Restoring the Forest Microbiome

Restoring the Forest Microbiome

Colin’s research focus is ecosystem ecology. He is especially interested and an expert in soil microbiomes and fungi!

By: Colin Averill, Postdoc and Ambizione Research Fellow at Crowther Lab

We are witnessing a global movement to protect what is left of nature, as well as restore as much as we can. When we work to restore natural ecosystems, we generally start with the plants. In tropical forest ecosystems, we are often logistically constrained to planting just a subset of the original tree species that were once present. The idea is that this initial planting will “jump-start” the natural process of forest succession, leading to the recruitment of even greater biodiversity than we put in at planting, and eventually develop into a thriving forest ecosystem. Yet, so many restoration efforts fail. The trees we plant often die in places they once thrived, outcompeted by new species that have invaded the site. However, perhaps only considering the vegetation is too limited a view of what an ecosystem is, and which parts of the ecosystem are missing.

When we think of forests, we generally focus on what we can see – the plants and animals inhabiting the aboveground. However, just below the earth live incredibly diverse and complex communities of bacteria and fungi. These microorganisms are essential to how plants interact with the soil environment, and are necessary to access critically limiting soil resources. Many soil fungi form belowground networks among trees, allowing trees to share resources and buffer one another in stressful environments. These microorganisms are the forest microbiome. Yet, many key forest microbial species are missing in the post-agricultural landscapes where most forest restoration happens. It begs the question, what would happen if while planting trees we also “planted” the forest microbiome, jumpstarting not just the plants, but also their associated bacteria and fungi?

Scenes from the field: preparing the soil for inoculation and the saplings for planting!

This is what our Ph.D. student, Felix Finkbeiner (also founder of Plant-for-the-Planet), is investigating with our team within the tropical dry forests of the Yucatán Peninsula of México. We’ve collected soil from intact forest remnants in the surrounding landscape, and use this soil as microbial inocula for soil microbiome restoration. The experimental setup is analogous to a randomized controlled drug trial. We’ve established 144 “blocks” of 100 trees across the landscape (14,400 trees!), and then randomly assigned the blocks to one of two treatment conditions. Half of the trees get a small scoop of forest inocula at the time of planting, while the other half gets a “placebo” dose of soil from the post-agricultural site we’re working to restore. Over the next several years we will be monitoring these trees to ask questions like:

  • Does soil microbiome inoculation increase the recovery of native forest microbial biodiversity?
  • Can microbiome inoculation increase tree growth, survival and carbon capture rates?
  • Will microbiome introduction increase the recruitment of other tree species into the plots, above and beyond what we planted?

We are excited to discover what happens. But, success or failure, we will learn more about how forest ecosystems assemble and gain a deeper knowledge of when restoration succeeds and fails. Beyond questions of the forest microbiome, this project is an example of how restoration and science can happen at the same time. By nesting experiments within larger restoration projects, we can learn more about how forests work on a fundamental level, while simultaneously learning how to do restoration better.

We’ve established a similar trial in Wales, UK in collaboration with The Carbon Community, a UK charity. We’re excited to replicate and expand this work across more restoration sites in diverse parts of the world. By doing so, we can generate truly general knowledge about how the global forest system works, and how best to restore and protect it.

Learn more about our soil microbiome research project in Yucatán, Mexico:

Covid-19 and the environment: causes and consequences

Covid-19 and the environment: causes and consequences

By Crowther Lab

In recent months, we’ve been asked many questions about Covid-19 and the environment. This Q&A is a brief review of what experts are saying – from science to policy. 

Several viruses exist in the coronavirus family. The respiratory disease called Covid-19 is caused by one of them: the SARS-CoV-2. Covid-19 is a zoonotic disease, meaning that the virus which is now spreading through human populations originated in another animal species. Coronaviruses are well-known to infect bats, and SARS-CoV-2 shows rather high similarity to viruses found in some bat populations, pointing to a likely bat origin (Latinne et al., 2020). What is still unclear is the chain of events that led to the transmission of SARS-CoV-2 to humans, and whether another species acted as an intermediate host. The first people to be infected seemed to have been in Wuhan, China. Many of them had had exposure to a market selling live animals, wild and farmed, but it is unknown whether the first human contamination did occur on the market (Huang et al., 2020).

While it will be difficult to ever fully pin-point the chain of events that led to the spillover of the Covid-19 disease to humans, scientists have long been warning about the risks of similar epidemics (e.g. Cheng et al., 2007). It is clear that environmental destruction, especially in the highly biodiverse tropics, is making the emergence of infectious diseases more likely (Morand et al., 2014). When humans disturb an ecosystem, it can modify the complex web of interactions between species, including interactions between pathogens and their hosts. Ecosystem degradation can also cause individuals of a species to migrate or forage closer to human settlements, carrying their pathogens with them. In this general context of disturbance, the more contact people or their farmed animals have with wildlife, the higher the chance of an eventual human contamination (Plowright et al., 2015). 

While images of animals reclaiming cities have been a joy to see, the benefits of reduced human activities will only be temporary and cannot be associated with lasting effects on biodiversity. Furthermore, wildlife could face an intensification of poaching, especially in the poorest countries. Lower surveillance of protected areas during the lockdown facilitates the operations of criminal organizations, although Covid-related travel restrictions also complicates international trafficking (Wildlife Justice Commission report, 2020). Additionally, the economic crisis could drive more people to small-scale poaching. Poaching can be a safety net for local populations during economic crises (Ballesteros & Rodríguez-Rodríguez, 2018), and poverty is a significant driver of illegal hunting and wildlife trade (Duffy et al., 2015). This is a good example to highlight how crucial the welfare of local communities is to any conservation goal.

Wildlife trade has been under scrutiny since the beginning of the Covid-19 outbreak, particularly around markets which deal in wild animal species. Early on, some international actors called for a general ban of wildlife markets. Others criticized this approach as simplistic and counter-productive. 

One of the arguments against a blanket ban is that it would likely drive the trade underground – an outcome made even more likely by the fact that large swaths of wildlife trade are already illegal, but nonetheless flourish in a multi-billion dollar criminal industry (‘t Sas-Rolfes et al., 2019). As researchers in ecology at the University of Oxford expressed in an opinion piece, “rushing to indiscriminately ban all wildlife trade in response to COVID-19 would not eradicate the risk of animal-to-human disease outbreaks. It could also have a severe impact on livelihoods and biodiversity.” Instead, they argue for “improved regulations that focus on health, [which] if implemented well, would avoid these effects while ensuring a low risk of future disease outbreaks.” 

Surely, stronger law enforcement against illegal trade and sanitary regulations of legal trade would be welcome improvements for biodiversity and human health.

As the world ground to a halt and over half of its population experienced a lockdown, pollution dropped. Globally, air quality went up, noise pollution went down and 2020 will see the biggest year-over-year greenhouse gas emissions drop ever recorded (between -5% and -10% compared to 2019, according to this Carbon Brief analysis). Some good news, among all the pain caused by the pandemic? Unfortunately, not really. This momentary drop in emissions has been purely incidental. It will be of little consequence in the long run if it is not followed by bold climate policies. In order to keep our planet’s warming within 1.5°C above pre-industrial temperatures, we need to decrease our emissions by nearly 8% per year, every year, starting now to reach carbon neutrality by 2050. Then, we must carry on by removing excess carbon that accumulated in the atmosphere (IPCC special report, 2018, UN Emissions Gap Report, 2019), a task for which the tools are yet far from ready (Fuss et al., 2018). However, we already know that among these tools, nature-based solutions like conservation and ecosystem restoration can play a key role while also benefitting biodiversity and human wellbeing (Griscom et al., 2017). Research from the Crowther lab has shown, for example, that there is significant potential to restore trees globally (Bastin et al., 2018).

Overall, the tremendous amount of work required to stabilize the climate may seem daunting. But in fact, the coronavirus crisis did deliver us one massive encouragement that this can be done. Why? Because this year, we saw substantial reductions in emissions, which were after all… a mere side-effect of temporary policies designed for a different goal entirely! This should make us confident that even larger reductions will be achieved, once ambitious and thoughtful public policies directly targeting emissions are finally put in place.

We are now at a turning point, where a lot will depend on the content of economic stimulus packages designed around the world to help economies recover. Will we choose the path to a sustainable future, or a return to a destructive business-as-usual?

In a guest article on IPBES (the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services),  four leading experts call for: “transformative change […]: fundamental, system-wide reorganization across technological, economic and social factors, including paradigms, goals and values, promoting social and environmental responsibilities across all sectors. As daunting and costly as this may sound – it pales in comparison to the price we are already paying.”

Some local governments are already taking bold, concrete steps. The city of Amsterdam for instance recently announced switching to a new economic model, called Doughnut Economics (Raworth, 2017), built explicitly around satisfying people’s needs within ecological boundaries. Meanwhile, experts in science, conservation and sustainability, including the Crowther Lab, have coalesced around strong principles to guide responsible action on nature-based solutions (Together With Nature). 

The tragedy of the COVID-19 pandemic and home confinement has heightened our collective awareness that our species, like any other, depends on the health of the ecosystems it lives in. Protecting our planet’s biodiversity and climate is ultimately protecting ourselves.

Get to know Tom ahead of his Inaugural Speech

Get to know Tom ahead of his Inaugural Speech

It’s one week until Tom’s Inaugural Speech on February 20, 2018! He will be talking about what makes the Crowther Lab unique, the work of the incredible scientists working together in the lab, and the impact we hope to have on combatting the issues around the climate.

While we want as many people as possible to come, it’s understandable that you may not want to if you have no idea who Tom is. So, here’s a brief blog through Tom’s background to get to know him a little better.

To kick things off

3 things you might not know about Tom:

  • He has played Andy Murray in tennis.
  • He had a stroke when he was 27.
  • He adopted a baby squirrel named Fran (scroll down for her photo).



Tom’s first year at Cardiff University was a bit of a blur. He wasn’t sure what he wanted to focus on academically, so football and socialising took precedence. In his final year, Tom was thrown out of one of his lectures for being too disruptive. After the lecture, he was given a dressing down by his professor Hefin Jones, who later went on to be his PhD advisor and now friend.

From Yale to ETH

After Tom’s PhD, he was accepted by the Yale School of Forestry and Environmental Studies in New Haven to carry out his post-doc. It was in Yale that Tom worked on what is still probably one of his most famous papers, ‘Mapping tree density at a global scale’ which was published in Nature.

After his time in Yale, Tom moved to Utrecht to continue his career in climate change ecology which finally led him to ETH, Zurich. Alongside University funding, Tom and the lab have also been granted 3 years of funding by the DOB Ecology. They have invested in the Crowther Lab to ensure it has the people and resources to carry out the research to better understand climate change and how to combat it.

If you are interested in coming, Tom will be presenting at 17:15 on the 19th February in the ETH Main Campus. We will be providing complimentary food and drink afterwards so if you come purely for the free fodder, we won’t judge you here. Those who find free dinners are most definitely winners.

We will be streaming the speech on Facebook, Twitter and Instagram so be sure to tune in.

Tom's adopted squirrel, Fran

Good News in a Bad Year

Good News in a Bad Year

Congrats! We’ve nearly made it to the end of a particularly challenging and exhausting year. For many, bad news – about a pandemic, political unrests, huge wildfires and as always, climate change – was even more part and parcel of their daily media consumption. But: not all is bleak. The Crowther Lab always tries to uncover and highlight hopeful and inspiring stories. So, here’s a list of recommended movies, podcasts and news articles that we’re featured in to end your year on a positive note. Some you might have already seen, but others may be worth a click now. 😉 Wishing you happy holidays and a pleasant end to 2020!

Documentaries and TV-Series

Can We Cool the Planet? – PBS Nova

We need thousands of solutions if we want to tackle climate change.

– Constantin Zohner, Can We Cool the Planet?

And guess what? These solutions do exist! Scientists all over the world are working hard to improve technologies and find new ways of drawing down or repurposing carbon from our atmosphere. PBS Nova’s Can We Cool the Planet? takes a look at the latest advances to mitigate climate change – from direct air capture to geoengineering, to carbon neutral fuel and nature based solutions (represented by Tom Crowther, Constantin and Johan from our lab). This documentary has super fascinating insights, a hopeful tone and great explainers. What it doesn’t have? A bleak perspective, that’s for sure!

The Age of Nature – PBS

Want to learn more about nature-based solutions? Look no further: Changing, the third episode of The Age of Nature is a great start into the topic. Equipped with gorgeous visuals, this documentary explores in which ways we can work with nature to bring back biodiversity and help mitigate climate change. From the forests of Bhutan to Tom Crowther in our lab, and from Borneo’s peatland forests to Belize’s coral reefs and Antarctica’s marine life: The Age of Nature highlights all nature does for us – and what we need to protect and restore it and its biodiversity.

Alien Worlds – Netflix

What could life look like on other planets? Netflix’ Alien Worlds explores just this question. A mix of sci-fi and documentary, the series takes a closer look at what we know about how life works on our planet – and how that knowledge might be applied to other worlds out there. Our favourite, of course, is episode 3, Eden. Among other things, Tom Crowther takes you on a walk in Scotland’s Rothiemurchus Forest to take a look at the soil beneath our feet to explain the fascinating role fungi and mycelial networks play in ecosystems. What’s that? Watch to find out!

Our lab's Tom Crowther in Netflix' Alien Worlds, looking for mycelial networks below ground!
Our lab’s Tom Crowther in Netflix’ Alien Worlds, looking for mycelial networks below ground!

News Articles

AI and machine learning constitute an enormous opportunity for scientists.

– Tom Crowther, Naratek Daily

As a global ecology lab, our main approach to better understand and address climate change is simple: look at data. Especially, big data. In an interview with Naratek Daily this spring, Tom talks about the importance of machine learning for our work at ETH Zurich and how we apply it to studying soils and forest ecosystems.

Our latest application of machine learning: building a new model, based on over 430’000 observations and our own experiments, to find out how climate change is affecting autumn onset and the leaf senescence of deciduous trees. As co-lead author Constantin Zohner explains in the Guardian and Inside Climate News autumn may, contrary to previous research, advance by 3-6 days by the end of the century. What does that mean? How is it connected to a self-regulating mechanism in trees? And what avenues does our study open for future research? Read the articles or check our summary on to find out!

Constantin Zohner, phenology expert at the Crowther Lab, checking up on an experiment. on the ETH Zürich terrace.
Constantin Zohner, phenology expert at the Crowther Lab, checking up on an experiment on an ETH Zurich terrace.

On the topic of trees: since the publication of our study on the global tree restoration potential in 2019, we have witnessed a growing interest in ecosystem restoration to help tackle the climate crisis. Indeed, conserving and restoring our ecosystems brings benefits beyond climate change mitigation. As Tom explains in the Financial Times agroforestry, for example, may result in improved agricultural yields. But of course, restoration has to be done right – that is in ecologically and socially responsible ways. And always in addition to cutting emissions, as we emphasise in this Rolling Stone article.

If tree planting is just used as an excuse to avoid cutting greenhouse-gas emissions, then it could be a real disaster.

– Tom Crowther, Rolling Stone

If you’re up for a longer read, we also recommend reading this article in The Washington Post. It covers the challenges of restoration but also shows why, despite them all, it is still an approach very much worth pursuing!

Restoring ecosystems also means restoring biodiversity. But what is biodiversity actually? How come there is so much of it in nature? If you ever wanted to learn more about biodiversity, this in-depth article in Quanta Magazine is one to check out – with great explainers from the Crowther Lab’s Dan Maynard and several other scientists on what biodiversity has to do with rock-paper-scissor games!

Collaboration, not competition, however, is the focus of this Science write-up all about the value of mycorrhizal networks of fungi for terrestrial ecosystems and how they’re affected by climate change. The article features several studies, including that of our lab’s Colin Averill, that showcase varying scenarios of how mycorrhizal associations may deprive trees of nutrients or support their drought resilience. All depends on a combination of factors involved – and on more research of what goes on below ground in the soil!


Episode 53: The Power of Nature – Outrage and Optimism Podcast

I’m fine if it’s really hard for us to achieve it. But if we are just going to give up before we even started, then that’s devastating.

– Tom Crowther, Outrage and Optimism Podcast

Prefer listening to podcasts instead of reading? No problem! Earlier this year, Tom Crowther talked with Christiana Figueres, Tom Rivett-Carnac and Paul Dickinson, hosts of the Outrage and Optimism podcast all about the power of nature-based solutions to tackle climate change. It’s a great episode that covers the value of scientific collaborations, the delicate balance of communicating science, the global restoration movement and how to positively cope with our fear of greenwashing. Give it a listen!

Episode 3: Why the world needs another trillion trees – House on Fire Podcast

Tree restoration has gained momentum as one of several ways to mitigate climate change. But restoring trees is not a simple one-time event: it takes time and care and goes beyond mere tree-planting. So how should we restore one trillion trees then? What kind of challenges may we run into? And how can we overcome them? Tom Crowther, Karen Holl, Pedro Brancalion and other ecology, forestry and restoration experts weigh in on an interesting conversation about the importance of biodiversity, the problem of deforestation, how to make use of natural regeneration and the need for local participation. A half hour well spent! Listen here to the House on Fire podcast.


The global restoration movement, machine learning, ecology and the power of collaboration: they all come together in Tom Crowther’s personal and inspiring talk at the launch event of TED Countdown! In an ode to the magic of biodiversity and networks, Tom elaborates on why we need to protect and restore our damaged ecosystems – not only to tackle climate change but also for the many other environmental, social and economic benefits ecosystems provide us with. One way to go forward in the future is with Restor, a new collaborative, open-data platform of ecological insights that we are excited to launch in 2021. Get a first glimpse of Restor in Tom’s speech.

One of our favourite talks this year: Tom Crowther at TED Countdown
One of our favourite talks this year: Tom Crowther at TED Countdown
What’s Mappenin’?

What’s Mappenin’?

Devin’s Geospatial Map

The Issue

Our predictions about climate change and how it is going to occur into the future are very uncertain. This is largely due to the fact that we don’t know how carbon storage on land is going to change, and so we don’t know how much carbon is going to be emitted into the atmosphere from the soil. One of the major drivers of change in soil carbon storage is nutrient enrichment, and as humans produce fertilisers and change the nutrient concentrations of the soils around the world, it is changing the ability of the soil to store carbon. But we don’t know the magnitude of this effect so we cannot predict how nutrient enrichment is going to change.


Data scientist Devin Routh and Prof. Thomas Crowther 

What the Crowther Lab are going to do?

We are doing a global study using the NUT NET data set. We are exploring how nitrogen, phosphorus and potassium are changing the amount of carbon stored in the soil all around the world. Devin is working to generate a global map of this effect so we can say where nutrient enrichment is increasing and decreasing carbon stocks. Once we have done that we will be able to add up all of the values from around the world to get a global understanding that can help us to understand how carbon stocks are going to change over the rest of the century. This will tell us a little bit more about how the climate is going to vary over the rest of this time.