Dataset Information

Degradation of C30 - Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities

ABSTRACT: A significant part of the heavier petroleum fraction resulting from offshore oil-spills sinks to the deep-sea. Its fate and biodegradation by microbial communities is unclear. In particular, the physiological and metabolic features of hydrostatic pressure (HP) adapted oil-degraders have been neglected. In this study, hydrocarbon-free sediment from 1km below surface water (bsl) was incubated at 0.1, 10 and 20MPa (equivalent to surface waters, 1 and 2km bsl) using triacontane (C30) as sole carbon source for a 3-month enrichment period. HP strongly impacted biodegration, as it selected for microbial communities with small cells, high O2 respiration and nutrients requirements, but low biomass and C30-degradation yields. The alkane-degrading metaproteome linked to β-oxidation was detected but its expression was reduced under HP contrary to several housekeeping genes. This was reflected in the enriched communities, as atmospheric pressure was dominated by hydrocarbonoclastic bacteria while non-specialized or previously unrecognized oil-degrading genera were enriched under HP.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Escherichia Coli

SUBMITTER: Robert Heyer

LAB HEAD: DIrk Benndorf

PROVIDER: PXD004328 | Pride | 2018-12-19

REPOSITORIES: Pride

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Publications

Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities.

Scoma Alberto A Heyer Robert R Rifai Ridwan R Dandyk Christian C Marshall Ian I Kerckhof Frederiek-Maarten FM Marietou Angeliki A Boshker Henricus T S HTS Meysman Filip J R FJR Malmos Kirsten G KG Vosegaard Thomas T Vermeir Pieter P Banat Ibrahim M IM Benndorf Dirk D Boon Nico N

The ISME journal 20181212 4

Petroleum hydrocarbons reach the deep-sea following natural and anthropogenic factors. The process by which they enter deep-sea microbial food webs and impact the biogeochemical cycling of carbon and other elements is unclear. Hydrostatic pressure (HP) is a distinctive parameter of the deep sea, although rarely investigated. Whether HP alone affects the assembly and activity of oil-degrading communities remains to be resolved. Here we have demonstrated that hydrocarbon degradation in deep-sea mi ...[more]

PMID: 30542078

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Project description:Microarrays have become established tools for describing microbial systems, however the assessment of expression profiles for environmental microbial communities still presents unique challenges. Notably, the concentration of particular transcripts are likely very dilute relative to the pool of total RNA, and PCR-based amplification strategies are vulnerable to amplification biases and the appropriate primer selection. Thus, we apply a signal amplification approach, rather than template amplification, to analyze the expression of selected lignin-degrading enzymes in soil. Controls in the form of known amplicons and cDNA from Phanerochaete chrysosporium were included and mixed with the soil cDNA both before and after the signal amplification in order to assess the dynamic range of the microarray. We demonstrate that restored prairie soil expresses a diverse range of lignin-degrading enzymes following incubation with lignin substrate, while farmed agricultural soil does not. The mixed additions of control cDNA with soil cDNA indicate that the mixed biomass in the soil does interfere with low abundance transcript changes, nevertheless our microarray approach consistently reports the most robust signals. Keywords: comparative analysis, microbial ecology, soil microbial communities We used lignin degradation as a model process to demonstrate the use of an oligonucleotide microarray for directly detecting gene expression in soil communities using signal amplification instead of template amplification to avoid the introduction of PCR bias. In the current study, we analyzed mRNA isolated from two distinct soil microbial communities and demonstrate our ability to detect the expression of a small subset of lignin degrading genes following exposure to a lignitic substrate. We also included purified control amplicons and mixed target experiments with pure P. chrysosporium genomic cDNA to determine the level of interference from soil biomass on target hybridization.

Dataset Information

Degradation of C30 - Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities

Publications

Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities.

Similar Datasets

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