David Coil edited Methods.md  over 8 years ago

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Cells were grown to post exponential phase (~72 hours) in 1 L of LB at 23 °C for large-scale biomass production, then centrifuged to pellet cells and lyopholized (VirTis Freezemobile). Analysis of respiratory quinones/polar lipids and fatty acids were carried out by the Identification Service, DSMZ, Braunschweig. Germany. Protocol details and references can be found at the following DSMZ pages; [polar lipids](https://www.dsmz.de/services/services-microorganisms/identification/analysis-of-polar-lipids.html), [respiratory quinones](https://www.dsmz.de/services/services-microorganisms/identification/analysis-of-respiratory-quinones.html), [cellular fatty acids](https://www.dsmz.de/services/services-microorganisms/identification/analysis-of-cellular-fatty-acids.html).  **16S rDNA rDNA, genome sequencing,  and Genome Sequencing** phylogenetic analysis**  Genomic DNA was extracted using a Wizard Genomic DNA Purification Kit (Promega). A nearly full-length 16S rRNA gene sequence was amplified using the 27F (5'-AGAGTTTGATCMTGGCTCAG-3') and 1391R (5'-GACGGGCGGTGTGTRCA-3') "universal" primers. **(add a citation for the primers)**. Sanger sequencing was provided by the College of Biological Science UC-DNA Sequencing Facility (UC Davis). This DNA was also used for Illumina sequencing of the draft genome as described elsewhere (Coil and Eisen, in press). The genome sequence was annotated using the RAST server \cite{Aziz_2008} \cite{Overbeek_2013}.