Nanopore metagenomic characterization of swine and poultry anaerobic digestate effluents and their agronomic valorization as stimulants and soil amendments

Anaerobic digestion of swine and poultry manure generates nutrient-rich liquid effluent and sludge that can be valorized as agricultural resources rather than treated as waste. This study evaluated their agronomic potential and biosafety using long-read nanopore metagenomics, field-scale fertigation, and long-term co-composting within a circular bioeconomy framework. Shotgun metagenomic sequencing of stabilized liquid effluent revealed diverse functional microorganisms, including methane-oxidizing and nitrogen-fixing bacteria ( Alcaligenes faecalis and Azospirillum sp. TSH100), lignocellulose degraders ( Cellulosilyticum sp. WCF-2, Burkholderia spp., and Bacillus subtilis ), probiotic Lactobacillus and Bifidobacterium spp., and the phytosanitary bacteriophage Xanthomonas phage GF2, indicating potential agricultural functionality and microbial risk mitigation. The effluent contained 103.6 mg L −1 total nitrogen, 135.4 mg L −1 phosphorus, and 656.4 mg L −1 potassium. In a 120-day field trial, diluted effluent fertigation increased mean papaya fruit yield by 52%, from 17.41 to 26.47 kg tree −1 , increased sweetness from 6.23 to 7.12°Brix and enhanced vegetative growth, with the Holland cultivar showing the highest productivity. A 10-month co-composting trial identified 20 kg sludge:8 kg leaf litter as the optimal mixing ratio. Yang Na ( Dipterocarpus alatus ) leaves produced compost with the highest organic carbon (34.42%) and organic matter (57.35%), with a mature C/N ratio of 21.86, although potassium remained low (0.25–0.30%). These findings demonstrate that properly characterized digestates can substitute for synthetic fertilizers, improve fruit quality and generate composts that return organic matter to soils, while reducing pollution risks and closing nutrient loops in intensive livestock systems, supporting sustainable waste management in tropical agricultural regions worldwide practice.