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

Vogel, Anjela L.; Thompson, Katharine J.; Straub, Daniel; App, Constantin B.; Gutierrez, Tony; Löffler, Frank E.; Kleindienst, Sara

doi:10.3389/fmicb.2023.1185619

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

Journal Article · Thu Jun 29 00:00:00 EDT 2023 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2023.1185619· OSTI ID:2471383

Vogel, Anjela L. ^[1]; Thompson, Katharine J. ^[1]; Straub, Daniel ^[2]; App, Constantin B. ^[3]; Gutierrez, Tony ^[4]; Löffler, Frank E. ^[5]; Kleindienst, Sara ^[1]

Eberhard Karls University of Tübingen (Germany); Univ. of Stuttgart (Germany)
Eberhard Karls University of Tübingen (Germany); Controlling Microbes to Fight Infection, Tübingen (Germany)
Eberhard Karls University of Tübingen (Germany)
Heriot-Watt University, Edinburgh (United Kingdom)
Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE; German Research Foundation (DFG)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 2471383

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 14; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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

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