High-temporal resolution of microbial food web dynamics and structure during phytoplankton blooms in the Baltic Sea

This dataset includes 8 files that contain data on environmental and biological variables, and diversity of eukaryotic microbes from samples collected in the coastal station in the Gulf of Gdańsk (Baltic Sea) during two high-frequency sampling campaigns in the Baltic Sea in 2023. 1. File “HFS-Baltic-environmentalabundanceandsize.xlsx”This file contains data on hydrological parameters, organisms count, nutrients concentration and cell sizes of heterotrophic nanoflagellates. It consists of four sheets: a. The "Parameters-Data" sheet lists all parameters for data presented in the "Data" sheet. Column A (Name) contains the variables names, column B (Unit) contains units in which they were measured, column C (Method/Device) contains information on the methodology, and column D (Comments) contains additional information; b. The "Data" sheet contains data in a wide format for all variables listed in the "Parameters-Data" sheet measured at sampling times. The first row contains variable names (listed in Column A of the Parameters-Data sheet) with units in square brackets; c. The "Parameter-Size" sheet lists parameters for data presented in the "Size" sheet in the same format as described for the "Parameters-Data" sheet. Starting from row 5 in columns A and B, the number of measured HNF cells for each sample is given; d. The "Size" sheet contains size measurements of HNF in the samples in a long format. The number of cells measured in each sample is provided in the "Parameter-Size" sheet. 2. File “Illumina-short-alleuks-Khanetal2025.rds”Phyloseq object containing information of amplicon sequence variance (ASV) read abundance of all eukaryotic sequences obtained from Illumina Miseq sequencing of the V6-V8 fragment of the 18S rRNA gene. Samples were rarefied to 25378 reads. 3. File “Illumina-short-aHNF-percent-Khanetal2025.rds”Phyloseq object containing information of amplicon sequence variance (ASV) read relative abundance (as percentage of reads of all eukaryotic sequences as in file “Illumina-short-alleuks-Khanetal2025.rds”) of the following eukaryotic groups: phyla Kathablepharidacea, Telonemia, Ancyromonadida, Apusomonada, Metamonada, Nibbleridia, Picozoa, Rhizaria, Rigifilida, Tubulinea, Opisthokonta; division Bigyra; families MAST-1, MAST-2,MAST-4, Basal_Cryptophyceae-1 and order Paraphysomonadales; obtained from Illumina Miseq sequencing of the V6-V8 fragment of the 18S rRNA gene. 4. File “LongAmpliconsASVtable.xlsx”This file contains information of amplicon sequence variance (ASV) read abundance of all eukaryotic sequences obtained from PacBio sequencing of the eukaryotic of rRNA operon sequences from V4 fragment of 18S rRNA gene to D9 fragment of 28S rRNA gene. It consists of four sheets: a. The "Parameters-Table" sheet lists all parameters for data presented in the "Data" sheet. Column A (Name) contains the variables names, column B (Unit) contains units in which they were measured, column C (Method) contains information on the methodology, column D (Comments) contains additional information and column e (Reference) contains reference to the methodology; b. The "Table" sheet contains data in a wide format for all variables listed in the "Parameters-Table" sheet measured at sampling times. The first row contains variable names (listed in Column A of the “Parameters-Table” sheet); c. The "Parameter-samplecodes" sheet lists parameters for data presented in the "samplecodes " sheet in the same format as described for the "Parameters-Table" sheet; d. The " samplecodes " sheet provides basic metadata for the samples. 5. File “KAT-fasta.clipkit.treefile”Maximum likelihood phylogenetic tree of rRNA operon sequences (from V4 fragment of 18S rRNA gene to D9 fragment of 28S rRNA gene) of Kathablepharidacea obtained from PacBio long amplicon sequencing. The tree was inferred using IQ-TREE with the TN+F+I+G4 model, automatically selected based on the Bayesian Information Criterion. The alignment used to build this tree is available in file “KAT-allignment.fasta”. 6. File “KAT-alignment.fasta”Alignment rRNA operon sequences (from V4 fragment of 18S rRNA gene to D9 fragment of 28S rRNA gene) of Kathablepharidacea. Sequences were aligned using the MAFFT online tool with default settings. The alignment was trimmed using ClipKIT (V.2.1.3) with the gappy parameter set to 0.9. 7. File “MAST-fasta.clipkit.treefile”Maximum likelihood phylogenetic tree of rRNA operon sequences (from V4 fragment of 18S rRNA gene to D9 fragment of 28S rRNA gene) of MAST-2 stramenopiles obtained from PacBio long amplicon sequencing. The tree was inferred using IQ-TREE with the TN+F+I+G4 model, automatically selected based on the Bayesian Information Criterion. The alignment used to build this tree is available in file “MAST-2.Allignment.fasta”. 8. File “MAST-2.alignment.fasta”.Alignment rRNA operon sequences (from V4 fragment of 18S rRNA gene to D9 fragment of 28S rRNA gene) of MAST-2 stramenopiles. Sequences were aligned using the MAFFT online tool with default settings. The alignment was trimmed using ClipKIT (V.2.1.3) with the gappy parameter set to 0.9. 9. File “MAST-2.alignment.fasta”.Alignment rRNA operon sequences (from V4 fragment of 18S rRNA gene to D9 fragment of 28S rRNA gene) of MAST-2 stramenopiles. Sequences were aligned using the MAFFT online tool with default settings. The alignment was trimmed using ClipKIT (V.2.1.3) with the gappy parameter set to 0.9.