Seasonal dynamics show diverse prokaryotic community linkages between surface and deep ocean water

The Munida Microbial Observatory Time-Series (MOTS) transect spans two horizontal surface ecotones: i) between coastal neritic and subtropical waters, ii) between subtropical and subantarctic waters. These surface horizontal ecotones are seasonally dynamic yet separate distinct microbial communities. However, less is known about the vertical ecotones between surface and mesopelagic waters, their seasonal dynamics and their strength as a boundary. Here, a three year time-series of prokaryotic community composition from surface and deep (500 m) subantarctic waters from MOTS was used to study the seasonality of epipelagic and mesopelagic communities. Both surface and deep prokaryotic communities had seasonal patterns and high levels of variance from year to year, particularly in surface waters. Most of the seasonal variability was associated with phytoplankton bloom periods. Various surface heterotrophic bacteria growing in response to phytoplankton blooms had a lagged peak in relative abundance in deep waters post bloom. While detection of some surface prokaryotes in the deep ocean seemed seasonally linked to phytoplankton blooms and subsequent sinking particles, other copiotrophic or typically algal-associated groups that bloomed in the surface were not detected in the mesopelagic suggesting only specific populations were surviving the migration down the water column, across the ecotone. Transfer is possibly not always unidirectional, with typically deep ocean microbes being seasonally abundant in surface waters. This indicates that the main mechanism linking surface and deep communities changes seasonally: sinking of organic particles during productive periods, and vertical convection during winter overturning. While horizontal marine ecotones are more like transition zones that vary over time and space, vertical marine ecotones separate distinct prokaryotic communities with a select few members transported across the border via different seasonal mechanisms.