Multi-omics highlights challenges in assessing the composition and performance of microbial consortia for commercial applications

The use of commercial microbial consortia in bioremediation is a promising method for addressing environmental pollution. These consortia are comprised of complex communities that include unculturable species that make it challenging to optimize consortia performance and carry out risk assessments for regulatory purposes. In this study, we provide a framework for using multi-omics to monitor the composition and performance of an aerobic ammonia oxidizing consortium in development for wastewater treatment. Long-read sequencing showed the consortium was dominated by an unclassified Nitrosospira species with the capacity for ammonia oxidation with many lower abundance taxa displaying the potential for denitrification. Considerable shifts in community composition and nitrogen cycling occurred when the consortium was grown along a redox gradient representative of wastewater for eight weeks. All aerobic and anaerobic cultures produced ammonia during the first four weeks and only aerobic cultures decreased ammonia concentrations after that time. Shotgun metagenomic sequencing showed the key ammonia oxidizing Nitrosospira sp. population decreased in abundance in aerobic cultures yet remained dominant in anaerobic cultures. Shotgun metatranscriptomic sequencing revealed that aerobic cultures decreased ammonia oxidation activity during the incubation and taxa that precluded detection in the starting material likely contributed to denitrification in anaerobic cultures. Metatranscriptomics showed that deamination of amino acids was an unexpected contributor to ammonia production that could negatively affect consortium performance. This study highlights how multi-omics provides insights that can be used to optimize performance and carry out risks assessments for consortia applied in different environmental settings.