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

• Published in: Frontiers in Microbiology
• Main Authors: Vogel, Anjela L., Thompson, Katharine J., Straub, Daniel, App, Constantin B., Gutierrez, Tony, Löffler, Frank E., Kleindienst, Sara
• Other Authors: German Research Foundation
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: Frontiers Media SA 2023
• Subjects: Microbiology (medical); Microbiology; Arctic
• Online Access: http://dx.doi.org/10.3389/fmicb.2023.1185619; https://www.frontiersin.org/articles/10.3389/fmicb.2023.1185619/full

Microbial degradation of petroleum hydrocarbons is a crucial process for the clean-up of oil-contaminated environments. Cycloclasticus spp. are well-known polycyclic aromatic hydrocarbon (PAH) degraders that possess PAH-degradation marker genes including rhd3α , rhd2α , and pahE . 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 Cycloclasticus pugetii 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 −2 , 1.80 × 10 −3 , and 3.20 × 10 −3 for rhd3α , rhd2α , and pahE , 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 in situ temperature conditions (i.e., 1.5°C), only detected Cycloclasticus spp. rhd2α genes and transcripts (mean TtG ratio of 4.15 × 10 −1 ). The other marker genes— rhd3α and pahE— were not detected, suggesting that not all Cycloclasticus 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.