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Supplemental Information

Figure 1: Growth curves of three phylogenetically distinct representatives of marine bacterioplankton in nutrient rich marine broth medium

Cells were harvested for proteomic analysis at the time points indicated by arrows for exponential phase (solid arrows) and stationary phase (hatched arrows) respectively. Error bars denote the standard deviation of three biological replicates. If not visible, error bars are within symbols.

DOI: 10.7287/peerj.preprints.1804v1/supp-1

Figure 2: Overall growth phase-associated changes in proteomes

(A, C, E) Relative abundances of detected proteins grouped into top level SEED categories: (A) MED92, (C) MED193 and (E) MED134. The three replicates are shown for exponential phase (open circles) and stationary phase (filled circles). Note the log scale on Y-axes. (B, D, F) Counts (y-axis) of increasing (right-pointing triangles), stable (circles) and decreasing proteins (left-pointing triangles) and relative abundances (size of symbols): (B) MED92, (D) MED193 and (F) MED134. Proteins that belong in more than one category were counted in all. Note that y-axes have been cut at 200; categories that exceed 200 were inserted at 200 with a label denoting the proper count.

DOI: 10.7287/peerj.preprints.1804v1/supp-2

Figure 3: Top 50 most abundant significantly differentially expressed proteins

Relative abundance and log2 fold changes for the top 50 most abundant significantly differentially expressed proteins. (A, C and E) proteins decreasing from exponential growth to stationary phase. (B, D and F) proteins increasing from exponential growth to stationary phase. (A, B) MED92; (C, D) MED193; and (E, F) MED134. Color codes denote the different functional categories in the SEED classification, Blue: Protein metabolism, Green: Membrane transporters, Orange: Stress response, Purple: Carbon metabolism, Grey: Amino acids and derivatives and Yellow: Respiration.

DOI: 10.7287/peerj.preprints.1804v1/supp-3

Figure 4: Changes in relative proportions of membrane transporter categories across growth phases

(A, C, E) Exponential phase in (A) MED92, (C) MED193 and (E) MED134. (B, D, F) Stationary phase in (B) MED92, (D) MED193 and (F) MED134. The areas of rectangles are proportional to relative abundances of categories at the three levels of the TC classification. Top-level categories are denoted with colored rectangles and labels in bold; second level categories are normal font labels spanning several rectangles; and third level categories have labels inside rectangles. Transporter identification according to TC categories.

DOI: 10.7287/peerj.preprints.1804v1/supp-4

Figure 5: Carbon metabolisms

(A, C, E) Relative abundances, averaged over triplicates for each growth phase, for enzymes in five important carbon metabolisms in (A) MED92, (C) MED193 and (E) MED134. Significantly differentially abundant proteins have names in bold font. (B, D, F) Glycolysis (EMP), TCA cycle and glyoxylate shunt BioCyc pathways in (B) MED92, (D) MED193 and (F) MED134. Heatmap indicating log2 fold changes of stationary phase in relation to exponential phase. Grey arrows indicate stable, i.e. not significantly differentially abundant proteins. Thin black arrows indicate non detected proteins.

DOI: 10.7287/peerj.preprints.1804v1/supp-5

Figure 6: Phosphorus metabolism in all three isolates

List of significantly increasing and decreasing proteins in the SEED category phosphorus metabolism during transition into stationary phase. (A) MED92; (B) MED193; (C) MED134.

DOI: 10.7287/peerj.preprints.1804v1/supp-6

Individual protein abundances in MED92

Identified proteins with estimated fold change (FC and log2FC columns), false discovery rate (localfdr), readings per sample (exp1-3 for exponential phase; stat1-3 for stationary phase) and various other statistics. Green shades in the log2FC column indicate higher abundance in stationary phase, yellow shades indicate lower; the stronger the color, the larger the difference between growth phases. False discovery rates less than 5% are indicated with green color, above with red.

DOI: 10.7287/peerj.preprints.1804v1/supp-7

Individual protein abundances in MED193

Identified proteins with estimated fold change (FC and log2FC columns), false discovery rate (localfdr), readings per sample (exp1-3 for exponential phase; stat1-3 for stationary phase) and various other statistics. Green shades in the log2FC column indicate higher abundance in stationary phase, yellow shades indicate lower; the stronger the color, the larger the difference between growth phases. False discovery rates less than 5% are indicated with green color, above with red.

DOI: 10.7287/peerj.preprints.1804v1/supp-8

Individual protein abundances in MED134

Identified proteins with estimated fold change (FC and log2FC columns), false discovery rate (localfdr), readings per sample (exp1-3 for exponential phase; stat1-3 for stationary phase) and various other statistics. Green shades in the log2FC column indicate higher abundance in stationary phase, yellow shades indicate lower; the stronger the color, the larger the difference between growth phases. False discovery rates less than 5% are indicated with green color, above with red.

DOI: 10.7287/peerj.preprints.1804v1/supp-9

Top SEED category summaries

Approximate (order of magnitude precision) relative abundances of proteins summed over top categories of the SEED classification. Proteins classified in more than one category were counted in all categories. The calculation of relative 54abundances counted each protein only once. Log2 fold changes (log2fc) calculated as the ratio between means in stationary phase divided by means in exponential phase. Counts and abundances of the three protein groups, increasing (“Up”), stable and decreasing (“Down”) in the three isolates.

DOI: 10.7287/peerj.preprints.1804v1/supp-10

Relative protein abundances summed over second level SEED categories

Approximate (order of magnitude precision) relative abundances of proteins summed over second level categories of the SEED classification. Proteins classified in more than one category were counted in all categories. The calculation of relative abundances counted each protein only once. Log2 fold changes (log2fc) calculated as the ratio between means in stationary phase divided by means in exponential phase.

DOI: 10.7287/peerj.preprints.1804v1/supp-11

Relative protein abundances summed over third level SEED categories

Approximate (order of magnitude precision) relative abundances of proteins summed over third level categories of the SEED classification. Proteins classified in more than one category were counted in all categories. The calculation of relative abundances counted each protein only once. Log2 fold changes (log2fc) calculated as the ratio between means in stationary phase divided by means in exponential phase.

DOI: 10.7287/peerj.preprints.1804v1/supp-12

Summary of transporter families

Number of detected and differentially abundant protein in the three strains per TCDB transporter family.

DOI: 10.7287/peerj.preprints.1804v1/supp-13

Proteins detected in MED92 with their TCDB classifications

The trsphierarchy field describes each protein's place in the TCDB hierarchy. See the TCDB website for explanations (http://www.tcdb.org/superfamily.php). All the other fields, except trspfamily, were taken from the corresponding MED92 SAM table (S1).

DOI: 10.7287/peerj.preprints.1804v1/supp-14

Proteins detected in MED193 with their TCDB classifications

The trsphierarchy field describes each protein's place in the TCDB hierarchy. See the TCDB website for explanations (http://www.tcdb.org/superfamily.php). All the other fields, except trspfamily, were taken from the corresponding MED193 SAM table (S2).

DOI: 10.7287/peerj.preprints.1804v1/supp-15

Proteins detected in MED134 with their TCDB classifications

The trsphierarchy field describes each protein's place in the TCDB hierarchy. See the TCDB website for explanations (http://www.tcdb.org/superfamily.php). All the other fields, except trspfamily, were taken from the corresponding MED134 SAM table (S3).

DOI: 10.7287/peerj.preprints.1804v1/supp-16

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Saraldevi Muthusamy conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Daniel Lundin analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Rui MM Branca conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Federico Baltar conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

José M González analyzed the data, reviewed drafts of the paper.

Janne Lehtiö conceived and designed the experiments, reviewed drafts of the paper.

Jarone Pinhassi conceived and designed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

Proteomics data not yet deposited, but will be.

Funding

This research was supported by the grants from the Göran Gustafsson Foundation for Research in Natural Sciences and Medicine, the Swedish Research Council VR, the Crafoord Foundation, and was also funded by the BONUS BLUEPRINT project, which has received funding from BONUS, the joint Baltic Sea research and development programme (Art 185), funded jointly from the European Union's Seventh Programme for research, technological development and demonstration and from the Swedish Research Council FORMAS to J.P. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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