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\section{Methods}  Experimental design  Triplicate leaf and root samples were taken from one of an  individual of each distinct species of SAV  found at each site. These site along the Potomac River. Twelve sites  were stored at room temperature visited  in total – 6 along  the Zymo Xpedition stabilization Potomac River,  and lysis buffer until 6 along the James River.  DNA extraction. The MoBio PowerSoil was extracted  from the samples and used as template in PCR amplification of upon return to  the V3-V4 region University  of the 16S SSU rRNA gene. Samples were cleaned and pooled to 1 ng/µL California, Davis.  DNA concentration and sequenced was PCR amplified, checked  on an Illumina MiSeq at a 1% agarose gel for amplification, cleaned, and pooled for sequencing. Sequencing was then done through  the UC Davis Genome Center Sequencing Core. Sequences weredemultiplexed using a custom in-house script. Fasta files were  then analyzed processed  using the QIIME a basic Qiime  workflow foranalyzing  microbial community data (an Ipython notebook detailing the scripts used for analysis is included in the data submission on Figshare. Figures ecology, and figures  and statistics were produced in R using the phyloseq package. Sampling protocol and storage  Any observed SAV species were sampled. Plants were drawn and distinguishing characteristics, like leaf morphology, were noted. A single plant of each species at a particular site 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 Lysis/Stabilization Solution (Zymo Research, Irvine, CA) in a 2 mL sterile tube until DNA extraction.  Nucleic acid isolation  DNA extraction was done using the Mo Bio PowerSoil DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, CA) with minor adjustments to the provided protocol. These adjustments included the following: heating the sample at 65ºC for 5 minutes after adding C1 solution to dissolve a precipitate that forms from C1 solution and Zymo Xpedition Lysis/Stabilization Solution; bead beating for 1 minute after heating with C1 solution; eluting in 50 µl of nuclease-free water instead of 100 µL of C6 solution. DNA concentration was determined using a Qubit fluorometer (Thermo Fischer Scientific, Carlsbad, CA).  Amplification  We use the bacterial/archaeal primers 515F/806R with an inhouse barcode system designed by Aaron Darling.   There are 25 each of forward and reverse primer barcodes that can be combined to make 625 total unique barcode combinations. The forward and reverse primers are at 10µM each and are mixed in equal parts to create the 10µM combinations (ex. one tube might contain a mix of F23 and R5). More about the primers can be found here: Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J.