Metagenomic approach unravelling bacterial diversity in combined composting and vermicomposting technology of agricultural wastes

Agricultural wastes and their valorization are at the heart of the EU policies related to the circular bioeconomy. Conversion of those wastes to products could be made through composting followed by vermicomposting. As the effectiveness mostly depends on the microorganisms involved, we aimed to identify the prokaryotic microbiome associated with four composting phases and one vermicomposting phase of wheat straw and cow manure composting. We used 16S rDNA PCR amplicon evaluation with the Illumina metagenomic technique generating a total of 653,057 sequences reads from the samples. Temperature had major role in the composting bacteriome changes influencing positively species abundance, Shannon and Simpson indices, and negatively Ace and Chao1. A reduction of C:N ratio from 25.94 to 14.24 and of pH and EC from 8.63 to 7.8 and from 2.26 mS.cm-1 to 1.7 mS.cm-1, respectively, were observed. Phylum Firmicutes (62%) and Actinobacteria (14%) prevailed in the source material (SM), while Proteobacteria (51%) and Bacteroidetes (8%) dominated in the first mesophilic phase (MP). Similarly to the SM, the thermophilic prokaryotes (TP) were represented by Firmicutes (54%) and Actinobacteria (9%), but also by Proteobacteria (6%). Principal coordinates analysis (PCoA) showed a significant weight of the total variation of bacterial taxa (PC1-68.16% and PC2-23.46%. Thus PCoA grouped together SM and TP, by one site, and both mesophilic phases and the vermicompost (COMP).