deletions | additions       diff --git a/Methods.md b/Methods.md  index d5ea323..4dea476 100644  --- a/Methods.md  +++ b/Methods.md 
...
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 10μl drop of fixed or unfixed sample was placed onto the grid and left in a dust-free environment for 10 min. Then excess was wicked off with filter paper. A 10μl 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.  Catalase Oxidase activity was measured using a solution of tetramethyl-p-phenylenediamine  and oxidase activity, as well as catalase activity was measured by  the hydrolysis addition of hydrogen peroxide to plated cells. The hydrolosis  of starch and casein, casein  were assayed measure  by standard methods. plate methods (beef agar with soluble starch and iodine staining, and milk agar with a pancreatic digest of casein respectively).  Carbon source utilization was assayed using the Phenotypic MicroArray(TM) services offered by Biolog, Inc. using their standard procedures for gram-negative bacteria as follows. Colonies were grown on blood agar at room temperature and suspended in IF-0a inoculating fluid (Biolog) to a density of 42% transmittance. The cell suspension was diluted 1:6 in IF-0a plus 1x Dye H (Biolog) and a carbon source utilization MicroPlate (PM1; Biolog) was inoculated with 100μl per well. The PM1 microplate was incubated at 23°C and read by the OmniLog instrument every 15 minutes for 96 hours. Duplicate sets of OmniLog data were converted to average read value and a threshold of 78 was required in both replicates for a positive call. **Respiratory quinones, polar lips, and fatty acids** 
...
FastTree \cite{19377059} was used with default settings to build an unrooted phylogeny. Dendroscope 3 \cite{22780991} was used to view and edit the phylogenetic tree in order to 1) root the tree with a clade that is sister to a well-supported clade containing strain Coronado(T), 2) prune the tree to remove taxa outside the clade containg the outgroup, and 3) "clean up" the tree.