Microbial Metagenomes across a Full Phytoplankton Bloom: High-Resolution Sampling Every 4 Hours for 22 Days

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.

数据集1——美国华盛顿州奥卡斯岛2021年近岸海域（2米水深）时间序列：YSI EXO1 Sonde探头（YSI EXO1 Sonde Probe）环境监测数据（文件：Nunn_OrcasIsland_Data_Probe.xlsx）：YSI探头采集的数据包含以下列：样品采集日期（Date）、采集时间（Time）、样品采集的日期时间组合字段（Date.Time）、叶绿素相对荧光单位（Chlorophyll (RFU)）、叶绿素浓度（单位：微克每升，Chlorophyll (ug L-1)）、电导率（Conductivity (us cm-1)）、样品采集水深（单位：米，Depth.m）、光学溶解氧饱和度（ODO (% saturation)）与光学溶解氧浓度（ODO (mg L-1)）、盐度（Sal (psu)）、pH值（pH）、摄氏温度（Temp (degrees Celsius)），以及样品采集位点的坐标（纬度与经度）。

数据集2——美国华盛顿州奥卡斯岛2021年近岸海域（2米水深）时间序列：SoundToxins浮游植物监测网络东湾报告（华盛顿海洋资助项目，文件：Nunn_OrcasIsland_Data_SoundToxins.xlsx）：该数据文件包含两个工作表。数据内容为公民科学志愿者在SoundToxins东湾监测站点获取的浮游植物相对丰度观测结果。需注意：所有观测的“丰度”数据均为基于显微镜镜检得到的分类丰度，无法直接反映对应类群在水体中的生物量。观测周期为2021年5月4日至2021年7月15日的每周站点走访。数据来源：SoundToxins浮游植物监测网络——华盛顿海洋资助项目。
- EastSound_Visits：包含SoundToxins项目使用的东湾县码头的走访记录，内容涵盖环境与水体状况、水体中浮游植物的常规观测结果。列信息包括：站点名称（Name）、所属项目（Program）、样品采集日期/时间（Date/Time）。描述站点物理环境的列包括：水温（Water）、气温（Air）、盐度（Salinity）、拖曳水深（单位：米，Depth Towed (m)）、拖网端（Cod End）、风速（Wind）、天气状况（Weather）、潮汐情况（Tide）以及观测记录（Obs.）。每次走访日期的详细评述均收录于“Visit Comments”列中。
- EastSound_Observations：包含以下列：所属项目（Program，固定为SoundToxins）、监测站点（Site，固定为County Dock – East Sound）、观测日期与时间（Date）。针对每个观测日期，样品中观测到的浮游植物将按分类群（Category）、属（Genus）与种（Species）进行记录。丰度测量值按照SoundToxins项目的定义表示浮游植物的相对丰度：“Bloom”指样品中的优势浮游植物，“Common”指样品中丰度较高的浮游植物，“Present”指样品中观测到的浮游植物。

数据集3——美国华盛顿州奥卡斯岛2021年近岸海域（2米水深）时间序列：营养盐分析（文件：Nunn_OrcasIsland_Data_Nutrients.xlsx）：按时间序列采集的营养盐浓度数据。列信息包括：样品采集日期（Date）、采集时间（Time）、样品采集的日期时间组合字段（DateTime）、磷酸盐浓度（PO4 [mM]）、硅酸盐浓度（Si.OH.4 [mM]）、硝酸盐浓度（NO3 [mM]）、亚硝酸盐浓度（NO2 [mM]）、铵盐浓度（NH4 [mM]），以及样品采集位点的坐标（纬度与经度）。

数据集4——美国华盛顿州奥卡斯岛2021年近岸海域（2米水深）时间序列：流式细胞术分析（Flow Cytometry Analysis，文件：Nunn_OrcasIsland_Data_FlowCytometry.xlsx）：列信息包括：样品采集日（共22天，Day）、采集日期（Collection Date）、采集小时（Hour）、样品采集的日期时间组合字段（DateID）。流式细胞术数据包含三类微生物的三次重复分析细胞计数（单位：细胞/毫升）：蓝细菌（Cyanobacteria Replicates 1-3）、微微型真核生物（Picoeukaryotes Replicates 1-3）、纳米级真核生物（Nanoeukaryotes Replicates 1-3），并附带对应的平均值与标准差。细菌采用两次重复分析，数据收录于“Bacteria Replicates 1-2”列，并附带平均值与标准差。此外还包含样品采集位点的坐标（纬度与经度）。

数据集5——美国华盛顿州奥卡斯岛2021年近岸海域（2米水深）时间序列：联合基因组研究所（Joint Genome Institute, JGI）宏基因组测序数据（文件：Nunn_OrcasIsland_Data_JGI_metadata）：该数据文件包含三个工作表。
- NCBI序列读取档案ID（NCBI Sequence Read Archive IDs）：收录隶属于单一生物项目（BioProject: PRJNA1093221）的NCBI序列读取档案ID编号。列信息包括：SRA实验登录号（SRA Experiment Accession number）、SRA实验标题（包含样品采集位点、采集日期、22天采样周期中的第几天、采样时间：1:00、5:00、9:00、13:00、17:00、21:00）、测序所用仪器（Instrument）、档案条目提交者（Submitter）、研究登录号（study accession number）、研究标题（study title）、样品登录号（sample accession number）、样品标题（sample title）、文件总大小（单位：兆字节，Mb）、运行总次数、斑点总数量、碱基总数量、文库名称（library name）、文库策略（library strategy）、文库来源（library source）、文库筛选方式（library selection），以及样品采集位点的坐标（纬度与经度）。
- IMG基因组ID（IMG Genome IDs）：按单个整合微生物基因组与微生物组（Integrated Microbial Genomes & Microbiomes, IMG）基因组ID列出每个时间点的JGI宏基因组数据集完整列表，列信息包含以下参数：JGI整合微生物基因组与微生物组识别号（IMG GenomeID）、样品采集的日期时间组合字段（DateID）、测序样品的类群（Domain）、该ID对应的JGI测序工作状态（Sequencing Status）、总研究项目名称（Study Name）、具体样品名称（包含标准注释：位置_样品_采集日期_采集日_采集时间，Genome Name / Sample Name）、测序中心（Sequencing Center）、样品ID号（IMG Genome ID）、提交ID（IMG Submission ID）、JGI基因组在线数据库（Genomes OnLine Database, GOLD）项目ID（GOLD Analysis Project ID）、JGI GOLD项目类型（GOLD Analysis Project Type）、JGI GOLD测序项目ID（GOLD Sequencing Project ID）、组装基因组大小（Genome Size * assembled）、宏基因组基因总数（Gene Count * assembled）、metaBAT计数数量（Genome MetaBAT Bin Count * assembled）、估计组装的基因组数量（Estimated Number of Genomes * assembled）、估计平均基因组大小（Estimated Average Genome Size * assembled）。
- 估计基因拷贝数：各时间点“细菌”（Bacteria）域所有类别的估计基因拷贝数。数据下载自JGI数据库，时间为2024年3月14日。首列为对应时间点的JGI样品ID（IMG Genome ID），随后为样品采集的日期时间组合字段（DateID），以及JGI识别的所有类别的对应估计基因拷贝数。