Biochar can potentially reduce heavy metals (HMs) mobility and bioavailability during composting. However, siderophores secreted by functional microbes might lead to the re-mobilization of metals like Cu and Zn. Therefore, this study intended to explore the impacts of Mikania micrantha Kunth (MM) and MM-derived biochar (MMB) in the reduction of Cu and Zn bioavailability, and siderophore-related gene abundances during composting. Compared with MM and corn straw (CS) composts, a significant decline was noticed in the extractable and reducible Cu [(2.3 mg kg−1 + 12.1 mg kg−1), and (3.3 mg kg−1 + 14.6 mg kg−1)], and Zn [(103.1 mg kg−1 + 110.1 mg kg−1), and (109.6 mg kg−1 + 117.2 mg kg−1)] in MMB and corn straw biochar (CSB) composts, respectively. Besides, the lowest relative abundance of HMs-resistant bacteria particularly Corynebacterium (0.40%), Pseudomonas (0.46%), and Enterobacter (0.47%), was noted in MMB compost. Also, a significant increase in sesquiterpenoid and triterpenoid biosynthesis abundance (5.77%) accompanied by a reduction in the abundance of clusters related to siderophore transport, and siderophore transmembrane transporter activity was detected in MMB compost. Multivariate analysis labeled temperature, moisture content, total organic carbon, Corynebacterium, and Bacillus as the primary factors significantly correlated with the Cu and Zn bioavailability (− 0.90 ≤ r ≤ 0.90, P < 0.05). The structural equation model revealed that physicochemical parameters, microbial abundance, and siderophores exert a substantial influence on Cu and Zn bioavailability. Accordingly, MM and its derived biochar are recommended as an effective approach for accelerating Cu and Zn bioavailability reduction and managing the growth and distribution of invasive plants.Graphical
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