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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 172.
Published online Apr 21, 2009. doi:  10.1186/1471-2164-10-172
PMCID: PMC2678164
Comparative metagenomics of Daphnia symbionts
Weihong Qi,1,4 Guang Nong,2 James F Preston,2 Frida Ben-Ami,3 and Dieter Ebertcorresponding author3
1Swiss Tropical Institute, Socinstrasse 57, 4002 Basel, Switzerland
2Department of Microbiology and Cell Sciences, University of Florida, Gainesvillle, FL 32611, USA
3Zoological Institute, Basel University, Vesalgasse 1, 4051 Basel, Switzerland
4Functional Genomics Center Zurich, UNI/ETH Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
corresponding authorCorresponding author.
Weihong Qi: weihong.qi/at/fgcz.ethz.ch; Guang Nong: gnong/at/ufl.edu; James F Preston: jpreston/at/ufl.edu; Frida Ben-Ami: frida.ben-ami/at/unibas.ch; Dieter Ebert: dieter.ebert/at/unibas.ch
Received March 4, 2008; Accepted April 21, 2009.
Abstract
Background
Shotgun sequences of DNA extracts from whole organisms allow a comprehensive assessment of possible symbionts. The current project makes use of four shotgun datasets from three species of the planktonic freshwater crustaceans Daphnia: one dataset from clones of D. pulex and D. pulicaria and two datasets from one clone of D. magna. We analyzed these datasets with three aims: First, we search for bacterial symbionts, which are present in all three species. Second, we search for evidence for Cyanobacteria and plastids, which had been suggested to occur as symbionts in a related Daphnia species. Third, we compare the metacommunities revealed by two different 454 pyrosequencing methods (GS 20 and GS FLX).
Results
In all datasets we found evidence for a large number of bacteria belonging to diverse taxa. The vast majority of these were Proteobacteria. Of those, most sequences were assigned to different genera of the Betaproteobacteria family Comamonadaceae. Other taxa represented in all datasets included the genera Flavobacterium, Rhodobacter, Chromobacterium, Methylibium, Bordetella, Burkholderia and Cupriavidus. A few taxa matched sequences only from the D. pulex and the D. pulicaria datasets: Aeromonas, Pseudomonas and Delftia. Taxa with many hits specific to a single dataset were rare. For most of the identified taxa earlier studies reported the finding of related taxa in aquatic environmental samples. We found no clear evidence for the presence of symbiotic Cyanobacteria or plastids. The apparent similarity of the symbiont communities of the three Daphnia species breaks down on a species and strain level. Communities have a similar composition at a higher taxonomic level, but the actual sequences found are divergent. The two Daphnia magna datasets obtained from two different pyrosequencing platforms revealed rather similar results.
Conclusion
Three clones from three species of the genus Daphnia were found to harbor a rich community of symbionts. These communities are similar at the genus and higher taxonomic level, but are composed of different species. The similarity of these three symbiont communities hints that some of these associations may be stable in the long-term.
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