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\section{Methods}  \subsection{Sample Collection}  Triplicate leaf and root samples were taken of an individual of each distinct species found at each site. A plant was uprooted with gloved hands and swirled in source river water to dislodge sediment. Alcohol-sterilized surgical scissors were used to cut approximately one inch of leaf tissue from the center of the length of the leaf. Alcohol-sterilized surgical scissors were also used to cut 5-10 roots. These were stored at room temperature in 500 µl of Zymo Xpedition buffer () in a 2 mL sterile tube until DNA extraction.  \subsection{Sample Processing}  DNA extraction was done using the MoBio PowerSoil DNA Extraction Kit () with minor adjustments to the provided protocol. Triplicate leaf and root samples were taken of an individual of each distinct species found at each site.  These adjustments included the following: heating the sample were stored  at 65ºC for 5 minutes after adding C1 solution to dissolve a precipitate that forms from C1 solution and Zymo; eluting room temperature  in 50 µl of nuclease-free water Zymo Xpedition buffer  () instead of 100 µL of C6 solution. [***<--Check these!!***]   The PCR protocol used was in  a combined and modified version of 2 mL sterile tube until DNA extraction. DNA was extracted from  the Earth Microbiome Project's PCR protocol () samples  and the Joint Genome Institute's PNA used as template in  PCR protocol (). We amplified amplification of  the [something, look [look  up] region on the 16S SSU rRNA gene using bacteria/archaeal primers 515F and 806R (Caporaso paper from protocol). Instead of using an annealing temperature of 50ºC from the EMB protocol, we used 55ºC. We also did not run the PCR reactions in triplicate as in the Earth Microbiome Project protocol. We used mitochondria and chloroplast PNA blockers (50µM). primers.  Samples were cleanedusing Ampure magentic beads  andadapter (). Samples were then  pooled to 1ng/µL DNA concentration and sequenced on an  Illumina MiSeq()  at the UC Davis Genome Center Sequencing Core (). To view the full sample processing protocol used, go to [?].  \subsection{Sample Analysis} Core.  Sequences were demultiplexed using a custom in-house script (github link from Guillaume). script.  Fasta files were then analyzed using the standard Qiime(ref qiime here?)  workflow for analyzing microbial community data (werner lab page??). data.  Figures and statistics  were produced in R using[some package]. We used unweighted UniFrac to produce  the PCoA plots and did some stats (adonis thing in R??). phyloseq package. The figures produced use unweighted UniFrac.