Multi-omics insights into livestock waste fermentation reveal microbial-metabolite interaction driving soil fertility and plant growth performance

Panchagavya (PG), a livestock-derived organic formulation, has potential as a sustainable bio-input; however, the relationships among its microbial dynamics, enzymatic activities, metabolite composition, and effects on soil and plant performance remain insufficiently characterized. This study therefore investigated the biochemical and functional characteristics of PG using complementary metagenomic, metabolomic, enzymatic, soil, and plant analyses. The growth of microbial populations was significantly high. During fermentation, microbial populations peaked on day 17. Bacterial counts increased by 3150%, with actinomycetes, a key bacterial group associated with soil health, increasing by 1122.2%, while fungal counts increased by 1507.8%. This was the most active metabolically and the enzyme activities, acid phosphatase (185.76 ug g − 1 ), alkaline phosphatase (146.10 ug g − 1 ), and dehydrogenase (441.30 ug g − 1 ) were highly related to microbial abundance (r 2 = 0.98). Metagenomic analysis revealed that Bacillota was the dominant phylum and identified genes related to nutrient cycling and physiological adaptation. Metabolomic profiling (GC–MS) identified various metabolites, including phenolics and fatty acids, which are involved in rhizosphere activities and plant resistance to stress. Optimal fermentation of PG (day 17) at 4% (v/v) had a significant positive effect on the growth of black gram, nutrient uptake and antioxidant enzyme activities at 30 and 45 days. The soil analysis also revealed that PG at 4% had a significant negative effect on the pH (saline to neutral) and electrical conductivity. Organic carbon and accessible nitrogen, phosphorus, iron and zinc were also increased suggesting enhanced soil nutrient status and nutrient availability following the PG treatment. In general, controlled fermentation was related with a better microbial and metabolite profile, enhanced soil biochemical characteristics and plant performance, supporting the promise of PG as a sustainable bio-input that can minimize dependence on synthetic agrochemicals.