Computational protocol: Isolation of Nitrospira belonging to Sublineage II from a Wastewater Treatment Plant

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Protocol publication

[…] Amplified PCR products were purified using the Wizard SV Gel and PCR Clean up System (Promega, Tokyo, Japan). Purified PCR products were sequenced using primers, 27f: 5′-AGAGTTTGAT CATGGCT-3′ and 1492r: 5′-TACGGTTACCTTGTTACGACTT-3′, by Fasmac (Kanagawa, Japan). Finally, the 16S rRNA gene sequences, comprising approximately 1,500 bases, were determined. Alignment editing and phylogenetic analyses were performed using ChromasPro version 1.4.1 software (Technelysium Pty, Tewantin, Australia) and MEGA4.0 software (). The bacterial 16S rRNA gene sequences were compared with those available from the DNA Data Bank of Japan (DDBJ) database. Genetic distance was calculated using a p-distance model of nucleic acid substitution. […]

Pipeline specifications

Software tools ChromasPro, MEGA
Databases DDBJ
Application Phylogenetics
Chemicals Nitrogen