David Coil edited Methods.md  over 8 years ago

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**METHODS**  Cells were initially grown on plates containing either Reasoner's 2A agar (R2A), or lysogeny broth agar (LB). LB was made with 10 g tryptone, 10 g NaCl, and 5 g yeast extract per liter. A clear preference for growth on LB was observed and so was used for all subsequent experiments. Salt tolerance was measured by growth in liquid media (25 °C) from 0% to 20% w/v NaCl. pH tolerance was measured by growth in liquid media (25 °C) from pH 3.4 to pH 8.0. Temperature preference was measured by growth in liquid culture across the range 4 °C to 30 °C. Growth in microgravity (OD600)  was measured aboard the International Space Station (ISS). Cell morphology, motility, and presence/absence of flagella were examined by light microscopy (Zeiss Axio Lab.A1) and transmission electron microscopy (TEM). Cell cultures in either exponential or stationary phase were prepared for TEM by the UC Davis Electron Microscopy lab as follows. 400 mesh copper grids with formvar/carbon support film (Ted Pella, Inc., Redding, Ca.) were placed on dental wax. A 10 μl drop of fixed or unfixed sample was placed onto the grid and left in a dust-free environment for 10 minutes. Then excess was wicked off with filter paper. A 10 μl drop of 1% PTA pH 5.8 (phosphotungstic acid) or 1% ammonium molybdate in double-distilled water was added to the grid and wicked off immediately. Grids were allowed to air-dry completely before viewing in a Philips CM120 (FEI/Philips Inc, Hillsborough, Or.) electron microscope at 80KV. 

**Respiratory quinones, polar lips, and fatty acids**  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). https://www.dsmz.de/services/services-microorganisms/identification/analysis-of-polar-lipids.html](https://www.dsmz.de/services/services-microorganisms/identification/analysis-of-polar-lipids.html), [https://www.dsmz.de/services/services-microorganisms/identification/analysis-of-respiratory-quinones.html](https://www.dsmz.de/services/services-microorganisms/identification/analysis-of-respiratory-quinones.html), [https://www.dsmz.de/services/services-microorganisms/identification/analysis-of-cellular-fatty-acids.html](https://www.dsmz.de/services/services-microorganisms/identification/analysis-of-cellular-fatty-acids.html).  **16S rDNA, genome sequencing, and phylogenetic analysis**