Soil Fertility, Biodiversity, and the Arc of Collapse and Recovery
Published:May 2025
The relationship between soil fertility and biodiversity is central to understanding how ecosystems function and change over time. Across many landscapes, ecosystems move through cycles of decline and recovery, shaped by shifts in nutrients, species composition and environmental conditions.
How ecosystems decline and recover over time
For the past 15 years, I’ve been gardening a small piece of land in the south-west of Ireland, in West Cork, and trying to coax life from a soil that just does not want to yield. The field and the garden I inherited had been treated the same way for decades: ploughed, planted, and served with synthetic fertiliser. In the field, animals had been kept pretty constantly — some donkeys, a pony or two, or some bullocks — but there was no rotation, no deliberate manuring, no return to the land of what was taken out. In the garden, there had been no animals at all. It had been worked and reworked, stripped bare and fed only chemical nutrients. A lot of the farm rubbish was buried there — I still dig up fertiliser sacks, bits of car, silage sheet, and pieces of farm machinery.
When I arrived, the pasture was poor. We kept sheep and pigs, but after ten years the sheep had destroyed the fences and the pigs had soured their ground. So the pasture is now planted as open woodland and allowed to revert, with some management. We have lizards and frogs, flowers, trees, and berries. But for the garden areas, even after five years of composting, mulching, and attempting to regenerate the land, many vegetables still do not grow well. Onions, peas, and beetroot will grow if given compost. Everything else either does not germinate, fails to thrive, succumbs to pests, or is hit with disease. Carrots and parsnips get carrot fly. Brassicas (apart from Brussels sprouts) fall to cabbage root fly. Potatoes are blighted and chewed by wasps. Slugs are rampant and leave their mark constantly on everything. The fruit trees — apple, pear, gooseberry, plum — are cankered and will not fruit. Some do not even flower. The only produce we get is blackcurrants and raspberries.
From Personal Experience to Research Question
This personal experience has become one of the entry points into my PhD study, which focuses on long-term ecological change and biodiversity, particularly through the use of sedimentary ancient DNA (sedaDNA) and microbial population analysis. But in addition to the stated objective of understanding how Ireland’s biodiversity has built up and responded to environmental change since the last glaciation, I realise now that a useful adjunct to this story is that of Ireland’s soil fertility.
By combining observations of contemporary soil degradation with the reconstruction of post-glacial ecosystems, I hope to understand not just what constitutes a healthy soil, but how soil forms, collapses, and regenerates through time.
Soil Had to Begin Again
During the last glaciation Ireland was covered entirely by ice as much as 1.2 kilometres thick, even as far out as the edge of the continental shelf. The land was scraped clean, as if an enormous bulldozer had traversed back and forth over the whole island. When the ice eventually melted, soil had to start again from nothing. Life returned slowly to the glacial gravels, sticky heavy boulder clay, and deep alluvial silts: lichens, mosses, microbial crusts. Then plants. Then fungi and insects. Over millennia, with the input of organic matter and build up of nutrients that had been pulled from deep in the sediment and left on the surface, the soil became rich and diverse.
Now, we appear to be reversing that trend at extraordinary speed.
And so the central question arises: if we understand how soil first formed, and what makes it functionally alive today, can we reverse the current collapse in soil fertility?
A Broken Soil
My investigations of my own soil, using microscopy and basic lab tests, revealed disturbing signs: very few fungal hyphae, almost no visible protozoa or nematodes, poor soil structure, compaction layers below the surface, sour smells, waterlogging in winter, and dry, cracked conditions in summer.
Even the no-dig method failed after a promising start. I mulched with cardboard and compost, and for two years the beds were productive. Then couch grass, buttercup, bindweed, and nettles broke through. The weeds became stronger. The crops weaker. I found that not disturbing the soil allowed the perennials to colonise at depth with a vengeance.
The revelation came slowly, but I finally realised: this soil is broken. Not in the superficial sense, but at a functional level. Its structure, its biology, its nutrient cycling — all disrupted. And the cause? Long-term negative management. Never before have I inherited a garden that had been managed like this. Fertiliser instead of manure. Overgrazing by animals without rotation. No return of organic matter. No time for recovery. Even well-intentioned interventions like mulching with compost were not enough to reverse it without deeper, systemic repair.
The Easy Fix — and Why I Rejected It
I might well have fixed the problem, temporarily anyway, with fertiliser, pesticide, herbicide, and fungicide. But that would just be propagating the problem. Did I want immediate results in vegetables grown with the aid of chemicals and made to produce in spite of the natural order? Or did I want to fix the problem and see that natural order return, allowing billions of years of natural evolution and symbiotic partnerships to manage it for me?
What is truly sobering is this: my garden and field are not the exception. They are the rule.
All across Ireland, and especially here in West Cork where we farm on siliceous bedrock — naturally low in calcium and high in iron — soils have been treated as inert, chemical-dependent substrates. Fertilisers have masked the decline, but the biology is gone. The structure is gone. The humus is gone. And so, quietly, the fertility is gone too.
Two Fields, Two Futures
Yet examples of regeneration do exist. Our neighbour, a dairy farmer, has taken a strikingly different path. He has focused on improving his herd through careful breeding and keeps his stocking rate low, lower than the optimum. He applies very little bagged fertiliser. Two years ago, he reseeded his poorest field — once conventionally managed for beef with fertiliser, heavy silage cuts, and poor drainage — with a diverse pasture mix: many species of grass, red and white clovers, hawkweeds, chickweeds, and a generous proportion of chicory.
Now that field is transformed. The pasture is thick, varied, verdant, and visibly alive. He notes that when the cows graze there, milk yield rises noticeably.
Next door is another field, managed conventionally, owned by a different farmer. It was a jumble of rocky outcrops covered by gorse and bramble, scrappy disjointed areas of grass, and poorly drained hollows. They removed the topsoil where it existed, smashed out the rock and spread the fragments around, levelled it, replaced the topsoil, and reseeded. It is ryegrass only. Mown three times already this year, after the latest cut it was quickly spread with slurry, and will soon receive bagged fertiliser. The grass looks stemmy and boring. There is no 'bottom' to it. No dandelions, no clover, not even docks. No biomass accumulating at the base. Just grass stems growing from bare soil.
What is the ryegrass feeding on? Slurry and fertiliser. But what is feeding the soil? Nothing. There are no deep-rooted plants to bring up minerals, no dying back to return organic matter. The system is one directional, linear and extractive.
Compare this to the chicory-clover pasture: tap-rooted plants cycle nutrients from depth. Leaves, stems, and flowers fall and decompose in place. Organic matter accumulates. The soil improves, year on year. One method gives back to the land. The other takes, and props up with chemistry.
If we ask which of these two management styles will impoverish the land, and which will improve it, the answer is obvious. And if we recognise that the ryegrass model dominates the national dairy system, the conclusion is deeply troubling.
Not Just a Farming Problem
This is not just my problem. It is not even just a farming problem. to quote this EU report - Urgent action needed to reverse soil degradation in Europe. "Nutrient imbalances are also on the rise: they are now estimated to affect 74% of agricultural land. These changes to the composition of soil can have negative consequences. For example, nitrogen surplus is increasing and can be harmful to human health, crops, eco-systems, and the climate. Meanwhile, soil organic carbon, which is essential to keeping soil healthy, is decreasing in agricultural areas. An estimated 70 million tonnes of this organic carbon were lost from the mineral soils of croplands across the EU and UK between 2009 and 2018."
This is an international ecological crisis in slow motion.
A soil that cannot grow food without chemicals is a soil on life support. A nation that cannot farm without inputs is a nation without resilience. And in a world of increasing population, rising input costs, extreme weather, and biodiversity collapse, this is not sustainable. It is an existential threat.
And now we are seeing the rising costs, and increasing unavailability, of fertilisers, produced by the use of fossil fuels and exported from the Middle East. This is a fragile linkage, upon which the world's food production depends.
Signs of a Different Direction
A blog titled How diverse is the soil life across Europe? A first continent-wide DNA analysis sheds light on the biodiversity below our feet was published a year ago on the GSBI website. This is another excellent blog from the Global Soil Biodiversity Initiative (GSBI) that is pointing in a very interesting direction. The launch of the First Local Soil Biodiversity Network: The Irish Soil Biodiversity Research Network (ISBRN).
How Soil Heals
The soil can be healed. It starts with awareness. Then with action. With compost, yes — but also with biology, with roots, with fungi, with time. It is essential to realise that fertility is not something to buy, but something to grow.
If we can successfully determine how to achieve good and sustainable fertility, then the power to restore the land is within reach. We need to understand that soil fertility is about biodiversity in the soil, as well as on it. The microbiota that do so much to release nutrients, enable gas exchange, ensure good soil structure at the micro level, and more than we even yet know about — that is what we need to focus on and learn about. There is so much we do not yet know, so much more to it than a bag of fertiliser and a dose of slurry.
The Heart of the Research
And perhaps by understanding the great cycles of collapse and regeneration that shaped Ireland’s soils over the last 12,000 years, we can learn how to restore them again — not just chemically, but biologically and systemically.
This, ultimately, is the heart of my research: to understand how natural systems dealt with deep systemic changes in the environment, and to learn how we can use that knowledge to mimic natural processes; to uncover how soils live, die, and might live again; and, hopefully, to halt the degradation that will otherwise eventually lead to ruin.