Substrate-independent expression of key functional genes in strain PS-1 limits their use as markers for PAH biodegradation.

Microbial degradation of petroleum hydrocarbons is a crucial process for the clean-up of oil-contaminated environments. spp. are well-known polycyclic aromatic hydrocarbon (PAH) degraders that possess PAH-degradation marker genes including , , and . However, it remains unknown if the expression of these genes can serve as an indicator for active PAH degradation. Here, we determined transcript-to-gene (TtG) ratios with (reverse transcription) qPCR in cultures of strain PS-1 grown with naphthalene, phenanthrene, a mixture of these PAHs, or alternate substrates (i.e., no PAHs). Mean TtG ratios of 1.99 × 10, 1.80 × 10, and 3.20 × 10 for , , and , respectively, were measured in the presence or absence of PAHs. The TtG values suggested that marker-gene expression is independent of PAH degradation. Measurement of TtG ratios in Arctic seawater microcosms amended with water-accommodated crude oil fractions, and incubated under temperature conditions (i.e., 1.5°C), only detected spp. genes and transcripts (mean TtG ratio of 4.15 × 10). The other marker genes- and were not detected, suggesting that not all spp. carry these genes and a broader yet-to-be-identified repertoire of PAH-degradation genes exists. The results indicate that the expression of PAH marker genes may not correlate with PAH-degradation activity, and transcription data should be interpreted cautiously.