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Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities

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Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities https://t.co/E0lVg0eVub The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex ch…
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Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities https://t.co/BUfDqcqLsn
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Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities https://t.co/4WFNOeBOv4
Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities https://t.co/E0lVfZXkCD The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex ch…
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Supplemental Information

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.

DOI: 10.7287/peerj.preprints.26950v2/supp-1

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.

DOI: 10.7287/peerj.preprints.26950v2/supp-2

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.

DOI: 10.7287/peerj.preprints.26950v2/supp-3

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.

DOI: 10.7287/peerj.preprints.26950v2/supp-4

A comparison of phototrophic mechanisms expanding on figure 2 (main text)

Normalized gene abundance (A) and expression (B) of phototrophic mechanisms per sample

DOI: 10.7287/peerj.preprints.26950v2/supp-5

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.

DOI: 10.7287/peerj.preprints.26950v2/supp-6

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.

DOI: 10.7287/peerj.preprints.26950v2/supp-7

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

DOI: 10.7287/peerj.preprints.26950v2/supp-8

Maximum-likelihood tree of PSII protein sequences (pufM and psbA) used to build the HMM and to recruit short reads with pplacer

pufM leaves are colored red and psbA leaves in black.

DOI: 10.7287/peerj.preprints.26950v2/supp-9

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Ella T Sieradzki conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Jed A Fuhrman conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Sara Rivero-Calle analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Laura Gómez-Consarnau conceived and designed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

All raw data (16S/18S, metagenomes and metatranscriptomes) can be found on EMBL-ENA under project number PRJEB12234. Metatranscriptomics sequences accession numbers are ERS1864892-ERS1864903, and negative control library sequences accession number is ERR2089009. Metagenomic sequences accession numbers are ERS1869885-ERS1869896 and negative control accession number is ERS1872073.

Assembled amino acid sequences of Prd, PsaA and RecA can be found at https://figshare.com/collections/Dimensions_of_Biodiversity_-_San_Pedro_Channel/4099757 .

Data Deposition

The following information was supplied regarding data availability:

Chlorophyll-A and nutrient measurements are provided in supplementary table S1.

Funding

This work was funded by NSF grant 1136818, NSF grant OCE1335269 and The Gordon and Betty Moore Foundation Marine Microbiology Initiative grant GBMF3779. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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