Mycolicibacterium sp. strain PAM1, an alfalfa rhizosphere dweller, catabolizes PAHs and promotes partner-plant growth

•PAH-degrading Mycolicibacterium sp. PAM1 was isolated from the alfalfa rhizosphere.•Degradation rate for pyrene and fluoranthene was 2 mg day−1.•Degradation rate for anthracene, fluorene, and phenanthrene was 1–27 mg day−1.•The nidAB-encoded enzyme might be responsible for the initial PAH oxidation in PAM1.•IAA-producing Mycolicibacterium sp. PAM1 promoted alfalfa growth. This research was focused on the isolation and characterization of a PAH-catabolizing mycobacterial strain from the petroleum hydrocarbon-contaminated rhizosphere of alfalfa, as well as on revealing some points of interaction between the microorganism and the plant. Mycolicibacterium sp. PAM1, a pyrene degrader isolated from the niche of interest to us, can catabolize fluoranthene, anthracene, fluorene, and phenanthrene. On the basis of curves of PAM1 growth with different PAHs as the sole carbon sources and on the basis of PAH-degradation rates, we found that pollutant availability to the strain decreased in the sequence phenanthrene > fluorene > fluoranthene ∼ pyrene > anthracene. For each PAH, the catabolic products were identified. PAM1 was found to have the functional genes nidA and nidB. New data modeling the 2D and 3D structures, intrinsic structural disorder, and molecular dynamics of the nidA and nidB gene products were obtained. The identified genes and intermediates of pyrene degradation indicate that PAM1 has a PAH catabolic pathway that is peculiar to known mycobacterial pyrene degraders. PAM1 utilized some components of alfalfa root exudates as nutrients and promoted plant growth. The use of mycobacterial partners of alfalfa is attractive for enhancing the phytoremediation of PAH-contaminated soils.