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. 

An extremely dry summer in Manchester

Right at the end of the extremely dry period we had this summer I decided to do a little experiment: I started taking a photo of the patch of grass in my street in Manchester, in the North West of England, every couple of days. I study the effects of drought on ecosystems (see my previous posts about the effects of drought belowground here and here) and I thought it would be nice to show how the grass in my street would bounce back after the rain had started.

Only… it didn’t. The rain did not come as intensely as I expected, and the grass did not bounce back as quickly as I expected. The first (top left) photo was taken on the 12^thof July, the last (bottom right) on the 20^thof August. And still you can see bare soil and brown patches! This patch of grass would look a lot lusher and greener during a normal Manchester summer.

The grass in my street in Manchester this summer. 

But, more importantly, while aboveground plant growth seems mostly recovered, the composition of the community has changed (which you can’t see in these photos), and as I’ve shown in my research, this might continue to affect belowground communities and the processes they perform.

Of course, this little patch of grass in Manchester is not that important for the functioning of our ecosystems. But it is a nice illustration of the impacts of an extremely dry summer on grassland and how long it takes for these fast-growing plants to regain their biomass!

Soil boring? My take on the image problem of soil science.

I am passionate about soil, especially about soil biodiversity and how soil organisms and plants interact and control C and N cycling. I have studied soils since I started my undergraduate in 1996, and I have witnessed a complete turnaround when it comes to interest in soil biodiversity and the functions it performs. When I started my PhD, no one was interested in soil organisms and how they regulate crucial ecosystem processes that also happen to be central to sustainable agriculture. Now, everyone is interested – from farmers, to policy makers, to fellow ecologists.

Well, I say everyone, but that is clearly not the case. Soil is still remarkably unsexy. I will illustrate this with a little anecdote.

Last Friday, I met the third year Zoology student who had been assigned to do a final year Science Media Education Project with me. As we walked up the stairs, I asked her what her background was, and she replied and said: “….. and you study soils, right?” in a slightly too upbeat manner. We went to my office, and after finding out that she’d like to interact with primary school children, I suggested organizing a book launch family activity or classroom activity linked to a children’s book about an earthworm that I provided scientific advice for. I explained to her what the book is about (it is about a little worm with low self-esteem, who goes on a journey and meets lots of impressive animals, but eventually finds out that worms are crucial for soil health and plant growth), that the authors are based in Manchester, and that it will come out in February. I saw her face light up as she got increasingly enthusiastic, and I said: “You probably thought, oh no, I have to do a project on soil” to which she replied that she had indeed been a bit worried. When she left, I felt happy that I had been able to excite her about the project, but sad that she had been worried about studying soil.

Sadly, I can’t really blame her.

I, too, often feel deeply bored when I read about soil.

Why is this?

Soil Carbon Storage: The Headache of Grazing

[This is a guest post by Thomas Ross, a 3rd year Biology student at The University of Manchester – he is currently doing a Science Media Project on the effects of grazing on soil C storage, which I am supervising. This blog post is part of his portfolio, and he has to reflect on its impact in his final submission. So don’t hesitate to leave your comment!]

The carbon stored in soil amounts to double that in the atmosphere and biomass combined and soil has the potential to sequester more. As atmospheric levels of carbon dioxide have been on the rise there has been an increase in global temperatures and climate change (here, the processes involved in soil carbon storage explained in more detail). The potential of the soil carbon reservoir to sequester this carbon from the atmosphere, and potentially ease the speed of climate change, can be influenced by our actions and the way in which we manage land. One such way is through the grazing of domestic livestock.

Grazing has the potential to modify ecosystems drastically and thus affect soil carbon storage. But how much is too much? Unfortunately, I cannot give you a definitive answer as the effects of grazing on soil carbon storage vary greatly. Some studies showing increases in soil carbon due to grazing, others decreases and some no changes at all. This causes a tricky problem when deciding how to manage livestock to ensure maximum soil carbon storage and withholding the interests of all stakeholders.

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.

Drought belowground

There is a heat wave in the UK, and at least in the north, where I live, not a single drop of rain has fallen for at least three weeks. I quite like it, especially since last year was basically one long, wet, windy autumn and I was craving for a real summer. But, with temperatures this high, and with this little rainfall, many plants are starting to look a bit poorly. Grass is turning brown, and forbs are hanging their heads. Especially in the north of England, where normally everything is lush and green around this time, this is an unusual sight.

I know this all too well, because I am running a drought experiment – our drought pots have been tortured to the max and we wouldn’t have needed the sturdy roofs, while we had to water our control pots.

Does this look dire? Then take a look at what’s happening belowground! Pots from my on-going drought experiment.

So, plants are having a hard time, and I can imagine farmers are becoming worried. Because summer droughts are expected to increase in the UK, and when crops are stressed to their limit, this will lead to yield reductions. Modern agricultural crops have evolved to be adapted to high-resource, low risk environments, and have very different properties than their wild ancestors (read this great paper by García-Palacios et al.) – properties that are not much good for resisting drought conditions.

However, if you think that carnage is going on aboveground, then take a look belowground.

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.

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.

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.