Lab in a tube: Monitoring soil chemistry without disturbing it

A team of researchers has developed a portable and automatic laboratory that can monitor soil chemistry in real time – and without expensive components. The aim is to give us easier access to follow the processes that usually take place hidden beneath our feet.

Imagine inserting a camera into the soil and continuously getting an overview of how oxygen moves between soil particles. Or how pH changes over a day as rainwater seeps through.
It sounds like a great idea, and a group of researchers at Aarhus University thinks so too. Together with German colleagues, they are now making it possible.

They have developed a portable and automatic mini-laboratory in tube form, called MARTINIS, which can measure specific chemical parameters in the soil in situ – that is, where they naturally occur – with minimal disturbance to the living microcosm that soil truly is.

“Soil is very complex – and as soon as we dig into it, we change it,” explains Associate Professor Klaus Koren from the Department of Biology at Aarhus University. “With MARTINIS, we can observe what happens over time, in high resolution, and without touching the samples.”

Klaus Koren is a co-author of the scientific paper on MARTINIS, published in Sensors and Actuators B: Chemical.

Sensor Film in the Soil

The system works using so-called planar optodes – thin sensors that light up or change colour when exposed to specific chemical substances such as oxygen, ammonia, or pH changes. This is a well-known technology that has long been used in laboratories.
But when analysing a soil sample in the lab, you only get data on what is present exactly where and when the sample was taken.

“We have scaled down the lab equipment to a cylinder 25 centimetres in diameter that can be buried in the soil, allowing continuous imaging of the surrounding soil environment,” explains PhD student Martin Reinhard Rasmussen, who has developed the system – and whose first name, incidentally, has nothing to do with the project name.

• How MARTINIS (Multi Analyte Real Time In-situ Imaging System) works:
• The optodes are mounted on the outside of a plexiglass tube, which is buried in the soil. Inside the tube sits an LED lamp that emits light at the wavelengths suited to the substances you want to detect, along with a camera that records the light emitted by the optode. The entire system is controlled by a Raspberry Pi computer, which automatically takes images and controls movement – the whole assembly can move up and down inside the tube and rotate 360 degrees.
• The advantage of planar optodes is that they do not just measure a single point but create two-dimensional images of the soil’s chemical conditions – which is crucial when describing complex soil processes. And because the camera can move and take images in sequences, it is possible to stitch together “panoramas” of entire soil profiles.

“It all runs automatically and costs only 5-600 euros to build yourself – and all parts and software are open source,” says Martin Reinhard Rasmussen.

In the first model, the system stores images on an SD card, but the goal is to equip it with a 5G card. A future vision is also to combine MARTINIS data with drone and satellite data.

MARTINIS is not yet fully developed as a commercial product. The researchers are currently seeking funding to further develop both the software and a more robust field-ready version.

The system has already been tested both in potting soil in the lab and in the field in Germany, where it measured oxygen dynamics in soil layers over several months without malfunctioning, even in rain and snow. It has also been trialled in the Rocky Mountains, where it tracked changes in soil chemistry after a forest fire.

From Compost to Consultancy

By monitoring pH and oxygen levels over time and across locations, it becomes easier to assess how soil chemistry changes – for example, after fertilisation or under different cultivation methods. A lot of oxygen, for instance, is needed to achieve effective composting.

The system clearly holds promise for agriculture, but it is unlikely that individual farmers will invest in it.
That is the view of Professor Klaus Butterbach-Bahl, a co-author of the study. He heads the Center for Landscape Research in Sustainable Agricultural Futures (Land-CRAFT) at Aarhus University – where Martin Reinhard Rasmussen is also affiliated.

“It will more likely be consultants and engineers who use the system and advise farmers based on the data they collect and analyse. And we will use it in our research at Land-CRAFT, where we can gain insight into redox reactions and changes in oxygen and pH levels,” he says.

At SEGES Innovation - an independent research and innovation company, which works for a sustainable and competitive agriculture and food production – Climate Specialist Franziska Petra Eller also sees great potential in the new invention:

“MARTINIS provides insight into an environment that is otherwise difficult to access: the soil. In situ use of planar optodes enables more realistic studies of the spatial and temporal dynamics of soil chemistry in agricultural fields. Applied research will undoubtedly benefit from this equipment, especially as it allows easy automatic collection of chemical soil data over longer periods with high temporal resolution.”

Monitoring Climate and the Environment

In addition to benefiting agriculture, measurements from MARTINIS could contribute to broader environmental and climate studies. When researchers monitor anoxic microenvironments – areas in the soil without oxygen – they gain insight into the processes that lead to the emission of the greenhouse gas nitrous oxide (N₂O), which plays a significant role in climate change. And pH data can help understand ammonia evaporation, which affects cloud formation in the atmosphere.

Facts:

• Klaus Koren is the supervisor of the paper’s lead author, Martin Reinhard Rasmussen.
• The Center for Landscape Research in Sustainable Agricultural Futures (Land-CRAFT) is a so-called Pioneer Centre, established and funded in collaboration between the Danish Minister for Higher Education and Science, the Danish National Research Foundation, the Carlsberg Foundation, the Lundbeck Foundation, the Novo Nordisk Foundation, the Villum Foundation, Aarhus University and the University of Copenhagen.
• The Land-CRAFT centre supports the green transition of agriculture by building the necessary fundamental and cross-disciplinary understanding of the processes that affect agricultural production and its environmental (e.g., nitrogen leaching), climate (greenhouse gas emissions), and biodiversity impacts. The centre particularly aims to understand how changes in agricultural practices affect nutrient and greenhouse gas flows across landscapes.
• Klaus Butterbach-Bahl’s work on mapping how agriculture impacts the climate through greenhouse gas emissions – and what can be done about it – earned him a Nobel Sustainability Award in 2024. The prize, established by descendants of Alfred Nobel’s brother Ludvig, has been awarded since 2022 to researchers who have made significant contributions to sustainable development.