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.

See methods section in the article.

File: Hegg_et _al-Microcystin_tolerance_assay.csv

Description: Data used for the Microcystin tolerance assay.

Columns:

1. individual_ID = individual identity
2. trial_number = trial number (0=week 0; 1 = week 4; 2 = week 8; 3 = week 12; 4 = week 16)
3. clone_ID = clone identity
4. treatment = experimental treatment (0 = non-toxic / no microcystin producing; 1 = toxic / microcystin producing)
5. bucket_ID = identity of the bucket the individual comes from
6. replicate_number = replication number (5 replications per trial per treatment)
7. days_of_survival = days of survival since the start of the experiment (19 = until the end of the assay)
8. number_of_broods = number of produced broods
9. average_brood_size = average brood size
10. total_number_of_offspring = total number of offspring (average_brood_size * number_of_broods)
11. survival_till_end = survival until the end of the assay (0 = no; 1 = yes)

File: Hegg_et_al-Microcystin_measurements.csv

Description: Measurements of Microcystin concentrations with ELISA-kit.

Columns:

1. elisa_sample = sample number on well plate (samples were randomized on plate: this is not the location on the plate)
2. elisa_number = identity of ELISA well plate
3. date = date of sampling (year-month-day)
4. enclosure = identity of enclosure
5. type = either inside the enclosure or in the surrounding water column.
6. Site = site identity (A or B)
7. Microcystin = average microcystin concentration (in microgram/liter)
8. microcystin_stddev =  standard deviation of microcystin concentration (in microgram/liter)

 File: Hegg_et_al-Overview_microbiome_samples.csv

Description: Overview of microbiome samples including data linked to these samples such as Microcystin concentrations and output of the tolerance assays.

Columns:

1. sample = sample file name
2. sample_id = sample identity (not for the control samples)
3. type = type of sample (gut = pooled gut samples; wf = water sample from the field; control = control samples)
4. date = date of sampling (year,month,day)
5. site = experimental site identity
6. enclosure = enclosure identity
7. clone = clone identity (only available for gut samples)
8. sequence_run = sequence run identity (1 or 2)
9. microcystin = Microcystin concentration (in microgram/liter) in enclosures.
10. offspring_tox = average number of offspring produced per individual in the toxic treatment  (from the tolerance assay)
11. offspring_nontox = average number of offspring produced per individual in the non-toxic treatment  (from the tolerance assay)
12. totalnumber_tox = total number of replicates in the toxic treatment (tolerance assay)
13. totalsurv_tox = number of replicates that survived until the end of the assay in the toxic treatment (tolerance assay)
14. totalrep_tox = number of replicates that reproduced before end of the assay in the toxic treatment (tolerance assay)
15. totalnumber_nontox = total number of replicates in the non-toxic treatment (tolerance assay)
16. totalsurv_nontox = number of replicates that survived until the end of the assay in the non-toxic treatment (tolerance assay)
17. totalrep_nontox = number of replicates that reproduced before end of the assay in the non-toxic treatment (tolerance assay)

File: Hegg_et_al-Phylogenetic_tree.tree

Description: Phylogenetic tree of all microbiome samples. This file is readable with the package “ape” in “R”.

File: Hegg_et_al-Microbiome_taxa_table.csv

Description: 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).