Composition and Stability of the Microbial Community inside the Digestive Tract of the Aquatic Crustacean Daphnia magna


Small filter-feeding zooplankton organisms like the cladoceran Daphnia spp. are key members of freshwater food webs. Although several interactions between Daphnia and bacteria have been investigated, the importance of the microbial communities inside Daphnia guts has been studied only poorly so far. In the present study, we characterised the bacterial community composition inside the digestive tract of a laboratory-reared clonal culture of Daphnia magna using 16S rRNA gene libraries and terminal-restriction length polymorphism fingerprint analyses. In addition, the diversity and stability of the intestinal microbial community were investigated over time, with different food sources as well as under starvation stress and death, and were compared to the community in the cultivation water. The diversity of the Daphnia gut microbiota was low. The bacterial community consisted mainly of Betaproteobacteria (e.g. Limnohabitans sp.), few Gammaproteobacteria (e.g. Pseudomonas sp.) and Bacteroidetes that were related to facultatively anaerobic bacteria, but did not contain typical fermentative or obligately anaerobic gut bacteria. Rather, the microbiota was constantly dominated by Limnohabitans sp. which belongs to the Lhab-A1 tribe (previously called R-BT065 cluster) that is abundant in various freshwaters. Other bacterial groups varied distinctly even under constant cultivation conditions. Overall, the intestinal microbial community did not reflect the community in the surrounding cultivation water and clustered separately when analysed via the Additive Main Effects and Multiplicative Interaction model. In addition, the microbiota proved to be stable also when Daphnia were exposed to bacteria associated with a different food alga. After starvation, the community in the digestive tract was reduced to stable members. After death of the host animals, the community composition in the gut changed distinctly, and formerly undetected bacteria were activated. Our results suggest that the Daphnia microbiota consists mainly of an aerobic resident bacterial community which is indigenous to this habitat.

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We thank S. Wiechmann for technical assistance, A. Held for experimental assistance and E. Hespeler (chair Prof. Meyer) for help with the Genetic Analyzer for T-RFLP analysis. We are grateful to Dr D. Martin-Creuzburg and T. Basen (Limnology department) for sharing their expertise in the cultivation of Daphnia magna and Scenedesmus obliquus. We also want to thank Dr D. Ebert, Basel, who kindly provided the bacterial 16S rRNA gene shotgun sequences from intact Daphnia. This study was supported by research grants of the University of Konstanz.

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Correspondence to Heike M. Freese.

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Supplementary Table 1

Relative fluorescence values of T-RFs from Msp1 digested bacterial 16S rRNA genes amplified from DNA extracts of Daphnia magna microbiota incubated with Scenedesmus obliquus in different experiments (E1–3; E3_30: double amount of dissected guts), with xenic Cryptomonas sp., and incubated without food in comparison to respective cultivation water and the algal culture used for feeding. T-RFs identified via clones were named after these clones; if T-RFs were identified via bacterial isolates from the gut, the name was placed in brackets. (DOC 26 kb)

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Freese, H.M., Schink, B. Composition and Stability of the Microbial Community inside the Digestive Tract of the Aquatic Crustacean Daphnia magna . Microb Ecol 62, 882 (2011).

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  • Bacterial Community
  • Clone Library
  • Bacterial Community Composition
  • Cultivation Water
  • Intestinal Microbial Community