February 17, 2023
Research Highlight

Soil Microbes as Drivers for the Formation of Mineral-Associated Organic Matter

Scientists studied how microbes break down minerals, with a focus on storing carbon in soils

soil microbes

Scientists discovered some surprising ways in which microbes interact with minerals, such as biotite, in soils. Their work could help lock organic carbon in soils and out of the atmosphere.

(Image: Pacific Northwest National Laboratory)

The Science

Toward an effort to stabilize carbon in soils, scientists are working to understand the complex interactions between microbes in the soil and the soil particles surrounding them. While these microbes can cause chemical weathering of minerals, thereby releasing important nutrients that keep them, plants, and other living organisms healthy, other aspects of the interactions between these microbes and soil minerals are not well understood. Following a six-month field-based study in the root zone of ponderosa pine, a multi-institutional team of researchers including scientists from Pacific Northwest National Laboratory (PNNL) used advanced instruments and determined that soil microbes were involved in the breakdown of minerals to form organic matter. The results could help scientists find ways to lock organic carbon in soil and prevent it from entering the atmosphere.

The Impact

In the face of global climate change, which is largely fueled by excess carbon, researchers are attempting to discover new ways to store carbon in soil over longer periods. However, the underground interactions can be surprisingly complex. For example, while it is well known that microbes decompose soil organic matter, there is limited understanding of how they are involved in mineral weathering. Nevertheless, these processes can result in soil clumps called aggregates and tinier clumps called microaggregates, which can serve to confine certain elements in the soil. Thus, understanding the relationship between microbes and minerals may hold the key to developing effective approaches to carbon storage.


A multi-institutional team of scientists used mesh bags filled with the mineral biotite and deployed them for six months in the root zone of ponderosa pine. These bags allowed fungal and soil microbes to enter but kept out tree roots. The team then compared chemical and functional changes in the contents of those bags with that of the surrounding soil. To discover the inner workings of the processes of weathering and aggregation, they studied samples using advanced instrumentation, such as Fourier transform ion cyclotron resonance mass spectrometry and high-resolution electron microscopes, available at EMSL, the Environmental Molecular Sciences Laboratory, a Department of Energy (DOE) Office of Science User Facility at PNNL. The results revealed that the microbial community had selectively colonized the minerals inside the bags and facilitated the production of soil organic matter, which acted as a conduit for nutrient extraction from the minerals and as a binding component in mineral aggregation. By contributing to the production of soil organic matter, the team demonstrated that the soil microbes were directly involved in the stabilization of soil organic carbon and mineral weathering. These insights will help scientists better understand complex underground interactions and could lead to approaches to stabilize carbon in soils.


Alice Dohnalkova, EMSL, alice.dohnalkova@pnnl.gov

Tamas Varga, EMSL, tamas.varga@pnnl.gov

Rosalie Chu, EMSL, rosalie.chu@pnnl.gov


This study was supported by the National Science Foundation and Laboratory Directed Research and Development funding at PNNL. Research was conducted at EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility.

Published: February 17, 2023

A.C. Dohnalkova, et al., “Effects of microbial-mineral interactions on organic carbon stabilization in a ponderosa pine root zone: A micro-scale approach.” Frontiers in Earth Science 10, 799694 (2022). [DOI: 10.3389/feart.2022.799694]