Genomic characterization of bacteria reveals their bioaugmentation and pre-treatment potential for improved hydrolysis and biomethanation of protein-rich substrates

The present study explored the genomic capacities of bacterial isolates Enterobacter cloacae AAK_M13, Bacillus subtilis AAK_M29, and Serratia marcescens EGD-HP20 for enhanced hydrolysis of proteinaceous wastes. Genome annotation showed conditionally expressed genes for degrading complex organic substrates thus indicating the metabolic versatility of the isolates which was also validated by plate assay. Of the different subsystems, 28, 24, and 54 annotation hits were associated with protein degradation in the three isolates respectively coding for peptidases of the di-, serine-, omega-, amino-, metalloendo-, and metallocarboxy-peptidase groups. Considering that high concentration of metals in the environment could interfere with the spatial structure of enzymes thereby inhibiting the microbial metabolism, the annotation of genes encoding metal resistance enzymes such as CopA (copper resistance), ArsC and ArsB (arsenic resistance), and yieF (chromium resistance) was significant. Validation of genomic capacities for extracellular proteolytic enzymes revealed the highest protease production between 100 and 200 U/mL min in case of strain EGD-HP20 that was also reflected from the highest soluble protein generation of 198–416 mg/mL during pre-treatment and hydrolysis of protein rich substrates (PRS). Batch studies on biomethanation led to highest methane yield from PRS hydrolysed in presence of strain EGD-HP20, such as soybean flour (270–275 mL/g VS added) followed by meat extract (266 mL/g VS added) and egg white (227 mL/g VS added) in comparison to the respective untreated/un-augmented PRS thus indicating the advantage of bioaugmentation/pre-treatment. The study suggests that deciphering the genes governing the protein degradation pathways and conversion of complex organics could enable the development of bioaugmentation strategies using bacterial strains for efficient biomenthanation.