Modelling the Effect of Vertical Mixing on Bottle Incubations for Determining in situ Phytoplankton Growth Rates and Primary Production

Abstract

The estimation of in situ phytoplankton growth rates and primary production is pivotal to many questions in biological oceanography and marine ecology both in a local and global context. A common approach is to incubate natural phytoplankton assemblages in clear bottles either at a single depth or at a range of fixed depths and to measure the increase in chlorophyll a (Chl a) (to determine the growth rate) or the uptake of carbon (14C) (to determine primary production) during the incubation period (typically 24 h). One of the main concerns with using fixed-depth bottle incubations is whether stranding samples at fixed depths biases the measured rates relative to the `true¿ in situ mixed conditions. Here we employ an individual based turbulence and photosynthesis model, which also accounts for photoacclimation and -inhibition, and apply it to dilution experiments performed to estimate the growth rates of the natural micro-phytoplankton community, including harmful taxa, in Alfacs Bay, Spain. In this micro-tidal coastal embayment, recurrent harmful outbreaks pose a threat to the local aquaculture. Based on the physical dynamics (light and turbulence profiles, wind and current intensities) operating during the dilution experiments, we discuss the error associated to the obtained growth rates. We show that the errors due to arresting the incubation bottles at fixed depths can be as large as 100%, depending on the method being used, the turbulence intensity, optical depth of the mixing layer, and incubation depth within the layer. We make recommendations for choosing the best depth for single-depth incubations. Furthermore we demonstrate that, if incubation bottles are being oscillated up and down through the water column, these systematic errors can be significantly reduced