The Center for International Forestry Research (CIFOR and World Agroforestry (ICRAF) joined forces in 2019, leveraging a combined 65 years’ experience in research on the role of forests and trees in solving critical global challenges.
Farm management and agroforestry can help soil biota to restore and sustain ecological functions

There are more microorganisms in one teaspoon of healthy soil than the entire human population of our planet. They include bacteria, fungi, actinomycetes (similar to fungi), protozoa (larger bacteria-eating microbes), nematodes (microscopic worms), and other invertebrates. Alongside soil macrofauna (organisms that are greater than 1 centimetre long, or have a width or diameter of more than 2 millimetres) such as earthworms, ants, beetles, earthworms, millipedes, centipedes, and termites, they play a major role in maintaining and improving soil health. The higher the population of beneficial organisms, the healthier the soil.
For over a decade, researchers at the Center for International Forestry Research and World Agroforestry (CIFOR-ICRAF) have been studying how living organisms in soil – such as earthworms, termites, fungi, and bacteria – restore and sustain ecological functions through farm management and agroforestry interventions. “Studying the physio-chemical characteristics of the soil alone will not yield its holistic health status,” said David Lelei, a CIFOR-ICRAF Junior Scientist in soil biology. “To find that out, soil biota studies must be conducted.”
“Studying soil biota is vital because these organisms play important roles in nutrient cycling, soil structure and health, carbon storage, water retention, and plant growth,” added CIFOR-ICRAF Research Associate Lukelysia Mwangi. “Soil biota also contributes to the overall biodiversity of ecosystems and supports many other ecological functions.”
The CIFOR-ICRAF Soil and Land Health Theme is committed to understanding the physical, chemical, and biological aspects of soil health – and the effects of land management on these. To that end, Living Soils Laboratory specialises in analysis to understand the role played by different species of soil biota in enhancing and sustaining critical ecosystem functions, and includes analysis of both macrofauna and microorganisms.
Over 4000 soil samples have been analysed so far; the findings are fundamental for better understanding these species’ interactions with soil and trees, with a view to improving overall farm productivity and effectively advising farmers – and addressing wider restoration, health, biodiversity, and climate challenges. “The ability to study [soil biota] changes in a given area as well as time will greatly enhance our capacity to understand the linkages between land use intensity, biodiversity and soil health,” said Lelei.
Monitoring microorganisms
In their analysis of microorganisms, the laboratory team focuses on arbuscular mycorrhizal fungi (AMF). AMF are the microbes that colonise plant roots and establish a connection between the plant and the soil) and bacteria: fungi ratios a higher ratio of fungi tends to imply greater fertility). The scientists analyse AMF by isolating spores and observing them under a microscope, which gives insights on species richness and diversity based on the different texture and colours of the specimens. For bacteria: fungi ratios, the team uses isolation and estimation of populations within their samples, which can help to project likely populations of these organisms within a landscape.
The researchers also carry out high-quality analysis of AMF and bacteria: fungi ratios in soil across diverse degraded landscapes. These biological indicator assessments are important tools for restoring damaged and degraded lands through improving plant nutrient uptake, water relations, ecosystem establishment, plant diversity, and productivity. AMF, for instance, plays a critical role in boosting plant growth and survival in harsh conditions; it also improves plants’ tolerance to abiotic stresses such as salinity and drought, as well as to root infections; and, it enhances soil structure by increasing soil aggregation and water-holding capacity.

Marvels of macrofauna
To analyse soil macrofauna, field sampling is conducted at the end of rainy seasons, when the macroinvertebrates are known to be active. Once they are moved to the laboratory, they are counted and their fresh weight from each strata layer is taken.
These organisms play major roles in maintaining and improving soil fertility, as well as cycling nutrients and carbon. They contribute to processes such as the maintenance of soil structure and incorporation of organic materials into the soil matrix, which are key in the restoration of degraded soils, as well as mitigating against climate change. As such, the laboratory is developing ways of maintaining them in soil.

Benefits for farmers – and beyond
Understanding soil biota can help farmers optimise nutrient management practices and reduce reliance on synthetic fertilisers, which can have negative environmental impacts over time. By contributing towards restoration of degraded soils, the soil biota contributes to improved agricultural productivity through beneficial soil ecosystem services.
The benefits of soil biota go beyond farming, too. Some soil bacteria have been found to produce antibiotics that are effective against human pathogens. Overall, the study of soil biota is important for understanding the functioning of ecosystems, supporting sustainable agriculture, mitigating climate change, and promoting human health.
“Our data shows that management techniques can improve soil health, reduce erosion, and increase crop yield,” said Mwangi. “On the other hand, degradation from activities such as overgrazing, deforestation, or inappropriate land use can have detrimental effects on the environment – including soil degradation, decreased biodiversity, and reduced productivity.”
Challenges and ways forward
One challenge of this vein of research is the complexity and variability of soil ecosystems. Funding for soil biota research can also be limited, and there is a need for greater public awareness of the importance of soil biodiversity for ecosystem functioning and human well-being.
Nonetheless, the research team plans to expand its scope to include investigating the impacts of climate change and land use change on soil biota; developing new sustainable agricultural practices that promote soil health and biodiversity; and upscaling analysis in the laboratory to include molecular techniques.
As soil health’s visibility increases on international agendas, the team hopes that funders will follow suit. “The UN CBD COP15 [the United Nations Convention on Biological Diversity’s 15th Conference of the Parties] in Montreal had several positive outcomes – including Target 2, which aims to restore at least 30 percent of degraded ecosystems in order to enhance biodiversity and ecosystem function,” said Leigh Winowiecki, Global Research Leader of Soil and Land Health at CIFOR-ICRAF and co-lead of the Coalition of Action 4 Soil Health (CA4SH). “Investing in soil health is key for achieving this on terrestrial systems.”
Learn more:
SEEING THE UNSEEN: Mysterious Mycorrhizal Community in Soil
Video: Soil Microfauna - Mycorrhizal Community in Soil
Video: Soil Macrofauna – Termites
Video: Soil Macrofauna - Millipedes, Centipedes