Genomic insights into heterotrophic nitrifying-aerobic denitrifying bacteria from petroleum terminal effluents

Heterotrophic nitrification-aerobic denitrification (HN/AD) is a single-organism process that converts ammonia into nitrogen gas under strictly aerobic conditions, playing a crucial role in biological ammonia removal from industrial wastewater. Despite several studies, significant knowledge gaps remain about the genes involved in the process. This study aimed to characterize the genomes of four HN/AD bacterial strains, <i>Pseudomonas stutzeri</i> UFV5, <i>Pseudomonas balearica</i> UFV3, <i>Rhodococcus ruber</i> UFV2, and <i>Gordonia amicalis</i> UFV4, and identify potential genes involved in the HN/AD process. Results revealed that shared genes of these strains were primarily involved in amino acid and protein biosynthesis. The two <i>Pseudomonas</i> strains had more genes linked to nitrogen metabolism than the others. Additionally, four strains showed a significant number of hypothetical proteins and genes related to oxidative stress. Notably, no common nitrogen metabolism genes were found among the strains, indicating a lack of a shared HN/AD pathway. However, comparing these genomes with previous transcriptomic data of the <i>P. stutzeri</i> UFV5 identified nine shared proteins as potential HN/AD pathway candidates. This study enhances our understanding of the genomes of these HN/AD-capable bacterial strains and identifies nine candidate genes as markers for the HN/AD process.