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\section{Methods}  Experimental design  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 was extracted from the samples upon return to the University of California, 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 were then processed using a basic Qiime workflow for microbial 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 \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.   Library preparation and sequencing  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.  Read quality assessment and Data Analysis  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 workflow for analyzing microbial community data (http://www.wernerlab.org/teaching/qiime/overview). Figures were produced in R using the phyloseq package. We used unweighted UniFrac to produce the figures for our data, and Qiime to calculate statistics on alpha and beta diversity data.