To observe or to extract? Different methods for studying soil organisms

Interest in characterising soil communities is booming, fuelled by the growing recognition that soil biota govern processes of carbon (C) and nitrogen (N) cycling – processes that underpin the delivery of soil-based ecosystem services such as climate mitigation and sustainable food production. Soils capture carbon, which can exacerbate climate change when released to the atmosphere, and they provide nitrogen and other nutrients for growing crops and feeding livestock – when these nutrients are lost from soils, they can pollute ground and surface water and cause a loss of biodiversity. Because soil microbes decompose organic matter, thereby releasing N for plant growth, and respiring C, they determine the balance between the release and retention of C and N in soils.

In my work, I have a particular interest in the role of soil fungi and bacteria in these processes. Moreover, I want to find out how land use change and climate change affect the relative abundance of fungi and bacteria, and the chain of soil fauna that feed on them (the fungal and the bacterial energy channel, respectively), and how these changes in turn affect processes of C and N cycling. For example, some of my recent work shows that fungal-dominated microbial communities of extensively managed grassland retain N better and have lower N leaching losses, about which you can read more in this old blog post. Also, I have shown that fungal-based soil food webs and the processes of C and N cycling that they carry out are less affected by drought, which is expected to increase with climate change, than bacterial-based soil food webs.

An example of a soil food web, with the fungal decomposition pathway (dashed arrows) and the bacterial decomposition pathway (solid arrows). Both fungi and bacteria are consumed by a chain of soil fauna, that consists of protozoa, nematodes, collembola, and mites.

An example of a soil food web, with the fungal decomposition pathway (dashed arrows) and the bacterial decomposition pathway (solid arrows). Both fungi and bacteria are consumed by a chain of soil fauna, that consists of protozoa, nematodes, collembola, and mites.

To do this type of work, obviously, you have to measure the composition of soil microbial communities, or even of entire soil food webs. This is not an easy task, as most of these organisms are not, or barely, visible for the naked eye. For decades, direct microscopy was the only possibility to quantify and characterise the composition of soil microbial and soil faunal communities. For microbial communities, this involves transferring a soil suspension onto a microscopic slide, staining the fungi and bacteria, and then counting their hyphae or cells using a microscope. I used this method during my PhD and spent weeks, if not months, looking through a microscope. Although still frequently used, in recent years, direct microscopy has been increasingly replaced by the measurement of phospholipid fatty acids (PLFAs), a component of the cell membranes of fungi and bacteria. Because different microbes have different PLFAs in their cell membranes, the PLFA composition of a soil sample can be used as a ‘fingerprint’ of the soil microbial community. In other words, it doesn’t only tell you about the relative abundance of fungi and bacteria, but also about the composition of the bacterial community. Continue reading