Additional file 1: of Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011

Detailed methods. Description of metagenome and metatranscriptome sample processing, sequencing, and data analysis, including internal standard additions and analyses. Figure S1. Hierarchical clustering of the Bray-Curtis dissimilarities in the taxonomic binning of transcripts from two microbial size fractions from 50 % water depth at each of five locations in the Amazon River and from the surface water at the Tapajós station

Transcriptomic versus biogeochemical data.

<p>Panel A: The correlation between diatom microscope counts and log RuBisCO Form ID transcripts counts. Panel B: The inverse relationship of carbonic anhydrase transcript abundance to DIC concentration. Panel C: The inverse relationship between polyphosphate kinase transcript abundance and phosphate concentration. Station 2 and 25 had little or no phosphate, due to the diatom bloom, however <i>ppk</i> was not upregulated.</p

Metadata for stations sampled in the ARP.

<p>Measurements taken in conjunction with the metatranscriptomes are listed here. Asterisks highlight where concentration of the variable was below limit of detection.</p

Sample size-normalized gene counts for the 31 biogeochemically-relevant genes.

<p>Values are the average of the duplicate samples, per 10 million sequences. Bolded/underlined numbers highlight the highest expression for that gene.</p

Salinity map of the May/June 2010 Amazon River Plume cruise aboard the RV Knorr.

<p>Salinity (PSU) from the underway system along the ship track was augmented with National Oceanographic Data Center profiles in regions of low coverage then interpolated and contoured.</p

Ratios of transcript abundance at stations 10:2 (black bars) and 25:2 (white bars).

<p>Station 10 has very high levels of eukaryotic nitrate transporter as well as chitin synthase compared to station 2. Note log scale. Stations 2 and 25 perform similar functions in the ARP. Thus the plot of the ratio of Station 25: Station 2 has smaller values than the ratio of stations 10 and 2.</p