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\section{Methods}  Triplicate leaf and root samples were taken of an individual of each distinct species of SAV found at each site along the Potomac River. Twelve sites were visited in total – 6 along the Potomac River, and 6 along the James River. DNA 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 extracted 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 samples upon return to center of  the University length  ofCalifornia, Davis. DNA was PCR amplified, checked on a 1\% agarose gel for amplification, cleaned, and pooled for sequencing. Sequencing was then done through  the UC Davis Genome Center Sequencing Core. Sequences leaf. Alcohol-sterilized surgical scissors  were then processed using a basic Qiime workflow for microbial ecology, and figures and statistics also used to cut 5-10 roots. These  were produced stored at room temperature  in R using the phyloseq package. 500 µl of Zymo Xpedition Lysis/Stabilization Solution (Zymo Research, Irvine, CA) in a 2 mL sterile tube until DNA extraction.  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 DNA  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 extracted  from the center of the length of the leaf. Alcohol-sterilized surgical scissors were also used samples upon return  to cut 5-10 roots. These were stored at room temperature in 500 µl the University  of Zymo Xpedition Lysis/Stabilization Solution (Zymo Research, Irvine, CA) in a 2 mL sterile tube until DNA extraction. California, Davis.  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). We use the bacterial/archaeal primers 515F/806R with an inhouse barcode system designed by Aaron Darling \cite{Caporaso_2012}. 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.   Samples were cleaned with Agencourt AMPure XP magnetic beads and adapter (Beckman Coulter, Indianapolis, IN) and quantified for amplicons with Qubit fluorometer (Thermo Fischer Scientific, Carlsbad, CA). Samples were pooled to 1 ng of DNA per sample, and sent in for sequencing on an Illumina MiSeq (Illumina, San Diego, CA) at the UC Davis Genome Center Sequencing Core.  Sequences were demultiplexed using a custom in-house script (https://github.com/gjospin/scripts/blob/master/Demul_trim_prep.pl), which automates quality assessment and trimming. Fasta files were then analyzed using a standard Qiime QIIME \cite{Caporaso_2010}  workflow for analyzing microbial community data (http://www.wernerlab.org/teaching/qiime/overview). Figures were produced in R \cite{}  using the phyloseq \cite{McMURDIE_2011}  package. We used unweighted UniFrac \cite{Lozupone_2005}  to produce the figures for our data, and Qiime QIIME  to calculate statistics on alpha and beta diversity data.