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Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia

(2010) FEMS MICROBIOLOGY ECOLOGY. 74(2). p.276-290
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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-1 alpha, IncP-1 beta, 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.
Keywords
petroleum, mangrove, rhizosphere, hydrocarbonoclastic bacteria, Guanabara bay, GRADIENT GEL-ELECTROPHORESIS, COMPLETE NUCLEOTIDE-SEQUENCE, HOST-RANGE PLASMIDS, BACTERIAL COMMUNITIES, ACINETOBACTER-CALCOACETICUS, PSEUDOMONAS-AERUGINOSA, MICROBIAL COMMUNITIES, MULTIVARIATE ANALYSES, RESISTANCE PLASMIDS, DIOXYGENASE GENES

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Citation

Please use this url to cite or link to this publication:

Chicago
Gomes, Newton CM, Cecilia G Flocco, Rodrigo Costa, Howard Junca, Ramiro Vilchez Vargas, Dietmar H Pieper, Ellen Krögerrecklenfort, Rodolfo Paranhos, Leda CS Mendonca-Hagler, and Kornelia Smalla. 2010. “Mangrove Microniches Determine the Structural and Functional Diversity of Enriched Petroleum Hydrocarbon-degrading Consortia.” Fems Microbiology Ecology 74 (2): 276–290.
APA
Gomes, N. C., Flocco, C. G., Costa, R., Junca, H., Vilchez Vargas, R., Pieper, D. H., Krögerrecklenfort, E., et al. (2010). Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia. FEMS MICROBIOLOGY ECOLOGY, 74(2), 276–290.
Vancouver
1.
Gomes NC, Flocco CG, Costa R, Junca H, Vilchez Vargas R, Pieper DH, et al. Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia. FEMS MICROBIOLOGY ECOLOGY. 2010;74(2):276–90.
MLA
Gomes, Newton CM, Cecilia G Flocco, Rodrigo Costa, et al. “Mangrove Microniches Determine the Structural and Functional Diversity of Enriched Petroleum Hydrocarbon-degrading Consortia.” FEMS MICROBIOLOGY ECOLOGY 74.2 (2010): 276–290. Print.
@article{4421150,
  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-1 alpha, IncP-1 beta, 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.},
  author       = {Gomes, Newton CM and Flocco, Cecilia G and Costa, Rodrigo and Junca, Howard and Vilchez Vargas, Ramiro and Pieper, Dietmar H and Krögerrecklenfort, Ellen and Paranhos, Rodolfo and Mendonca-Hagler, Leda CS and Smalla, Kornelia},
  issn         = {0168-6496},
  journal      = {FEMS MICROBIOLOGY ECOLOGY},
  keywords     = {petroleum,mangrove,rhizosphere,hydrocarbonoclastic bacteria,Guanabara bay,GRADIENT GEL-ELECTROPHORESIS,COMPLETE NUCLEOTIDE-SEQUENCE,HOST-RANGE PLASMIDS,BACTERIAL COMMUNITIES,ACINETOBACTER-CALCOACETICUS,PSEUDOMONAS-AERUGINOSA,MICROBIAL COMMUNITIES,MULTIVARIATE ANALYSES,RESISTANCE PLASMIDS,DIOXYGENASE GENES},
  language     = {eng},
  number       = {2},
  pages        = {276--290},
  title        = {Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia},
  url          = {http://dx.doi.org/10.1111/j.1574-6941.2010.00962.x},
  volume       = {74},
  year         = {2010},
}

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