Leisha In this article, I explore the intricate relationships between the soil microbiome, plants, and human health. Through recent discoveries and personal experience, I share how restoring healthy soil is about more than adding microbes, it is about rebuilding the living terrain itself. Together we are learning that the health of plants, soil, and people depends on fostering natural processes, diversity, and ancient microbial partnerships.
If you have been reading my articles here at Living Ground, you know I often write about bacteria, fungi, archaea, and the intricate microbial communities that shape both our bodies and our soils. Every day I see a deeper connection to the soils healh, plant and human health. And, I am beginning to realize we need to create compost right in our garden or farm just as Nature does it.
The human microbiome, with its bustling diversity of bacteria, bacteriophages, viruses, archaea, and fungi, has been at the forefront of biological research for the past decade. These discoveries have reshaped our understanding of health, teaching us that no organism is an island. A living system cannot be fully understood without including its microbial cohabitants. Some biologists now call this new way of seeing holobiont biology, life seen not as singular, but as symbiotic.
As science enters the public conversation, though, we often find that its subtleties are lost. Complex systems get simplified into quick fixes, and that is where problems begin.
Take iron deficiency in infants, for example. On the surface, it seems simple: if iron levels are low, supplement with iron. Yet, nature is never that simplistic. While iron is essential for oxygen transport, growth, and redox reactions, iron cannot be properly utilized by the human body without adequate copper.
Copper is the hidden key that unlocks iron’s biological functions. It is copper-dependent enzymes, like ceruloplasmin and hephaestin, that make iron usable, shuttling it into cells, loading it onto hemoglobin, and regulating its transport. Without enough bioavailable copper, supplemented iron often sits inert, or worse, feeds pathogenic bacteria rather than nourishing human tissues.
Copper itself exists in soils primarily in two oxidation states: Copper I (Cu⁺) and Copper II (Cu²⁺). In well-aerated soils, copper is usually found in the oxidized Cu²⁺ form, often tightly bound to organic matter or clay particles. In this state, it can be difficult for plants to access. Microbial activity plays a vital role in the soil copper cycle. Certain soil microbes help reduce Cu²⁺ to Cu⁺, the more bioavailable form for plants, especially under low-oxygen conditions or through microbial redox reactions.
Plant roots, aided by mycorrhizal fungi and rhizobacteria, secrete organic acids and enzymes that further solubilize copper, making it available for uptake. Once absorbed, copper becomes an indispensable micronutrient in plants, enabling photosynthesis, respiration, lignin formation, and, importantly, setting the stage for the copper-dependent pathways that later allow animals, including humans, to properly utilize iron.
In degraded soils, where microbial communities are broken and organic matter is scarce, copper availability plummets. Plants grown in such soils may be copper-deficient, and so too will the people eating them. Without copper, no amount of iron supplementation can truly solve anemia or restore robust health. Instead, it sets up a terrain ripe for microbial imbalance in both soil and gut.
This deeper layer shows why terrain always comes first. Fixing symptoms without restoring systems leads us deeper into imbalance.
When it comes to supporting this hidden terrain, the role of mycorrhizal fungi and rhizobacteria is critical. These symbiotic partners extend the root systems of plants, dramatically increasing their access to water and minerals like copper, phosphorus, and zinc. However, what often goes unsaid is that the very fertilizers and amendments we apply, even so-called natural ones, can disrupt these delicate relationships.
High levels of nitrogen, phosphorus, or potassium from chemical fertilizers, and even from strong natural fertilizers like manure teas or blood meal, can overwhelm the signaling pathways between plant roots and fungi. The plant, sensing an abundance of nutrients, may “shut off” its investment in microbial partnerships. Without the need to exchange sugars for minerals, the ancient alliances between plant and microbe collapse. When these relationships die back, the long-term resilience of the soil begins to erode.
Thus, whether in human health or soil health, the message repeats: shortcuts break systems.
The same caution applies to probiotics after antibiotics. We know antibiotics devastate the gut microbiome. So, the thinking goes, replenish it with store-bought probiotics. Yet, research shows that doing so can actually slow the gut’s return to its natural balance. Five months after antibiotic treatment, those taking probiotics had not yet recovered their native microbial diversity. Those who let their bodies self-restore, or who used their own pre-antibiotic stool sample for transplantation, rebounded faster.
Nature’s designs are often slower, subtler, and far wiser than we give them credit for.
The soil is no different.
We have long known that soil is alive with bacteria, archaea, bacteriophages, fungi, and viruses. Nitrogen-fixing relationships, like those between legumes and rhizobia, are commonly understood. Yet the soil biome, like the human one, is even more complex than we imagined.
Fungi create compounds that inhibit bacterial overgrowth. In response, bacteria evolve resistance strategies. This dynamic tension keeps life in balance. Regions differ. Bacteria thrive in temperate zones, fungi in cooler climes. Every soil carries its own distinct microbial fingerprint, shaped by microclimate, rainfall, plant life, disturbance, and time.
When we till the soil, we tear apart fungal networks that hold soil structure together and moderate microbial populations. When we compact the earth, we favor anaerobic organisms, changing the very nature of the underground world.
Even something as simple as iron moves through this hidden dance. In well-aerated soils, iron exists in a form (Fe3+) that plants cannot easily absorb. Under brief anaerobic conditions fostered by microbial activity, it is reduced to Fe2+, available to plant roots. Without the microbes, plants would struggle to draw life from the earth.
No two soils are the same, just as no two human microbiomes are identical. Soil is shaped by rainfall, sunlight, seasons, parent material, plant communities, and every living thing that touches it. Soil can rebound after fire, drought, or trauma, but it remembers. And over time, as climates shift, microbial populations change in response.
Plant life too is a powerful sculptor of the microbiome. Studies in coffee plantations show that native shade trees enrich microbial diversity far better than introduced species. Different plants invite different microbial symphonies.
Even annual crops like tomatoes leave microbial fingerprints. Grow tomatoes year after year in the same spot, and microbial shifts from previous seasons can reduce yields. Soil has memory. Soil carries stories.
The tomato study makes it clear. A plant is never just a plant. It is a living system enmeshed with its microbial environment, leaving echoes in the soil that persist long after the plant itself is gone. This insight mirrors a larger shift in biology: the growing recognition that all living beings are holobionts, collaborative organisms composed of both their own cells and vast microbial partnerships. To truly restore soils, we must begin to think like holobionts ourselves.
As we deepen into this exploration, it becomes important to expand our very definition of life itself. The traditional scientific view has long treated organisms as individual, self-contained units. Yet this lens is shifting. The concept of the holobiont offers a more natural, ecological understanding of life — seeing an organism and its microbial partners as a single, integrated living system.
Every plant, every animal, every human is a host not just to cells bearing their own DNA, but to a vast and essential community of bacteria, fungi, archaea, and viruses. These microbial communities are not passive passengers. They shape the growth, metabolism, immunity, and behavior of their hosts. In return, the host shapes the microbial community. It is a dynamic, co-evolved relationship — a true partnership.
Ecologists are beginning to embrace the holobiont perspective because it mirrors the complexity they observe in natural systems. Forests, grasslands, coral reefs, and even agricultural fields are not collections of isolated individuals but networks of mutualistic relationships, where cooperation, communication, and co-dependence are the rule rather than the exception.
In the context of soil and agriculture, this changes everything. If we see the plant not as an individual but as a holobiont, then our focus must shift from simply feeding the plant to feeding the entire living system that supports it. Building soil health is no longer about inputs alone. It becomes about cultivating relationships — between roots and microbes, between soil structure and water, between minerals and enzymes, between plants and the unseen life that sustains them.
This is the path forward. Not force-feeding plants with soluble fertilizers. Not sterilizing the soil with chemicals. But reweaving the web of life at every scale. When we tend to the whole — the holobiont — we heal ourselves, our gardens, and our world.
Plants have their own strategies for survival. Arabidopsis, a wild mustard relative, secretes natural coumarins that help it scavenge iron from alkaline soils, while simultaneously deterring bacterial freeloaders.
And all of this brings me to the heart of what I am discovering.
At Living Ground, we produce powerful microbe composts, rich with life, diversity, and the potential to awaken tired soils. Yet, as our work deepens, it is becoming clear that microbes alone are not enough.
If the underlying terrain, the soil structure, the plant diversity, the living root systems, is unhealthy, then applying microbes is like seeding a symphony into a broken instrument. The true health of the soil, plants, and even ourselves must begin by rebuilding the terrain first.
Nature already knows how to compost. I am increasingly guided by the realization that our gardens and farms must mirror these natural processes, not override them.
That means:
- Prioritizing green manure crops, plants grown not for harvest but to feed the soil.
- Leaving weeds, without seeds, on the surface, allowing their roots to break compacted layers and their decomposing tissues to enrich the microbial feast.
- Encouraging plant diversity, so that a broad, resilient web of life can take root.
Many weeds, often seen as nuisances, are actually master mineral harvesters. They mine the subsoil for nutrients that shallow-rooted crops could never reach. They are gifts, not enemies.
Living Ground’s microbe composts thrive best when applied to such healthy, diverse terrains. In living soils with green manures, weeds, root exudates, and decaying organic matter, the microbes we apply can integrate naturally, supporting and strengthening the whole system.
Bokashi composting, vermicompost, hot compost, all have their place. But none of them create soil on their own. True soil health comes from microbial integration into a living, breathing, plant-rooted community.
Some evolving practices I recommend:
- Use composts and microbial inoculants thoughtfully, always paired with living green plants.
- Favor vermicompost where possible, worms create a microbe-rich, plant-ready amendment.
- Grow green manures. Let weeds work for you. Leave their cuttings on the soil surface as living mulch.
- Prioritize perennial crops when you can. They weave deep, lasting relationships with soil microbes.
- Celebrate biodiversity in your garden. Diversity above supports diversity below.
- Avoid tilling or compacting your soil. Treat it as the living, breathing skin of the Earth that it is.
- And most of all, trust that what works in one place may not work the same way somewhere else. Listen to your land. Watch. Adapt.
Long before we were farmers, gardeners, or scientists, we were participants in this great microbial dance. Somewhere along the way, we forgot, but the memory is still alive, waiting for us to return.
The research is still unfolding. Every answer opens a dozen new questions. But one truth is already clear: The future of soil, plant, and human health lies in restoring not just the microbes, but the living landscapes they call home.
Long live the Holobiont. Long live Living Ground.
LINKS
https://www.mdpi.com/2073-4395/12/5/994
https://www.tandfonline.com/doi/full/10.1080/17429140802272717#d1e287
