Structure and succession of the microbiome during the millicomposting of agricultural and urban wastes

This study characterized the bacterial microbiome during the complete millicomposting process of agricultural and urban waste using high-throughput sequencing and bioinformatics tools, marking a pioneering global investigation. Microbial diversity peaked at 90 days, declined after 120 days, and stabilized by 150–180 days. Alpha and beta diversity, richness (Chao1), and Shannon indices were analyzed using Microbiome Analyst and visualized in R (Phyloseq and ggplot2 packages). Principal Coordinate Analysis (PCoA) used Jensen-Shannon distance, and differences between millicomposting stages were assessed with the Scott-Knott test (p < 0.05). Proteobacteria and Actinobacteria dominated (70%), with Alphaproteobacteria (order Rhizobiales) and Actinomycetales prevalent early and Acidimicrobiales increasing later. Other significant phyla included Bacteroidetes, Planctomycetes, Firmicutes, and Acidobacteria (~5%). Acidobacteria's abundance at 180 days correlated with millicompost maturity (C/N ratio = 15). Unclassified bacteria rose to 55% at the process's end, while Streptomyces and Bacillus were key genera (4% each). These findings provide unprecedented insights into microbial succession in millicomposting mediated by Trigoniulus corallinus , highlighting microbial roles in organic matter transformation and potential as bio-inputs for sustainable waste management. This work advances the understanding of microbiome contributions to sustainable agriculture and seedling production. • For the first time the bacterial microbiome of millicomposting was investigated. • The alpha diversity of the millicomposting was greater at 90 days. • The Proteobacteria and Actinobacteria phyla represent 70% of the microbiome. • Proteobacteria and Actinobacteria are related to the degradation of lignocellulose. • At the end of millicomposting there is an increase in Acidobacteria.