Conserving Earth’s microbial biodiversity before it’s too late

Microbes are central to life on Earth, but their biodiversity is threatened by anthropogenic activities. Can international efforts in conservation and restoration curb this incalculable loss?

Author: Vilhelmiina Haavisto. Vilhelmiina is a freelance science writer and PhD student at ETH Zürich in Switzerland, where she works with marine microbial communities.

You would be hard-pressed to find an ecosystem on Earth uninhabited by microbes. From cycling essential elements to helping us digest our food and producing important industrial compounds, the services that microscopic organisms provide to all of Earth’s inhabitants is staggering in its scale and complexity. Putting numbers on the world’s microbial diversity is difficult, as the very definition of a microbial “species” is fraught with disagreement in the scientific community. They are capable of an incredibly vast variety of lifestyles and can rapidly evolve to occupy new niches, making them a rich and diverse group of organisms.  

However, much like the biodiversity of larger organisms that we hear so much about, microbial biodiversity is also on the decline worldwide. The threats are familiar, and anthropogenic – climate change, urbanization, and changes in land use, among many others. The threats extend to virtually all microbial ecosystems — soils, animal-associated microbiomes, and even fermented foods, to name a few — and are leading to homogenization of the microbial biodiversity pool, the loss of what makes different locations around the world microbiologically special.

Gathering information about the microbial makeup of different regions and ecosystems has never been easier, as genetic sequencing technologies become increasingly widespread and cost-effective. For example, the Earth Microbiome Project crowd-sources environmental and human-associated samples to systematically catalogue the microbial life on our planet. Meanwhile, more local efforts such as the African Microbiome Institute at Stellenbosch University in South Africa aim to stimulate microbiome research in ecosystems and populations that are historically underrepresented in microbiome datasets. Together, such efforts contribute to a deeper understanding of the microbial diversity that surrounds us, and highlight what we risk losing.

A microbial vault for humanity

Luckily, conservation can happen in the literal sense for microbes, just as it does for animals and plants. Enter the Microbiota Vault Initiative. Inspired by the Svalbard Global Seed Vault, a collection of over 1 million plant seeds from around the world, the Initiative “aims at conserving the world’s human-beneficial microbes for future generations”, explains Prof. Pascale Vonaesch, one of the Initiative’s core members. “The aim is to safeguard microbes [from] around the world, especially from communities still living a traditional lifestyle and having an especially rich microbiome.” In contrast to existing projects such as the Global Microbiome Conservancy, who mainly store single-strain samples of microbes, the Microbiota Vault Initiative seeks to store entire complex communities from human, food, and environmental samples.

Image Credit: Prof. Pascale Vonaesch

The Initiative, currently in its launch phase, is composed of three core research groups across three Swiss institutions, and one at Rutgers University in the United States, each contributing their own expertise. For example, dedicated members of Vonaesch’s group at the University of Lausanne in Switzerland focus on the practical aspects of sample collection and storage, such as optimizing freezing protocols and working with collaborators in Laos and Ethiopia to collect some first samples. Outside of their work with the Initiative, the Vonaesch lab specializes in the role of the human microbiome in health, particularly in terms of undernutrition in low- and middle-income countries, as well as developing microbiota-targeted treatments. “There is a very nice complementarity to the Vault,” Vonaesch notes.

If not now, when?

Meanwhile, the research group of Prof. Nicholas Bokulich, based at ETH Zürich, provides bioinformatics expertise to manage all the Vault’s sample-associated data. “The goal is to find a sweet spot between comprehensive and feasible methodologies for sample cataloguing,” explains Dr Anton Lavrinienko, a postdoctoral researcher in the group. His job is to review and develop robust pipelines and metadata standards for the Initiative, which is critical for the organization and retrieval of information regarding the precious samples. As the samples are of complex microbial communities, associated data, such as metagenomic sequencing results, require careful curation to keep them organized and accessible.

During his PhD, Lavrinienko analysed how wildlife microbiomes change in disturbed habitats; the parallels between his prior work and the Initiative are clear. “The threats are the same,” he says. “Socioeconomic transitions lead to lifestyle changes, effectively changing microbial habitats and causing losses of biodiversity and ancestral microbiome states across the board.” His inspiration by the Initiative’s mission, as well as the sense of time running out, are palpable; “it’s really, really urgent…there won’t be an undisturbed human microbiota on Earth in 20 years anymore,” he adds. “If not now, then when?”

Vonaesch echoes this sentiment; “I think that microbiomes will drastically decrease in diversity in the future…in a time when we’re only starting to understand their importance for health,” she notes. Ultimately, the mission of the Initiative is to save the scientific potential in microbiome samples that current technologies cannot make use of, in the hopes that future technological developments can help us to harness their full potential. “Microbiota Vault is not a research project,” Lavrinienko stresses – “it’s about preservation.”

Restoration for conservation

In addition to creating a comprehensive collection of Earth’s microbial diversity, there are other actions we can take to conserve this rich resource. For example, microbes can be re-introduced to depleted areas to restore upended ecosystems and expand reservoirs of microbial life across the planet. Indeed, 2020-2029 marks the United Nations Decade of Ecosystem Restoration, which aims to promote the “protection and revival of ecosystems all around the world” – in which microbes play an indispensable part.

Indeed, a meta-analysis conducted by Averill, other members of the Crowther Lab and their collaborators showed that restoring depleted soils with their native microbiomes could accelerate plant growth by an average of 64%, though growth benefits exceeded 500% in some cases. The Crowther Lab has also run large field trials to show that soil restoration can accelerate forest growth, contributing to ‘natural’ climate solutions by capturing carbon dioxide. Besides soils, microbiome restoration has also shown promise in other ecosystems such as coral reefs, agricultural environments, and even the human gut.

“Restoration is a wonderful option for promoting biodiversity both above- and belowground,” says Crowther, “but it works best when people use local, natural and diverse soil communities, rather than simplified synthetic communities.” Indeed, regionality is also important to consider, as the results of microbiome restoration can vary considerably depending on their context. “We need to know which regions and ecosystems benefit most…to identify key priority regions,” he explains. 

Matters of scale

Even once one has considered regionality and the use of local soil mixes, the continued and widespread success of restoration techniques boils down to one critical factor: scalability. Although small experiments and field trials are relatively easy to conduct, the areas that need restoration can be incredibly vast. “Right now, much of soil microbiome restoration relies on soil transplants,” explains Averill. Transplants entail moving soil, along with its complex microbiota, from an intact ecosystem to a microbiota-depleted one in bulk. “While this can be really, really effective,” Averill adds, “it’s not clear that it will scale…we can’t dig up our intact ‘source’ ecosystems forever!” Finding ways to sustainably source local soils for restoration, or emulate their microbial composition, is at the forefront of research priorities.

Averill’s time in the Crowther Lab inspired him to found Funga, a start-up dedicated to improving forestry outcomes using soil microbes, with a particular focus on scalability. “While academia is incredible at challenging old paradigms and generating new ways to understand the world, it’s not designed to massively scale discoveries on the timelines needed to meaningfully address the biodiversity and climate crises,” he explains. “Funga is a chance…to realize climate and biodiversity action quickly, and at a meaningful scale.”

In February 2023, Funga secured $4 million in seed funding to further their goal of sequestering 3 billion tons of carbon dioxide by 2050, using the power of forest soil fungi. “Building experimentation into the process of scaling,” Averill notes, “allows us to test and iterate at a speed not possible in academic science.” However, the benefits of restoration are clear, and motivation is not lacking by any means. “Microbiome restoration can actually be used to accelerate forest growth, and has the potential to be a massively scalable natural climate solution,” Averill explains.

Restoring together

Both microbiome conservation and restoration efforts cannot proceed without collaboration, and are by no means at odds with one another – quite the opposite. “The more people bringing novel approaches to protecting microbial biodiversity, the better”, exalts Averill; “We need a global microbiome restoration movement!” Crowther also praises the “thousands of inspiring people around the world who have committed their lives to promoting biodiversity for the wellbeing of local communities,” who he has been fortunate to work alongside through his UN board position and other engagements. 

However, with collaboration on a global effort comes a pressing need for responsible work. “The restoration of nature can only work in the long term when it is done in a socially and ecologically responsible way,” notes Crowther. “When healthy biodiversity becomes the preferred option for local communities around the world, that is when it will propagate in the long term.” Long-standing management practices can be slow to change, but Crowther emphasizes that understanding how different ecological management strategies will play out in the environment will make these decisions easier for local communities.

One major step towards local-yet-global restoration is the launching of Restor, a science-based open data platform founded by Crowther to accelerate the global restoration movement. “[Restor] plays an essential role in building connections within the restoration movement,” Averill explains, “and making the best scientific information…easily available.” The platform facilitates knowledge transfer between the many actors involved in restoration, from research scientists to NGOs, governments, and practitioners on the ground, and currently has 1,000 participating organisations, with 130,000 sites sampled across 140 countries.

No progress without trust

The Microbiota Vault Initiative also centers responsible practices, particularly with regards to sample collection and ownership. Many of the samples already acquired come from low- or middle-income countries in the global South, where human populations and their microbiomes may still be relatively close to their ancestral states. However, these populations have also been marginalized and exploited by researchers in the global North throughout history. “[As] these samples come from vulnerable populations,” explains Vonaesch, “all samples are owned by the original collection and only stored in the Vault [on their behalf].”

Frameworks such as principles for ethical fieldwork and the Nagoya Protocol, as well as an open-access policy to the Vault’s content catalogue, are essential for the Initiative to build trust and ensure that the people to whom the samples belong are included and respected throughout the process. “The entire thing relies on trust,” emphasizes Lavrinienko, “but trust wouldn’t exist without getting local people involved.” Indeed, field partners are an essential part of the Initiative’s work, and efforts are ongoing to share knowledge and techniques. “[The Initiative] aims to disseminate the newest research and analysis techniques for microbiomes, especially to places where less microbiome research has been performed thus far,” Vonaesch explains. Vonaesch also praises the Initiative’s capacity building activities, such as the Global Microbiome Network symposia, that aim to promote microbial biodiversity conservation and build connections around the world.

The road ahead

Unlike conservation of large mammals and other so-called “charismatic” species, it may be harder to drum up enthusiasm about conserving microbial life; especially when microbes have a general, though skewed, reputation for causing disease. However, their conservation is critically important for life on Earth as we know it. “Microbes provide these services without knowledge of whether you’re a scientist or not, whether or not we understand the mechanisms by which they do so,” emphasizes Lavrinienko. “Everything is interconnected.”

The key challenges lie in funding, scalability, and cultivating trust with local communities to ensure that the diversity of collections and restoration approaches mirrors that of real microbial ecosystems. However, the passion driving those involved in microbiome conservation and restoration efforts, not to mention the urgency of the matter, are well-poised to help overcome these difficulties and ensure that microbial biodiversity, and everything it offers us, is here to stay.