A field experiment reveals seasonal variation in the Daphnia gut microbiome

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.