DOI: 10.5061/dryad.6tn7c
title: Data from: Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities

description: In order to characterize copepod feeding in relation to microbial plankton
 community dynamics, we combined metabarcoding and metabolome analyses
 during a 22-day seawater mesocosm experiment. Nutrient amendment of
 mesocosms promoted the development of haptophyte (Phaeocystis pouchetii)-
 and diatom (Skeletonema marinoi)-dominated plankton communities in
 mesocosms, in which Calanus sp. copepods were incubated for 24 h in
 flow-through chambers to allow access to prey particles (&lt;500 μm).
 Copepods and mesocosm water sampled six times spanning the experiment were
 analysed using metabarcoding, while intracellular metabolite profiles of
 mesocosm plankton communities were generated for all experimental days.
 Taxon-specific metabarcoding ratios (ratio of consumed prey to available
 prey in the surrounding seawater) revealed diverse and dynamic copepod
 feeding selection, with positive selection on large diatoms, heterotrophic
 nanoflagellates and fungi, while smaller phytoplankton, including P.
 pouchetii, were passively consumed or even negatively selected according
 to our indicator. Our analysis of the relationship between Calanus grazing
 ratios and intracellular metabolite profiles indicates the importance of
 carbohydrates and lipids in plankton succession and copepod–prey
 interactions. This molecular characterization of Calanus sp. grazing
 therefore provides new evidence for selective feeding in mixed plankton
 assemblages and corroborates previous findings that copepod grazing may be
 coupled to the developmental and metabolic stage of the entire prey
 community rather than to individual prey abundances.
description: SRP076974Sequence Read Archive containing sequence flowgram files for copepod gut content ("COP") and filterable plankton biomass from mesocosm seawater ("FIL") eukaryotic microbial communities. Sequences were generated from amplicon libraries generated using PCR primers targeting the V7 region of the eukaryote small subunit rRNA gene (SSU rRNA). Each flowgram file contains sequence information for 24 biological samples which were pooled and indexed prior to sequencing.Sequence read identifiers and CREST taxonomic assignmentsThis zipped archive contains 48 taxonomic assigment text files: one taxonomic assignment file (sequence identification number and taxonomy with tab separation) for each sample used in this study (24 copepod gut content samples and 24 filterable seawater plankton biomass samples). Taxonomic assignment of quality-trimmed sequences was performed using the CREST classifier with Silvamod reference database.Taxonomic_assignments.zipAmpliconNoise OTU tableThis table summarizes OTU (98% cut-off) abundance in all sequence samples used for this study. Rows of the table are OTUs and columns of the table are samples. Column names consist of "TYPE_TreatmentDate". TYPE indicates sample type ("COP" - copepod gut content or "FIL" - filterable seawater plankton biomass). Treatment designations indicate mineral nutrient additions for each treatment: "blank" - Control mesocosms that received no mineral nutrients, "NP" - mesocosms that received N + P addition, "NPSi" - mesocosms that received N + P + Si addition, "fjord" - samples taken from the adjacent Raunefjorden. Dates indicate sampling date in March 2012.Ray_et_al-AmpliconNoise_OTUs_cutoff98.csvTaxonomic assignments for AmpliconNoise OTUsThis file contains taxonomic assignments for AmpliconNoise-identified OTUs (98% cut-off). Taxonomic assignment of OTUs was performed using the CREST classifier with Silvamod reference database.Ray_et_al-AmpliconNoise_OTUs_taxonomic_assignments.txtCREST taxonomic assignments tableThis table shows the abundance of highest-rank CREST taxonomic assignments of sequence reads for all samples.CREST_taxonomy_table.csv