Plant-soil interactions: the cycle of life

Last spring, I gave a TED talk about plant-soil interactions and their importance in the global carbon cycle at a TEDx event organised by Amsterdam University College. You can watch the video below, but for those of you who rather read (actually, I am one of those people, as I never have the patience to watch a video from beginning to end!) you can also read the full text below.

Do you ever think about soils? Do you ever think about soils, other than, when your boots are muddy, or your vegetables dirty? Well, I’m going to talk about soils.

Soils! Without soils, we would not be here. Soils sustain all life on land. And that is because all energy flows through soils, via photosynthesis and respiration.

Have soils always been here?

No!

Have you ever thought about how soils are formed? Where plants came from? And the tiny invisible microbes that live in the soil?

More than 4.5 billion years ago, there was no soil. There wasn’t even life. There were only oceans. But somewhere between 4.5 and 3.5 billion years ago, the first microorganisms appeared in the oceans. There wasn’t even free oxygen at that time! But then, photosynthesis evolved in bacteria, and cyanobacteria started producing oxygen around 2.7 billion years ago. About 1.5 billion years ago, the first fungi appeared, and much later, around 500 million years ago, the first land plants arose. Probably, photosynthesis in these plants was derived from photosynthetic bacteria inside plant cells (the endosymbiosis theory). Those first land plants – like this little liverwort – had no, or very rudimentary roots (remember, there was no soil that they could grow their root in, only rock!), and were likely helped on land by symbiotic fungi. 

And this is where soil started to form. 

Why are Dutch farmers and builders angry and why have I started tweeting in Dutch? The Dutch nitrogen crisis.

You might have seen it in the news: Dutch farmers ravaging cities with their tractors. But this week also builders, contractors, dredgers, and gardeners have protested in The Hague, where our government is based. They are angry, because a lot of their activities and projects have been halted, and farmers in the vicinity of protected natural (Natura 2000) areas might have to move or be bought out.

Why? Because of the Programma Aanpak Stikstof (PAS), a programme designed to reduce nitrogen deposition in Natura 2000 (a European network of protected natural areas) areas while still allowing economic growth and development. Cleverly, this programme allowed nitrogen-emitting activities in the vicinity of these areas if there were planned compensating measures to reduce future emissions, as well as future measures to reduce the degradation of Natura 2000 areas. So, essentially, taking a mortgage on future compensating measures. But on the 29^thof May 2019, the Council of State judged that the PAS could no longer be used to allow nitrogen-emitting activities, because this is challenging European law.

So now, according to some people, The Netherlands is in lock-down. Building projects have been halted, and Dutch livestock numbers need to be reduced. Of course it is understandable that builders and farmers are upset; they are just trying to protect their livelihood.

What is the current weather doing to our soils?

There has been plenty of media coverage of the current extremely hot and dry weather. The drought is revealing archaeological features, (see also here), and we can even see the browning of our landscape from space. But this drought is not good news for our ecosystems at all, and one example of that are the recent wildfires in the Peak District. These fires are not just bad news for the plants and animals that live there, but also they make large amounts of carbon that have been sequestered over many years go up in the air as CO₂, and this can amplify climate change. Drought also affects our ecosystems more subtly than that, but the long-term consequences might be as severe.

We can all see the effect the drought is having on plants: lawns are turning yellow, corn leaves are rolling, and in extreme cases, trees even lose their leaves. They become inactive, and can even die. This is not just bad news for the plants, it is also bad news for the soil. When plants stop growing, they are not photosynthesing, and when they are not photosynthesising, they are not removing CO₂from the atmosphere. A large part of this photosynthesised CO₂ goes straight into the soil to fuel the activities of microbes, which carry out important functions such as the decomposition of plant litter and the release of nutrients for plant growth.

Blood, sweat, and tears: the story behind the paper

I have already hinted at it in a previous post, and I have been tweeting a lot about it during the past couple of days: our paper ‘Soil food web properties explain ecosystem services across European land use systems’ is now online on the PNAS website! The paper is about, well, soil food webs, and how important they are for ecosystem services. Of course, I already knew that, as did many others, and relationships between groups of soil organisms and ecosystem processes have been shown before. But in this paper, we show that there are strong and consistent relationships between soil food web properties and processes of carbon and nitrogen cycling on a European scale!

Anyway, this is all pretty exciting, but I don’t want to write about the actual content and message of the paper here. No. Because when you see a paper like this, nice and shiny and with a blue PNAS logo on the side, with slick figures, a list of references, online supplementary information, and a small box detailing the contribution of each author, oh, and not to forget the acknowledgements thanking the funder, the landowners, and the people who helped in the lab, you don’t think about all the blood, sweat, and tears that went into putting together such a paper. And blood, sweat, and tears went in it.

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.

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.

The diversity beneath our feet

Yesterday, Georgina Mace gave a seminar in the Faculty of Life Sciences at the University of Manchester. Of course, I was at the front row (well, almost), as I have only just started at Manchester and I was employed to reinforce ecology and environmental sciences in the Faculty. I have seen Georgina Mace speak before, and today she spoke about biodiversity, and specifically, the decline of it.

In her talk, she highlighted trends in the decline of plants, birds, mammals, reptiles, fish, and amphibians, mainly as a result of habitat destruction. She spoke about mechanisms of these organisms to cope with disturbances; some species just cope with changing circumstances, some move away to new habitats, and some (or, rather a lot, as evidenced by the graphs in her presentation) go extinct. At the end of her talk, she spoke about why biodiversity is important for humans. First of all, humans value biodiversity because of its intrinsic value – we simply want to know that there are elephants in Africa, or panda bears in China (although personally, I couldn’t care less about panda bears).  Second, we want to conserve species because we want to preserve the genetic library of life, and all the information about its evolution that is locked up in genes. And finally, we want to conserve biodiversity because it provides ecosystem services that are directly beneficial for humans, although the science underpinning this relationship is still thin on the ground.