Extending conservation to include Earth's microbiome

Global assessments of biodiversity pay scant attention to the microbial world, and many conservation organizations are largely uninterested in extending their work to microbes. This, despite the fact that all animals and plants, including humans, evolved and now survive in a world dominated by microbes that is inextricably linked to their functioning and survival. Microbes make up much of the world's biodiversity and include bacteria, fungi, viruses, archaea, and protozoa. The microbial world is a focus of industry and of medicine, which has medicalized microbes, making them the province primarily of doctors, public health professionals, and drug companies. Conservation has been drawn into this medicalization of microbes through One Health, with its focus on human, wildlife, and domestic animal disease. The conservation community must expand its horizon to give greater attention to the rich, dynamic, and vital microbial world. Microbes are highly diverse, with estimations of upward of 1 trillion species (Locey & Lennon, 2016), the vast majority of which are still unrecognized. They are also ubiquitous. The atmosphere is rich with microbes and transports and deposits many of them throughout Earth's surface in unbelievable numbers: hundreds of millions of viruses and tens of millions of bacteria per square meter per day (Reche et al., 2018). In marine ecosystems, microbes, mostly bacteria, account for approximately 70% of marine biomass and are critical in marine nutrient cycling. Even tiny viruses have a global biomass of 0.2 gigatons of carbon, representing 10% of the biomass of all animals (Bar-On et al., 2018). Microbes comprise a significant percentage of Earth's species and regulate major biogeochemical and global nutrient cycles, greenhouse gas exchange, and disease dynamics. In soils, they are essential to plant growth, including major human food crops. They are critical to many aspects of food security, and they are sources of evolutionary innovation in many taxa through horizontal gene transfer (Averill et al., 2022). Microbes that live in intimate association with their hosts as microbiomes contribute to their hosts’ disease resistance and nutrition and influence their behavior, among many other functions. The limited attention microbes have gotten that is not human-disease related has focused primarily on human, domestic animal, and crop plant microbiomes. Conservation practice should strengthen its duty of care to the microbial world because of its intrinsic and instrumental values. Microbes have value in their own right, as part of microbial communities, and as part of coupled systems with other nonmicrobial species. They have instrumental values as providers of services or contributions to all 3 components of biodiversity: genes, species, and ecosystems. They are critical providers of services to humans through their roles in food production, physiology, climate, and nutrient cycling. But all is not well in the microbial world. It is facing the same set of threats as the rest of biodiversity, including extinction caused by land-use change, pollution, ocean warming and acidification, invasive species, and “co-extinction” driven by loss of host species (Cavicchioli et al., 2019). With their vital roles well documented, why are microbes so little considered in much of conservation? The answer lies in multiple places, including the tenacious boundaries between disciplines such as microbiology and soil science—where microbes are prime topics for study—and conservation, with its well-known bias toward larger organisms and expansive ecosystems. Additionally, the concept of species is difficult to define with microbes because of their ability to exchange genetic material and because so many occur in tightly organized communities, such as biofilms. As a result, the category of species, so beloved of conservationists, is more difficult to deploy and work with. Although recent advances are changing this, microbes are harder to count with traditional conservation methods (they cannot be observed via satellite), making them even further outside the comfort zone for traditional conservation. Finally, conservation efforts at all scales have not had sufficient resources to achieve their goals, so there is an understandable reluctance to add additional efforts focused on microbial diversity that do not come with dedicated funding, which has been very limited. There have been repeated attempts to get the conservation community to engage in microbial conservation (e.g., Cockell & Jones, 2009), but these calls have found limited traction. Exceptions include a growing interest in the relationship between microbiomes and conservation as a key component of species conservation (e.g., Redford et al., 2012) and the rich microbial diversity in soils (e.g., Krzywoszynska, 2019). What should conservation do to enable a renaissance in interest in microbes? First would be to recognize and embrace the importance of building out the discipline and practice of conservation to include microbes. A key step would be for the International Union for the Conservation of Nature to build interest and capacity in microbes in its membership and volunteer network as part of their species and ecosystem work. This could be kicked off through a primer or meeting that brings together experts from outside conservation and a key set of conservation change makers. Second would be to learn about, and build on, existing important work in arenas often not on conservation's radar, such as the Global Microbiome Network, Society for the Protection of Underground Networks, Earth Microbiome Project, Beneficial Microbes for Marine Organisms Network, and Mangrove Microbiome Initiative. Special sections or issues in journals of the Society for Conservation Biology (SCB) and development of interest groups within SCB would help in this regard. Part of this work could include development of modules on microbes to be included in courses taught on conservation biology. Third would be to develop research and monitoring and expand research focus beyond disease-causing microbes. Promising work, such as identification of global hotspots for soil nature conservation by Guerra et al. (2022), provides an important basis for expanding priority setting to include microbes. Fourth, pay specific attention to the role of microbes in ecosystem structure and function and hence in conservation outcomes. Consider microbes essential to restoration and rewilding of species and ecosystems. For example, habitat suitability measures should be extended to contain a specific microbial component. Fifth, explain the importance of and ways to maximize the role of microbes in current approaches, such as nature-based solutions and the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services’ Nature's Contributions to People, which would substantially increase the range of biodiversity that needs to be incorporated into frameworks detailing human reliance on nature—both as services and disservices. Sixth, extend conservation's work with partners on traditional ecological knowledge to include the knowledge and management of the microbial world. Finally, engage with the synthetic biology community in collaborative work on potential conservation applications of engineered microbes and the imperative to invest in microbial conservation. The just-negotiated Kunming–Montreal Global Biodiversity Framework provides a perfect place to begin this new facet of vital conservation work. We have been engaging in decades of conservation work with a profound lack of knowledge of the microbial world. Our conservation gaze has been directed at large, charismatic species and ecosystems for too long. A grand challenge for conservation will be to extend its duty of care to include the too often maligned or ignored microbial world. Microbes too are part of the biodiversity we are so dedicated to saving.

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