title: Characterization of para-Nitrophenol-Degrading Bacterial Communities in River Water by Using Functional Markers and Stable Isotope Probing.
abstract: Microbial degradation is a major determinant of the fate of pollutants in the environment. para-Nitrophenol (PNP) is an EPA-listed priority pollutant with a wide environmental distribution, but little is known about the microorganisms that degrade it in the environment. We studied the diversity of active PNP-degrading bacterial populations in river water using a novel functional marker approach coupled with [(13)C6]PNP stable isotope probing (SIP). Culturing together with culture-independent terminal restriction fragment length polymorphism analysis of 16S rRNA gene amplicons identified Pseudomonas syringae to be the major driver of PNP degradation in river water microcosms. This was confirmed by SIP-pyrosequencing of amplified 16S rRNA. Similarly, functional gene analysis showed that degradation followed the Gram-negative bacterial pathway and involved pnpA from Pseudomonas spp. However, analysis of maleylacetate reductase (encoded by mar), an enzyme common to late stages of both Gram-negative and Gram-positive bacterial PNP degradation pathways, identified a diverse assemblage of bacteria associated with PNP degradation, suggesting that mar has limited use as a specific marker of PNP biodegradation. Both the pnpA and mar genes were detected in a PNP-degrading isolate, P. syringae AKHD2, which was isolated from river water. Our results suggest that PNP-degrading cultures of Pseudomonas spp. are representative of environmental PNP-degrading populations.
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, United Kingdom AKowalcz@scj.com.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Kowalczyk
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, United Kingdom.
authors.forename: Özge
authors.initials: Ö
authors.lastname: Eyice
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, United Kingdom.
authors.forename: Hendrik
authors.initials: H
authors.lastname: Schäfer
authors.affiliation: Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, United Kingdom.
authors.forename: Oliver R
authors.initials: OR
authors.lastname: Price
authors.affiliation: Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, United Kingdom.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Finnegan
authors.affiliation: Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, United Kingdom.
authors.forename: Roger A
authors.initials: RA
authors.lastname: van Egmond
authors.affiliation: Department of Geography and Environmental Science, University of Reading, Whiteknights, Reading, Berkshire, United Kingdom.
authors.forename: Liz J
authors.initials: LJ
authors.lastname: Shaw
authors.affiliation: Department of Geography and Environmental Science, University of Reading, Whiteknights, Reading, Berkshire, United Kingdom School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire, United Kingdom.
authors.forename: Glyn
authors.initials: G
authors.lastname: Barrett
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, United Kingdom.
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bending
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001673:Biodegradation, Environmental; D002247:Carbon Isotopes / Q000032:analysis / Q000378:metabolism; D008969:Molecular Sequence Data; D009596:Nitrophenols / Q000378:metabolism*; D010802:Phylogeny; D011549:Pseudomonas / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D045483:Rivers / Q000382:microbiology*
chemical_list: D001426:Bacterial Proteins; D002247:Carbon Isotopes; D009596:Nitrophenols; D012336:RNA, Ribosomal, 16S; C024836:4-nitrophenol