title: Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data.
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.
authors.affiliation: Systems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas Madrid, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Bargiela
authors.affiliation: School of Biological Sciences, Bangor University Bangor, UK.
authors.forename: Christoph
authors.initials: C
authors.lastname: Gertler
authors.affiliation: EcoTechSystems Ltd., Ancona Italy.
authors.forename: Mirko
authors.initials: M
authors.lastname: Magagnini
authors.affiliation: Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Mapelli
authors.affiliation: Beijing Genomics Institute Shenzhen, China.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy ; Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal, Saudi Arabia.
authors.forename: Daniele
authors.initials: D
authors.lastname: Daffonchio
authors.affiliation: School of Biological Sciences, Bangor University Bangor, UK.
authors.forename: Peter N
authors.initials: PN
authors.lastname: Golyshin
authors.affiliation: Systems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas Madrid, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Ferrer
keywords: Mediterranean Sea; ammonium; biostimulation; crude oil degradation; enrichment; metagenomics; microcosm; uric acid