Anaerobic biodegradation of crude oil under sulphate-reducing conditions leads to only modest enrichment of recognized sulphate-reducing taxa

Crude oil degradation under sulphate-reducing conditions was investigated in microcosms, amended with North Sea crude oil and inoculated with estuarine sediment from the River Tyne, UK. Linear-alkanes (nC7-nC34) were degraded over a 686 day period in oil-amended microcosms, in contrast alkane degradation was minimal in microcosms which were inhibited with sodium molybdate. Libraries of PCR-amplified 16S rRNA genes were prepared from DNA extracted from oil-amended microcosms at day 176, when the systems were actively sulphate-reducing (17.7 ± 0.9 μmol L−1 SO42− day−1 g−1 wet sediment) and at day 302, by which point sulphate was depleted. Bacteria from the phyla Chloroflexi, Firmicutes, Proteobacteria (Delta-, Gamma- classes) were enriched in oil-degrading microcosms relative to control microcosms to which no oil was added. Sequences of 16S rRNA genes from conventional sulphate-reducing microorganisms (SRM) such as Desulfotomaculum, Desulfosporomusa, Desulfosporosinus, Desulfovibrio, Desulfobulbus, Desulfobacter and Desulfobacterium, which have previously been implicated in oil degradation in other hydrocarbon-impacted environments, were not dominant in clone libraries prepared from oil-amended microcosms that were actively reducing sulphate at day 176. Instead sequences from Gammaproteobacteria (∼34%), most closely related to Marinobacterium sp. and members of the family Peptostreptococcaceae within the Firmicutes (∼27%), were detected at highest frequency. By day 302, when sulphate was depleted and the majority of n-alkane degradation had already occurred, a shift in community composition was apparent in oil-amended microcosms with sequences from Chloroflexi (family Anaerolineaceae) being most frequently encountered (24%), together with Firmicutes (20%) and the more conventional SRM; Deltaproteobacteria (19%). These data suggest that other groups of organisms in addition to conventional sulphate-reducing microorganisms play a role in the anaerobic degradation of crude oil in some sulphate-containing environments. ► Oil degradation with sulphate leads to only modest enrichment of known sulphate-reducers. ► Alkane degradation in sulphate-reducing, oil-amended microcosms took c. 300 days. ► Bacteria related to Marinobacterium may have a role in anaerobic oil degradation. ► Bacteria related to Clostridiales (Peptostreptococcaceae) may play a role in anaerobic oil degradation. ► Bacteria related to Chloroflexi (Anaerolineaceae) may play a role in anaerobic oil