DOI: 10.5061/dryad.1zcrjdfrc
title: Seasonal turnover in community composition of stream-associated macroinvertebrates inferred from freshwater environmental DNA metabarcoding

description: Macroinvertebrate communities are crucial for biodiversity monitoring and
 assessment of ecological status in stream ecosystems. However, traditional
 monitoring approaches require intensive sampling and rely on invasive
 morphological identifications that are time consuming and dependent on
 taxonomic expertise. Importantly, sampling is often only carried out once
 in a year, namely during late winter – spring, where most indicator taxa
 have larval stages in the streams. Hence, species with divergent phenology
 might not be detected. Here, we use environmental DNA (eDNA) metabarcoding
 of filtered water samples collected in both spring and autumn from five
 streams in Denmark to address seasonal turnover in community composition
 of stream macroinvertebrates. We find that eDNA read data from the same
 stream sampling site clearly show different communities in spring and
 autumn, respectively. For three of the five streams, season even appears
 to be a more important factor than sampling site for explaining the
 variation in community composition. Finally, we compare eDNA data with a
 near-decadal dataset of taxon occurrences in the same five streams based
 on kick sampling conducted through a national monitoring program. This
 comparison reveals an overlap in species composition, but also that the
 two approaches provide complementary rather than identical insights into
 community composition. Our study demonstrates that aquatic eDNA
 metabarcoding is useful for species detection across highly diverse taxa
 and for identifying seasonal patterns in community composition of
 freshwater macroinvertebrates. Thus, our results have important
 implications for both fundamental research in aquatic ecology and for
 applied biomonitoring.
description: This dataset represents environmental DNA sequencing data from
 spring and autumn sampling at five stream sites in Denmark (see connected
 publication for details). DNA has been amplified with
 primers BF1 (5'-ACWGGWTGRACWGTNTAYCC-3') and BR1
 (5'-ARYATDGTRATDGCHCCDGC-3'), targeting a 217 bp fragment of the
 COI. The libraries have been sequenced using paired end NovaSeq 6000
 sequencing (150 BP PE). The dataset consists of eight
 zipped libraries (four PCR replicates of the same samples for the
 two seasons) and eight txt files that can be used for demultiplexing
 purposes for each library. Libraries are named K2-K9,
 and each contain two sequence data files (paired end sequencing) and an
 MD5 file. K2* --&gt; Spring samples PCR
 replicate one K3* --&gt; Spring samples PCR
 replicate two K4* --&gt; Spring samples PCR
 replicate three K5* --&gt; Spring samples PCR
 replicate four K6* --&gt; Autumn samples PCR
 replicate one K7* --&gt; Autumn samples PCR
 replicate two K8* --&gt; Autumn samples PCR
 replicate three K9* --&gt; Autumn samples PCR
 replicate four If you would like to
 demultiplex this data, we refer to the eight txt files named according to
 libraries. Each file contains 20 real samples (four samples per site:
 Borre, Boege, Tjaer, Jeks, and Faebaek). Each site contains one field
 blank (referred to as location name followed by "K"), and there
 is a total of four extraction blanks (CNE_P16 - CNE_P19). We also included
 two PCR blanks (NTCs). In total, after demultiplexing, there should be 31
 data files per library (20 samples, five field blanks, four extraction
 blanks and two PCR blanks). The txt files include the
 sample name followed by the PCR replicate number. The two following
 columns represent the tags used for individual samples. Tags are
 consistent across PCR replicates. After demultiplexing,
 you should be able to do as you please with the data.
description: If you want to follow the exact filtering and data analysis done
 in our study, we refer to the manuscript for further details after the
 demultiplex step. If you have any questions, feel free to send an email to
 Mads Reinholdt Jensen with any questions you may have.