Computational protocol: Biodegradation of Phenol by Bacteria Strain Acinetobacter Calcoaceticus PA Isolated from Phenolic Wastewater

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Protocol publication

[…] The genomic DNA of strain PA was extracted as previously described []. DNA was used as template to amplify bacterial 16S rDNA with universal primers 27F (5′-AGAGATTGATCCTGGCTCTG-3′) and 1492R (5′-GGTTTCCTTGTTACGACAT-3′) on a Mastercycler gradient thermocycler (Eppendorf, Hamburg, Germany). The amplification reaction was performed in 25 μL volume PCR buffer containing 1.5 mM MgCl2, 0.2 mM of each deoxynucleoside triphosphate, 1 μM each of the forward and reverse primers. An initial denaturation step of 5 min at 94 °C was conducted, followed by 35 cycles of 94 °C for 30 s, 55 °C for 45 s and 72 °C for 90 s. The procedure was completed with a final elongation step at 72 °C for 10 min. The PCR products were sequenced, and the sequences were compared with bacterial 16S rDNA sequences in GenBank using the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) program []. Neighbor-joining phylogenetic trees [] were constructed using the Molecular Evolutionary Genetics Analysis (MEGA) program version 4 []. The reliability of phylogenetic reconstructions was estimated through bootstrap analysis (1000 replicates). The 16S rDNA sequence of the strain PA was available under GenBank accession numbers KT878384. […]

Pipeline specifications

Software tools BLASTN, MEGA
Application Phylogenetics
Organisms Acinetobacter calcoaceticus
Chemicals Carbon, Phenol