Computational protocol: Enhancement mechanisms of short-time aerobic digestion for waste activated sludge in the presence of cocoamidopropyl betaine

Similar protocols

Protocol publication

[…] For the DNA extractions, sludge samples in both STAD reactors were collected with the aerobic digestion time of 0, 8, and 12 h. 10 mL of sludge sample was centrifuged at 12000 × g for 20 min at 4 °C. The supernatant were removed and the pellets were resuspended using PBS buffer (molar ratio of Na3PO4, Na2HPO4, NaCl, and KCl is 2:4:9:1). The total genomic DNA of each sample was extracted using Fast DNA® Spin Kit for Soil (MP Biomedicals, USA) following the manufacturer’s instructions. DNA samples were sent to Beijing Genewiz biological technology (Beijing, China) to perform sequencing library preparations and standard Illumina MiSeq sequencing protocols. The forward primers containing the sequence “CCTACGGRRB GCASCAGKVRVGAAT” and reverse primers containing the sequence “GGACTAC NVGGGTWTCTAATCC” were used to amplify the V3 and V4 regions, while the forward primers containing the sequence “GTGYCAGCMGCCGCGGTAA” and reverse primers containing the sequence “CTTGTGCGGKCCCCCGYCAATTC” were used to amplify the V4 and V5 regions of bacterial 16 S rRNA genes. DNA libraries were validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit and real time PCR (Applied Biosystems, Carlsbad, CA, USA). DNA libraries were multiplexed and loaded on an Illumina MiSeq instrument (Illumina, San Diego, CA, USA) according to manufacturer’s instructions. Sequencing was performed using a 2 × 250 paired-end (PE) configuration; Image analysis and base calling were conducted by the MiSeq Control Software (MCS) on the MiSeq instrument. We evaluated the overall community using the unweighted UniFrac distance matrix and the relationships among samples with Cytoscape and principle coordinate analysis (PCoA). All the 16 S rRNA gene-sequencing data were analyzed using the QIIME 1.7 software as described by Lai et al.. […]

Pipeline specifications

Software tools UniFrac, QIIME
Application 16S rRNA-seq analysis
Diseases Protein Deficiency, Wasting Syndrome
Chemicals Oxygen