README: Organic compounds drive growth in phytoplankton taxa from different functional groups

https://doi.org/10.5061/dryad.zkh1893g8

Raw data, R scripts and supplementary material

Description of the data and file structure

This data contains:
-Raw data of cell counts (ecoplates) and the associated R script to e.g. apply the t-test, plotting etc.#

-Sequencing data (1 fasta document, 15 sequence PDFs named by strain ID)

-Supplementary figures (S1-S3)

-Supplementary tables (S1 - S4)

Sequencing data refers to the identification of the strains as indicated in the supplementary data table S1. The fasta data contains the strain ID in the header of each sequence which connects it with table S1. The fasta data can be used with the ncbi database to identify sequences (ncbi blast). Results of this process and further information included (e.g. morphology) are shown in the supplementary data (tab. S1). The PDFs are provided by the sequencing company and imply the quality of each base identified by the colour code. Again, the name of the PDF contains the strain ID and therefore can be linked with table S1. Note that two of our 17 strains could not be sequenced (see information in table S1).

Further information concerning the raw data of cell counts

This document shows the raw data i.e. cell counts from the EcoPlates

Column A, B and C show the strain ID, taxon and functional group. See also supplementary data tab. S1 for further details.

Column D names the plate replicate. Each strain and light treatment contains (at least) 3 valid plate replicates. See also tab. S2.

Column E indicates the light treatment.

Column F shows the well. Each well contains a certain organic compound (or none in case of the control). This information can be obtained from the R script or online sources.

Column G shows the actuall cell count / 10 µL.

Column H indicates if the plate was valid. Further information about how this was decided can be obtain from further supplementary data (tab. S2).

Further information concerning supplementary fig. S1.1-S1.24:

These figures show raw cell count data per plate and data merged across plates for each strain and light treatment.

Further information concerning supplementary fig. S2:

Figure S2 shows the developement of cell counts of the different strains and light treatment prior to the transfer to the ecopltes, which was used to evaluate if the strain was growing sufficiently.

Further information concerning supplementary fig. S3.1-S3.2:

These figures show the number of posititive and negative effects per strain and cell density.

Further information concerning supplementary fig. S3.3-S3.10:

Figures S3.3-S3.7 show additional graphical data for the cases were significantly positive or negative effects were exclusively achieved in the densest culture included (per strain and light treatment) as derived from S3.1 and S3.2 . This is to show that the overall results discussed in this study – i.e. data merged across plates – cannot be primarily lead back to significant effects found on the plates with the densest culture alone (i.e. those where nutrient limitation and growth promotion by bacterial remineralisation could play a role). Where effects were significant in the data merged across plates, patterns of being higher or lower than the control can be observed across different plates in most cases (and not only in the densest plate), though they were not always significant on single plate level. The other way around, significant effects on the densest plates did not lead to significant results across the plate, if they were not reflected to certain (not significant) degree on the other plates. This is precisely/ exemplarily highlighted by the annotations in the plots, with the colour scheme shown here.

Note that in all other strains, significant effects appeared across strain densities. For these cases we only show three examples (fig. S3.8-S3.10) to furthermore highlight that there is no overall positive correlation of effects with strain density across strains. Data from other strains are not explicitely shown here, but the plots with the final results (normalised and merged data; including assignment of significance) can be found in the supplementary data (fig. S1.1-S1.23) where also the data of the single plates is shown (without assignment of significance, but to show general patterns).

While some effects only appearing on single plates might be interesting ecologically, by merging the data across the different plates our results became more independent of potential random effects, i.e. we significantly diminished the chance of identifying false positive effects. This was our primary aim and we do in turn accept the loss of details to be discussed in the manuscript.

Further information concerning supplementary tab. S1:

This document shows relevant information concerning the strains cultivation, origin and identification.

Clumn A, G, O, V, Y show the strain ID. The repeat is needed to be able to display the table as pdf version, in case neither csv nor xls are readable.

The strain ID which connects this table with tab. S2 and tab S3 as well as provided sequencing data.

Final strain identity

Column B shows the functional group, which is based on the genus (column C) and size (column T)

Column C and D show the identified genus and possible taxon based on the identification process showed in columns L – S

Environmental & cultivation parameters

Column E shows the origin (i.e. sampling station in the Elbe estuary), while the number indicates the approximate distance to the spring of the Elbe river.

Column F shows the season the strain originated from

Column H and I show the latitude and longitude.

Columns J and K show the incubation temperature and temperature in the original water sample, respectively.

Columns L and M show the turbidity and salinity during sampling.

Identification process

Column P show the DNA concentration in the extract used for sequencing.

Column Q indicates the type of primer used.

Column R shows a subjective proxy for the quality of the sequences obtained based on the clarity of identification of the singles bases (and length). Respective PDF data showing the sequences and quality of base identification are provided with the additional data.

Column S and T show the query length and % overlap with data base sequences (based on highest e value)

Column U indicates which database sequence (taxon) the strains sequence best fitted to (based on O and P)

Column W shows morphological criteria included in the taxa identification process.

Column X gives further information why we assigned a certain taxon rather than another, and why/where certain strains could not be identified.

Column Z shows which taxon where identified as pico or nano (criterion see there)

Other

Column AA gives further ecoplate related comments about e.g. which strains where included in dark experiments.

Further information concerning supplementary tab. S2:

Here we provide metadata for the ecoplates experiments including e.g. culture preparation.

Each Line indicates an ecoplate measured with it’s additional information.

Column A, J, L, W and AG show the row number for orientation in the pdf version of this table.

Column B shows the strain ID. The strain ID connects this table with tab. S1 and tab. S3. Further Infos about the strains can be found in tab. S1, where e.g. the taxon is shown, that is needed to relate the data to what is written in the manuscript. (In the manuscript, the strain ID is only use where necessary to differentiate different strains of the same genus)

Column C shows the light treatment, which either 100 % (159 µEinstein/ m2*s) or reduced (usually -75% except for pilot studies)

Column D shows the replicate number of the ecoplates. Usually replicates have consecutive numbers. Ecoplates run under reduced light availability are additionally labeled with ‘D’ for dark. A is used to imply Ampicillin.

Column E – H indicate when the culture was prepared i.e. added to the ecoplates on day 0 (d0) and when it was prepared for measurement on day 1 (d1).

Column I shows if the ecoplate run was valid i.e. included in the paper.

Column K gives further information, e.g. why measurement is invalid.

Column M-V and X-AF show cell counts/ 20 µL conducted prior to, during and after the ecoplates measurements. This was done to track the development of the cultures and ensure exponential growth. The data is shown graphically in the supplementary figure S2. Note that in some cases data is upscaled from 10 µL measurements.

Column AH shows examples for the change in cell count within 24 h as % as derived from cell count information in M-V and X-AF. Which days this concerns is shown in AI (e.g. d0 – d(-1) means cell count of day of plating minus cell count on day before plating).

Further information concerning supplementary tab. S3:

This documents shows all p-values of the t-test conducted in the data analyses.

Row 2-8 show the p-values that refer to the comparison between the dark and light experiment. Those do not refer to a certain compound but the overall ratio between organic carbon treatments and the control.

Row 9-721 show the p-values that refer to the comparison of the cell counts achieved in the presence of a certain organic compound compared to the cell count in the organic-free control. Data was merged across plates (after normalizing by the plates mean) per strain and light treatment before the t-test was carried out. That means that each p-value refers to the comparison of 9 organic treatment values (3 wells per plate * 3 plates) with the respective 9 control values.

Column A shows the strain concerned. The strain ID connects this data sheet with tab. S1 and tab. S2. Tab. S1 gives further information about the strains, e.g. the taxon, relevant to relate the results to the manuscript text. (In the manuscript, the strain ID is only use where necessary to differentiate different strains of the same genus)

Column B and C indicate the compound and compound type referred to. As described above, row 2-8 concern all compounds.

Column D indicates which light treatment the data refers to. In row 2-8 it aditionally shows which light treatments were compared in the t-test.

Column E shows the p-value.

Column F shows if the p-value was <=0.05 (significant) or >0.05 (not significant)

Column G indicates if the p-value refers to a comparison of organic compound vs. organic-free control or to a comparison between different light treatments. As mentioned above that differs between the different rows.

Column H shows if effects were negative or positive. This includes non-significant effects. In row 9-721 a positive effect for instance means that the normalized mean cell count in the treatment with the compound was higher than the mean cell count of the organic-free control. In row 2 for instance, “negative effect” indicates that ratio between organic treatments and controls was overall lower in the dark than in the light in strain N7.

Further information concerning supplementary tab. S4:

Column A shows the strain ID (see also supplementary table S1)

Column B shows the date when the measurements were carried out

Column C-E show the cell counts of the 3 replicates à 10 µL each

Column F shows the standard deviation in % referring to the mean

Column G gives further descriptive information

Sharing/Access information

Data is original and not available elsewhere.

Code/Software

Cytometric data (cell counts) from the ecoplates of the ecoplates were processed and analysed in R (version 4.1.3), including the packages tidyverse (version 1.3.2), stats (version 4.1.3) and ggplot2 (version 3.4.0). The R script is structured by different headers/ comments leading through the script. The R script can be used to process the raw data table (after transformation to csv) and reproduce results.