Mesozooplankton is a key component of the ocean, regulating global
processes such as the carbon pump, and ensuring energy transfer from
lower to higher trophic levels. Yet, despite the importance of
understanding mesozooplankton diversity, distribution and connectivity
at global scale to predict the impact of climate change in marine
ecosystems, there is still fragmented knowledge. To fill this gap, we
applied DNA metabarcoding to mesozooplankton samples collected during
the Malaspina-2010 circumnavigation expedition across temperate and
tropical oceans from the surface to bathypelagic depths. By conducting a
hidden diversity analysis, we highlight the still scarce knowledge on
global mesozooplankton diversity and identify the Indian Ocean and the
deep sea as the most understudied areas. By analysing mesozooplankton
community spatial distribution, we confirm global biogeographical
patterns across the temperate to tropical oceans both in the vertical
and horizontal gradients. Additionally, we reveal a consistent increase
in mesozooplankton beta-diversity with depth, indicating reduced
connectivity at deeper layers, and identify a water mass type-mediated
structuring of bathypelagic communities, instead of an oceanic
basin-mediated as observed at upper layers. This suggests limited
dispersal at deep ocean layers, most likely due to weaker currents and
lower mixing of water mass types. Overall, our work supports the neutral
theory of biodiversity and thus the importance of oceanic currents and
barriers in dispersal in shaping global plankton communities, and
provides key knowledge for predicting the impact of climate change in
the deep-sea.