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software package using the Mothur NAST aligner  \citep{DeSantis2005,schloss2009}. Reads that did not align to the expected  region of the SSU rRNA gene were discarded. After expected error and alignment  based quality control. The remaining quality controlled  reads were annotated using the “UClust” taxonomic annotation framework in \citep{caporaso2010,edgar2010}. We used 97\% cluster seeds from the Silva SSU  rRNA database (release 111Ref)  \citep{quast2013} as reference for taxonomic annotation (provided on the QIIME website) \citep{quast2013}. Quality control  screening filtered out 344,472 or 1,720,480 raw sequencing reads. Reads  annotated as "Chlorloplast", "Eukaryota", "Archaea", "Unassigned" or  "mitochondria" were culled from the dataset.  Sequences were distributed into OTUs with a centroid based clustering algorithm (i.e. UPARSE \citep{edgar2013}). The centroid selection also included robust chimera screening \citep{edgar2013}. OTU centroids were established at a threshold of 97\% sequence identity and non-centroid sequences were mapped back to centroids. Reads that could not be mapped to an OTU centroid at greater than or equal to 97\% sequence identity were discarded. For phylogenetic reconstruction, alignment was performed with SSU-Align \citep{nawrocki2009,nawrocki2013}. Columns in the alignment that were aligned with poor confidence ($<$ 95\% of characters had posterior probability $>$ 95\%) were not considered when building the phylogenetic tree. FastTree Additionally, the  alignment was trimmed to coordinates such that all sequences in the alignment  began and ended at the same positions.FastTree  \citep{price2010} was used with default parameters to build the phylogeny. NMDS ordination was performed on weighted Unifrac \citep{lozupone2005} distances between samples. The Phyloseq \citep{mcmurdie2013} wrapper for Vegan \citep{oksanen2015} (both R packages) was used to compute sample values along NMDS axes. The 'adonis' function in Vegan was used to perform Adonis tests (default parameters) \citep{Anderson2001a}. We used DESeq2 (R package), an RNA-Seq differential expression statistical  framework \citep{love2014}, to identify OTUs that were enriched in high