We live in an era of rapid and continuous global change. Temperatures are rising, severe and extreme climate events are increasing in frequency, and pollution with toxic chemicals and plastics is affecting ecosystems worldwide, from the air to water and soil. Exacerbating this situation is the fact that the world’s population is increasing and, with it, so is the demand for more and better food production. Meeting this need relies on natural and agricultural systems, of which soils are a key component, that can sustain global demands while withstanding multiple anthropogenic and environmental stressors. Human activities have substantially degraded soil ecosystems, with lasting impacts on soil biodiversity, soil fertility, carbon sequestration capacity and, ultimately, food security and climate change mitigation1.
Soil harbours an incredible diversity of microorganisms — bacteria, archaea, fungi, viruses, protists and microalgae — which transform the physical and chemical properties of soils2 and regulate processes that are essential for ecosystem health and functioning, including nutrient cycling and carbon dynamics3. As fundamental as they are for soil ecosystems, microorganisms are highly vulnerable to global change. Warming can substantially reduce microbial diversity in soil4, multiple environmental stressors modify the functional and metabolic profile of soil microbiomes5,6, and global change factors can increase the abundance of potentially pathogenic microbial species6,7. Recognizing the growing threats facing soil ecosystems, Nature Reviews Microbiology highlights advances in our knowledge of how soil microbiomes are being transformed by anthropogenic pressures, and what the implications are for ecosystem functioning and services. This Focus issue brings together articles that examine how global change is affecting microbial communities in soil, and discuss challenges, knowledge gaps and opportunities to improve soil health in our rapidly changing world.
Agricultural intensification has been a major pressure on soil ecosystems. Although it has greatly facilitated increased food production, intensive agriculture is affecting soil resilience and biodiversity. In their Perspective, Banerjee, Dasgupta and van der Heijden explain the concept of microbial homogenization and discuss how agricultural intensification is causing the loss of rare and beneficial taxa, with wider implications for ecosystem functioning and food security. The conservation of belowground microorganisms is important, as emphasized by Chen and colleagues in their Comment, in which they identify key challenges to soil microbial conservation and call for the integration of soil microbiology into conservation policies.
Soil microorganisms are also increasingly exposed to a wide range of pollutants, such as heavy metals, pesticides and microplastics. In their Review, Zhu et al. examine through a One Health lens how pollution is affecting the soil microbiome, highlighting the consequences for environmental, animal and human health, and exploring microbiome-informed strategies for pollution mitigation and sustainable soil management.
When assessing the many effects of global change on soil microorganisms, analysis should extend beyond microbial communities as a whole and consider specific taxa, which may exhibit different responses. Soil fungi, for example, are very sensitive to physical, chemical and biological anthropogenic stressors, with implications for planetary health, as discussed in a Review by Rillig. Ecological relationships within the soil microbiome and between microorganisms and other organisms, such as plants, are also fundamental to understanding the effects of global change on soil communities, as highlighted by Honda in this issue’s Genome Watch.
As accumulating evidence illustrates the impact of global change on soil microbial communities, attention is increasingly turning towards restoration8. In their Review, Breed and colleagues examine how human activities are degrading soil and sediment microbiomes, as well as current restoration approaches, and they highlight the importance of integrating the microbiome into restoration science, practice and policy for more effective and resilient outcomes. In a Comment, Babalola and Oribhabor discuss the opportunities and barriers to implementing microbiome-informed approaches for sustainable soil management and restoration in low-income settings, where land degradation disproportionately affects food security and human well-being. The need for microbial restoration is also relevant in urban environments, where soils are particularly affected by human activity and yet are critical components of the urban infrastructure. In their Comment, Schulz and Schloter reflect on the pressing need to integrate microbial science and knowledge into urban design to develop climate-resilient cities. As efforts to harness microorganisms for soil restoration and management accelerate, an important question remains: how can microbial interventions be implemented safely and effectively within a complex ecological system such as soil? In their Comment, He and Falcao Salles examine the ecological consequences and unintended effects of introducing microorganisms into soils, advocating a deeper understanding of soil ecology.
Together, the articles in this Focus issue illustrate the urgency of safeguarding and restoring soil microbial communities, to enhance the resilience of soil ecosystems in response to global environmental pressures. Growing recognition of the importance of soil microorganisms has sparked the development of initiatives for the characterization and conservation of microbial diversity: The UK Crop Microbiome CryoBank, the Caatinga Microbiome Initiative9 in Brazil, and the China Soil Microbiome Initiative reflect efforts to advance our understanding of the microbial communities that are so important for soil ecosystems. Importantly, any progress on this front will help to advance United Nations Sustainable Development Goals (SDGs), including SDG 15 (Life on Land), SDG 13 (Climate Action), SDG 2 (Zero Hunger) and SDG 6 (Clean Water and Sanitation). However, further research efforts and concrete actions are urgently needed to improve soil health, protect soil microbial communities and ensure ecosystem services: from advancing our understanding of how different microbial groups respond to individual and multiple global change drivers, to integrating microbial biodiversity into conservation frameworks, incorporating microbiome science into soil restoration and urban planning strategies, and developing ecologically informed approaches for safe and effective use of microbial interventions. Close collaboration between researchers, local farmers, land managers, industry and policymakers from both high-income and middle- and low-income settings will be key to establishing effective and sustainable ways to protect the biodiversity of soil ecosystems.
