title: Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation.
abstract: Microbial metabolism in aromatic-contaminated environments has important ecological implications, and obtaining a complete understanding of this process remains a relevant goal. To understand the roles of biodiversity and aromatic-mediated genetic and metabolic rearrangements, we conducted 'OMIC' investigations in an anthropogenically influenced and polyaromatic hydrocarbon (PAH)-contaminated soil with (Nbs) or without (N) bio-stimulation with calcium ammonia nitrate, NH(4)NO(3) and KH(2)PO(4) and the commercial surfactant Iveysol, plus two naphthalene-enriched communities derived from both soils (CN2 and CN1, respectively). Using a metagenomic approach, a total of 52, 53, 14 and 12 distinct species (according to operational phylogenetic units (OPU) in our work equivalent to taxonomic species) were identified in the N, Nbs, CN1 and CN2 communities, respectively. Approximately 10 out of 95 distinct species and 238 out of 3293 clusters of orthologous groups (COGs) protein families identified were clearly stimulated under the assayed conditions, whereas only two species and 1465 COGs conformed to the common set in all of the mesocosms. Results indicated distinct biodegradation capabilities for the utilisation of potential growth-supporting aromatics, which results in bio-stimulated communities being extremely fit to naphthalene utilisation and non-stimulated communities exhibiting a greater metabolic window than previously predicted. On the basis of comparing protein expression profiles and metagenome data sets, inter-alia interactions among members were hypothesised. The utilisation of curated databases is discussed and used for first time to reconstruct 'presumptive' degradation networks for complex microbial communities.
authors: Department of Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain.
authors: María-Eugenia
authors: ME
authors: Guazzaroni
authors: Florian-Alexander
authors: FA
authors: Herbst
authors: Iván
authors: I
authors: Lores
authors: Javier
authors: J
authors: Tamames
authors: Ana Isabel
authors: AI
authors: Peláez
authors: Nieves
authors: N
authors: López-Cortés
authors: María
authors: M
authors: Alcaide
authors: Mercedes V
authors: MV
authors: Del Pozo
authors: José María
authors: JM
authors: Vieites
authors: Martin
authors: M
authors: von Bergen
authors: José Luis R
authors: JL
authors: Gallego
authors: Rafael
authors: R
authors: Bargiela
authors: Arantxa
authors: A
authors: López-López
authors: Dietmar H
authors: DH
authors: Pieper
authors: Ramón
authors: R
authors: Rosselló-Móra
authors: Jesús
authors: J
authors: Sánchez
authors: Jana
authors: J
authors: Seifert
authors: Manuel
authors: M
authors: Ferrer
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D001673:Biodegradation, Environmental; D044822:Biodiversity; D056186:Metagenomics; D008969:Molecular Sequence Data; D009281:Naphthalenes / Q000378:metabolism / Q000633:toxicity*; D010802:Phylogeny; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000378:metabolism
chemical_list: D009281:Naphthalenes; D012987:Soil; D012989:Soil Pollutants; C031721:naphthalene