Computational protocol: Biosurfactant production from marine hydrocarbon-degrading consortia and pure bacterial strains using crude oil as carbon source

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Protocol publication

[…] Total genomic DNA was extracted according to (). DNA yield and quality was determined by agarose gel electrophoresis of 5 μl of DNA extract. DNA extracts were stored at 4°C until use.PCR and pyrosequencing were performed in Research and Testing Laboratory (Lubbock, TX, USA) on an FLX Titanium platform, for the V4 hypervariable region of the 16S rRNA gene using primers 515F (5′-GTGCCAGCMGCCGCGGTAA-3′) and 806R (5′-GGACTACHVGGGTWTCTAAT-3′) which are known to have reduced bias and cover a wide range of bacterial and archaeal phyla (). Noise filtering and chimera removal (using the AmpliconNoise package ), operational taxonomic unit (OTU) clustering (at 97% similarity, using uclust ), OTU table construction, Good’s coverage index estimation () and phylogenetic assignments (comparing against the latest Greengenes database release with uclust) were performed in QIIME v1.8 (). The samples for the whole project have been deposited in the NCBI short read archive (SRA) database under the BioProject accession number PRJNA190077. […]

Pipeline specifications

Software tools AmpliconNoise, UCLUST, QIIME
Databases Greengenes
Application Phylogenetics
Organisms Paracoccus marcusii
Chemicals Carbon, Silica Gel