A field experiment reveals seasonal variation in the Daphnia gut microbiome

Abstract

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 large‐scale experiments under natural conditions.

Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance

“…4 ), but the Shannon Index did not vary by genotype or sediment layer of origin. Overall, Daphnia bacterial community composition reported in this study is similar to those found in other Daphnia studies, particularly the dominance of Betaproteobacteria in Daphnia guts and Actinobacteria in the medium [ 22 , 24 , 26 ].…”

“…The community composition of gut bacteria in D. magna is influenced by both the host genotype and by a variation in environmental bacteria [ 21 , 22 ]. However, the extent of host genotype influence on Daphnia bacterial communities is debated, with a laboratory study revealing no variation in whole D. magna bacterial communities by host genotype [ 23 ] and a recent mesocosm study showing no variation by host genotype in D. magna gut bacterial communities raised in natural lake water [ 24 ].…”

Natural diversity of the honey bee (Apis mellifera) gut bacteriome in various climatic and seasonal states

“…We assumed that a seasonal shift in gut bacteriome would be identified as such differences have been observed in many other invertebrate and vertebrate species. For instance, seasonal variation of the gut bacteriome was found in humans [47,48], non-human primates [49,50], other mammalian species [51,52], fishes [15], birds [53] and arthropods as well [54,55]. However, seasonal changes are most likely linked to other factors, such as changes in the feeding habit of the animal or its lifestyle.…”

Combined Effects of Polystyrene Nanoplastics and Enrofloxacin on the Life Histories and Gut Microbiota of Daphnia magna

“…The isolated DNA was then mixed v/v to obtain a representative sample and was then sequenced. In order to analyse the microbiota, we used a standard Miseq illumine sequencing method used in numerous previous studies, e.g., in [62][63][64][65]. The D. magna, the digestive tracts were collected in 1.5 mL Eppendorf and stored at −20 • C. Afterwards, the DNA extraction was performed in the spin-column-based method using the GeneMATRIX DNA Purification kit (EurX, Gda ńsk, Poland), according to the manufacturer's procedure.…”