Linking the bottom to the top in aquatic ecosystems

Linkages between benthic and pelagic habitats occur in both freshwater and marine systems across multiple spatial and temporal scales, and are influenced by a number of chemical, biological, and physical forces. We identified three major mechanisms of benthic-pelagic coupling: (1) organism movement, (2) trophic interactions, and (3) biogeochemical cycling. We also explore the implications of several stressors, including invasive species and climate change that will inevitably impact the linkages between benthic and pelagic habitats. We identify critical research gaps that need to be addressed to quantify the habitat coupling of these ecosystems. We advocate for more collaboration among scientists with expertise in benthic and pelagic habitats in both freshwater and marine ecosystems to fully understand the cycles, interactions, processes, and functions of benthic-pelagic coupling in ecosystems. Finally, we suggest targeted research needs for better capturing of cross-ecosystem linkages in aquatic ecology.