Identification of protein-degraders in an anaerobic digester by protein stable isotope probing combined with metagenomics

Abstract

Abstract Background Presence of carbohydrates hampers protein degradation in anaerobic digesters. To understand this phenomenon, we used proteogenomics to identify the active protein-degraders in the presence of low and high carbohydrates concentrations. Active metabolic pathways of the identified protein-degraders were investigated using proteomics with 13C-protein substrates (protein stable isotope probing). Results Acinetobacter was identified as the main protein-degraders under both protein-fed and protein-glucose mixture-fed conditions. The incorporation of the 13C-labelled protein substrate was predominantly observed in outer membrane-bound proteins and porin proteins, which are associated with proteinases or the transportation of amino acids across the cell wall. The Acinetobacter metabolic model and the incubation conditions suggested that glucose and proteins were degraded through anaerobic respiration. Conclusions The unfavourable effect of the presence of carbohydrates on protein biodegradation was attributed to Acinetobacter’s preference for substrate. This work highlights that efficient degradation of protein and carbohydrate mixtures in anaerobic digesters requires a staged or time-phased approach and enrichment of active protein-degraders.