The Plant-Microbe Alliance for Environmental Restoration: From Nature-Inspired Solutions to Engineered Ecological Recovery.

According to the United Nations, up to 40% of the world's terrestrial ecosystems are degraded and in need of ecological restoration. Here, we argue that ecosystem restoration requires not only the reintroduction of plant species but also the recovery of the biological interactions that sustain ecosystem functioning. Plants and their associated microbiomes form integrated functional units in which microorganisms contribute to nutrient cycling, stress tolerance, contaminant degradation and ecosystem resilience. These plant-microbe partnerships therefore represent a new opportunity for environmental biotechnology. Advances in microbiome engineering, multi-omics and artificial intelligence are enabling the identification, design and management of microbial communities with complementary functions adapted to specific restoration contexts. However, the complexity of environmental microbiomes, the technical limitations of multi-omics in contaminated environments and the gap between computational predictions and ecological performance highlight the need for experimental and field-scale validation. In this context, we propose Holobiont Engineering for Ecosystem Restoration (HEER) as a conceptual framework that treats plants and their microbiomes as functional units and makes ecological interactions explicit targets of restoration. This perspective positions microbial biotechnology at the interface between ecological restoration and environmental engineering, supporting a shift from species-focused approaches towards the recovery of ecosystem functions.

© 2026 The Author(s). Microbial Biotechnology published by John Wiley & Sons Ltd.