Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities

Abstract

The analysis of microbial assemblages in industrial, marine, and medical systems can inform decisions regarding quality control or mitigation. Modern molecular approaches to detect, characterize, and quantify microorganisms provide rapid and thorough measures unbiased by the need for cultivation. The requirement of timely extraction of high quality nucleic acids for molecular analysis is faced with specific challenges when used to study the influence of microorganisms on oil production. Production facilities are often ill equipped for nucleic acid extraction techniques, making the preservation and transportation of samples off-site a priority. As a potential solution, the possibility of extracting nucleic acids on-site using automated platforms was tested. The performance of two such platforms, the Fujifilm QuickGene-Mini80™ and Promega Maxwell®16 was compared to a widely used manual extraction kit, MOBIO PowerBiofilm™ DNA Isolation Kit, in terms of ease of operation, DNA quality, and microbial community composition. Three pipeline biofilm samples were chosen for these comparisons; two contained crude oil and corrosion products and the third transported seawater. Overall, the two more automated extraction platforms produced higher DNA yields than the manual approach. DNA quality was evaluated for amplification by quantitative PCR (qPCR) and end-point PCR to generate 454 pyrosequencing libraries for 16S rRNA microbial community analysis. Microbial community structure, as assessed by DGGE analysis and pyrosequencing, was comparable among the three extraction methods. Therefore, the use of automated extraction platforms should enhance the feasibility of rapidly evaluating microbial biofouling at remote locations or those with limited resources.

Municipal Solid Waste Landfills Harbor Distinct Microbiomes

“…Each sample (filter and DNAzol) was vortexed for 30 s at full speed upon thawing at room temperature. DNA was extracted from 1 mL of the DNAzol solution in each replicate sample using an automated Maxwell 16 Cell total RNA LEV Purification Kit (Promega, Madison, WI, USA), omitting the final DNase step as described in Oldham et al ( 2012 ). Extracted DNA ranged in detected concentration from 1.04 to 12.3 ng/μL, with three samples that failed to quantify (Table S1 ).…”

Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies

“…Fecal DNA was extracted from 0.25 g of stool using the PowerBiofilm TM DNA Isolation Kit (MOBIO laboratories, Carlsbad, USA), as described by the manufacturer 36 .…”

Genome Sequence of Clostridium sp. Strain P21, a CO-Fermenting Acetogen Isolated from Old Hay

“…Cells were washed, and RLA lysis buffer (Maxwell 16; Promega) was added. DNA extraction was performed using the automated Maxwell 16 tissue LEV total RNA purification kit (Promega) purification system v4.90 modified from the manufacturer’s instructions as described by Oldham et al ( 3 ). DNA library preparation and genome sequencing were performed at Oklahoma Memorial Research Foundation Next-Generation Sequencing Core using the NEBNext Ultra II library prep kit (New England BioLabs) and MiSeq reagent kit v3 (Illumina) on an Illumina MiSeq instrument as per the manufacturer’s instructions.…”