Computational protocol: Enhanced electrical power generation using flame-oxidized stainless steel anode in microbial fuel cells and the anodic community structure

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Protocol publication

[…] Next-generation sequencing was performed by the MiSeq Illumina sequencing platform (Illumina Inc., CA, USA) using the V4 region of the 16S rRNA gene []. The cubic MFCs with the membrane, fed with the peptone medium, were operated at 25 °C. The MFCs reached a stable performance after 2 months, and were cultured for a further 2-month period. The biofilms formed on the anodes were extensively washed with distilled water, and the genomic DNA of the bacteria tightly adhering to the anodes was extracted using an UltraClean™ Soil DNA Isolation kit (Mo Bio Laboratories, Carlsbad, CA, USA). Libraries were constructed from the bacterial genomic DNA by polymerase chain reaction using 563F and 802R primers, which included the Illumina overhang adapter sequences, according to the manufacturer’s instructions. The libraries were sequenced on 300PE MiSeq run, and paired-end read data were processed with the QIIME software []. The read sequences were joined, quality-checked, and clustered into OTUs by the Uclust method []. After chimera check, taxonomic classification, rarefaction curves, and alpha diversity indices were computed with QIIME. Beta diversity analysis was calculated using a weighted UniFrac distance matrix [], and the result was visualized with a principal coordinate (PCo) plot. Taxonomic assignment to the Geobacter species was conducted by a BLAST search at a similarity threshold of 97 %. […]

Pipeline specifications

Software tools QIIME, UCLUST, UniFrac
Application 16S rRNA-seq analysis
Organisms Dipturus trachyderma, Geobacter metallireducens
Chemicals Carbon