Metagenomic analysis reveals the linkages between bacteria and the functional enzymes responsible for potential ammonia and biogenic amine production in alfalfa silage.

Abstract

To clarify the molecular mechanisms underlying ammonia (NH3 ) and biogenic amines (BAEs) formation in alfalfa silage, whole metagenomic sequencing analysis was performed to identify the linkages between functional bacteria and their responsible enzymes in alfalfa silage prepared with and without sucrose addition. Genes encoding nitrite reductase (nirB) resulting in NH3 formation were the most abundant and were mostly assigned to Enterobacter cloacae and Klebsiella oxytoca. Putrescine-related genes, classified mainly to encode ornithine decarboxylase (odcA), were predominantly carried by Escherichia coli, Ent. cloacae and Citrobacter sp. Escherichia coli and Kl. oxytoca were the important species responsible for cadaverine and tyramine formation. Ent. cloacae, E. coli, and Kl. oxytoca dominated the bacterial community in naturally fermented alfalfa silage, whilst sucrose-treated silages greatly inhibited the growth of these species by promoting the dominance of Lactobacillus plantarum, thus decreasing the concentrations of NH3 , cadaverine, putrescine and tyramine. Enterobacteriaceae bacteria are mainly responsible for the NH3 , putrescine, cadaverine and tyramine formations in alfalfa silage. Whole metagenomic sequencing analysis served as a useful tool to identify the linkages between functional bacteria and associated enzymes responsible for NH3 and BAEs formation.