Microbial conservation is essential for sustaining ecosystem functions and services

Microorganisms are fundamental to life on earth, playing crucial and irreplaceable roles in biogeochemical cycles, climate, ecosystem services, and human health. Their diversity and functionality are increasingly threatened by human activities. Yet, microbes remain largely excluded from nature conservation efforts.

A world without microorganisms would lack essential life-supporting processes. Yet, despite being threatened by global change, microbes remain largely excluded from conservation efforts. Crucial steps are needed to establish microbial conservation. Image credit: Shutterstock/luchschenF.

This challenge is gaining attention, and others have recommended to conserve microbes—most recently, with the establishment of a “Microbial Conservation Specialist Group” by the International Union for Conservation of Nature (IUCN). The IUCN suggests raising awareness of the need for microbial conservation within the global conservation community, given that they are exposed to the same threats as plants and animals. And the IUCN recommends extending conservation practice to microbes by highlighting their intrinsic and instrumental values for life on earth.

We support this call, as well as the adoption of microbial conservation as a coherent scientific discipline and a practical field of application. But we need to go further. Here, we propose a conceptual framework and a roadmap for microbial conservation that builds on and extends contemporary nature conservation efforts. Specifically, we outline how microbes can support traditional conservation goals and suggest adaptations to conserve microorganisms themselves.

Prioritizing Nature Protection

Nature conservation began with the protection of habitats—marked by the designation of Yellowstone as the world’s first national park in 1872—and soon expanded to include species protection (from 1929 onward), becoming embedded in international agreements, constitutions, and national laws from around 1948. These formal frameworks will need changes to effectively conserve microbes.

Only this integrated approach can protect entire ecosystems and all their interacting constituents—advancing nature conservation to the next level with positive impacts on ecosystem functions and services.

As a first step, we reviewed how microbial conservation could be achieved through four existing strategies: habitat protection; species protection; legal and policy frameworks; and public awareness, education, and citizen science. Here, we highlight how microbes already support existing conservation efforts. For instance, microbes help maintain the health of terrestrial and marine macrobiological species, as well as the functioning of habitats (1). We also propose necessary adaptations to account for the unique characteristics of microorganisms and discuss potential challenges (see also SI Appendix).

In doing so, we demonstrate that traditional conservation concepts—such as the IUCN approach—provide a useful framework for microbial conservation. But to be effective, they must be updated to include the unique characteristics of microbes and their habitats. This includes the limitations of the species concept when applied to many microbes, as well as the different spatial scales that must be considered when protecting plants and animals versus microbes. Microbial diversity and composition vary between micro-niches; this changes their characteristics, often on a micrometer to centimeter scale.

Only this integrated approach can protect entire ecosystems and all their interacting constituents—advancing nature conservation to the next level with positive impacts on ecosystem functions and services.

Habitat Protection

Ecosystem functions strongly depend on microbes (1); hence, considering microbial diversity and community composition will clearly support habitat protection. And conserving areas with a high diversity of progenitors of crop plant species will also protect host-associated microorganisms and could protect future food security (2). One strategy for microbial conservation is to designate habitats that harbor unique microbial taxa as protected such as salt lakes (3), hydrothermal vents (4), or polar and high-elevation regions (5).

Beyond such specific habitats, research efforts must focus on hotspots that harbor a particularly high microbial (taxonomic and functional) diversity or areas and structures that serve as reservoirs for bacteria that help to maintain ecosystems and hosts. It’s hard to determine whether current conservation efforts also protect and promote microbial diversity. That’s because plant and animal diversity are often uncorrelated or poorly correlated with microbial diversity (6).

Biodiversity hotspots are currently defined as areas containing a high level of species of selected plant and animal groups, particularly endemic and threatened species or both, which often do not overlap with hotspots of soil microorganism diversity and function. This leaves more than 70% of these areas unprotected. Future projections based on scenarios of global climate and ecosystem change suggest that the current microbial hotspots will strongly decline, mainly due to net area losses, with severe negative consequences for ecosystem services (7). The drivers of such microbiological diversity loss overlap with those related to the decline in macrobiological diversity. These drivers include habitat loss (8), as well as direct effects of global change factors such as pollution, drought, land-use changes, and climate warming (9, 10).

A recent study exposed soil samples to 10 different global change treatments (warming, drought, N-deposition, salinity, heavy metal, microplastics, antibiotics, fungicides, herbicides, and insecticides) individually and in combination to simulate multifactorial stress conditions. Responses of microbial communities to multifactorial stresses could not be predicted based only on their responses to individual stresses, both in direction and magnitude, and were characterized by more pathogens and antibiotic-resistance genes (10).

To better define global hotspots of microbial diversity, we need more research on the distribution of species, genes, and functions within and across ecosystems (11). However, our understanding of microbial biogeography at the strain level remains rudimentary, and microbial abiotic niches are poorly defined (12). On a smaller scale, the multiple micro-niches that exist on a single host (e.g., ref. 13) or within an ecosystem are often unexplored but would provide valuable information on overall microbial diversity.

For instance, every single plant individual provides multiple micro-niches for microbial colonization, and each plant species hosts a specific microbiome. The diversity of a single leaf microbiome can depend on the total microbiome diversity at a site, which is positively affected by the number of micro-niches available within the site (14). Thus, healthy soils and a high plant diversity increase the number of micro-niches in an ecosystem and serve as microbial reservoirs. It’s hard to assess if microbial diversity is declining or shifting in taxonomic and functional composition without a robust baseline (15).

The United Nations dedicated this decade to ecosystem restoration. But these projects often fail to recover microbial diversity, composition, and functionality, despite specific management practices such as soil amendments and inoculations (16). Likewise, microbial transplants or probiotic treatments often fail to have a positive impact (8). This is partly down to the stochasticity of microbial communities (17). The upshot: We need a mechanistic understanding of microbial community assembly that also accounts for functional consequences of different assembly trajectories.

Species Protection

Selected wild species are protected by law, making it illegal to kill, injure, capture, or damage these plants and animals. But the traditional biological species concept, e.g. based on reproductive isolation, doesn’t readily apply to microorganisms that primarily reproduce asexually. This may prevent the targeted protection of microbes, except for ex situ conservation of individual strains or whole microbial communities that would conserve their genetic diversity and their functions for future use. However, most microorganisms are notoriously hard to culture under standard laboratory conditions, as they have specific requirements on their environment or are “viable but nonculturable” (VBNC), also known as in deep dormancy.

Ex situ conservation of many microorganisms is thus hampered by these limitations, and research is needed to increase the taxonomic range of culturable microbes. Alternatively, the isolation and long-term storing of VBNCs—or even whole microbial communities—without cultivation may allow for successful reintroductions. For plants and animals, Red Lists serve as vital monitoring tools for population trends of species with categories ranging from being extinct to being of least concern. While fungi have been included into the IUCN Red List of Threatened Species (18), the consideration of other microorganisms such as bacteria remains challenging. Thus, the protection of microbial functions and whole communities generally should be the highest priority.

A minority of microbes is pathogenic or has negative impacts on the environment or human health (19). Nonetheless, microbial diversity bears the dangers of diseases, a risk that will increase due to global change (20). Furthermore, the spread of antibiotic-resistance genes constitutes a danger for environmental and human health and thus requires close monitoring (21). To avoid jeopardizing environmental and public health, microbial conservation must therefore be accompanied by comprehensive risk assessments.

The role that microbiomes play in the conservation of many animal species is largely unrecognized. For instance, captivity tilts the gut microbiome of cheetahs toward a higher abundance of pathogenic bacteria and disease-associated functional pathways, which is one reason for their high mortality and low rates of reproduction in zoos. Altered diets and increased contacts with dogs, cats, and humans also disrupt the cheetah gut microbiome (22). Thus, host-associated microbiomes must be considered in both the in situ and ex situ conservation macrobiological species.

Legal and Policy Frameworks

A starting point to introduce microbes into conservation agreements could be the Kunming-Montreal Global Biodiversity Framework (GBF; ref. 23). The GBF identified 23 global targets for consistent implementation in international conservation frameworks. Many of these targets, such as those addressing the biodiversity loss, restoration, reduction of pollution, or impacts of climate change, aim to maintain biodiversity and ecosystem functions and services—and thus also include microbes, although they are not specifically mentioned.

Such international agreed-upon frameworks need to be implemented into national targets (24). This requires a significant increase in financial resources for conservation in general, including payments for vital ecosystem functions and services, such as biogeochemical cycles or climate regulation (25), provided by microbiological diversity.

Public Awareness, Education, Citizen Science

Despite the importance of microbes, the general public is receptive to messages that they need to “kill 99.9% of all microbes” in many situations. In fact, allergies, asthma, and autoimmune disorders can be prevented by microbial exposure (26).

Successful microbial conservation needs greater awareness of these beneficial effects and a realistic assessment of potential risks. This can support action to preserve habitats such as diversity hotspots or specific reservoirs that host beneficial microbiomes (26). Researchers and teachers could emphasize the advantages of diverse microbiomes in school programs and citizen science projects (27).

Conservation biology is deeply rooted in the perception and experience of nature, yet microbes are mostly not included, with rare exceptions such as edible mushrooms and lichens (26). We can change that by training a new generation of nature educators that appreciate and teach microbial contributions. For example, an important perception of nature stems from the smell of soil after rain, called petrichor. This earthy aroma would not emerge without geosmin and other volatile organic compounds released by Actinobacteria (28).

More than 20 years ago, the British astrobiologist Charles Cockell said that “without lions there is life, but without microorganisms there can be no higher life forms” (29). He was astonished that microbes were not part of conservation efforts. Nothing has really changed since then; microbes are still largely ignored in conservation biology and policy, despite the increasing threat of global change. That must change. Nature conservation is not working unless it protects entire ecosystems with all their interacting members—big and small.

Supplementary Material

Appendix 01 (PDF)