Nutrients and Chlorophyll-A concentrations measured in samples collected in this study
All Chl-A measurements as well as nutrient measurements in October through April are courtesy of the Caron lab, USC. Values in bold are below the instrument detection limit.
Comparison between read recruitment to functional genes using a protein HMM vs. reciprocal blast
Total reads per sample for normalization purposes are indicated in the bottom row.
Placement of assembled proteorhodopsin ORFs in the MicRhoDE tree clusters indicates that locally assembled rhodopsins represent much of the Prd diversity
The number of reads (pooled from all samples) that mapped to the assembled ORFs from metatranscriptomes (MT) and metagenomes (MG) was significant compared to number of pooled reads mapped to the curated proteins from MicRhoDE.
Evenness of rhodopsins by clade across samples
Each bar represents the Shannon index of evenness based on relative abundance of rhodopsin clades by site and month. Evenness in metagenomes is denoted by full bars, and in metatranscriptomes by striped bars.
A comparison of phototrophic mechanisms expanding on figure 2 (main text)
Normalized gene abundance (A) and expression (B) of phototrophic mechanisms per sample
Normalized relative abundance of phototrophic mechanisms per sampling site expanding on figure 2 (main text)
Variability of phototrophic mechanisms per genome in metagenomes from the three sampling locations of the San Pedro Channel (n=4, shown in Figure 1: the Y-axis denotes the percentage of genomes with the particular phototrophic mechanism normalized to recA gene (see methods). psaA for oxygenic photosynthesis, prd for proteorhodopsin and pufM for aerobic anoxygenic photosynthesis.
Maximum-likelihood tree of PSI protein (psaA) sequences used to build the HMM and to recruit short reads with pplacer
Bacterial sequences appear in blue, viral in red, eukaryotic in green and assembled ORFs in black.
Read recruitment to functional genes using a Hidden Markov Model (HMM) vs. reciprocal blast
Comparison of relative abundance (number of reads recruited over total number of reads per sample) of functional genes using reads recruited by HMM or reciprocal blast in (A) metagenomes and (B) metatranscriptomes