Substrate-independent expression of key functional genes in Cycloclasticus pugetii 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. Cycloclasticus spp. are well-known polycyclic aromatic hydrocarbon (PAH) degraders that possess PAH-degradation marker genes including rhd3α, rhd2α, and pahE. However, it remains u...
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ftdoajarticles:oai:doaj.org/article:eb44927dc6eb4aa5848fab995c8edcf2 2023-07-23T04:18:00+02:00 Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation Anjela L. Vogel Katharine J. Thompson Daniel Straub Constantin B. App Tony Gutierrez Frank E. Löffler Sara Kleindienst 2023-06-01T00:00:00Z https://doi.org/10.3389/fmicb.2023.1185619 https://doaj.org/article/eb44927dc6eb4aa5848fab995c8edcf2 EN eng Frontiers Media S.A. https://www.frontiersin.org/articles/10.3389/fmicb.2023.1185619/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2023.1185619 https://doaj.org/article/eb44927dc6eb4aa5848fab995c8edcf2 Frontiers in Microbiology, Vol 14 (2023) PAH-degrading bacteria process-specific marker genes transcript-to-gene ratio biodegradation marine environment aromatic ring-hydroxylating dioxygenases Microbiology QR1-502 article 2023 ftdoajarticles https://doi.org/10.3389/fmicb.2023.1185619 2023-07-02T00:35:18Z 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. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Frontiers in Microbiology 14 |
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Directory of Open Access Journals: DOAJ Articles |
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English |
topic |
PAH-degrading bacteria process-specific marker genes transcript-to-gene ratio biodegradation marine environment aromatic ring-hydroxylating dioxygenases Microbiology QR1-502 |
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PAH-degrading bacteria process-specific marker genes transcript-to-gene ratio biodegradation marine environment aromatic ring-hydroxylating dioxygenases Microbiology QR1-502 Anjela L. Vogel Katharine J. Thompson Daniel Straub Constantin B. App Tony Gutierrez Frank E. Löffler Sara Kleindienst Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation |
topic_facet |
PAH-degrading bacteria process-specific marker genes transcript-to-gene ratio biodegradation marine environment aromatic ring-hydroxylating dioxygenases Microbiology QR1-502 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Anjela L. Vogel Katharine J. Thompson Daniel Straub Constantin B. App Tony Gutierrez Frank E. Löffler Sara Kleindienst |
author_facet |
Anjela L. Vogel Katharine J. Thompson Daniel Straub Constantin B. App Tony Gutierrez Frank E. Löffler Sara Kleindienst |
author_sort |
Anjela L. Vogel |
title |
Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation |
title_short |
Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation |
title_full |
Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation |
title_fullStr |
Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation |
title_full_unstemmed |
Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation |
title_sort |
substrate-independent expression of key functional genes in cycloclasticus pugetii strain ps-1 limits their use as markers for pah biodegradation |
publisher |
Frontiers Media S.A. |
publishDate |
2023 |
url |
https://doi.org/10.3389/fmicb.2023.1185619 https://doaj.org/article/eb44927dc6eb4aa5848fab995c8edcf2 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Frontiers in Microbiology, Vol 14 (2023) |
op_relation |
https://www.frontiersin.org/articles/10.3389/fmicb.2023.1185619/full https://doaj.org/toc/1664-302X 1664-302X doi:10.3389/fmicb.2023.1185619 https://doaj.org/article/eb44927dc6eb4aa5848fab995c8edcf2 |
op_doi |
https://doi.org/10.3389/fmicb.2023.1185619 |
container_title |
Frontiers in Microbiology |
container_volume |
14 |
_version_ |
1772180117452226560 |