There is much discussion about soil biology in Agriculture, and for those of us following one of the many natural approaches, soil biology sits at the core of our systems.  Nature is a complex set of systems and there are a range of different doctrinal approaches that have evolved to support sympathetic agriculture.
For me, one of the trickiest things is understand what is going on in the soil in order to decide what, if any, intervention is needed. The big challenge is that much of the active component of soil is microscopic and dynamic so we cant see it.
I found myself coming up against this same challenge time again; what does healthy soil look like and how do I measure, or at least monitor it?
There are a number of biological and organic matter tests from a range of providers, but none gave me a clear and timely picture of what I am working with.  Whilst many natural processes occur over significant time spans, some are pretty rapid and these are the things that provide an indication as to how the soil is reacting to our intervention.
Many folk are happy to discuss soil health as either a theoretical or generic level, but real time observation was limited to a few indicators such as worm counts, smell and feel and colour.  These are useful, having served us for millennia but still not really providing the feedback I crave.  Don’t get me wrong, a spade, a nose and a bit of intuition have alwasy provided a huge amount of information, but I am after a bit more.
The blinding conclusion I have come to is that whilst many of us talk about soil biology, very few of us actually know what it looks like (or what it should look like) at a microscopic level.   This line of reasoning brought me into contact with, amongst others, the work of Dr Elaine Ingham and her work with The Soil Food Web.  This approach involves lookng at soil and soil amenments through a microscope to understand what conditions exist in the soil and compare this with the conditions that the plants we are trying to grow prefer.  I listened to much of her material on the dreaded interweb and found it resonated for me.

So I signed up for the Soilfoodweb foundation course and scales fell from my eyes.  Within a few weeks I had bought a shadowing microscope (which now sits on my desk and which I use almost every day).  I am now doing further training which has been incredibly instructive and seems to resonate with what I have been feeling but not seeing on the ground!  

Seeing what is living in the soil and beginning to understand the role that things play has provided a stunning insight into what is actually happening in and on my ground.  Whilst some things weren’t a surprise, many  were.  I have started looking at farming at Mindrum in a completely different way and am beginning to understand the logic and the contraditions behind a number of the extant theories, many of which had previously required an act of faith with a veneer of logic (or should that be the other way round!).  Some examples:

Organic Matter in the flesh - Meet the Aggregates

Having heard (and talked!) much about soil organic matter, its exciting to see it in action and see what it does.  Having always assumed it was just a question of getting muck and mulch onto the ground, it suddenly became clear that it is about much more than that….  much dead organic matter oxidises rapidly and disappears into the atmosphere unless there is a functional soil biology which can turn it into Aggregates which persist in the soil for much longer.  Simplistically, Micro Aggregates are created as Soil Bacteria glue pieces together, and are then stitched together by fungi to form Macro Aggregates.  Significantly, this is augmented by materials such as humic acids which are generated as the fungal community processes decaying material and also the sugary exudates emitted by plant roots.   These Macro Aggregates may tie carbon up for centuries unless destroyed, and which provide incredible structure for the soil and the organisms that live in it.

Soil Bacteria - part of the base of the pyramid

Soil Bacteria are amongst the first things to colonise soil,  in some soils they are the only things that can survive.  This is particularly true in some of the disfunctional soils in which the rest of the soil food web has been inadvertently demolished by catastrophic events, whether natural or manmade.

Bacteria (especially beneficial bacteria) form a critical layer at the base of the soilfood web, but much of their benefit is only realised if the other functional layers are there to release the goodness they have mined from the soil.

I found to my horror that one of the fields that, in a conventional system, had been one of my best (aka flattest and least stony!) arable fields had bacteria but little else (picture above).  If we look at successional theory (covered in a later piece) the soil profile I was looking at would suggest that I have created ideal conditions for weeds to out compete the crops I am trying to produce.  In a conventional system this didn’t really matter as we threw lots of herbicides at the problem, but in an organic or natural model, more thought is clearly required!

I am now working hard to build a functional food web in this soil which will provide a diverse environment which encourages mid successional grasses and cereals as part of a much wider rotation.  This should create conditions where the target crops outcompete the weeds automatically.

There are good bacteria and bad bacteria – which can tell a story about what has or is happening in the soil.


Fungi - binding and mining

One of the next things to grow in healthy soil are the Fungi.  There are a vast number of types with many roles, both beneficial and others which may cause disease. 

Like bacteria, Fungi in a functional soil have a mining role, taking unavailable nutrients from the soil and converting them to a form that can be used by plants.

Above we see a fungal Hypha growing through micro aggregates, stitching them together.  in time, these may well form a macro aggregate which will provide soil structure and house much more soil biology.

Michorrizal fungi in the soil form symbiotic (mutually supportive) relationships with a range of mid and later successional plants and, in exchange for sugary exudates from the plant roots, provide a significant proportion of the water and nutrients needed by the plant.  Many of these nutrients are not available to plants unless via these fungal relationships.

When we were conventionally farming, the fungicide seed dressings we used killed these michorrizal fungi as well as the bad ones and as a result the crops were entirely dependent on the “fast food” artificial nutrients provided.

One of the other functions of the fungi are to convert the sugars provided by the plants to the dark brown humic acid which locks up carbon in many soils, and provides the soil structure that is so clear in health soil.

Fungi and Bacteria exist towards the base of the trophic system,  mining unavailable nutrients from the soil.  If these nutrients are to be made available to plants, however,  we need some predators to eat them and release some of the nutrients into the soil.

Protozoa - Hunters of all shapes

Healthy soil contains a range of protozoa of many sizes and types.  This is an arcella, which is quite big, but a huge range of flagellates, amoeba of various types and other single celled organisms predate on smaller organisms including bacteria.  Protozoa have a much wider ratio of Carbon to Nitrogen atoms so they excrete much of the spare nitrogen and nutrients from the bacteria they consume in a form which is ideally suited for use by plants.

There are a myriad of different protozoa in good healthy soils or in good compost. They range in sizes from some small flagellates measuring 5 microns  to huge ciliates which may be over 100 microns long.

Many different forms of amoeba, some completely naked and others live protected in simple or ornamented shells or tests they have created from material in the soil.

Understanding what conditions different signature protozoa prefer enables us to read a little about the conditions that have existed in the soil.  As an example, ciliates are able to operate in anaerobic conditions, so the presence of ciliates would indicate that the soil is, or has recently been Anaerobic.

Friendly Nematodes in the Food Web

Having considered Nematodes in soil to be a generally bad thing it has become clear that there are many more types of beneficial nematodes than bad and that these  play a critical nutrient cylcing role in healthy soil.  Bacterial Feeders, Fungal Feeders and predatory nematodes (the character in this picture is a young bacterial feeder) form a key part of the soil foodweb, releasing nutrients that have been mined by the lower trophic layers in the food web as they eat lower organisms.

I now find myself excitedly searching soil samples for these characters.  And as they take different times to mature, they are great indicators of how the soil microbiome is evolving and how healthy soil really is.  Instructive and entertaining – what more can one ask!


I have barely scratched the surface of what is a vast and complex are.  I have, I’m afraid, cherry picked from some of the lower layers of the soil foodweb – there are many more layers and organisms in them.  I have no doubt that we will meet more and hear their stories at a later stage!

It has been staggering to be able to see the organisms that we are sharing our ground with.  Having met some of them, eyeball to eyeball (figuratively of course – many of them don’t need eyes!) it brings a completely new perspective into the ground and how we manage it. 

Excitingly, this is the view from the rock under which I often find my self (literally).  It may not be a classic view – but it never stops changing… or communicating!