Simulations of phytoplankton seasonal cycle with multi-level and multi-layer physical-ecosystem models: the Black Sea example

A generic framework for individual-based modelling and physical-biological interaction

The increased availability of high-resolution ocean data globally has enabled more detailed analyses of physical-biological interactions and their consequences to the ecosystem. We present IBMlib, which is a versatile, portable and computationally effective framework for conducting Lagrangian simulations in the marine environment. The purpose of the framework is to handle complex individual-level biological models of organisms, combined with realistic 3D oceanographic model of physics and biogeochemistry describing the environment of the organisms without assumptions about spatial or temporal scales. The open-source framework features a minimal robust interface to facilitate the coupling between individual-level biological models and oceanographic models, and we provide application examples including forward/backward simulations, habitat connectivity calculations, assessing ocean conditions, comparison of physical circulation models, model ensemble runs and recently posterior Eulerian simulations using the IBMlib framework. We present the code design ideas behind the longevity of the code, our implementation experiences, as well as code performance benchmarking. The framework may contribute substantially to progresses in representing, understanding, predicting and eventually managing marine ecosystems.

Venice and I: How a City Can Determine the Fate of a Career

Quoting the ancient Romans: Audentes Fortuna iuvat. Being in the right place at the right time is useless if you do not grasp your Fortuna and build upon it. In this article, I expound on the milestones of my multiform research career, which over more than 40 years brought me from Venice to California to MIT; from the Venice problem to highly nonlinear, coherent structures in the ocean and atmosphere; and from the mare nostrum (the Mediterranean Sea), a laboratory for global processes, to the tropical ocean-atmosphere systems and regional coupled climate models of the Maritime Continent. The climate system, with its daunting complexity, is arguably the greatest challenge for, and the future of, the entirety of the earth sciences. Finally, living in and working for Venice has been the privilege and Fortuna of my life.

Microphytoplankton variations during coral spawning at Los Roques, Southern Caribbean

Phytoplankton drives primary productivity in marine pelagic systems. This is also true for the oligotrophic waters in coral reefs, where natural and anthropogenic sources of nutrients can alter pelagic trophic webs. In this study, microphytoplankton assemblages were characterized for the first time in relation to expected coral spawning dates in the Caribbean. A hierarchical experimental design was used to examine these assemblages in Los Roques archipelago, Venezuela, at various temporal and spatial scales for spawning events in both 2007 and 2008. At four reefs, superficial water samples were taken daily for 9 days after the full moon of August, including days before, during and after the expected days of coral spawning. Microphytoplankton assemblages comprised 100 microalgae taxa at up to 50 cells per mL (mean ± 8 SD) and showed temporal and spatial variations related to the coral spawning only in 2007. However, chlorophyll a concentrations increased during and after the spawning events in both years, and this was better matched with analyses of higher taxonomical groups (diatoms, cyanophytes and dinoflagellates), that also varied in relation to spawning times in 2007 and 2008, but asynchronously among reefs. Heterotrophic and mixotrophic dinoflagellates increased in abundance, correlating with a decrease of the diatom Cerataulina pelagica and an increase of the diatom Rhizosolenia imbricata. These variations occurred during and after the coral spawning event for some reefs in 2007. For the first time, a fresh-water cyanobacteria species of Anabaena was ephemerally found (only 3 days) in the archipelago, at reefs closest to human settlements. Variability among reefs in relation to spawning times indicated that reef-specific processes such as water residence time, re-mineralization rates, and benthic-pelagic coupling can be relevant to the observed patterns. These results suggest an important role of microheterotrophic grazers in re-mineralization of organic matter in coral reef waters and highlight the importance of assessing compositional changes of larger size fractions of the phytoplankton when evaluating primary productivity and nutrient fluxes.