title: Detection by denaturing gradient gel electrophoresis of ammonia-oxidizing bacteria in microcosms of crude oil-contaminated mangrove sediments.
abstract: Currently,  the effect of crude oil on ammonia-oxidizing bacterium communities from  mangrove sediments is little understood. We studied the diversity of  ammonia-oxidizing bacteria in mangrove microcosm experiments using mangrove  sediments contaminated with 0.1, 0.5, 1, 2, and 5% crude oil as well as  non-contaminated control and landfarm soil from near an oil refinery in Camamu  Bay in Bahia, Brazil. The evolution of CO(2) production in all  crude oil-contaminated microcosms showed potential for mineralization. Cluster  analysis of denaturing gradient gel electrophoresis-derived samples generated  with primers for gene amoA, which encodes the functional enzyme ammonia  monooxygenase, showed differences in the sample contaminated with 5% compared  to the other samples. Principal component analysis showed divergence of the  non-contaminated samples from the 5% crude oil-contaminated sediment. A Venn  diagram generated from the banding pattern of PCR-denaturing gradient gel  electrophoresis was used to look for operational taxonomic units (OTUs) in  common. Eight OTUs were found in non-contaminated sediments and in samples  contaminated with 0.5, 1, or 2% crude oil. A Jaccard similarity index of 50%  was found for samples contaminated with 0.1, 0.5, 1, and 2% crude oil. This is  the first study that focuses on the impact of crude oil on the  ammonia-oxidizing bacterium community in mangrove sediments from Camamu Bay.
authors.affiliation: Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brasil.
authors.forename: A C F
authors.initials: AC
authors.lastname: dos Santos
authors.forename: E L S
authors.initials: EL
authors.lastname: Marques
authors.forename: E
authors.initials: E
authors.lastname: Gross
authors.forename: S S
authors.initials: SS
authors.lastname: Souza
authors.forename: J C T
authors.initials: JC
authors.lastname: Dias
authors.forename: M
authors.initials: M
authors.lastname: Brendel
authors.forename: R P
authors.initials: RP
authors.lastname: Rezende
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D020562:Betaproteobacteria / Q000235:genetics*; D044822:Biodiversity; D001938:Brazil; D004269:DNA, Bacterial / Q000235:genetics*; D058645:Denaturing Gradient Gel Electrophoresis / Q000379:methods; D019015:Geologic Sediments / Q000382:microbiology; D010084:Oxidation-Reduction; D010088:Oxidoreductases; D010578:Petroleum / Q000378:metabolism* / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D043982:Rhizophoraceae / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D010578:Petroleum; D012336:RNA, Ribosomal, 16S; D000641:Ammonia; D010088:Oxidoreductases; C045582:ammonia monooxygenase