Engineering of Soil Microbiomes: From Conservation to Productivity

Soil contamination with hazardous inorganic and organic compounds, including emerging pollutants, poses a serious threat to ecosystem functioning and sustainable land use. Established remediation practices have primarily been focused on removing or stabilizing contaminants, often neglecting or ignoring the need to restore soil biological functions. However, soils are biologically active systems, and their capacity to support nutrient cycling, plant productivity, and ecosystem resilience is fundamentally determined by complex microbial communities. In this context, numerous studies have shown that remediation measures can remodel soil microbiomes, with implications for ecosystemic services and ecological processes. Consequently, there is growing interest in reducing the contribution of chemical-only outcomes to the restoration of functional soils through microbiome recovery and bioaugmentation with specialized beneficial microbes. Recent advances in microbial ecology and engineering in microbiomes now offer new perspectives to monitor, detect, and promote recovery of soil microbial communities toward resilient and functional states. The goal of this Research Topic is to improve soil remediation strategies, focusing not just on contaminant removal but on restoring soil health, functional resilience and ecosystemic services. Even after long-term remediation efforts, many soils remain ecologically affected by contamination, exhibiting disrupted microbial activities, impaired nutrient processing, and ultimately weakened ecosystem functioning. Latest progress in microbial ecology and ecological engineering now provide opportunities to understand and manage soil microbiomes, shaping their recovery to functional and resilient states. This Research Topic welcomes research articles that explore innovative strategies for restoring soil microbial diversity and function, including engineered microbial consortia, bioremediation approaches, and microbiome-informed management practices, including ecological interactions between and microbes and higher organisms, such as plants and soil invertebrates (e.g., earthworms, nematodes and insects). Studies that assess microbial community responses, functional restoration, and ecosystem-level impacts are particularly appreciated. By combining mechanistic viewpoints with applied methodologies, this collection aims to establish new benchmarks for successful soil remediation that prioritize both contaminant reduction and long-term rehabilitation of soil ecosystem processes. This Topic encourages submissions of research papers that contribute to the understanding of soil microbiome recovery as a key component of soil ecology after pollution events or under anthropogenic pressure. We support research that combines microbial ecology, soil science, biotechnology, bioengineering and remediation strategies to evaluate, monitoring and tracking, microbial communities and their associations for ecosystem reliability and functioning. Representative topics include: The effects of pollutants and remediation strategies on the structure and function of microbial communities; Innovative bioremediation and phytoremediation approaches; microbial community interactions and dominant species in polluted soils; Ecologically guided management practices for lasting soil health. Microbial communities as a relevant member of holobiomes of higher organisms, such as plants and invertebrates (e.g., earthworms, nematodes and insects) in polluted soils. Developing of novel or innovative molecular, physics and or chemical–based methodologies to evaluate the microbial communities and their functions and interactions in real-time and/or at field level. We welcome submissions of disciplinary or interdisciplinary original research, reviews, conceptual models and methodological studies that offer insights, empirical or field-based evidence. Contributions that combine ecological modelling, machine learning and neural network ecology-based approaches as well as contributions under a perspective at global level, such as One-Health, EcoHealth and/or Planetary Health, are also particularly appreciated. Topic editors: Emilia Neag, Zamfira Stupar, Marcos Pileggi, Milko Alberto Jorquera Source: https://www.frontiersin.org/research-topics/79812/engineering-of-soil-microbiomes-from-conservation-to-productivity