Visualising soil aggregates: shedding light on soil structure
Jul 1, 2025
Experiments at I14 beamline reveals how organic matter binds soil
Have you ever wondered how the soil you walk on was formed? Soil is a mixture of organic matter, minerals, gases, water and organisms that support the life of plants and soil organisms. Soil is an essential resource for, among other things, food production, water filtration, nutrient cycling and carbon sequestration. Healthy soil is the cornerstone of sustainable agriculture and climate resilience, and its physical structure, especially the formation of aggregates, is key to its function. Soil aggregates are clusters of soil particles that bind together, influenced by biological, chemical, and physical processes. They affect water retention, aeration, root penetration, and microbial habitats. Understanding how these structures form is crucial for improving soil health and productivity, but their development at the microscale remains poorly understood.
In an article recently published in the journal Soil Biology and Biochemistry, researchers from Lund University used advanced imaging at Diamond Light Source to track organic matter within forming soil aggregates. By labelling plant litter with rare earth elements and tracing their distribution using synchrotron radiation-based nano X-ray Fluorescence (nano-XRF) at the beamline I14, they visualised how organic matter physically embeds into soil particles.
Understanding soil better through high-resolution visualisation
Before this study, researchers had observed that organic matter inputs, such as plant litter, can stimulate aggregate formation. However, the exact mechanisms, particularly the role of particulate organic matter (POM) and microbial activity in initiating and stabilising aggregates, were largely speculative. The field lacked detailed, spatially resolved analyses that could directly visualise how inputs become integrated into soil microstructures.
Historically, studies relied on bulk chemical analysis and low-resolution imaging to assess organic matter in soil. However, these methods lacked the spatial precision to identify where and how litter becomes part of the aggregate matrix. As a result, researchers couldn’t fully determine whether physical incorporation, microbial binding, or chemical interactions were the main drivers.
This research addressed that gap using nano-XRF imaging, allowing scientists to distinguish between particulate litter, mineral particles, and microbial hotspots in forming aggregates. The central scientific question was: what mechanisms underlie the physical integration of organic matter into soil structure, and how do different types of litter influence this process?
This insight is crucial for land management and soil carbon storage strategies. By pinpointing the types of organic inputs that most effectively promote aggregation, the research provides a pathway to improving soil function and resilience.
The role of Diamond synchrotron techniques in this study
- Overlay image of Sm (blue) and Nd (yellow) binary nXRF intensity maps of a small microaggregate; magenta colour indicates area where Sm and Nd overlap
The use of nano-XRF at Diamond’s I14 beamline enabled the team to track rare earth-labelled litter with high spatial resolution. This technique allowed for precise visualisation of micron-scale structures within soil aggregates, something traditional imaging could not achieve. The beamline’s capabilities in elemental mapping and chemical speciation were essential for distinguishing between organic particles and mineral matter.
The imaging revealed that soil aggregates often formed around organic matter particles, with straw being embedded into the larger ones (>250 μm) to a higher extent. A known fungal preference for straw suggests their contribution to the process via physical binding of particles within their hyphal networks. Surprisingly, while microbial activity is typically assumed to be a major driver, the study found that microbial community composition had overall limited influence over the short duration (seven weeks) of the incubation period of the experiments.
Building better soil: future implications and applications
This study opens up important avenues for applied and fundamental soil science. Understanding the physical role of plant litter in aggregate formation has immediate relevance for agriculture. For instance, incorporating litter inputs into soil could promote structure, reduce erosion, and enhance water retention, especially important in drought-prone areas. In carbon management, fostering soil aggregation may help lock organic carbon into stable forms, aiding climate mitigation efforts.
Future research may focus on longer-term dynamics, different types of litter, and interactions with climate variables like moisture and temperature. The methods developed here could also be applied to contaminated soils, helping scientists understand how pollutants bind to or move through structured soil.
To find out more about the I14 beamline please contact the Principal Beamline Scientist Majid Kazemian: majid.kazemian@diamond.ac.uk
Related Publication:
Pucetaite, M. et al. Visualization of soil aggregate structures provides insights into their formation mechanisms induced by litter inputs. Soil Biology and Biochemistry 2025
Image credits: this publication: 10.1016/j.soilbio.2024.109686 under CC BY 4.0 license
Diamond Light Source is the UK's national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire.
Diamond Light Source Ltd
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE
Copyright © Diamond Light Source. Diamond Light Source® and the Diamond logo are registered trademarks of Diamond Light Source Ltd
Registered in England and Wales at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom. Company number: 4375679. VAT number: 287 461 957. Economic Operators Registration and Identification (EORI) number: GB287461957003.