Physiological and transcriptomic insights into the cold adaptation mechanism of a novel heterotrophic nitrifying and aerobic denitrifying-like bacterium Pseudomonas indoloxydans YY-1

Development of low-temperature biological nitrogen removal processes is of scientific and engineering importance. Cold-adapted heterotrophic nitrifying and aerobic denitrifying (HNAD) bacteria have attracted increasing interest. However, the nitrogen metabolism and cold adaption mechanisms of HNAD bacteria remain unclear. In this article, a novel cold-adapted HNAD-capable bacterium, Pseudomonas indoloxydans YY-1, was isolated. Analyses of draft whole-genome features indicated that strain YY-1 was capable of complete dissimilatory nitrate reduction, ammonium assimilation, and cyanate decomposition. The gene cluster of napABCDE and gene norR, which encode for the periplasmic nitrate reductase and nitric oxide reductase transcription regulator, were identified in the YY-1 genome. Adenosine triphosphate levels increased fivefold, and polysaccharide content significantly rose in the extracellular polymeric substances of strain YY-1 when temperature decreased from 25 °C to 5 °C. Comparative transcriptional profiles of the strain grown at 25 °C and 10 °C revealed that the genes involved in tricarboxylic acid cycle, cytochrome reductase, transhydrogenase, and adenosine triphosphate synthesis were overexpressed, whereas the genes that encod for nicotinamide adenine dinucleotide dehydrogenase, cytochrome reductase, and the functional proteins of nitrate assimilation were downregulated. For ammonium assimilation of strain YY-1 at 10 °C, transcriptional data revealed the overexpression of glutamate dehydrogenase and glutamate synthase genes. This study highlights the potential nitrogen metabolic diversity of HNAD bacteria and expands the understanding of physiological and transcriptional strategies of cold adaption of those bacteria.