogen cycling, because that's why I and my coworkers study.

You've got microbes that take atmospheric nitrogen and turn it into stuff plants can use (nitrogen fixation, these include the critters that live in legume roots), and then you've got several other kinds of microbes that shuffle nitrogen from one form to another (nitrifiers, denitrifiers, probably others I'm not aware of). Carbon cycling involves SO MANY TYPES OF MICROBES, it's ridiculous, but my favorites are the methanogens - the ones that make methane. There are also methanotrophs, the ones that eat methane.

Here’s the background information from my blog post earlier this year. You can see the full piece here. Read the method and rationale then see the results of my challenge below.

Officials are encouraging people to “soil their undies”—but the suggestion is not as unseemly as it sounds. To help gauge the health of local soils, the U.S. Department of Agriculture recommends planting a pair of fresh cotton underpants 3 inches deep in the ground. Wait at least 60 days, then dig them up.

Healthy soil contains billions of microbes that will break down organic material like cotton, so the more holes-filled and threadbare your unearthed undies, the heartier your soil. And the heartier your soil, the bigger the role it can play in producing nutritious plants, reducing erosion and storing carbon. Source: The Nature Conservancy Magazine

Here’s the how-to:

Plant a pair of new, cotton underwear horizontally about 3 inches deep in the site you're curious about. Don't forget to mark the spot you planted!

Wait at least 60 days. This gives your soil microbes time to do their magic! Then dig the undies back up.

Share your results by sending us a photo of your "harvest" and a little info about your operation to [email protected].

My Soil Your Undies Challenge

This is how I started my Soil Your Undies Challenge—a little boy’s pair of 100% cotton briefs. I removed the elastic waistband but left the leg bands in place. On May 30, I buried the undies three inches deep and marked the spot with a large rock. A butternut squash plant covered the area all summer.

Then it was time to prepare the bed for cool season crops so on October 8 I removed the marker rock and excavated for the briefs.

This is what I found. The little chunk of brief had worked to the surface but otherwise, only the narrow elastic band around the leg openings survived. I dug around the soil and could find no other evidence of the brief. The soil microbes took care of all that cotton, suggesting my soil is pretty darn good.