Anaerobic digestate fertilization reshapes the rhizosphere bacterial communities of Lolium perenne L. at compositional and predicted functional potential levels

Abstract

The effects of anaerobic digestates on soil microbial communities have received increasing attention due to their potential impacts on soil health and antibiotic resistance. To date, no integrated analysis of rhizosphere bacterial community structure, antibiotic resistance genes (ARGs), and mobile genetic elements has been conducted in digestate-treated perennial ryegrass (Lolium perenne L.). We analyzed rhizosphere bacterial communities of this pasture using metabarcoding to study the effects of a manure-derived digestate on community structure and predicted functions. We also explored the association between digestate-enriched taxa and explanatory variables, including the abundance of two ARGs, class 1 integrons, and IncP-1ε plasmids. The greenhouse study included an unfertilized control and three fertilization treatments: digestate, inorganic fertilizer, and combined fertilizer (digestate + inorganic fertilizer). The results indicated a significant effect of the fertilizer type on bacterial communities and a stimulation of predicted functions related to genetic information processing by digestate and its combination. Digestate application resulted in the greatest differentiation in bacterial community structure relative to the unfertilized control and shifted communities toward amplicon sequence variants (ASVs) positively associated with class 1 integrons. Differential abundance analysis identified three ASVs and three genera (Arenimonas, Algoriphagus and Novosphingobium) that were significantly enriched under digestate treatment, relative to both urea and the unfertilized control. Our results demonstrate that anaerobic digestate application alters bacterial community structure and highlight the need for further studies to elucidate the potential adaptive role of class 1 integrons in rhizosphere microbiomes following digestate fertilization, including their contribution to antibiotic resistance.