Comparison of different protocols for the extraction of microbial DNA from reef corals

This study aimed to test different protocols for the extraction of microbial DNA from the coral Mussismilia harttii. Four different commercial kits were tested, three of them based on methods for DNA extraction from soil (FastDNA SPIN Kit for soil, MP Bio, PowerSoil DNA Isolation Kit, MoBio, and ZR Soil Microbe DNA Kit, Zymo Research) and one kit for DNA extraction from plants (UltraClean Plant DNA Isolation Kit, MoBio). Five polyps of the same colony of M. harttii were macerated and aliquots were submitted to DNA extraction by the different kits. After extraction, the DNA was quantified and PCR-DGGE was used to study the molecular fingerprint of Bacteria and Eukarya. Among the four kits tested, the ZR Soil Microbe DNA Kit was the most efficient with respect to the amount of DNA extracted, yielding about three times more DNA than the other kits. Also, we observed a higher number and intensities of DGGE bands for both Bacteria and Eukarya with the same kit. Considering these results, we suggested that the ZR Soil Microbe DNA Kit is the best adapted for the study of the microbial communities of corals.

Comparison of different protocols for the extraction of microbial DNA from reef corals

This study aimed to test different protocols for the extraction of microbial DNA from the coral Mussismilia harttii. Four different commercial kits were tested, three of them based on methods for DNA extraction from soil (FastDNA SPIN Kit for soil, MP Bio, PowerSoil DNA Isolation Kit, MoBio, and ZR Soil Microbe DNA Kit, Zymo Research) and one kit for DNA extraction from plants (UltraClean Plant DNA Isolation Kit, MoBio). Five polyps of the same colony of M. harttii were macerated and aliquots were submitted to DNA extraction by the different kits. After extraction, the DNA was quantified and PCR-DGGE was used to study the molecular fingerprint of Bacteria and Eukarya. Among the four kits tested, the ZR Soil Microbe DNA Kit was the most efficient with respect to the amount of DNA extracted, yielding about three times more DNA than the other kits. Also, we observed a higher number and intensities of DGGE bands for both Bacteria and Eukarya with the same kit. Considering these results, we suggested that the ZR Soil Microbe DNA Kit is the best adapted for the study of the microbial communities of corals.

Comparison of different protocols for the extraction of microbial DNA from reef corals.

This study aimed to test different protocols for the extraction of microbial DNA from the coral Mussismilia harttii. Four different commercial kits were tested, three of them based on methods for DNA extraction from soil (FastDNA SPIN Kit for soil, MP Bio, PowerSoil DNA Isolation Kit, MoBio, and ZR Soil Microbe DNA Kit, Zymo Research) and one kit for DNA extraction from plants (UltraClean Plant DNA Isolation Kit, MoBio). Five polyps of the same colony of M. harttii were macerated and aliquots were submitted to DNA extraction by the different kits. After extraction, the DNA was quantified and PCR-DGGE was used to study the molecular fingerprint of Bacteria and Eukarya. Among the four kits tested, the ZR Soil Microbe DNA Kit was the most efficient with respect to the amount of DNA extracted, yielding about three times more DNA than the other kits. Also, we observed a higher number and intensities of DGGE bands for both Bacteria and Eukarya with the same kit. Considering these results, we suggested that the ZR Soil Microbe DNA Kit is the best adapted for the study of the microbial communities of corals.

Action of antimicrobial substances produced by different oil reservoir Bacillus strains against biofilm formation.

Microbial colonization of petroleum industry systems takes place through the formation of biofilms, and can result in biodeterioration of the metal surfaces. In a previous study, two oil reservoir Bacillus strains (Bacillus licheniformis T6-5 and Bacillus firmus H(2)O-1) were shown to produce antimicrobial substances (AMS) active against different Bacillus strains and a consortium of sulfate-reducing bacteria (SRB) on solid medium. However, neither their ability to form biofilms nor the effect of the AMS on biofilm formation was adequately addressed. Therefore, here, we report that three Bacillus strains (Bacillus pumilus LF4 -- used as an indicator strain, B. licheniformis T6-5, and B. firmus H(2)O-1), and an oil reservoir SRB consortium (T6lab) were grown as biofilms on glass surfaces. The AMS produced by strains T6-5 and H(2)O-1 prevented the formation of B. pumilus LF4 biofilm and also eliminated pre-established LF4 biofilm. In addition, the presence of AMS produced by H(2)O-1 reduced the viability and attachment of the SRB consortium biofilm by an order of magnitude. Our results suggest that the AMS produced by Bacillus strains T6-5 and H(2)O-1 may have a potential for pipeline-cleaning technologies to inhibit biofilm formation and consequently reduce biocorrosion.

Characterization of Gordonia sp. strain F.5.25.8 capable of dibenzothiophene desulfurization and carbazole utilization.

A dibenzothiophene (DBT)-degrading bacterial strain able to utilize carbazole as the only source of nitrogen was identified as Gordonia sp. F.5.25.8 due to its 16S rRNA gene sequence and phenotypic characteristics. Gas chromatography (GC) and GC-mass spectroscopy analyses showed that strain F.5.25.8 transformed DBT into 2-hydroxybiphenyl (2-HBP). This strain was also able to grow using various organic sulfur or nitrogen compounds as the sole sulfur or nitrogen sources. Resting-cell studies indicated that desulfurization occurs either in cell-associated or in cell-free extracts of F.5.25.8. The biological responses of F.5.25.8 to a series of mutagens and environmental agents were also characterized. The results revealed that this strain is highly tolerant to DNA damage and also refractory to induced mutagenesis. Strain F.5.25.8 was also characterized genetically. Results showed that genes involved in desulfurization (dsz) are located in the chromosome, and PCR amplification was observed with primers dszA and dszB designed based on Rhodococcus genes. However, no amplification product was observed with the primer based on dszC.

Production of antimicrobial substances by Bacillus subtilis LFE-1, B. firmus HO-1 and B. licheniformis T6-5 isolated from an oil reservoir in Brazil.

AIMS: Forty Bacillus strains isolated from a Brazilian oil reservoir were tested against each other to select strains producing antimicrobial substances (AMS). Three strains, Bacillus subtilis (LFE-1), Bacillus firmus (H2O-1) and Bacillus licheniformis (T6-5), were selected due to their ability to inhibit more than 65% of the Bacillus strains tested. These three strains were also investigated for their capability to inhibit sulphate-reducing bacteria (SRB). Furthermore, physiological and biochemical characteristics of the antimicrobial compounds produced by the selected strains were determined. METHODS AND RESULTS: Among the forty strains tested, 36 (90%) strains were able to inhibit at least one Bacillus strain used as indicator in plate assays and three of them (LFE-1, T6-5 and H2O-1) were able to inhibit 65, 70 and 97.5% of the 40 strains studied here respectively. Clear zones of inhibition were observed when H2O-1 was tested against SRB-containing consortium T6-lab and Desulfovibrio alaskensis strain NCIMB 13491, while strain T6-5 was able to inhibit only the D. alaskensis strain. The three substances showed to be insensitive to different enzymes and chemicals, were heat stable and the substances produced by strains T6-5 and H2O-1 were active over a wide pH range. CONCLUSIONS: Three different AMS produced by Bacillus strains from an oil reservoir, two of them with activity against SRB, are presented here. SIGNIFICANCE AND IMPACT OF THE STUDY: The preliminary characterization of these AMS points to their potential use as biocides in the petroleum industry for controlling problems associated with SRB.

Influence of petroleum contamination and biostimulation treatment on the diversity of Pseudomonas spp. in soil microcosms as evaluated by 16S rRNA based-PCR and DGGE.

AIMS: The aim of this study was to apply a group specific PCR system followed by denaturing gradient gel electrophoresis (DGGE) analysis to evaluate the effect of oil contamination and the biostimulation process on the diversity of Pseudomonas populations in soil ecosystems. METHODS AND RESULTS: Direct DNA extraction from biostimulated- and oil-contaminated soil samples was performed. Primers specific for the genus Pseudomonas spp. were used to amplify 16S rRNA genes and then a semi-nested PCR reaction was applied to obtain smaller fragments for comparing the PCR products by DGGE. Whether in bulk, oil-contaminated or biostimulated soils, the DGGE profiles revealed little change in Pseudomonas community throughout the 270 days of experiment. The presence of a few additional bands observed only in treated samples indicated that a bacterial shift occurred with the addition of nutrients and with oil contamination. CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY: The combination of semi-nested PCR and DGGE was found to be a rapid and sensitive technique to study the diversity within the genus Pseudomonas and may be suitable for further studies concerning the role of this bacterial group in large-scale oil-contaminated areas.

Production of biosurfactant from a new and promising strain of Pseudomonas aeruginosa PA1.

The Pseudomonas aeruginosa PA1 strain, isolated from the water of oil production in Sergipe, Northeast Brazil, was evaluated as a potential rhamnolipid type of biosurfactant producer. The production of biosurfactants was investigated using different carbon sources (n-hexadecane, paraffin oil, glycerol, and babassu oil) and inoculum concentrations (0.0016-0.008 g/L). The best results were obtained with glycerol as the substrate and an initial cell concentration of 0.004 g/L. A C:N ratio of 22.8 led to the greatest production of rhamnolipids (1700 mg/L) and efficiency (1.18 g of rhamnolipid/g of dry wt).