Each of the farmers were interested in how the soils from different fields varied, the amount of plant material present in the soil, the spread of mycelium (a network of fungal hyphae), and the bulk composition of the soils. Using our in-house knowledge of geoscience, we were also able to interpret the soils in the greater geological context - understanding the rocks that the soils were derived from and how they impact the landscape around the farms.
Electron microscopy isn't usually employed by farmers, so this was a valuable opportunity for both them and for PEMC and we are very grateful for their enthusiasm in this project.
The first step of investigating the soils we were sent was to simply look at them. All the farmers we worked with are from the local area, so all the soils were quite similar and could be most easily be described as clays. Clay-rich soils are high in nutrients and can retain a lot of water as we learnt during preparation of the samples before putting them into our
JEOL IT510 LV SEM to image.
In this image, we can see individual tiny mineral crystals that make up the soil. These little flat minerals are collectively called "clay minerals" and can include minerals such as mica and chlorite. We also found small crystals of harder, more angular sandy minerals such as quartz and feldspar. The abundance of clay minerals in the soil determines how clayey it is.
Into the roots
As well as minerals, soils also contain organic matter. All the soils we investigated had an abundance of plant material as seen in this image. Because these soils were dried out prior to analysis, the structure of the roots and so on collapses as the water is removed which gives this easily identifiable wrinkled appearance.
In order to analyse plant material in its hydrated state, PEMC uses
Cryo-Scanning Electron Microscopy (Cryo-SEM). Cryo-SEM involves freezing the sample in a liquid nitrogen slush and requires some additional preparation of the instrument.
If you think cryo-SEM could be beneficial for your experiment, please discuss it with your contact at PEMC to organise the necessary logistics.
Another key feature of soils are the fungal networks called mycelium. Mycelium can be beneficial for soil health, and one farmer we worked with was interested in seeing how quickly these networks grow and re-establish after ploughing.
We were able to find an expansive network throughout the soil complete with spores as seen in this image. We were also able to find spores in the other soil samples, as well as smaller networks and fragments of hyphae - the branching structure of the fungus. In fact, the more we looked them more we found, and we were fascinated by the diversity of the fungal spores that we could see.
Signs of life
We didn't just find minerals, plants, and fungus; we also found a diverse range of invertebrates like this small worm (as well as some worm eggs) and this gave us a snap shot into the complicated ecosystem at play in these soils.
There are multiple applications of electron microscopy for biology, most notably
Transmission Electron Microscopy (TEM). This is a high magnification, high resolution technique that allows researchers to image cells and much more. A JEOL 1400 TEM is available at PEMC for students, researchers, and for commercial purposes.
Whilst we were able to identify minerals based on their appearance during the imaging stages of these investigations, it was also important for us to conduct compositional analysis. This meant that we had to homogenise the soils to get an average composition that would be less biased by large minerals.
We used an agate mortar and pestle to grind the soils into a fine powder that could be mounted and analysed using
Energy Dispersive Spectroscopy (EDS) to calculate a bulk composition. Having an agate mortal and pestle is key, as it's stronger than a porcelain or ceramic one and wouldn't cause any contamination as could happen if the softer minerals in a stone mortar and pestle (as you can buy for your kitchen) broke apart during grinding.
One of the farmers we worked with kindly supplied us with a sample of the bedrock from their farm. We carried out
compositional analysis, explored scientific literature, and delved into the geological maps of the local area to establish the history of the bedrock.
In this case, we were able to identify the bedrock as a Devonian mudstone and shale, some 420-320 million years old. This element map shows the distribution of different minerals in the sample, including quartz, muscovite mica, biotite mice, chlorite, and a rare earth element-bearing mineral that was likely weathered out from the nearby Dartmoor granites. This bedrock weathers into soil, so these minerals were also identified in the soil itself.
How to work with PEMC
PEMC gladly supports UK-based and international businesses looking to access electron microscopy at competitive rates, offering our full complement of
analytical techniques. Working with PEMC puts you in touch with an expert in electron microscopy and relevant experience in your field. Our team will develop creative solutions and ensure that you get the best data possible with a quick turnaround.