Computational protocol: Methanocella conradii sp. nov., a Thermophilic, Obligate Hydrogenotrophic Methanogen, Isolated from Chinese Rice Field Soil

Similar protocols

Protocol publication

[…] DNA extraction, PCR amplification, terminal restriction fragment length polymorphism (T-RFLP) analysis, cloning and sequencing were performed as previously reported . Sequences were either aligned with RDP's aligner tool using the Ribosomal Database Project (RDP 10) for 16S rRNA gene or with the Mega 4.0.2 software package for the deduced McrA amino acid. All sequence alignments were analyzed with the Mega 4.0.2 software package . Distances were calculated using the Jukes-Cantor correction. For phylogenetic analysis, the near full length 16S rRNA gene was amplified using the universal archaeal primer pair Arc21f/1492r . The mcrA gene was amplified with MCRf/MCRr . Phylogenetic trees were produced using the neighbor-joining and maximum-parsimony methods by bootstrap re-sampling analysis with 1000 replicates. 16S rRNA gene and mcrA gene sequences of strain HZ254T have been deposited in GenBank under the accession numbers of JN048683 and JN081865, respectively. [...] Complete genomes of HZ254T (accession number: CP003243) , SANAET (accession number: AP011532) and MRE50T (accession number: AM114193) were used to calculate the ANI (Average Nucleotide Identity) values by the Blast-based method with the Jspecies package . Please note, although the genome for MRE50T was constructed as a complete metagenome from an enrichment before its isolation , the fact that MRE50T was the only archaeal member in that enrichment includes that its genome was well represented by the metagenome , . […]

Pipeline specifications

Software tools MEGA, JSpeciesWS
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Methanocella conradii, Oryza sativa, Methanocella paludicola
Chemicals Methane