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

Two careers, one journey

A career in academia means choosing to be flexible. I have already written about the drawbacks and benefits of short-term research contracts and moving around a lot in terms of having a social life and maintaining friendships, but when it comes to maintaining your relationship, things can become a lot more complicated. Especially when both partners have a career, and are driven and ambitious about it.

Of course, it is fairly common for couples to move abroad for one partner’s career, if that partner has a high-earning job in business or industry. In general, it will be the husband that has the career, and the wife that follows, whether or not with children. If you think this is not the case anymore, you’d be surprised how many people responded with ‘normally, it’s the other way around’ when my partner and I announced that we were moving to England for my job (for the record: I am a woman).

However, maybe things are different in academia, and maybe the choice between the man’s or the woman’s career is more balanced. You might expect this to be true, because I like to believe that academics are rational, thoughtful, and generally quite liberal when it comes to equality issues. On the other side, there are fewer women in professorial positions than men, and this is largely because when women have children, they choose to work fewer hours whereas men generally don’t (note that I am not in any way judging this decision, but the facts are the facts – if you want to read more about this, have a look at the most recent special issue in Nature). At a younger age, men are more likely to be more advanced in their career because in couples, generally the man tends to be older than the woman. Because it makes sense to give priority to the most advanced, or well-earning, career, it is therefore likely that partners that both have a job in academia move for the man’s career. Continue reading

A very short history of creativity in science

Is science creative? I know that the process of scientific discoveries can be, or ought to be – is inherently? – creative. You can find some interesting opinions here, but it boils down to having to be resourceful and imaginative to design experiments for answering difficult, or big questions. I agree. However, I think that increasingly, the process of scientific discovery is constrained and pushed into a straight jacket, with implications for the creativity that is necessary to come to great scientific discoveries. Who still has time to wander through nature, observing and thinking? To have long discussions during coffee breaks, and philosophise about new ideas and approaches?

Yet this is what early scientists did. They studied the patterns they observed in nature, through spending time in nature. Think about Newton being sat under a tree when the apple fell on his head, or about Darwin and his voyage on the Beagle. Think about their books, that read like adventure novels. In the early days of the Royal Society, in the 1600’s, science and philosophy, or metaphysics, were inseparable, and doing science consisted for a large part of talking about it. Later, there were close ties between poets and scientists, and romanticism had a major impact on 19th century science. For example, the romantic poet Samuel Coleridge travelled to Germany and presumably influenced natural scientists such as Alexander Humboldt. Coleridge and his friend Wainwright got their inspiration while going on long and exhausting walks, often for weeks on end, and having opium-fuelled discussions through the night. Continue reading