Organic amendments influence soil properties, soil microbial diversity, and winter barley traits in a five-year field trial with contaminated soils at a former wood preservation site

Abstract Background Soil contamination with metal(loid)s and organic pollutants creates environmental and health concerns, driving the need for sustainable remediation strategies. Organic amendments can mitigate contamination effects, enhancing soil quality, and potentially increasing biomass production; however, their long-term influence remains an open question. In a five-year field experiment at a former wood-preservation site, this study evaluates the effects of five organic amendments—fresh pig manure (PM), biodigested pig manure (PD), compost (C), compost pellets (Pt), and green waste compost (G)—on Cu-contaminated soils. Here, we evaluated their impacts on physico-chemical soil properties, metal bioavailability, microbial community structure, plant growth and soil fertility. Results All amendments led to an overall soil improvement, including enhanced physico-chemical properties, increased enzyme activities. The amendments promoted the concentration of soil 16S bacterial genes and improved the yield of winter barley cultivated in the plots. The most abundant phyla detected across soil samples were Actinobacteriota , Proteobacteria , and Firmicutes , with Bacillus , Streptomyces , and Bradyrhizobium among the dominant genera. Compost-based amendments at 5% w/w addition rate (C5 and Pt5) showed the most promising results, significantly increasing soil carbon, nitrogen, and phosphorus contents, while reducing bioavailability of Cd, Ni, Pb, and Zn compared with untreated control plots ( p < 0.01). A decrease in Cu availability was observed but it was not significant. The Pt5 soils exhibited the highest 16S rRNA gene copy number ( p < 0.01). Both compost and compost pellets amendments enriched microbial communities associated with soil quality and plant yield, leading to significant improvements in soil fertility and barley yield (+ 200% on average). Conclusion This integrative approach identified organic amendments, notably compost and pelleted compost, that effectively contribute to soil remediation from multiple perspectives: chemical properties (pH, organic content, nutrients), reduction of bioavailable soil Cd and Zn, enzyme activities, microbial abundance and diversity (16S rRNA), and winter barley yield. The study evidenced signature biomarkers characteristic of healthy soils ( Paenibacillus , Lysinibacillus , and Agromyces ) and polluted soils ( Candidatus Solibacter and Mycobacterium ). Our findings support the use of compost (raw and pelleted) as a balanced approach for phyto-managing metal-contaminated soils, reducing 1 M NH 4 NO 3 -extractable soil Cd and Zn while enhancing microbial activity and soil fertility. Graphical Abstract