Microbial Residues Last Longer in Soil When Bound to Noncrystalline Minerals

The Science

Soil organic matter is the key to healthy soil and therefore bioenergy crop yields as it provides essential nutrients, retains water, and supports plant growth. Much of it originates from microorganisms and their residues after death. A multi-institutional team of scientists led by Pacific Northwest National Laboratory (PNNL) studied how farming can enhance microbial contributions to soil organic matter. Using isotopic tracers, spectroscopy, and nanoscale imaging, the team showed that microbial residues last longer in soil when bound to noncrystalline minerals. In farm fields, fine-textured silty soils rich in these minerals can hold more microbial carbon overall than sandy soils. However, sandy soils still showed strong evidence that fresh microbial residues can bind quickly to the mineral surfaces present.

The Impact

This study reveals a major mechanism behind soil carbon storage: microbial interactions with highly reactive hydroxyl-rich iron minerals can stabilize microbial residues. Microbial residues, enriched with nitrogen-containing compounds like peptides and amino sugars, attach to mineral surfaces through interactions with reactive hydroxyl groups on poorly crystalline iron minerals, forming stable organo-mineral complexes. The dispersed nature of poorly crystalline minerals creates extensive reactive areas, allowing microbial residue compounds, particularly those with amide and carboxylic functional groups, to adsorb effectively. Although fine-textured silty soils have greater surface area and hold more microbial residues, fresh microbial residues could also rapidly bind to mineral surfaces in sandy soils. Understanding this mechanism of soil organic matter formation and retention opens new opportunities to manage soils for both bioenergy crop productivity and long-term fertility.

Summary

Healthy soils depend not just on plant inputs, but also on the remains of microbes. This study found that microbial residues build up when they bind to fine-textured, noncrystalline minerals that are rich in reactive iron. Researchers at PNNL used advanced tools at the Environmental Molecular Sciences Laboratory (EMSL) and the Stanford Synchrotron Radiation Lightsource (SSRL), both Department of Energy (DOE) Office of Science user facilities. Researchers used EMSL’s nanoscale secondary ion mass spectrometry to map the spatial distribution of ¹³C-labeled microbial residues at the submicron scale. X-ray diffraction and Mössbauer spectroscopy were used to characterize the mineral phases involved, with a specific focus on identifying noncrystalline iron minerals. Isotope ratio mass spectrometry was used to quantify the incorporation of labeled carbon across different soil fractions. At SSRL, researchers used synchrotron-based μ-X-ray fluorescence and X-ray absorption near edge structure spectroscopy to determine the spatial distributions of iron mineral phases in light and heavy mineral-associated organic matter fractions from sandy and silty soils. Together, these tools enabled the team to link microbial residues to mineral types and soil textures. By identifying this mineral-mediated mechanism of microbial carbon retention, the study provides a foundation for developing soil management practices that enhance carbon storage in bioenergy cropping systems and beyond.

Contacts

Kirsten S. Hofmockel  
Pacific Northwest National Laboratory  
kirsten.hofmockel@pnnl.gov

Qian Zhao  
Environmental Molecular Sciences Laboratory and The University of Texas at Dallas  
qian.zhao@utdallas.edu

Funding

The research was supported by the Department of Energy (DOE), Office of Science, Biological and Environmental Research Genomic Science program under FWP 68292 and 07880. Additional support was provided by an Exploratory Research award 51095 from the Environmental Molecular Sciences Laboratory, a DOE Office of Science user facility sponsored by the Biological and Environmental Research program. PNNL is a multiprogram national laboratory operated by Battelle for DOE under Contract DE-AC05-76RLO 1830. Additionally, research was conducted as part of user proposal S-XV-ST-5898 through the Stanford Synchrotron Radiation Lightsource, a DOE Office of Science user facility at the SLAC National Accelerator Laboratory supported by the DOE, Office of Science, Office of Basic Energy Sciences under contract DEAC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by DOE-BER and by the National Institutes of Health, National Institute of General Medical Sciences (NIGMS; P30GM133894).