Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Braz J Microbiol
2016 Jan 01;473:712-23. doi: 10.1016/j.bjm.2016.04.004.
Show Gene links
Show Anatomy links
Evaluation of bacterial diversity recovered from petroleum samples using different physical matrices.
Dellagnezze BM
,
Vasconcellos SP
,
Melo IS
,
Santos Neto EV
,
Oliveira VM
.
???displayArticle.abstract???
Unraveling the microbial diversity and its complexity in petroleum reservoir environments has been a challenge throughout the years. Despite the techniques developed in order to improve methodologies involving DNA extraction from crude oil, microbial enrichments using different culture conditions can be applied as a way to increase the recovery of DNA from environments with low cellular density for further microbiological analyses. This work aimed at the evaluation of different matrices (arenite, shale and polyurethane foam) as support materials for microbial growth and biofilm formation in enrichments using a biodegraded petroleum sample as inoculum in sulfate reducing condition. Subsequent microbial diversity characterization was carried out using Scanning Electronic Microscopy (SEM), Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rRNA gene libraries in order to compare the microbial biomass yield, DNA recovery efficiency and diversity among the enrichments. The DNA from microbial communities in petroleum enrichments was purified according to a protocol established in this work and used for 16S rRNA amplification with bacterial generic primers. The PCR products were cloned, and positive clones were screened by Amplified Ribosomal DNA Restriction Analysis (ARDRA). Sequencing and phylogenetic analyses revealed that the bacterial community was mostly represented by members of the genera Petrotoga, Bacillus, Pseudomonas, Geobacillus and Rahnella. The use of different support materials in the enrichments yielded an increase in microbial biomass and biofilm formation, indicating that these materials may be employed for efficient biomass recovery from petroleum reservoir samples. Nonetheless, the most diverse microbiota were recovered from the biodegraded petroleum sample using polyurethane foam cubes as support material.
Fig. 1. SEM analyses of different bacterial enrichments from Campos Basin oil. (a, b) Oil without support; (c, d) oil added with polyurethane foams; (e, f) oil added with shale; (g, h) oil added with arenite. Arrows indicates biofilm formation.
Fig. 2. (a) DGGE analyses showing the distinct band profiles. M: marker; Lanes 1–3: WS enrichments; lanes 4–6: PF enrichments; lanes 7–9: S enrichments; lanes 10–12: A enrichments. (b) Dendrogram showing the grouping of different profiles among the enrichments and distinct matrices.
Fig. 3. Occurrence of bacterial genera in the petroleum enrichments: (a) Enrichment without support material (WS) (95 clones, 7 ribotypes); (b) enrichment with polyurethane foams (PF) as support material (46 clones, 15 ribotypes); (c) enrichment with shale (S) as support material (63 clones, 3 ribotypes); and (d) enrichment with arenite (A) as support material (50 clones, 3 ribotypes).
Fig. 4. Phylogenetic analysis based on partial bacterial 16S rRNA sequences of clones from diverse enrichment samples and related species. Bootstrap values greater than 70% are listed. GenBank accession numbers are listed after species names. Numbers in brackets correspond to additional clones presenting. 97% sequence similarity with the clones represented in the tree. Letters PF, WS, A and S correspond to the sample libraries. Methanohalophilus portucalensis was used as outgroup.
Aitken,
Anaerobic hydrocarbon biodegradation in deep subsurface oil reservoirs.
2004, Pubmed
Aitken,
Anaerobic hydrocarbon biodegradation in deep subsurface oil reservoirs.
2004,
Pubmed
Annweiler,
Identical ring cleavage products during anaerobic degradation of naphthalene, 2-methylnaphthalene, and tetralin indicate a new metabolic pathway.
2002,
Pubmed
Bieszkiewicz,
An attempt to use selected strains of bacteria adapted to high concentrations of petroleum oil to increase the effective removal of petroleum products in excess activated sludge in laboratory conditions.
1998,
Pubmed
Chamkha,
Isolation of a thermophilic and halophilic tyrosol-degrading Geobacillus from a Tunisian high-temperature oil field.
2008,
Pubmed
Dahle,
Microbial community structure analysis of produced water from a high-temperature North Sea oil-field.
2008,
Pubmed
Ewing,
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
1998,
Pubmed
Ferrari,
Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria.
2005,
Pubmed
Gieg,
Methanogenesis, sulfate reduction and crude oil biodegradation in hot Alaskan oilfields.
2010,
Pubmed
Gieg,
Biological souring and mitigation in oil reservoirs.
2011,
Pubmed
Gordon,
Consed: a graphical tool for sequence finishing.
1998,
Pubmed
Gro kopf R,
Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms.
1998,
Pubmed
Gössner,
Thermicanus aegyptius gen. nov., sp. nov., isolated from oxic soil, a fermentative microaerophile that grows commensally with the thermophilic acetogen Moorella thermoacetica.
1999,
Pubmed
Heuer,
Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients.
1997,
Pubmed
Janbandhu,
Biodegradation of phenanthrene using adapted microbial consortium isolated from petrochemical contaminated environment.
2011,
Pubmed
Jang,
Identification of Weissella species by the genus-specific amplified ribosomal DNA restriction analysis.
2002,
Pubmed
Jones,
Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs.
2008,
Pubmed
Kaster,
Characterisation of culture-independent and -dependent microbial communities in a high-temperature offshore chalk petroleum reservoir.
2009,
Pubmed
Korenblum,
Bacterial diversity in water injection systems of Brazilian offshore oil platforms.
2010,
Pubmed
L'Haridon,
Petrotoga olearia sp. nov. and Petrotoga sibirica sp. nov., two thermophilic bacteria isolated from a continental petroleum reservoir in Western Siberia.
2002,
Pubmed
Lima,
Evaluation of bacterial surfactant toxicity towards petroleum degrading microorganisms.
2011,
Pubmed
Liu,
Molecular characterization of the alkB gene in the thermophilic Geobacillus sp. strain MH-1.
2009,
Pubmed
Lu,
Enhanced biodecolorization of azo dyes by anthraquinone-2-sulfonate immobilized covalently in polyurethane foam.
2010,
Pubmed
Ma,
Pseudomonas, the dominant polycyclic aromatic hydrocarbon-degrading bacteria isolated from Antarctic soils and the role of large plasmids in horizontal gene transfer.
2006,
Pubmed
Magot,
Microbiology of petroleum reservoirs.
2000,
Pubmed
Martínez-Checa,
Yield production, chemical composition, and functional properties of emulsifier H28 synthesized by Halomonas eurihalina strain H-28 in media containing various hydrocarbons.
2002,
Pubmed
Meckenstock,
Oil biodegradation. Water droplets in oil are microhabitats for microbial life.
2014,
Pubmed
Miranda-Tello,
Petrotoga halophila sp. nov., a thermophilic, moderately halophilic, fermentative bacterium isolated from an offshore oil well in Congo.
2007,
Pubmed
Najafi,
Interactive optimization of biosurfactant production by Paenibacillus alvei ARN63 isolated from an Iranian oil well.
2011,
Pubmed
Nazina,
[Phylogenetic diversity of aerobic saprotrophic bacteria isolated from the Daqing oil field].
2002,
Pubmed
Nazina,
[The phylogenetic diversity of aerobic organotrophic bacteria from the Dagan high-temperature oil field].
2005,
Pubmed
Neria-González,
Characterization of bacterial community associated to biofilms of corroded oil pipelines from the southeast of Mexico.
2006,
Pubmed
Ogier,
Safety assessment of dairy microorganisms: the Leuconostoc genus.
2008,
Pubmed
Orphan,
Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs.
2000,
Pubmed
Pham,
Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods.
2009,
Pubmed
Röling,
The microbiology of hydrocarbon degradation in subsurface petroleum reservoirs: perspectives and prospects.
2003,
Pubmed
Sette,
Analysis of the composition of bacterial communities in oil reservoirs from a southern offshore Brazilian basin.
2007,
Pubmed
Silva,
Evaluation of support materials for the immobilization of sulfate-reducing bacteria and methanogenic archaea.
2006,
Pubmed
Voget,
Prospecting for novel biocatalysts in a soil metagenome.
2003,
Pubmed
Wang,
Comparison of bacterial community in aqueous and oil phases of water-flooded petroleum reservoirs using pyrosequencing and clone library approaches.
2014,
Pubmed
Widdel,
Anaerobic biodegradation of saturated and aromatic hydrocarbons.
2001,
Pubmed
Wu,
Rhamnolipid production with indigenous Pseudomonas aeruginosa EM1 isolated from oil-contaminated site.
2008,
Pubmed
Yun,
Screening for novel enzymes from metagenome and SIGEX, as a way to improve it.
2005,
Pubmed
Zinder,
Methanogenesis in a Thermophilic (58 degrees C) Anaerobic Digestor: Methanothrix sp. as an Important Aceticlastic Methanogen.
1984,
Pubmed
von der Weid,
Molecular diversity of bacterial communities from subseafloor rock samples in a deep-water production basin in Brazil.
2008,
Pubmed