Harnessing Microbiomes for Soil Carbon Sink Enhancement and Contaminant Mitigation in Agro‑Forest Ecosystems

Agroforestry is the integration of trees with crops and/or livestock within the same land-use system, including practices such as alley cropping, trees within crop fields, silvopasture, and homegardens. These systems can support carbon storage, food production, and ecological stability, yet intensive management and external inputs may contribute to soil carbon depletion and the accumulation of antibiotic resistance genes (ARGs), heavy metals (HMs), and persistent organic pollutants (POPs). ARGs may enter through livestock manure, wastewater irrigation, and antibiotic use, while HMs and POPs can derive from fertilizers, pesticides, irrigation water, atmospheric deposition, and other sources. Soil microbiomes influence carbon transformation, pollutant fate, and the decomposition of crop residues. Straw and other organic matter—including prunings, leaf litter, roots, and manure—may be retained on the soil surface or incorporated into soils, shaping carbon cycling and storage. Despite substantial progress, integrated knowledge linking these processes remains fragmented, calling for focused, up-to-date evidence across agroforestry systems.This Research Topic intends to address key bottlenecks restricting microbiome-driven soil functions in agroforestry systems, including limited mechanistic understanding of carbon sequestration, multi-pollutant mitigation, organic matter decomposition, and molecular regulatory pathways. We aim to collect multidisciplinary research to reveal how microbiomes and bioactive molecules reshape soil carbon cycling and contaminant fate. By integrating empirical experiments and macro-level bibliometric syntheses, we hope to bridge laboratory discoveries and practical field solutions. The ultimate goal is to provide theoretical foundations for improving soil carbon sink capacity and reducing pollution risks in agroforestry soils.We welcome Original Research, Review, Mini-Review, Meta-Analysis, and bibliometric studies. Contributed work should focus on microbiome-oriented soil carbon-sink improvement; mitigation of ARG, HM, and POP pollution; microbial degradation of crop straw and other organic inputs; regulatory effects of high-activity small-molecule carbon and bioactive molecules; and bibliometric analysis of these themes. Both field investigations and laboratory mechanistic research are encouraged. Descriptive studies without mechanistic insight are discouraged. Topic editors: Xuehao Zheng, Qing Luo, Belay Tafa Oba Source: https://www.frontiersin.org/research-topics/87025/harnessing-microbiomes-for-soil-carbon-sink-enhancement-and-contaminant-mitigation-in-agro-forest-ecosystems