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Not AvailableAccumulation of nitrogenous metabolites is considered as one of the limiting factors in the intensification of shrimp aquaculture worldwide. The present study reports the development and evaluation of microbial consortium containing ammonia oxidising bacteria (AOB), nitrite oxidising bacteria (NOB) and denitrifying bacteria (DNB) to mitigate total ammonia nitrogen (TAN) in commercial Penaeus vannamei shrimp farms. Oxidation rates of NH3-N and NO2 due to with AOB and NOB enrichment in the spiked media was 1.57 ppm day−1 and 1.46 ppm day−1 respectively under experimental conditions. The nitrite reduction rate due to Marinobacter spp. in the DNB consortia was 3–4.5 ppm h−1. The AOB and NOB consortia carried out ammonia oxidation and nitrite oxidation at salinities between 2 and 35‰ while DNBs were active above 15‰ salinity. DGGE analysis of the consortium showed the presence of eight AOB and 11 NOB and two DNB groups and metagenome analysis revealed the presence of more than 3000 OTUs at 97% similarity index. Eubacteria dominated the enrichment (>95%) while Proteobacteria were the predominant phylum. Nitrosomonas and Nitrosococcus (AOB) and Nitrospira (NOB) and ammonia oxidising archaea like Nitrosopumilus and Nitrososphaera were detected in addition to several unclassified species. Significant reduction in the levels of TAN (p < 0.05) was observed following application (at 5 L ha−1 week-1) of the microbial consortia (formulation) in four commercial P. vannamei shrimp farming sites having the salinity between 15 and 62‰. Results of the study suggests that the AOB, NOB and DNB formulation developed microbial formulation developed in the study could efficiently mitigate the toxic ammonia species in commercial P. vannamei shrimp culture farms.Not AvailableICA