Woulds, C., Bouillon, S., Cowie, G. L., Drake, E., Middelburg, J. J., Witte, U., Schwartz, M. C., Jeffreys, R., Larkin, K., Gooday, A. J., and Whitcraft, C 2016 http://doi.org/10.5518/92 Clare Woulds: 0000-0002-3681-1468 Steven Bouillon Gregory Cowie Bert Drake Jack Middelburg Ursula Witte: Matthew Schwartz Rachel Jeffreys Kate Larkin Andy Gooday Christine Whitcraft Digital data underpinning the findings in Woulds et al. (2016): Woulds, C., Bouillon, S., Cowie, G. L., Drake, E., Middelburg, J. J., and Witte, U.: Patterns of carbon processing at the seafloor: the role of faunal and microbial communities in moderating carbon flows, Biogeosciences, 13, 4343-4357, doi:10.5194/bg-13-4343-2016, 2016. http://doi.org/10.5194/bg-13-4343-2016 The data are derived from sediment cores and extracted from two places in Scotland: Loch Etive (https://en.wikipedia.org/wiki/Loch_Etive) and Ythan (https://en.wikipedia.org/wiki/Ythan) estuary. The physical samples were processed in a number of ways for specific purposes as outlined in Woulds et al. (2016). Some of the analyses are destructive, and the remaining physical samples have not been preserved. The files are of two types: 1. Excel Files, which contain 1, 2, 3, or 5 sheets; and, 2. CSV Files which are conversions of the Excel files into comma separated version (CSV) format which is a more preservation friendly format. The files contain data that underpin the findings in Woulds at al. (2016). Edited versions of Original Excel Files developed and used by a project team. Considered to be more user friendly versions of the Original Excel Files. During the process of preparing the data for sharing, the file "Ythan Fauna Data.xlsx" was converted from Microsoft Excel Worksheet to Microsoft Excel 97-2003 Worksheet format so it was the same format as all the other Excel files. The filenames of some files were changed as follows: "Loch Etive Airds Bay DIC and respiration data.xls" changed to "Loch Etive Airds Bay DIC and respiration.xls" "Loch Etive Airds Bay Fauna datasheet.xls" changed to "Loch Etive Airds Bay raw total fauna extracted.xls" "Loch Etive Airds Bay isotope tracing experiment fauna isotope data.xls" changed to "Loch Etive Airds Bay isotope tracing experiment faunal isotopes.xls" "Ythan Fauna Data.xlsx" changed to "Ythan isotope tracing experiment faunal isotopes.xls" "Ythan PLFAs and bacterial uptake.xls" changed to "Ythan PLFAs and bacterial C uptake.xls" Known to exist at the time of data ingest and may be available on request from the corresponding author - Clare Woulds. Contain some implementations of formulae which are not in the edited versions. (The equations of important formulae are provided in Woulds et al. (2016).) Contain more comments added by the project team as they cleaned and prepared the data. The CSV files contain individual Sheets of the Excel Files that have been saved in a Commma Seperated Version (CSV) format. Fields containing commas are enclosed in double quotation marks, but otherwise fields are separated using a comma. For Excel files containing only one Sheet, the CSV file saved is given the same name as the Excel file except it has a ".csv" file extension instead of a ".xls" one. For Excel files containing more than one Sheet, the name of the Sheet (or a substitute) is appended to the name of the file before the file extension. The name modification was an attempt to standardise between the two sets of data and make it more intuitive with regard what each file contains. Some of the CSV files are rectangular data, i.e. they are made up of rows with the same number of columns in each row (often with first row being a header). However, some of the Excel Sheets effectively contain multiple tables as described below. It should be possible to clean the data further and produce a cleaner rectangular only set of CSV files. Perhaps others who use this data may help to produce this cleaner version of CSV Files. Excel file detailed descriptions and a list of CSV Files are provided below. There are 5 files for "Loch Etive Airds Bay" and 3 files for "Ythan": The 3 files for Ythan have files with the same filename endings as for three of the Loch Etive Airds Bay files. Although the corresponding files contain data about the same things, their form and layout are not always consistent. All filenames begin "Loch Etive Airds Bay". <"Loch Etive Airds Bay DIC and respiration.xls"> 1 sheet: "Overlying Water Data". Header: Sample,pos,intended,actual,Actual time (h),Del 13C DIC,At % DIC,Volume Removed (ml),Cumulative vol replacement added BEFORE sampling (ml),Average DIC from Westerschelde Expt. mM,Average DIC from Ythan Expt. mM,Water Column Height (cm),Overlying Water Vol (ml),Uncorr. 13C Present m moles ,13C DIC conc. mM ,Corrected 13C DIC content. m moles,Added C content m moles,Added C content in mg,Core Overlying Water Respiration (mg C h-1) ,Respiration rate mg C m-2 h-1,Total Respiration in Experiment mg C m-2 Notes: There are individual empty lines separating groups of 7, 7, 6 and 6 rows with records. These records are grouped by sediment cores and each row represents a different time in which the core was sampled/tested. For the last record for each sediment core, there are summary data which provides summaries for all records of the core. These summary data are provided in the final 3 fields which are otherwise blank. Respiration rates were calculated using regressions, as that averages out for change in rate through the experiment. An additional row of data in row 34 provides the average of the summaries for the 4 cores. This is saved in CSV format as: "Loch Etive Airds Bay DIC and respiration.csv". <"Loch Etive Airds Bay isotope tracing experiment faunal isotope.xls"> 2 Sheets: "Compiled Fauna Data"; "Summarised". Header: Batch,Tray ID,Vial No,Depth,Sampling Date,Processing Date,Core no.,time series,Vertical,Median Depth,sieve,Dry Weight / mg,Group,taxon,#,Fate,Photo #,Notes,,mg N,mg N Blank Corr.,mg C,mg C Blank Corr.,At % 13C,d 13C,Natural Abundance At %,Excess At %,mg Added (Excess) 13C,mg Added C Notes: There is 1 row for each sample sent for faunotype analysis. Rows are separated into 5 groups for different time series. This is saved in CSV format as: "Loch Etive Airds Bay isotope tracing experiment faunal isotope Compiled Fauna Data.csv". Notes: There are effectively 6 tables of data in the sheet and 4 graphs. This sheet contains formulae which shows how data in some tables are derived from other values in the sheet. Rows 3 to 9, columns B to M inclusive. Contains raw data from samples that have been summarised and include summed totals of Carbon 13 (C13) uptake by core broken down by grouping. Rows 14 to 20, columns B to M inclusive. The same values as in Table 1, but multiplied by 2. For the main experiment, core samples were divided in half. One half was frozen and the other parts was not. So the multiplication by 2 provides estimates of the total masses for all the samples. Rows 14 to 20, columns O to Q inclusive. Additional Bacteria data that shows the uptake of carbon by bacteria from the different cores. Rows 14 to 20, columns X to AA inclusive. Provides the percentage of the mass of carbon in each Rows 14 to 20, columns AC to AF inclusive. Provides the percentage of uptake of C13 by broad taxonomic group. This is one of the key parts of the data that underlies the findings in Woulds et al. (2016). This is saved in CSV format as: "Loch Etive Airds Bay isotope tracing experiment faunal isotope Summarised.csv". <"Loch Etive Airds Bay raw total fauna extracted.xls"> There is no similar file for Ythan. 2 Sheets: "Data entry - natural"; "Data entry - sf13". Both have the same header: Tray ID,Vial No,Depth,Sampling Date,Processing Date,Core no.,time series,Vertical,sieve,Group,taxon,#,Fate,Photo #,Notes Both are sheet created via the digitisation of data from laboratory microscope note books. This records basic isotropes. This is saved in CSV format as: "Loch Etive Airds Bay raw total fauna extracted Data entry - natural.csv". This records details for the C13 tracing experiments. sf13 is the lab notebook code. This is saved in CSV format as: "Loch Etive Airds Bay raw total fauna extracted Data entry - sf13.csv". <"Loch Etive Airds Bay natural abundance faunal isotopes.xls"> 1 Sheet: "Compiled Natural Abundance" Header: Tray ID,Vial No,Depth,Sampling Date,Processing Date,Core no.,,Vertical,,Dry Weight / mg,sieve,Group,taxon,#,Notes,,,ug N,ug C,Del 13C,At % 13C Notes: Rows are grouped by broad fauna taxonomic group. Each group of rows have a summary row that separates each group of rows that contains the mean isotropic signature for each broad taxonomic group. This is saved in CSV format as: "Loch Etive Airds Bay natural abundance faunal isotopes.csv". <"Loch Etive Airds Bay PLFAs and bacterial C uptake.xls"> Spreadsheet for mud to lipid extraction processing. where samples were profiled using a gas chromatograph which splits samples by their chemical composition. Concentrations are effectively graphed over time. 4 Sheets: "area", "Delta", "Incorp", "Sample IDs" Samples are in the columns, chemical components are the rows. Row 4 gives the Sample Number (1 to 28) in Columns C to AC inclusive. This sheet is effectively the area under the concentration over time graph for each chemical for each sample. The values have been 'calibrated' and has concentrations in given uits. It contains some cells which contain "#DIV/0!" values which is where the area could not be calulated due to a dividion by zero in the calculation. This is saved in CSV format as: "Loch Etive Airds Bay PLFAs and bacterial C uptake Concentrations.csv". This sheet has the same layout as the area sheet: Samples are in the columns, chemical components are the rows. Row 4 gives the Sample Number (1 to 28) in Columns C to AC inclusive. These are data from the radio mass spectrometer processing providing details of isotropic compositions of samples. The name for this sheet becomes "del13C" when converted to CSV format. Using a lower case d is intentional here as del stands for the Greek letter delta for which the lower case version has a special meaning in this context. This is saved in CSV format as: "Loch Etive Airds Bay PLFAs and bacterial C uptake delta13C.csv". Incorp is short for Incorporation and is a result of a calculation of Delta multiplied by concentration. Key data underlying Woulds et al. (2016) is given in the last 4 rows (rows 56 to 59 inclusive) of the sheet: total Measured Uptake in to Bacterial PLFAs Total Uptake into All Bacterial PLFAs Total bacterial uptake of 13 C Total bacterial uptake of C "There are 4 bacterial incorporations and 2 transfer functions and these effectively measure how much added carbon is eaten by bacteria." This is saved in CSV format as: "Loch Etive Airds Bay PLFAs and bacterial C uptake Incoporation.csv". The Sample Number column corresponds to the Row 4 in the other sheets. The rows are grouped by core and details of samples are provided along with core summaries for the last record in each core. Porosity is used to calculate the wet weight from the dry sample. In row 34, column H a value has been added using an interpolation method. This is saved in CSV format as: "Loch Etive Airds Bay PLFAs and bacterial C uptake Sample IDs.csv". All filenames begin "Ythan". <"Ythan isotope tracing experiment faunal isotopes.xls"> 2 Sheets: "Collected data Only and AVGs"; "Fauna Samples and Isotopes" These are very similar to the "Loch Etive Airds Bay isotope tracing experiment faunal isotope.xls" Compiled Fauna Data Sheet. One differences is that the Batch field is not included. Header: Tray,Well/vial,Date picked/put away,site,Experiment,replicate,Depth horizon,Sieve,Taxon,Number,Photo (.jpg),Dry Weight / mg,w/w %C,d13C,At % 13C,w/w %N,d15N,At % 15N,ug C,ug N,Taxon,Avg %C,Avg d13 C,Avg %N,Avg del 15N Rows are grouped according to the Replicate column with blank lines tht separate these groups. This is saved in CSV format as: "Ythan isotope tracing experiment faunal isotopes Collected data Only and AVGs.csv". Notes: The header is on row 2. Rows 93 to 97, columns A to E inclusive provide summary data. This is saved in CSV format as: "Ythan isotope tracing experiment faunal isotopes Fauna Samples and Isotopes.csv". <"Ythan DIC and respiration.xls"> 1 Sheet: "Lab Experiment" Header: Experiment,Core,Treatment,wat col. Height / cm,Wat vol. / cm3,Sample date,Time,Time since start resp. measurement / h,Vol / ml,DIC Vial,WHCO3 (µmol CO2/l),WISOC (delta 13 C o/oo),13C Atom %,Amount (micro moles) 13C in chamber prior to sampling,Amount (micro moles) 13C removed at sampling,Amount (micro moles) 13C introduced at sampling,Corrected micro moles 13C present in chamber immediately prior to sample,Trendline micromoles 13DIC/h,Micromoles total micromoles C/h (scaled up for algae labelling level,Respiration rate in micrograms m-2 h-1,Respiration rate in mg m-2 h-2,Core Average Respiration rate in mg m-2 h-3,mg added C respired over whole experiment in chamber (452 cm 2) Notes: This Sheet contains tabular data and graphs. There is one main table and a small summary table after row 43 at the end. The samples were incubated twice. So for each core there are two sets of rows of data. All Core field values containing a 1 are for one type of incubation and those without a 1 are for the other type of incubation. This is saved in CSV format as: "Ythan isotope tracing experiment faunal isotopes Fauna Samples and Isotopes.csv". <"Ythan PLFAs and bacterial uptake.xls"> There are 5 sheets: "Concentrations"; "Del"; "At %"; "Incorporation"; "Summary and sample details" This is like the "Loch Etive Airds Bay PLFAs and bacterial C uptake.xls" "area" Sheet. Samples are in the columns, chemical components are the rows. This is saved in CSV format as: "Ythan PLFAs and bacterial uptake.csv". This is like the "Loch Etive Airds Bay PLFAs and bacterial C uptake.xls" "Delta" Sheet. This is saved in CSV format as: "Ythan PLFAs and bacterial uptake Concentrations.csv". Atom Percent is a different way of expressing isotopic composition. The del notation is parts per thousand relative to an international standard, whereas atom percent is literally the percentage of the Carbon atoms present that are the Carbon 13 (13C) isotope). This is saved in CSV format as: "Ythan PLFAs and bacterial uptake Atom Percentage.csv". This is like the "Loch Etive Airds Bay PLFAs and bacterial C uptake.xls" "Incorp" Sheet. This is saved in CSV format as: "Ythan PLFAs and bacterial uptake Incorporation.csv".

header: Experiment,Core,Med Depth,Total bacterial uptake of C ug / g sed,Bac Biomass ug C/g sed.,Porosity,Total bacterial Uptake in horizon/ mg C,Total bacterial Uptake in chamber/ mg C,Total bacterial Biomass in horizon/ mg C,Total bacterial Biomass in chamber/ mg C,,,,,,,,,,,,,,,,,,,,,,,,, This is saved in CSV format as: "Ythan PLFAs and bacterial uptake Summary and sample details.csv".

<"Ythan PLFAs and bacterial uptake.xls">