Molecular basis of 1-nitronaphthalene and 2-nitronaphthalene biodegradation by Burkholderia pseudomultivorans M3 and its bioremediation potential.

Nitro-polycyclic aromatic hydrocarbons (nitro-PAHs) are toxic and persistent environmental contaminants of increasing concern because of their widespread occurrence and ecological risks. Nitronaphthalene, a representative nitro-PAH, occurs as positional isomers, yet microbial degradation studies have mainly focused on 1-nitronaphthalene (1-NN), leaving the basis for biodegradation of 2-nitronaphthalene (2-NN) largely unresolved. In this study, Burkholderia pseudomultivorans M3 was isolated from river sediment in Anhui Province, China, and was found to efficiently degrade both 1-NN and 2-NN, indicating an expanded degradation range for nitronaphthalene isomers. Genome analysis identified a novel nitronaphthalene degradation gene cluster (nnd) that is phylogenetically related to reported nin- and nag-type gene clusters but differs functionally from both. Gene knockout and complementation experiments demonstrated that nndAc, encoding the catalytic α-subunit of a Rieske-type dioxygenase, is essential for degradation of both isomers. Heterologous expression and metabolite identification further showed that the NndAB system transforms 1-NN and 2-NN into 1,2-dihydroxynaphthalene via the corresponding nitro-dihydrodiol intermediates, with concomitant nitrite release. Site-directed mutagenesis revealed that the ability of NndAc depends on the coordinated effects of multiple active-site residues, with F200 being particularly important for 2-NN transformation. Moreover, strain M3 maintained substantial removal efficiency in synthetic wastewater containing mixed nitro-, carboxyl-, and hydroxyl-substituted naphthalene compounds, supporting its applicability in complex contaminated matrices. These findings reveal the molecular basis underlying the broadened substrate range of nitronaphthalene degradation and highlight the potential of strain M3 for remediation of wastewater containing mixed substituted naphthalene pollutants.