Substrates and pathways preference of two novel species of Rhodococcus for aromatic compounds degradation

The coexistence of multiple compounds in various environments reinforces the difficulty of bioremediation. To better understand the processes of degrading multiple compounds, two strains (designated NM-2^T and LJ-10^T) that can degrade multiple types of aromatic compounds were isolated from common field soil. Strains NM-2^T and LJ-10^T were identified as two novel species named Rhodococcus mengyinensis sp. nov. and Rhodococcus shunpengi sp. nov., respectively. Both strains degrade benzoic acid using the catechol pathway with ortho-cleavage, vanillic acid and p-hydroxybenzoate via the protocatechuate pathway with ortho-cleavage, and m-hydroxybenzoate and 2,5-dihydroxybenzoate via the gentisate pathway with meta-cleavage. Additionally, strain NM-2^T degrades naphthalene and o-hydroxybenzoate via catechol-mediated pathways, while strain LJ-10^T metabolizes biphenyl utilizing benzoate as an intermediate. They degrade polycyclic aromatic hydrocarbons (PAHs, mostly bicyclic) through initial meta-cleavage followed by ortho-cleavage. Both strains prefer monohydroxylated benzoates, degrading them at rates significantly higher than other compounds. The presence of monoaromatic phenolic acids accelerates their degradation of PAHs, increasing the rates of naphthalene and biphenyl degradation by twofold and threefold. This work systematically illuminates the preferences of compounds, ring-cleavage methods and key genes utilization.