The soil’s early warning system: microbes can predict desertification before plants start to die

Microbial ecology (the study of how tiny microbes interact with each other and their environment) underpins the health of every ecosystem on Earth. The microbes living in soil recycle nutrients, support plant growth and help ecosystems respond to environmental change. In this explainer, microbial ecologist Marc Van Goethem tells us why microbes are critical to human life. They can also provide an early warning if Africa's drylands are approaching ecological tipping points, offering new ways to monitor and protect vulnerable landscapes.

What is microbial ecology, and why is it an important field of research?

Microbial ecology is the study of how microorganisms, like bacteria, fungi and the viruses that infect them, interact with one another and their environment. Together, microorganisms exert considerable influence on their immediate environment. Some examples include the breakdown of organic matter to release nutrients into the soil, digesting the food in our guts, and storing carbon dioxide.

Studying microbial ecology is an effort to make sense of these combined biological and chemical processes in nature. This information can then be used to predict how an environment might respond to future changes or why, for example, crops grow better in one field compared to another. Microorganisms quietly shape our lives even though they get less recognition than more easily observed animals and plants.

What are soil microbes and why do they matter?

Soil microorganisms are very small (micrometres); we can only see them under powerful microscopes. Their small sizes, however, make their roles in nature even more profound. In soils, bacteria, fungi and viruses form microbial communities that operate like mini-cities. We call these communities “microbiomes”.

On a single grain of sand you could find thousands of bacterial cells interacting by sharing nutrients and genetic material. They also compete for space and resources by producing antibiotics, which are compounds that kill other bacteria. Around 70%-80% of clinically used antibiotics originate from soil bacteria like Streptomyces.

The soil microbiome is central to the carbon cycle. Microbes can absorb carbon and bury it in the soil, or degrade plant and animal matter, which releases carbon into the atmosphere. These processes are extremely sensitive to environment changes. Increasing temperatures, caused by global warming, may increase microorganism activity. Buried carbon may be sent back into the atmosphere. Too much atmospheric carbon acts as a blanket and increases global temperatures – and the cycle escalates.

Your work suggests that changes in microbial communities could provide an early warning of desertification. How can organisms we can't see tell us so much about the health of an ecosystem?

My work hinges on the knowledge that microorganisms respond fast to environmental changes – faster than plants or animals can. Microorganisms detect and react to signals that we can't perceive. Some examples include changes in soil pH, moisture content or temperature.

Microbial responses are leading indicators of changes to temperature, water or physical disturbance in soil and the health of the above-ground ecosystem. I believe we can use this knowledge before we see visible changes like plant death.

What do you hope your work will reveal about how Africa's drylands respond to climate change and how could that knowledge help scientists and policymakers better protect these landscapes?

The central aim of this work is to identify the tipping points at which drylands begin to lose the resilience provided by the soil microbiome. The proposed research will collect representative soil samples from four African deserts: the Namib, Kalahari, Sahara and Sahel. I hope to provide meaningful data points, like data about which microbes are present or absent in soils, and what they are doing under various environmental conditions across drylands to map the microbiome across stages of desertification. Desertification is the process in which fertile lands in dry areas completely lose the ability to support plant, animal and human life.

These samples I hope to collect will come from

• intact ecosystems

• at-risk ecosystems

• degraded soils.

Through metagenomic sequencing (where we sequence the genomes of the entire microbiome simultaneously) and associated metadata (climate and soil chemistry information) we hope to identify the markers of desertification. This could be in the form of a specific microorganism disappearing and the mini-city then collapsing, or the microbiome losing an important function such as making nitrogen available to a plant.

Using these insights, I hope to provide a measure that shows the difference between healthy dryland microbiomes and those actively experiencing desertification.

This information will be provided as a reference accessible by researchers and policymakers to compare data from their drylands to estimate whether their landscapes are at risk of desertification.

Marc Van Goethem does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.

By Marc Van Goethem, Microbial ecologist, University of Pretoria