DOI: 10.5061/dryad.9s4mw6mg5
title: A field experiment reveals seasonal variation in the Daphnia gut microbiome

description: The gut microbiome is increasingly recognized for its impact on
 host fitness, but it remains poorly understood how naturally
 variable environments influence gut microbiome diversity and
 composition. We studied changes in the gut microbiome of ten
 genotypes of water fleas (Daphnia magna) in submerged mesocosm
 enclosures in a eutrophic lake over a period of 16 weeks, from
 early summer to autumn. The microbial diversity increased when
 Daphnia were reintroduced from the laboratory to the lake, and
 the composition of gut microbes drastically changed. Both gut
 microbiome diversity and composition continued to change over the
 16-week period, with alpha diversity peaking in late summer.
 The gut microbiome community was clearly distinct from that of
 the surrounding water, and temporal changes in the two
 communities were independent of each other. There were no
 consistent differences in the gut microbiomes among Daphnia
 genotypes in the lake environment. The change in gut microbiome
 over the season was accompanied by a decline in reproductive
 output and survival. There were weak, but statistically
 supported, effects of microbiota composition on Daphnia fitness,
 but there was no evidence that natural variation in
 microbiome diversity or composition was associated with tolerance
 to the cyanotoxin microcystin. We conclude that the gut
 microbiome of Daphnia is highly dynamic in a natural lake
 environment, but that host genetic effects on microbiome
 diversity and composition between genotypes within a population
 can be vanishingly small. These results emphasize
 that establishing the ecological effects of gut microbiota will
 require largescale experiments under natural conditions.
description: See methods section in the article.
description: <strong>File: Hegg_et _al-Microcystin_tolerance_assay.csv
 </strong>
 <strong>Description:</strong> Data used for the
 Microcystin tolerance assay. <strong>Columns:
 </strong> individual_ID = individual
 identity trial_number = trial number (0=week 0; 1 =
 week 4; 2 = week 8; 3 = week 12; 4 = week 16)
 clone_ID = clone identity treatment =
 experimental treatment (0 = non-toxic / no microcystin producing; 1 =
 toxic / microcystin producing) bucket_ID = identity
 of the bucket the individual comes from
 replicate_number = replication number (5 replications per trial
 per treatment) days_of_survival = days of survival
 since the start of the experiment (19 = until the end of the
 assay) number_of_broods = number of produced
 broods average_brood_size = average brood
 size total_number_of_offspring = total number of
 offspring (average_brood_size * number_of_broods)
 survival_till_end = survival until the end of the assay (0 = no;
 1 = yes) <strong>File:
 Hegg_et_al-Microcystin_measurements.csv</strong>
 <strong>Description:</strong> Measurements of
 Microcystin concentrations with ELISA-kit.
 <strong>Columns:</strong> 
 elisa_sample = sample number on well plate (samples were
 randomized on plate: this is not the location on the plate)
 elisa_number = identity of ELISA well plate
 date = date of sampling (year-month-day)
 enclosure = identity of enclosure type =
 either inside the enclosure or in the surrounding water column.
 Site = site identity (A or B) Microcystin =
 average microcystin concentration (in microgram/liter)
 microcystin_stddev =  standard deviation of microcystin
 concentration (in microgram/liter) 
 <strong> File: Hegg_et_al-Overview_microbiome_samples.csv
 </strong> <strong>Description:
 </strong>Overview of microbiome samples including data linked to
 these samples such as Microcystin concentrations and output of the
 tolerance assays.
 <strong>Columns:</strong> 
 sample = sample file name sample_id =
 sample identity (not for the control samples) type =
 type of sample (gut = pooled gut samples; wf = water sample from the
 field; control = control samples) date = date of
 sampling (year,month,day) site = experimental site
 identity enclosure = enclosure identity
 clone = clone identity (only available for gut
 samples) sequence_run = sequence run identity (1 or
 2) microcystin = Microcystin concentration (in
 microgram/liter) in enclosures. offspring_tox =
 average number of offspring produced per individual in the toxic treatment
  (from the tolerance assay) offspring_nontox =
 average number of offspring produced per individual in the non-toxic
 treatment  (from the tolerance assay) totalnumber_tox
 = total number of replicates in the toxic treatment (tolerance
 assay) totalsurv_tox = number of replicates that
 survived until the end of the assay in the toxic treatment (tolerance
 assay) totalrep_tox = number of replicates that
 reproduced before end of the assay in the toxic treatment (tolerance
 assay) totalnumber_nontox = total number of
 replicates in the non-toxic treatment (tolerance assay)
 totalsurv_nontox = number of replicates that survived until the
 end of the assay in the non-toxic treatment (tolerance assay)
 totalrep_nontox = number of replicates that reproduced before
 end of the assay in the non-toxic treatment (tolerance assay)
 <strong>File: Hegg_et_al-Phylogenetic_tree.tree
 </strong> <strong>Description:
 </strong>Phylogenetic tree of all microbiome samples. This file is
 readable with the package “ape” in “R”.
 <strong>File:
 Hegg_et_al-Microbiome_taxa_table.csv</strong>
 <strong>Description: </strong>List of all taxa
 present in the dataset and their 16S amplicon sequences. Row names are 16S
 amplicon sequences. Columns indicate taxonomic ranks (Kingdom, Phylum,
 Class, Order,Family and Genus).