DOI: 10.5061/dryad.zkh1893g8
title: Organic compounds drive growth in phytoplankton taxa from different functional groups

description: Phytoplankton are usually considered autotrophs, but an increasing number
 of studies shows that many taxa are able to also utilise organic carbon.
 Acquiring nutrients and energy from different sources might enable an
 efficient uptake of required substances and provide a strategy to deal
 with a varying resource availability, especially in highly dynamic
 ecosystems such as estuaries. In our study we investigated the effects of
 31 organic carbon sources on the growth (proxied by differences in cell
 counts after 24 h exposure) of 17 phytoplankton strains from the Elbe
 estuary spanning four functional groups. All of our strains were able to
 make use of at least 1 and up to 26 organic compounds for growth.
 Pico-sized green algae such as Mychonastes, as well as the nano-sized
 green alga Monoraphidium in particular were positively affected by a high
 variety of substances. Reduced light availability, typically appearing in
 turbid estuaries and similar habitats, resulted in an overall poorer
 ability to utilise organic substances for growth, indicating that organic
 carbon acquisition was not primarily a strategy to deal with darkness. Our
 results give further evidence for mixotrophy being an ubiquitous ability
 of phytoplankton and highlight the importance to consider this trophic
 strategy in research.
description: # Organic compounds drive growth in phytoplankton taxa from different
 functional groups 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 &lt;=0.05 (significant) or &gt;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.