title: Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia.
abstract: In this study, the combination of culture enrichments and molecular tools was used to identify bacterial guilds, plasmids and functional genes potentially important in the process of petroleum hydrocarbon (PH) decontamination in mangrove microniches (rhizospheres and bulk sediment). In addition, we aimed to recover PH-degrading consortia (PHDC) for future use in remediation strategies. The PHDC were enriched with petroleum from rhizosphere and bulk sediment samples taken from a mangrove chronically polluted with oil hydrocarbons. Southern blot hybridization (SBH) assays of PCR amplicons from environmental DNA before enrichments resulted in weak positive signals for the functional gene types targeted, suggesting that PH-degrading genotypes and plasmids were in low abundance in the rhizosphere and bulk sediments. However, after enrichment, these genes were detected and strong microniche-dependent differences in the abundance and composition of hydrocarbonoclastic bacterial populations, plasmids (IncP-1α, IncP-1β, IncP-7 and IncP-9) and functional genes (naphthalene, extradiol and intradiol dioxygenases) were revealed by in-depth molecular analyses [PCR-denaturing gradient gel electrophoresis and hybridization (SBH and microarray)]. Our results suggest that, despite the low abundance of PH-degrading genes and plasmids in the environmental samples, the original bacterial composition of the mangrove microniches determined the structural and functional diversity of the PHDC enriched.
authors.affiliation: CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. gomesncm@ua.pt
authors.forename: Newton C M
authors.initials: NC
authors.lastname: Gomes
authors.forename: Cecilia G
authors.initials: CG
authors.lastname: Flocco
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Costa
authors.forename: Howard
authors.initials: H
authors.lastname: Junca
authors.forename: Ramiro
authors.initials: R
authors.lastname: Vilchez
authors.forename: Dietmar H
authors.initials: DH
authors.lastname: Pieper
authors.forename: Ellen
authors.initials: E
authors.lastname: Krögerrecklenfort
authors.forename: Rodolfo
authors.initials: R
authors.lastname: Paranhos
authors.forename: Leda C S
authors.initials: LC
authors.lastname: Mendonça-Hagler
authors.forename: Kornelia
authors.initials: K
authors.lastname: Smalla
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D001938:Brazil; D004269:DNA, Bacterial / Q000032:analysis; D004785:Environmental Pollutants / Q000378:metabolism; D019015:Geologic Sediments / Q000382:microbiology*; D006838:Hydrocarbons / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D010578:Petroleum; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D043982:Rhizophoraceae / Q000382:microbiology*; D058441:Rhizosphere; D017422:Sequence Analysis, DNA; D014871:Water Microbiology
chemical_list: D004269:DNA, Bacterial; D004785:Environmental Pollutants; D006838:Hydrocarbons; D010578:Petroleum; D012336:RNA, Ribosomal, 16S