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bioRxiv · 10.1101/2025.07.12.664532

Transcriptomic analyses unveil hydrocarbon degradation mechanisms in a novel polar Rhodococcus sp. strain R1B_2T from a high Arctic intertidal zone exposed to ultra-low sulfur fuel oil.

Freyria, N. J.·Lirette, A. O.·O'Connor, B. R. W.·Greer, C. W.·Whyte, L. G.
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Abstract

As Arctic shipping increases due to climate change, characterized by rising temperature and decreasing sea-ice coverage, the risk of oil spills through the Northwest Passage in this fragile ecosystem grows, necessitating effective bioremediation strategies. Research on bioremediation using Arctic coastal sediment bacteria has gained attention, particularly Rhodococcus species that play key roles in hydrocarbon degradation (HD) under extreme conditions. This study investigates the HD capabilities of a novel cryophilic Arctic Rhodococcus sp. strain R1B_2T isolated from Canadian high Arctic beach sediment in Resolute Bay, exposed to ultra-low sulfur fuel oil for three months at 5 {degrees}C. Comparative transcriptomics analyses revealed dynamic responses and metabolic plasticity, with upregulation of genes for aliphatic, aromatic, and polycyclic aromatic hydrocarbons, biosurfactant production (rhamnolipid), cold adaptation, and stress responses. The strain possesses several key alkane degradation genes (alkB, almA, CYP153, ladA), with co-expression network analysis highlighting synergistic mechanisms between alkB and CYP153 that target different chain-length alkanes (alkB: [~]C5-C20; CYP153: [~]C5-C12 and >C30) demonstrating complementary degradation strategies. The findings reveal adaptive mechanisms and degradation kinetics of native Arctic bacteria, highlighting the potential of Arctic cryophilic and halotolerant Rhodococcus species for oil spill remediation in polar marine environments. HIGHLIGHTS- Novel cryophilic Arctic Rhodococcus strain R1B_2T demonstrates robust hydrocarbon degradation capabilities at 4{degrees}C - Transcriptomic analysis reveals upregulation of key genes for aliphatic, aromatic, and PAH degradation pathways - Synergistic expression between alkB, almA and CYP153 genes enables efficient degradation of varied hydrocarbon chain lengths - Concurrent upregulation of biosurfactant production linked to hydrocarbon biodegradation, cold adaptation, and stress response mechanisms GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/664532v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@16fa663org.highwire.dtl.DTLVardef@114e2a2org.highwire.dtl.DTLVardef@2b244borg.highwire.dtl.DTLVardef@5bb803_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Freyria, N. J., Lirette, A. O., O'Connor, B. R. W., Greer, C. W., Whyte, L. G.. 2025-07-13. Transcriptomic analyses unveil hydrocarbon degradation mechanisms in a novel polar Rhodococcus sp. strain R1B_2T from a high Arctic intertidal zone exposed to ultra-low sulfur fuel oil.. https://doi.org/10.1101/2025.07.12.664532

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