When the Soil Breathes Again
- Florian Strobel
- Dec 5, 2025
- 5 min read
How Microbes Stop Surface Sealing, Build Humus, and Keep Water in the System
Water is rarely the problem. Soil function is.
Agriculture is experiencing two extremes at the same time: long dry periods, and then rain that arrives too fast. That sounds like weather, but it is often infrastructure. A soil that functions can absorb water, distribute it, store it, and release it again. A soil that does not function responds with crusting, runoff, erosion, patches of waterlogging, or dry spots.
The key point is systemic: soil is not a “substrate”, soil is a living operating system. And microbes in that system are not an “ingredient”, they are the process engine.
1) The ideal outcome: a “chamber sponge” made of pores
A healthy soil has a hierarchical pore system:
Macropores for fast water and air transport
Mesopores for plant-available water
Micropores for very tightly bound residual water
In practice, that means: water enters, finds pathways, spreads out, and remains available within a usable range.
Important for interpretation: plant-available water is the water held between field capacity and the permanent wilting point. Some of the water stored in soil can be bound so tightly that plants can access it only to a limited extent.
2) What a microbial consortium actually does in soil
A microbial consortium does not work through individual “tricks”, but through coupled processes that reinforce each other. The key is that biological activity in soil acts exactly where structure is created or lost: on particle surfaces, inside pores, and at the interface of water, air, minerals, and organic matter.
A) Preventing surface sealing means binding particles before pores clog
Surface sealing (crusting) occurs when fine particles become mobile, “glue shut” pores, and the surface collapses during the first strong contact with water. That reduces infiltration, increases runoff, and promotes crust formation.
Microbes can have a structure-building effect here, mainly via extracellular polymeric substances (EPS) and biofilm:
EPS are natural biopolymers that can act as a binding matrix and bring particles together into more stable associations.
This matrix supports aggregate stability. More stable aggregates break down less during heavy rain, pores stay more open, and the surface seals less easily.
Translated into practice: less crust, less “smearing shut”, better water intake even during more intense rainfall events.
B) Building humus instead of “just collecting residues”: the biological transformation process
Humus formation is not only the accumulation of plant residues, but a biological pathway of transformation and stabilization.
A central long-term mechanism is microbial turnover:
Microbes grow, use organic substrates, form biomass, and in doing so transform complex organic structures.
Part of the biomass dies and becomes microbial necromass.
These cell components can transition into more stable organic fractions and bind to mineral surfaces. This makes organic matter less “fleeting” and more a part of the soil matrix.
Important: this is not an overnight effect. Speed and magnitude depend on the starting soil, organic inputs, climate, water regime, and management.
C) Stabilizing soil function (“soil cleansing” in a functional sense)
“Soil cleansing” here does not mean sterilizing, but functionally stabilizing. The goal is not “everything gone”, but “the system becomes resilient again”.
This includes typical ecological mechanisms:
competition for food and space
occupation of ecological niches
changes in micro-environments within the pore space, for example local pH and redox conditions
breakdown of organic “loads” that can trigger unstable microbial surges or unwanted dynamics
This is compatible with the well-known framework that soils can become more stable, or even more disease-suppressive, through microbially mediated processes, without using a kill-based approach.
Inoculated microbes do not establish permanently in every soil. In some cases, what changes is the system function rather than the long-term community composition. That is why the goal is not “one strain wins”, but “soil function stabilizes.”
3) Why infiltration and water storage go hand in hand
It seems like a trade-off: if more water is stored, water would have to infiltrate more slowly.
In a well-structured pore system, it is the opposite:
Macropores allow rapid entry and drainage of excess water.
Meso- and micropores provide distribution and retention.
EPS, stable aggregates, and the organic matrix help prevent this pore structure from smearing shut.
That is why the major practical lever is often not only “hold more”, but structure better and distribute better.
4) The biological process step by step: from first contact to regeneration
Phase 1: Contact and activation in the topsoil
After application, microbes move into the top millimeters and encounter substrates such as dead roots, organic residues, root exudates, and different oxygen micro-zones.
Phase 2: Breakdown of unstable organic matter
Microbes break down organic materials through enzymes and metabolic processes. This reduces unstable organic “loads” and frees up resources for structure-building.
Phase 3: EPS, biofilm, micro-aggregates
Now the structural effect emerges:
EPS and biofilm bind particles and organic molecules.
Micro-aggregates form and can contribute to more stable aggregate structures.
Phase 4: Turnover and humus formation via microbial necromass
During growth, microbes die. Part of their cell components becomes part of more stable organic fractions. Over time, this can create a functional, “sponge-like” soil matrix.
Phase 5: Rebalancing the microbiome
Through competition, niche occupation, and resource steering, a more robust microbial balance can develop that stabilizes soil function in the long term.
5) Legend: technical terms in plain language
Infiltration: water entering the soil at the surface.
Macropores: larger pores for fast transport of water and air.
Mesopores/Micropores: smaller pores for storage and tightly bound water.
Field capacity: water content after free drainage has stopped.
Permanent wilting point: water content at which plants permanently wilt because they cannot take up enough water.
Plant-available water capacity (AWC): water held between field capacity and wilting point.
Aggregates: crumb structures made of mineral particles and organic bindings.
EPS: biopolymers secreted by microbes outside the cell.
Biofilm: microorganisms embedded in an EPS matrix on surfaces and within pores.
Microbial necromass: dead microbial cell components that can contribute to soil organic matter.
6) Self-tests: how to check structure, infiltration, and trend changes yourself
These tests are intended as on-farm screening. They show trends and differences, not perfect absolute values.
Test 1: Slake test (10 minutes)
You need: 2 glasses/bowls, water, a small shovel, a smartphone.How to do it:
Take 2–3 dry soil crumbs (do not crush).
Gently place one crumb into the water.
Observe for 5–10 minutes: stable, partial breakdown, rapid breakdown.
Document with photo/video.
Why it matters: aggregate stability is closely linked to crusting and surface sealing risk.
Test 2: Ring infiltration (comparison test)
You need: a ring (pipe section), hammer + wooden block, measuring cup, stopwatch, water, plastic sheet/film.
How to do it:
Insert the ring a few centimeters into the soil so it seals well.
Do not disturb the surface inside the ring.
Add water gently (over plastic sheet or a spoon).
Measure the time for a defined volume to infiltrate.
Measure multiple points per zone, with the same starting moisture.
Note: a single-ring setup can include lateral flow. That makes it ideal for before/after and area comparisons.
Bonus: Spade test
Roots, crumb structure, compaction zones, visible pores. Often the fastest system diagnosis.
Sources for further reading
NRCS definitions and classification of AWC, field capacity, and wilting point.
FAO slake test protocol.
Minasny & McBratney on the on-average moderate increase of AWC with higher SOC.
Reviews on EPS and soil aggregation.
Microbial biofilms and hydraulic soil processes.
Microbial necromass as a major SOC contribution.
Suppressive soils and microbiome-mediated stability.
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