Two decades of describing the unseen majority of aquatic microbial diversity



    1. Microbial Habitat Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
    Search for more papers by this author
    • L. Zinger and A. Gobet contributed equally to this work.


    1. Evolution du Plancton et PaléoOcéans (EPPO), Station Biologique de Roscoff, UMR7144 Centre National de la Recherche Scientifique (CNRS) et Université Pierre et Marie Curie (UPMC), Place Georges Teissier, 29680 Roscoff, France
    2. Genoscope (CEA), CNRS UMR 8030, Université d’Evry, 2 rue Gaston Crémieux, BP5706, 91057 Evry, France
    Search for more papers by this author
    • L. Zinger and A. Gobet contributed equally to this work.


    1. Microbial Ecology UMR 5557 CNRS-Université Lyon 1; USC 1193 INRA, Bat G. Mendel, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
    Search for more papers by this author

Lucie Zinger, Fax: +49 421 2028 690; E-mail:


Aquatic environments harbour large and diverse microbial populations that ensure their functioning and sustainability. In the current context of global change, characterizing microbial diversity has become crucial, and new tools have been developed to overcome the methodological challenges posed by working with microbes in nature. The advent of Sanger sequencing and now next-generation sequencing technologies has enabled the resolution of microbial communities to an unprecedented degree of precision. However, to correctly interpret microbial diversity and its patterns this revolution must also consider conceptual and methodological matters. This review presents advances, gaps and caveats of these recent approaches when considering microorganisms in aquatic ecosystems. We also discuss potentials and limitations of the available methodologies, from water sampling to sequence analysis, and suggest alternative ways to incorporate results in a conceptual and methodological framework. Together, these methods will allow us to gain an unprecedented understanding of microbial diversity in aquatic ecosystems.