DOI: 10.6084/m9.figshare.26882737
title: Microbial Metagenomes across a Full Phytoplankton Bloom: High-Resolution Sampling Every 4 Hours for 22 Days

description: Dataset 1 - Orcas Island, WA, USA 2021 Coastal Ocean (2m depth) Time Series - Environmental YSI EXO1 Sonde Probe Data (Nunn_OrcasIsland_Data_Probe.xlsx): Data collected by the YSI Probe includes columns for the date (Date) and time (Time) the sample was collected, a character value for the combined date and time of sample collection (Date.Time), chlorophyll relative fluorescence units (Chlorophyll (RFU)), chlorophyll µgL (Chlorophyll (ug L-1)), electrical conductivity (Conductivity (us cm-1)), depth the sample was collected in meters (Depth.m), optical dissolved oxygen (ODO (% saturation)) and (ODO (mg L-1), salinity (Sal (psu)), pH (pH), the temperature in degrees Celsius (Temp (degrees Celsius),), and coordinates (Latitude and Longitude) of sample collection site.



Dataset 2 – Orcas Island, WA, USA 2021 Coastal Ocean (2m depth) Time Series - SoundToxins Phytoplankton Monitoring Network East Sound Report, Washington Sea Grant (Nunn_OrcasIsland_Data_SoundToxins.xlsx): Data file consists of two tabs. Data includes relative abundance observations of phytoplankton at the SoundToxins East Sound Monitoring Site by citizen science volunteers. Note that all observational “Abundance” data is reported as categorical abundances based on microscopy and does not directly reflect the amount of biomass present in the water as represented by taxonomic group. Observations included for weekly site visits from 5/4/21 – 7/15/21. Credit: SoundToxins Phytoplankton Monitoring Network – Washington Sea Grant


- EastSound_Visits: Includes visit comments on environmental and water conditions and general observations of phytoplankton present in the water for the East Sound County Dock utilized by the SoundToxins program. Columns include site location (Name), Program, and Date/Time of sample collection. Columns detailing physical conditions at the site include Water, Air, Salinity, Depth Towed (m), Cod End, Wind, Weather, Tide, and Obs. General commentary for each visit date included in “Visit Comments” column. 


- EastSound_Observations: Includes columns for Program (SoundToxins), Site (County Dock – East Sound), and date and time of observation (Date). For each Date, the phytoplankton observed in the sample are reported as Category, Genus and Species. Abundance measurements reflect the relative abundance of phytoplankton observed in sample as defined by SoundToxins Program (“Bloom” = dominant phytoplankton in sample, “Common” = phytoplankton abundant in sample, “Present” = phytoplankton observed in sample). 




Dataset 3 – Orcas Island, WA, USA 2021 Coastal Ocean (2m depth) Time Series - Nutrient Analysis (Nunn_OrcasIsland_Data_Nutrients.xlsx): Nutrient concentrations collected across time. Columns include the date the sample was collected (Date) and time of collection (Time), and a character value for the combined date and time of sample collection (DateTime). Phosphate concentrations (PO4 [mM]), silicate concentrations (Si.OH.4 [mM]), nitrate concentrations (NO3 [mM]), nitrate concentrations (NO2 [mM]), ammonium concentrations (NH4 [mM]), and coordinates (latitude and longitude) of sample collection site.



Dataset 4 – Orcas Island, WA, USA 2021 Coastal Ocean (2m depth) Time Series - Flow Cytometry Analysis (Nunn_OrcasIsland_Data_FlowCytometry.xlsx): Columns for the day the sample was collected (1 of 22; Day), the date (Collection Date), and time (Hour) the sample was collected, a character value for the combined date and time of sample collection (DateID) are reported. Flow cytometry data includes cell counts (cells/mL) for triplicate analyses of cyanobacteria (Cyanobacteria Replicates 1-3), picoeukaryotes (Picoeukaryotes Replicates 1-3), nanoeukaryotes (Nanoeukaryotes Replicates 1-3), their averages and standard deviations. Bacteria were analyzed in duplicate and are included (Bacteria Replicates 1-2) with the average and standard deviation reported. Coordinates (latitude and longitude) of sample collection site are also included. 



Dataset 5 – Orcas Island, WA, USA 2021 Coastal Ocean (2m depth) Time Series - Joint Genome Institute Metagenomic Sequencing (Nunn_OrcasIsland_Data_JGI_metadata): Data file consists of three tabs. 


- NCBI Sequence Read Archive IDs: Includes NCBI Sequence Read Archive ID numbers, grouped under a single BioProject: PRJNA1093221. Columns include the SRA Experiment Accession number, SRA Experiment Title (which indicates the location the sample was taken, the date the sample was taken, the day number the sample was taken out of 22 days, and the time the sample was taken 1:00, 5:00, 9:00, 13:00, 17:00, 21:00), instruments sequencing was completed on (Instrument), who submitted the archive entry (Submitter), study accession number, the study title, the sample accession number, the sample title, the total size of the file (Mb), the total number of runs, total spots, total bases, library name, library strategy, library source, library selection, and coordinates (latitude and longitude) of sample collection site.


- IMG Genome IDs: Complete list of JGI metagenomic datasets for each time point are listed by individual Integrated Microbial Genomes & Microbiomes (IMG) Genome IDs and include columns for the following parameters: JGI Integrated Microbial Genomes & Microbiomes identification number (IMG GenomeID), character value for the combined date and time of sample collection (DateID), type of sample sequenced (Domain), status of JGI sequencing effort for this ID (Sequencing Status), the name of the umbrella project study (Study Name), name of the specific sample includes standard annotation location_sample_datecollected_daycollected_timecollected (Genome Name / Sample Name), location of sequencing (Sequencing Center), Sample ID number (IMG Genome ID), Submission ID (IMG Submission ID), Joint Genome Institute Genome OnLine Database project ID (GOLD Analysis Project ID), type of Joint Genome Institute Genome OnLine Database project (GOLD Analysis Project Type), Joint Genome Institute Genome OnLine Database project ID (GOLD Sequencing Project ID), size of assembled genome (Genome Size * assembled), number og genese in metagenome (Gene Count * assembled), number of metaBAT counts, (Genome MetaBAT Bin Count * assembled), estimated number of genomes assembled (Estimated Number of Genomes * assembled), estmated average genome size (Estimated Average Genome Size * assembled).


- Estimated Gene Copy Number: The Estimated gene copies for all classes in the domain “Bacteria” for each time point. Data downloaded from JGI 3.14.2024. The first column is the JGI sample ID for the specified timepoint (IMG Genome ID) followed by a character value for the combined date and time of sample collection (DateID) and all the classes identified by JGI with their respective estimated gene copy numbers.