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In this paper, we focus on the current understanding of the microbial diversity of bacte- rioplankton and its link to the biogeochemistry of the pelagic zone of aquatic ecosystems. During the last 2 decades, a large array of molecular approaches has been developed and applied to assess the diversity of bacterioplankton. One key result of the classical molecular approaches, such as commu- nity fingerprints and environmental clone libraries, is that the bacterioplankton community contains only a few abundant species and a large number of less abundant to rare members. This is in contrast to soil bacterial communities, where no abundant species are detected and the total number of spe- cies is substantially larger. New approaches, such as metagenomics and pyrosequencing, are dis- cussed in terms of their ability to determine the diversity and abundance of the rare members of the community and the biogeochemical potential of the community. Several new approaches, such as sta- ble isotope probing (SIP) and multi-isotope imaging mass spectrometry (MIMS), have been devel- oped to study structure-function relationships of microbial communities. The combination of biogeo- chemical stimulation experiments with these functional and/or molecular approaches has the potential to elucidate the role of specific microorganisms concerning specific biogeochemical func- tions. These experimental analyses, together with in situ measurements of molecular and biogeo- chemical markers, enable the identification of key catalysts of pelagic biogeochemical processes and determination of their regulatory factors. Based on our current understanding of the structure- function links in bacterioplankton, we hypothesize that any local bacterial community comprises 2 parts: the abundant members form a core community that carries out the ongoing biogeochemical functions, and the rare members form a seedbank that provides the genetic potential to respond to any change in the system. Together, both parts form a pan community that is able to mediate the biogeochemical processes in the pelagic ecosystems of the earth.

Molecular diversity of bacterioplankton: link to a predictive biogeochemistry of pelagic ecosystems