title: Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation.
abstract: Crude oil is one of the most important natural assets for humankind, yet it is a major environmental pollutant, notably in marine environments. One of the largest crude oil polluted areas in the word is the semi-enclosed Mediterranean Sea, in which the metabolic potential of indigenous microbial populations towards the large-scale chronic pollution is yet to be defined, particularly in anaerobic and micro-aerophilic sites. Here, we provide an insight into the microbial metabolism in sediments from three chronically polluted marine sites along the coastline of Italy: the Priolo oil terminal/refinery site (near Siracuse, Sicily), harbour of Messina (Sicily) and shipwreck of MT Haven (near Genoa). Using shotgun metaproteomics and community metabolomics approaches, the presence of 651 microbial proteins and 4776 metabolite mass features have been detected in these three environments, revealing a high metabolic heterogeneity between the investigated sites. The proteomes displayed the prevalence of anaerobic metabolisms that were not directly related with petroleum biodegradation, indicating that in the absence of oxygen, biodegradation is significantly suppressed. This suppression was also suggested by examining the metabolome patterns. The proteome analysis further highlighted the metabolic coupling between methylotrophs and sulphate reducers in oxygen-depleted petroleum-polluted sediments.
authors.affiliation: Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Bargiela
authors.affiliation: Department of Proteomics, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany.|Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
authors.forename: Florian-Alexander
authors.initials: FA
authors.lastname: Herbst
authors.affiliation: Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain.
authors.forename: Mónica
authors.initials: M
authors.lastname: Martínez-Martínez
authors.affiliation: Department of Proteomics, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany.|Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Seifert
authors.affiliation: Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Madrid, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Rojo
authors.affiliation: Institute for Coastal Marine Environment, CNR, Messina, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Cappello
authors.affiliation: Institute for Coastal Marine Environment, CNR, Messina, Italy.
authors.forename: María
authors.initials: M
authors.lastname: Genovese
authors.affiliation: Institute for Coastal Marine Environment, CNR, Messina, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Crisafi
authors.affiliation: Institute for Coastal Marine Environment, CNR, Messina, Italy.
authors.forename: Renata
authors.initials: R
authors.lastname: Denaro
authors.affiliation: School of Biological Sciences, Bangor University, Gwynedd, UK.
authors.forename: Tatyana N
authors.initials: TN
authors.lastname: Chernikova
authors.affiliation: Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Madrid, Spain.
authors.forename: Coral
authors.initials: C
authors.lastname: Barbas
authors.affiliation: Department of Proteomics, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany.|Department of Metabolomics, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: von Bergen
authors.affiliation: Institute for Coastal Marine Environment, CNR, Messina, Italy.
authors.forename: Michail M
authors.initials: MM
authors.lastname: Yakimov
authors.affiliation: Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Ferrer
authors.affiliation: School of Biological Sciences, Bangor University, Gwynedd, UK.
authors.forename: Peter N
authors.initials: PN
authors.lastname: Golyshin
mesh_terms: D001673:Biodegradation, Environmental; D019015:Geologic Sediments / Q000382:microbiology; D007558:Italy; D008522:Mediterranean Sea; D055432:Metabolomics; D010578:Petroleum / Q000633:toxicity; D059392:Petroleum Pollution; D040901:Proteomics; D014871:Water Microbiology
chemical_list: D010578:Petroleum
keywords: Anaerobic; Crude oil; Hydrocarbonoclastic; Mediterranean Sea; Metabolomics; Microbiology