“Soil reminds me of land, it reminds me of crops, it also reminds me of the ground — something that provides a foundation.”
“When I think about soil, what comes to mind are cornfields and coffee plantations from my childhood. I remember soil preparation, but with a lot of difficulty.”
“When talking about soil, I remember my plants, my vegetable garden, my flowers, my garden. And all of that is wonderful.”
MARIANA – Soil means something different to each person. But there is one part of this story that almost no one imagines. Just a few centimeters below our feet lies one of the most diverse environments on the planet — a microscopic kingdom capable of shaping forests, feeding crops, and storing the carbon responsible for global warming.
Today, I invite you to look at soil through a different lens and discover this invisible universe that sustains life — and that can help save the planet.
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MARIANA – Hello, I’m Mariana Pollo, and this is Ccarboncast, the podcast that connects you to climate and carbon science. (brief pause)
For a long time, science viewed soil only as a physical support. Today, we know it is a living, pulsating ecosystem.
Close your eyes for a moment and imagine a vast underground world where bacteria, fungi, archaea, and even viruses coexist in a complex network of billions of microorganisms.
PROF. ANDREOTE – When we use the concept of the soil microbiome, that is exactly what we mean: a view of how this living fraction of the soil exists and interacts with it, changing its characteristics.
It is a very broad biological fraction, made up of enormous biodiversity. We can list thousands of species coexisting in the soil and even millions of living cells in just a single gram of soil.
Obviously, the interaction between minerals and the biological component gives rise to functions that are essential for soil quality, across its different uses and for agriculture as a whole.
Within this soil biology — within this soil microbiome — we find a series of processes that benefit both the soil and plant development.
MARIANA – This is Professor Fernando Andreote, a professor at ESALQ and a researcher at CCARBON. He will be our guide on this deep dive to unravel the mysteries of soil — and there are many.
In just one gram of soil, there can be between 10 million and 1 billion microorganisms. They work together as a diverse community, exchanging nutrients, forming biofilms, and interacting with the environment. In doing so, they help structure the soil, retain water, and store carbon in a more stable form.
And here’s an important clarification: when we talk about microbiota, we are referring only to the set of microorganisms present in the soil.
The microbiome, on the other hand, includes everything they do — their genes, their functions, and the interactions that keep the soil alive.
In other words, microbiota tells us who is there; the microbiome explains how this invisible world works.
Just as the microbiome of our own bodies influences our health, soil also has its own microbiome — and the vitality of crops and the carbon cycle depend on it.
PROF. ANDREOTE – Within the biological fractions of the soil and their functions, one of the most important and most studied aspects is how soil biology interferes with carbon transformation in this environment.
If we take a broader view, we can see two different and highly complementary processes.
The first involves macro-organisms — which, although small, are considered macro within the soil matrix — and they are responsible for fragmenting and incorporating organic material, greatly increasing the contact surface between organic residues and the soil.
The second, complementary stage is carried out by microorganisms, mainly bacteria and fungi, but also other important groups. Through enzymatic attack, they complete the decomposition of organic matter.
So, if in the first stage the material is fragmented and incorporated into the system, its decomposition and mineralization — the finer breakdown of organic matter — occurs through microorganisms. Bacteria and fungi that produce enzymes related to carbon cycling are especially important here.
Obviously, this biology–carbon connection gives rise to different forms of carbon. Part of this carbon is incorporated into the microbial biomass itself, as microorganisms feed and generate new cells.
Part of it goes into the atmosphere, mainly as CO₂, and in a few cases as other compounds such as methane. And a large fraction — depending on the original material — remains stabilized in the soil, either as mineral-associated organic matter or what we previously referred to as humic material: a more stable, more recalcitrant fraction that persists in the soil for much longer periods. There is, therefore, a clear connection between biological processes and carbon flows within the soil environment.
MARIANA – Even though invisible to the naked eye, this process is one of the keys to tackling climate change.
What is most fascinating is that microorganisms use very different strategies to deal with different types of carbon. Some are opportunistic and act quickly — they are the first to arrive when there is an input of easily degradable carbon, such as fresh leaves or recent organic residues.
Others work over the long term and prefer compounds that are harder to degrade. These slow-growing microorganisms are primarily responsible for transforming carbon into stable forms that can remain in the soil for decades or even centuries.
When carbon stays in the soil instead of returning to the atmosphere, it helps mitigate global warming. But for this to happen, it must be fixed more permanently — and that depends on the biological activity happening underground.
PROF. ANDREOTE – All biological activity that promotes plant growth also contributes to this process, because within the same time frame, plants accumulate much more biomass — both in roots and aboveground — increasing carbon inputs into the soil system.
This includes nutrient availability processes, plant growth promotion, and biological protection of plants. All of this greatly enhances a plant’s potential to convert resources into biomass.
So, we see a very significant gain at this point.
MARIANA – To ensure that soil maintains its capacity to capture carbon, it is essential to maintain microbial activity.
And the way to do that is by investing in agricultural practices that stimulate life in the soil.
PROF. ANDREOTE – Soil management is an extremely important practice. Perhaps it is within soil management that we find many of the innovations that have taken agriculture to new levels of productivity and, more recently, to new levels of sustainability and agronomic efficiency.
And when we look at soil management, it includes different components.
MARIANA – Sustainable agricultural practices play a central role in creating environments that are favorable to microorganisms. A great example is integrated systems, such as Crop–Livestock–Forest Integration (ILPF).
ILPF combines different land uses in rotation or intercropping. As a result, it keeps the soil covered and adds various types of organic residues and plant species. All of this favors multiple ecological niches for microorganisms, increasing their diversity and functionality.
Reducing excessive use of chemical pesticides is also important, as these inputs can kill beneficial microorganisms or inhibit their natural functions. By adopting more sustainable practices, such as bioinputs combined with planned chemical use, it is possible to protect and even restore microbial communities.
PROF. ANDREOTE – What we are seeing today is the development of biological soil management, an area that is very important, rapidly growing in both the market and scientific knowledge, full of innovations and possibilities.
When we look at it, we can divide biological soil management into two major blocks of action. One of them focuses on caring for the soil as an environment — in other words, promoting the native biological activity of that soil to a higher level.
MARIANA – Biological management values natural processes and views soil as a living ecosystem that can be strengthened and regenerated by stimulating the biodiversity already present there.
PROF. ANDREOTE – How do we do that? Primarily by restoring the soil’s own characteristics. If I were to give a very general recipe, I would say that for grain crops, no-tillage is the best system we have to promote soil biology. It provides thermal comfort, moisture retention, and a diversity of carbon sources — everything we value when thinking about biodiversity and biological activity.
For other crops, however, it is not always possible to maintain a no-tillage system.
MARIANA – The no-tillage system is indeed one of the most powerful tools in this regard. Temperature becomes more stable, moisture is conserved for longer, and crop residues serve as both food and shelter for microorganisms.
But Professor Andreote points out that not all crops allow for the adoption of this system. In horticulture and other crops, soil preparation is still common, which creates challenges for the adoption of conservation practices.
PROF. ANDREOTE – For horticulture, it is challenging. For sugarcane, soil preparation is always part of the renewal phase.
So even if we can’t achieve the ideal, what should we focus on to maintain biodiversity and biological activity at their maximum potential?
Diversity of carbon sources is extremely important, maximum soil stability is essential, and soil cover is fundamental — especially when possible with living plants.
This is one aspect: caring for soil and understanding it as an environment.
MARIANA – The key is to seek balance across three fundamental pillars: diversity of carbon sources, and physical and chemical soil stability.
When this foundation is well structured, the benefits become evident.
Soils with greater microbial diversity are more resilient to environmental stresses, such as droughts, sudden temperature fluctuations, or intensive input use.
In addition, these systems keep carbon stabilized, making biological management an important ally in climate change mitigation.
This type of management also involves a second, more technological axis, based on the application of biological products — this is where bioinputs come in.
PROF. ANDREOTE – Finally, and no less important, we must understand that much of the technology linked to soil biology — now from a more applied perspective, in bioinputs — allows for the complementation or even partial or total replacement of chemical tools.
And if we remember how chemical inputs are produced, they carry a very heavy carbon and energy cost.
So when we remove a chemical molecule with a large carbon footprint from its production and replace it with a biological tool that has a much smaller carbon footprint, we also contribute positively to the carbon balance of that agricultural area.
Bioinputs are products developed from living organisms or their metabolites. They include biofertilizers, biostimulants, and biological control agents.They are used to stimulate everything from root growth to pest and disease control, and they serve as an alternative or complement to conventional chemical inputs.
PROF. ANDREOTE – This has grown exponentially in recent years. Everyone knows that over the past decade this market has expanded, and today it offers producers a wide range of products for different purposes.
Identifying which biological products make sense for a given production area is an efficient and well-proven way to stimulate specific and desired processes in cropping systems.
Analyzing soil microbiology has always been a challenge, but advances over the last 20 years have paved the way for a new generation of much more comprehensive analyses.
That’s because traditional methods relied on culturing microorganisms in the laboratory — and less than 1% of them grow on plates.
With new techniques, science can observe biological processes directly in the soil and analyze the DNA of the entire microbial community, including species that were previously invisible to classical laboratory methods.
This is where biological indicators come in — essential tools for evaluating soil health and functioning under different management systems.
PROF. ANDREOTE – That means I go into the soil and measure activity without culturing the organism. So I am capturing all organisms that produce that process. In addition, we combine these analyses with molecular methods — we extract genetic material from the soil and use molecular biology techniques to obtain DNA sequences. Depending on what we want to analyze, we have different strategies — it’s a very broad field of research. Based on this genetic information, we reconstruct the biological composition of the soil and infer changes caused by management practices.
This allows us to monitor processes, understand differences in biodiversity and biological balance, and evaluate disease suppression. These are all critical functions for agriculture that we map through biological indicators and molecular biology, enabling us not only to monitor changes but also to predict them — generating predictive management strategies.
MARIANA – All of this knowledge does not happen in isolation. It is the result of years of research and the collective work of groups dedicated to soil microbiology, such as the Soil Microbiology Extension Group at ESALQ, coordinated by Professor Fernando Andreote.
In addition to outreach, the group conducts experiments, laboratory analyses, and develops technical materials based on current scientific methodologies. It is also a training space for students to engage with research and understand firsthand how soil microbiology directly influences agriculture.
PROF. ANDREOTE – Within my research group at ESALQ today, the central question is how agricultural practices shape the soil microbiome. This unfolds in several directions. We have projects focused on fertilizers and how different nutrition systems shape soil biological composition and balance.
We have also conducted projects with pesticides and are resuming some of them to understand the real impact of these products on the soil biological system. We work extensively with production systems — integrated and non-integrated — to understand carbon flow and how biology adapts in these systems.
And we have a very interesting project on how carbon is stabilized in the soil based on microbial necromass. This is a relatively new topic worldwide. We are beginning to understand which residual fractions of bacterial and fungal cells remain in the soil after they die — what stable carbon remains. The data are very interesting and show that much of stabilized organic matter may be derived from microbial activity.
MARIANA – In other words, we no longer view plant residues as the only source of stable carbon; microbial fractions are also extremely important. This opens new questions: how can we manipulate this process? Can we accelerate it? Stabilizing carbon in the soil brings enormous benefits — both for carbon cycling and for soil quality gains associated with higher organic matter content.
In short, soil is no longer seen merely as a physical support, but as a living, dynamic system that responds strongly to sustainable management.
These practices not only help maintain soil health, they also create an ideal environment for the microbiome to do its work: transforming organic matter, promoting fertility, and sequestering carbon.
PROF. ANDREOTE – One important thing is that the microbiome will always be there. If we do nothing to consider it, it will be unbalanced and hinder our processes.
But if we focus on biological soil structuring and learn how to manage it to reach its maximum potential, it becomes a partner to the farmer, delivering services that directly support what we seek: soil quality and plant performance.
MARIANA – The soil microbiome not only sustains plant life — it is also essential in addressing the climate crisis. Microorganisms are responsible for fixing carbon, balancing nutrients, and strengthening crop resilience. Caring for life in the soil is caring for the future.
In the next episode, you will learn about the history of planted forests in Brazil and how they contribute to carbon sequestration.
CLOSING
Ccarboncast is produced by the dissemination team of CCARBON/USP. This episode was written and narrated by Mariana Pollo, with content review by Rodolfo Fagundes and Juliana Ramiro. Recording took place at TV USP studios, with editing and sound design by Soupods. This project is supported and funded by FAPESP.
