This readme.txt file was generated on 2022-02-21 by Salvador Espada-Hinojosa GENERAL INFORMATION 1. Title of Dataset: Primary Data. Host-symbiont response to lack-of-sulfide stress in the giant ciliate mutualism 2. Author Information A. Principal Investigator Contact Information Name: Monika Bright Institution: Department of Functional and Evolutionary Ecology. University of Vienna Address: Djerassiplatz 1, A-1030 Vienna (Austria) Email: monika.bright@univie.ac.at B. Associate or Co-investigator Contact Information Name: Salvador Espada-Hinojosa Institution: Department of Functional and Evolutionary Ecology. University of Vienna Address: Djerassiplatz 1, A-1030 Vienna (Austria) Email: salvador.espada@univie.ac.at 3. Date of data collection (YYYY-MM-DD): The data concerning host response to sulfide starvation were collected between 2015-04-25 and 2021-08-19. The data concerning symbiont response to sulfide starvation were collected approximately between 2012-01-01 and 2014-12-31. 4. Geographic location of data collection: Zoothamnium niveum colonies were collected from Piran, Slovenia: from the estuarine canal Sv. Jernej (45°29'48.6"N, 13°35'57.0"E) and from the mudflat in Strunjan (45°31'44.0"N, 13°36'13.2"E). Experiments were performed in the Marine Biology Station of Piran. FISH and SEM were performed in the University of Vienna. 5. Information about funding sources that supported the collection of the data: Funding came from two Austrian Science Fund projects FWF P24565 B22 and FWF 32197 granted to MB. (https://www.fwf.ac.at). SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: This dataset is available under the CC0 1.0 Universal (CC0 1.0) Public Domain Dedication. https://creativecommons.org/publicdomain/zero/1.0/legalcode 2. Links to publications that cite or use the data: Espada-Hinojosa et al. (2022). "Host-symbiont stress response to lack-of-sulfide in the giant ciliate mutualism". PLoS (in press). 3. Was data derived from another source? no 4. Recommended citation for this dataset: Espada-Hinojosa et al. (2022). "Primary Data. Host-symbiont stress response to lack-of-sulfide in the giant ciliate mutualism". Dryad. DOI:10.5061/dryad.vt4b8gts8 DATA & FILE OVERVIEW 1. File List: Countings.csv SEM counting observations for sulfide starvation experiments, including coverage and frequency of dividing cells Environment.csv Physical and chemical monitoring of the sulfide starvation and sulfidic control experiments Espada-Hinojosa_et_al_2022.Rmd Rmarkdown report code Espada-Hinojosa_et_al_2022.html Rmarkdown report outcome in html format Experiments.csv Sulfide starvation and sulfidic control experiments additional information Measurements.csv SEM counting observations for sulfide starvation experiments, including cell dimensions and elongation and volume derived from them SulfidicControlColonies.csv Sulfidic control experiments overall performance of individual colonies SulfidicControlSwarmers.csv Sulfidic control experiments offspring recording of relevant events, such as swarmer release, and settlement as a new colony SulfidicControlTimes.csv Accurate account of the sulfidic control experiments timepoints StarvingColonies.csv Sulfide starvation experiments data for 120 colonies, including colony sizes, survival and reproductive performance StarvingSwarmers.csv Sulfide starvation experiments offspring recording of relevant events, such as swarmer release, and settlement as a new colony MD5 (Countings.csv) = ad4fbe105ad390b59aaf377d87732e3a MD5 (Environment.csv) = 05054f9bb9e3dae612ef2d551c710aaf MD5 (Espada-Hinojosa_et_al_2022.Rmd) = 627344bfbed0a78846ff2abe6517b061 MD5 (Espada-Hinojosa_et_al_2022.html) = 4e0bf9f974613b40db9405f34677b2db MD5 (Experiments.csv) = d03f17a6c28576117724ebad5c667833 MD5 (Measurements.csv) = c15d58269847d58dfc1f7876df2f46c5 MD5 (StarvingColonies.csv) = 37eaf6e908ee85c4ff4a940ecf10d46c MD5 (StarvingSwarmers.csv) = cec73153f2d8a64a81af794e59b7bb4c MD5 (SulfidicControlColonies.csv) = fc32b11cb7bb6c28e7998c7b12ad53f1 MD5 (SulfidicControlSwarmers.csv) = 77bb8d685b37eda69ee21beaab8fd25b MD5 (SulfidicControlTimes.csv) = 7665737b0b0f57ea2784da69b1b920e4 2. Relationship between files, if important: The file Espada-Hinojosa_et_al_2022.Rmd requires all the .csv files to load the data and generate the Rmarkdown html report (Espada-Hinojosa_et_al_2022.html additionally provided). 3. Are there multiple versions of the dataset? no METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: Host (Zoothamnium niveum colonies) performance through sulfide starvation and under a sulfidic control experiment was characterized through observation under dissection microscope. Symbiont performance was characterized through Scanning Electron Microscopy (SEM) and Fluorescence in situ hibridization (FISH). 2. Methods for processing the data: Generalized linear models and ordinary least square regressions are employed. Statistical significance tests are also employed. 3. Instrument- or software-specific information needed to interpret the data: R version 3.6.0 - https://www.r-project.org/ knitr R package version 1.23 tidyr R package version 1.1.3 kableExtra R package version 1.1.0 seqinr R package version 3.4-5 MASS R package version 7.3-54.4 All R packages available in CRAN - https://cran.r-project.org/mirrors.html 4. Environmental/experimental conditions: As indicated in Environment.csv 5. People involved with sample collection, processing, analysis and/or submission: Salvador Espada-Hinojosa, Judith Drexel, Julia Kesting, Edwin Kniha, Iason Pifeas, Lukas Schuster, Jean-Marie Volland, Helena C. Zambalos, Monika Bright. DATA-SPECIFIC INFORMATION FOR: Countings.csv 1. Number of variables: Six 2. Number of cases/rows: 180 3. Variable List: Treatment Either "in situ" or "48h oxic" SEMColonyID Running number ID for the individual colony for SEM characterization Part Localization on the host cell, either "oral" or "aboral" SymbiontCells Number of symbiont cells inside of a grid of 70 square micrometers Coverage Percent of the host surface covered by symbiont cells FDC Frequency of dividing cells 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: None DATA-SPECIFIC INFORMATION FOR: Environment.csv 1. Number of variables: Eight 2. Number of cases/rows: 158 3. Variable List: date_hour Time point ColoniesIDs Running number ID for the individual colony Water Either "In" or "Out" for each "Swarmer" or "Colony" pH Measurement of the pH Salinity Measurement of the salinity Temp_C Measurement of the temperature in Celsius degrees O2_perCentSat Measurement of the oxygen concentration in percent of saturation Sulfide_uM Measurement of the sulfide concentration in micromolar 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: None DATA-SPECIFIC INFORMATION FOR: Experiments.csv 1. Number of variables: Six 2. Number of cases/rows: Nine 3. Variable List: ColoniesIDs Running number ID for the individual colony ranges SamplingSite Either "Strunjan" or "Sv. Jernej" Start Timepoint of the beginning of the experiment, as DD/MM/YYYY_HH:MM End Timepoint of the end of the experiment, as DD/MM/YYYY_HH:MM SwarmersAgeWhenKilled_hours Range of hours for the age of the swarmer in the moment of sacrifice for size measurement SwarmerGroup Either "A", "B", "C" or "D" according to the sulfide starvation experiment design. "--" if not applicable for the sulfidic control experiment 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: None DATA-SPECIFIC INFORMATION FOR: Measurements.csv 1. Number of variables: Seven 2. Number of cases/rows: 9271 3. Variable List: Treatment Either "in situ" or "48h oxic" SEMColonyID Running number ID for the individual colony for SEM characterization Part Localization on the host cell, either "oral" or "aboral" Width_Um Measured symbiont cell width in micrometers Length_Um Measured symbiont cell length in micrometers ElongationFactor Calculated length between width elongation ratio Volume_Um3 Calculated volume in cubic micrometers assuming cilinder plus two hemispheres cell shape 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: None DATA-SPECIFIC INFORMATION FOR: StarvingColonies.csv 1. Number of variables: Eight 2. Number of cases/rows: 120 3. Variable List: ColonyID Running number ID for the individual colony MacrozoidsAtStart Number of macrozooids present in the colony at the beginning of the experiment BranchesAtDeath Number of branches present in the colony once it dies MacrozoidsAtDeath Number of macrozooids present in the colony once it dies ColonySurvival_hours Range of hours comprising the survival of the colony in hours ReleasedSwarmers Number of macrozooids released as swarmers by the colony during the experiment DeltaM Net production of macrozooids by the colony during the experiment DeltaS Net production and release of swarmers by the colony during the experiment 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: None DATA-SPECIFIC INFORMATION FOR: StarvingSwarmers.csv 1. Number of variables: Nine 2. Number of cases/rows: 310 3. Variable List: SwarmerID Running number ID for the individual swarmer SwarmerSizeGroup Category within the experimental design for the swarmer size ColonyID Running number ID for the individual colony from which the swarmer originated ColonyTimeUnderOxic_hours Time in hours of the colony being exposed to oxic conditions when the swarmer dettached from it (upper bound) SwarmerAgeWhenKilled_hours Age range in hours of the swarmer once sacrificed for size measurement SwarmerSize_Um2 Size of the swarmer in square micrometers once mounted in a slide and observed and photographed under a optical microscope DeadUp Upper bound of the time the swarmer lived in hours Lifespan_hours Time range in hours for the swarmer life EdwinColony ID from the original records 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: None DATA-SPECIFIC INFORMATION FOR: SulfidicControlColonies.csv 1. Number of variables: Eight 2. Number of cases/rows: 60 3. Variable List: ColonyID Running number ID for the individual colony MacrozooidsAtStart Number of macrozooids present in the colony at the beginning of the experiment BranchesAtDeath Number of branches present in the colony once it dies MacrozooidsBeforeDeath Number of macrozooids present in the colony before it died DeathTimePoint Upper bound in hours of the moment of colony death ReleasedSwarmers Number of macrozooids released as swarmers by the colony during the experiment DeltaM Net production of macrozooids by the colony during the experiment DeltaS Net production and release of swarmers by the colony during the experiment 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: None DATA-SPECIFIC INFORMATION FOR: SulfidicControlSwarmers.csv 1. Number of variables: Eight 2. Number of cases/rows: 2803 3. Variable List: Timepoint Running number of the timepoint of the experiment, roughly each 12 hours ColonyID Running number ID for the individual colony WellID Specification of the well being observed in the recorded event SwarmerID Running number ID for the individual swarmer Event N, swimming; S, settlement; T, transfer; D, death Page Page number from the original records Evidence Either "Observation" or "Reconciled" Notes Comments 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: For the "Event" variable: N, swimming; S, settlement; T, transfer; D, death DATA-SPECIFIC INFORMATION FOR: SulfidicControlTimes.csv 1. Number of variables: Four 2. Number of cases/rows: 12 3. Variable List: Timepoint Running number of the timepoint of the experiment, roughly each 12 hours Date Date of the experiment as DD/Month3leters/YYYY StartingHour Starting moment of the timepoint recording as HH:MM AccumulatedHours Number of hours since the beginning of the experiment 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: Months are expressed as their 3 letters abbreviations