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A Molecular Approach to Identify Active Microbes in Environmental Eukaryote Clone Libraries

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Abstract

A rapid method for the simultaneous extraction of RNA and DNA from eukaryote plankton samples was developed in order to discriminate between indigenous active cells and signals from inactive or even dead organisms. The method was tested using samples from below the chemocline of an anoxic Danish fjord. The simple protocol yielded RNA and DNA of a purity suitable for amplification by reverse transcription-polymerase chain reaction (RT-PCR) and PCR, respectively. We constructed an rRNA-derived and an rDNA-derived clone library to assess the composition of the microeukaryote assemblage under study and to identify physiologically active constituents of the community. We retrieved nearly 600 protistan target clones, which grouped into 84 different phylotypes (98% sequence similarity). Of these phylotypes, 27% occurred in both libraries, 25% exclusively in the rRNA library, and 48% exclusively in the rDNA library. Both libraries revealed good correspondence of the general community composition in terms of higher taxonomic ranks. They were dominated by anaerobic ciliates and heterotrophic stramenopile flagellates thriving below the fjord’s chemocline. The high abundance of these bacterivore organisms points out their role as a major trophic link in anoxic marine systems. A comparison of the two libraries identified phototrophic dinoflagellates, “uncultured marine alveolates group I,” and different parasites, which were exclusively detected with the rDNA-derived library, as nonindigenous members of the anoxic microeukaryote community under study.

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Acknowledgments

We thank U. Frisenette, Captain of the RV Maria for all his support during sampling in Mariager and providing his expertise and all facilities that enabled sampling of the Mariager Fjord. We are grateful to Anika Knapp for initial RNA work. K. Jürgens provided valuable comments on an earlier draft of the manuscript and E. Jarroll helped to improve the language. We greatly appreciate the comments of two anonymous reviewers, who helped to significantly improve our manuscript. This study was funded by grants from the Deutsche Forschungsgemeinschaft (DFG) to TS (STO414/2-2) and the Stiftung Rheinland-Pfalz für Innovation (project 736).

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Stoeck, T., Zuendorf, A., Breiner, HW. et al. A Molecular Approach to Identify Active Microbes in Environmental Eukaryote Clone Libraries. Microb Ecol 53, 328–339 (2007). https://doi.org/10.1007/s00248-006-9166-1

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