Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data

Handle URI:
http://hdl.handle.net/10754/592618
Title:
Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data
Authors:
Bargiela, Rafael; Gertler, Christoph; Magagnini, Mirko; Mapelli, Francesca; Chen, Jianwei; Daffonchio, Daniele ( 0000-0003-0947-925X ) ; Golyshin, Peter N.; Ferrer, Manuel
Abstract:
Biostimulation 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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data 2015, 6 Frontiers in Microbiology
Publisher:
Frontiers Media SA
Journal:
Frontiers in Microbiology
Issue Date:
24-Nov-2015
DOI:
10.3389/fmicb.2015.01270
Type:
Article
ISSN:
1664-302X
Additional Links:
http://journal.frontiersin.org/Article/10.3389/fmicb.2015.01270/abstract
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorBargiela, Rafaelen
dc.contributor.authorGertler, Christophen
dc.contributor.authorMagagnini, Mirkoen
dc.contributor.authorMapelli, Francescaen
dc.contributor.authorChen, Jianweien
dc.contributor.authorDaffonchio, Danieleen
dc.contributor.authorGolyshin, Peter N.en
dc.contributor.authorFerrer, Manuelen
dc.date.accessioned2015-12-28T14:31:06Zen
dc.date.available2015-12-28T14:31:06Zen
dc.date.issued2015-11-24en
dc.identifier.citationDegradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data 2015, 6 Frontiers in Microbiologyen
dc.identifier.issn1664-302Xen
dc.identifier.doi10.3389/fmicb.2015.01270en
dc.identifier.urihttp://hdl.handle.net/10754/592618en
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.en
dc.language.isoenen
dc.publisherFrontiers Media SAen
dc.relation.urlhttp://journal.frontiersin.org/Article/10.3389/fmicb.2015.01270/abstracten
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.en
dc.subjectammoniumen
dc.subjectbiostimulationen
dc.subjectcrude oil degradationen
dc.subjectenrichmenten
dc.subjectMediterranean Seaen
dc.subjectmetagenomicsen
dc.subjectmicrocosmen
dc.subjecturic aciden
dc.titleDegradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Dataen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalFrontiers in Microbiologyen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionSystems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spainen
dc.contributor.institutionSchool of Biological Sciences, Bangor University, Bangor, UKen
dc.contributor.institutionEcoTechSystems Ltd., Ancona, Italyen
dc.contributor.institutionDepartment of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italyen
dc.contributor.institutionBeijing Genomics Institute, Shenzhen, Chinaen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorDaffonchio, Danieleen
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