Guide to soil biology and how to protect it

Many farms are closer to being “regenerative” than they might think, says a leading soil scientist.

Ian Bell of Northern Soil Regen told delegates at Carbon Calling in Cumbria last month that regenerative agriculture is not simply avoiding certain conventional methods.

He said it is about developing a thought process that acknowledges and limits damage (see “How conventional farming can damage the soil food web”) done to soil biology.

See also: 7 farmer tips on moving to regenerative farming

The regenerative thought process starts with the soil food web (see diagram), developed by US soil scientist Elaine Ingham, said Mr Bell.

The focus should then be on limiting inputs and getting soil biology going again (see “How good farming practice can help”).

“Humic and fulvic acids can be applied to the land to buffer the damage of weedkillers, and compost extracts and biochars [high-carbon residues produced by pyrolysis] can get soil biology moving again, too,” said Mr Bell.

What is the soil food web?

Once the soil food web is in place and balanced, the claim is that this helps the soil to be structured optimally, suppressing weeds and inhibiting disease.

Organic farmers growing 9t dry matter/ha with no chemical inputs is testament to the productivity of soil food webs, the conference heard.

Every living thing has its place providing it is in balance, said Mr Bell. “Only 3-4% of bacteria are disease-causing. The rest are essential to us and essential to plants and soil health.”

In productive grass and arable land, the bacteria and fungi are in balance, whereas bare soil after an earthquake is dominated by bacteria, and woodland soil, by fungi.

The soil food web is made up of a complex range of organisms:


Plant leaves, shoots and roots

  • Plants act like solar panels. The more diversity in their size and shape – for example, clover, ryegrass and fescue – the better, as this creates diverse root systems.
  • Plants strip carbon out of the atmosphere through photosynthesis.
  • Carbon is converted into sugars in the roots. Up to 40% of these sugars are sent out into the soil as exudates. This is not because the roots have too much sugar, but because they want to trade food with bacteria.

Bacteria, fungi and nematodes

  • Bacteria and decomposing fungi are attracted to these sugars and live off them, processing them to produce enzymes.
  • The enzymes solubilise plant food (nitrogen, sulphur, sodium, boron, iron and so on) from soil particles (sand, silt and clay).
  • Fungi is also responsible for breaking down fibrous material (wood/straw).
  • Basic soil tests only look for water-soluble nutrients, and do not find these plant nutrients locked up in the soil particles.
  • The plant trades with the soil microbes: sugar and carbohydrate for minerals.
  • Productive grassland and cereal ground have a balance of bacteria and fungi (typically 600mg/g of soil each).
  • Each sugar the plant sends out is a specific request for a trace element. For example, the plant may need calcium, so it attracts a bacterium that is full of calcium.
  • Root-feeding nematodes cycle nutrients but also eat the roots.

Mycorrhizal fungi

  • Arbuscular mycorrhizal fungi (AMF) are different to decomposing fungi. They work symbiotically with plants, creating drip lines extending for many metres through the soil, with plants allowing them inside their roots.
  • The plants give the AMF sugars and in return the AMF pass on water, phosphorous and other nutrition. Without AMF there is hardly any phosphorous available for plants.

Arthropods, nematodes and protozoa

  • The plants cannot yet access the traded nutrients. They rely on protozoa (for example, amoeba and flagellates) to ingest the water-soluble nutrients, and excrete them in plant-available forms.
  • Just like a cow, the protozoa graze and pass out valuable nutrients for the plant. This happens in the rhizosphere around the plant roots.
  • Bacteria-feeding, fungi-feeding and predatory nematodes (roundworms) pass out nutrients as plant-available food. Predatory nematodes eat root-feeding nematodes.

Mycorrhizal pods (insects)

  • Insects and larger organisms (also called arthropods) – for example, worms, spiders and beetles – eat bacteria, nematodes and fungi and pass more nutrients on to plants

Birds and mammals

  • Birds and mammals, such as rabbits, foxes and cows, are also part of the soil food web.

How conventional farming can damage the soil food web

Applying synthetic fertiliser


  • Ammonium nitrate is a salt, which kills soil bacteria. Without these bacteria, the food cannot be solubilised for the plant, so the food must come from fertiliser
  • As an oxidising agent, ammonium nitrate skews the balance of oxidation and reduction. This means carbon is not pulled down into the soil as effectively and pH is less stable
  • It makes plants “lazy” and stops them putting sugars out to feed microbes

Weedkillers (glyphosate)


  • Blanket glyphosate applications kill off the living plants above the soil meaning carbon is not pulled down to the roots and there are no sugars for microbial populations on which to feed

Using anthelmintics


  • Nematodes are roundworms that are critical to controlling soil pests. They are killed by roundworm wormers. The first nematodes to return following the use of wormers are the root feeders and they can thrive in the absence of predatory nematodes



  • The physical action of inversion ploughing breaks up the soil structure and interrupts the balance of the soil food web

Anaerobic slurry


  • Dairy cows are fed mineralised feed, so slurry contains salts. Salinity, if too high, can upset the flow of water through the soil
  • The slurry, if full of anaerobic bacteria, creates an anaerobic environment. Anaerobic bacteria thrive in compacted soils where oxygen is limited
  • Large machinery compacts soil further, producing more anaerobic conditions

How good farming practice can help

Sustainable control of parasites (Scops) principles

Limiting wormer use by conducting faecal egg counts and targeting treatments at slow-growing lambs limits the amount of product used

Rotational grazing

Rotational grazing allows grassland rest periods of 21 days on average. During this time it can regenerate leaf mass for stock to eat and grow root mass, capturing more sunlight and carbon to feed the soil biology

Spot spraying

Targeting weeds with knapsack sprayers or weedwipers limits the amount of chemical being applied to the farm

Slurry additives

Various slurry additives are applied by some farmers to aerobically digest slurry in the store, claiming it converts ammonia into bacterial protein


More farms are trialling composting to increase bacterial, and particularly fungal, populations in soils. This is added to the land as extracts, teas or whole


Direct-drilling and min-till cultivations with strip-till drills are used on some farms to keep living roots in the soil and minimise disturbance to arbuscular mychorrhizal fungi

Alleviating compaction

Many ways to minimise and address compaction are widely used by farmers, including wider/double tyres, subsoiling and aeration