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dc.contributor.authorBargiela, Rafael
dc.contributor.authorGertler, Christoph
dc.contributor.authorMagagnini, Mirko
dc.contributor.authorMapelli, Francesca
dc.contributor.authorChen, Jianwei
dc.contributor.authorDaffonchio, Daniele
dc.contributor.authorGolyshin, Peter N.
dc.contributor.authorFerrer, Manuel
dc.date.accessioned2015-12-28T14:31:06Z
dc.date.available2015-12-28T14:31:06Z
dc.date.issued2015-11-24
dc.identifier.citationDegradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data 2015, 6 Frontiers in Microbiology
dc.identifier.issn1664-302X
dc.identifier.pmid26635742
dc.identifier.doi10.3389/fmicb.2015.01270
dc.identifier.urihttp://hdl.handle.net/10754/592618
dc.description.abstractBiostimulation with different nitrogen sources is often regarded as a strategy of choice in combating oil spills in marine environments. Such environments are typically depleted in nitrogen, therefore limiting the balanced microbial utilization of carbon-rich petroleum constituents. It is fundamental, yet only scarcely accounted for, to analyze the catabolic consequences of application of biostimulants. Here, we examined such alterations in enrichment microcosms using sediments from chronically crude oil-contaminated marine sediment at Ancona harbor (Italy) amended with natural fertilizer, uric acid (UA), or ammonium (AMM). We applied the web-based AromaDeg resource using as query Illumina HiSeq meta-sequences (UA: 27,893 open reading frames; AMM: 32,180) to identify potential catabolic differences. A total of 45 (for UA) and 65 (AMM) gene sequences encoding key catabolic enzymes matched AromaDeg, and their participation in aromatic degradation reactions could be unambiguously suggested. Genomic signatures for the degradation of aromatics such as 2-chlorobenzoate, indole-3-acetate, biphenyl, gentisate, quinoline and phenanthrene were common for both microcosms. However, those for the degradation of orcinol, ibuprofen, phenylpropionate, homoprotocatechuate and benzene (in UA) and 4-aminobenzene-sulfonate, p-cumate, dibenzofuran and phthalate (in AMM), were selectively enriched. Experimental validation was conducted and good agreement with predictions was observed. This suggests certain discrepancies in action of these biostimulants on the genomic content of the initial microbial community for the catabolism of petroleum constituents or aromatics pollutants. In both cases, the emerging microbial communities were phylogenetically highly similar and were composed by very same proteobacterial families. However, examination of taxonomic assignments further revealed different catabolic pathway organization at the organismal level, which should be considered for designing oil spill mitigation strategies in the sea.
dc.language.isoen
dc.publisherFrontiers Media SA
dc.relation.urlhttp://journal.frontiersin.org/Article/10.3389/fmicb.2015.01270/abstract
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
dc.subjectammonium
dc.subjectbiostimulation
dc.subjectcrude oil degradation
dc.subjectenrichment
dc.subjectMediterranean Sea
dc.subjectmetagenomics
dc.subjectmicrocosm
dc.subjecturic acid
dc.titleDegradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.identifier.journalFrontiers in Microbiology
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionSystems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spain
dc.contributor.institutionSchool of Biological Sciences, Bangor University, Bangor, UK
dc.contributor.institutionEcoTechSystems Ltd., Ancona, Italy
dc.contributor.institutionDepartment of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
dc.contributor.institutionBeijing Genomics Institute, Shenzhen, China
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personDaffonchio, Daniele
refterms.dateFOA2018-06-13T12:39:17Z


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