ALBERT

Description: Biodiversity is one of the key mechanisms that facilitate the adaptive response of planktonic communities to a fluctuating environment. How to allow for such a flexible response in marine ecosystem models is, however, not entirely clear. One particular way is to resolve the natural complexity of phytoplankton communities by explicitly incorporating a large number of species or plankton functional types. Alternatively, models of aggregate community properties focus on macroecological quantities such as total biomass, mean trait, and trait variance (or functional trait diversity), thus reducing the observed natural complexity to a few mathematical expressions. We developed the PhytoSFDM modelling tool, which can resolve species discretely and can capture aggregate community properties. The tool also provides a set of methods for treating diversity under realistic oceanographic settings. This model is coded in Python and is distributed as open-source software. PhytoSFDM is implemented in a zero-dimensional physical scheme and can be applied to any location of the global ocean. We show that aggregate community models reduce computational complexity while preserving relevant macroecological features of phytoplankton communities. Compared to species-explicit models, aggregate models are more manageable in terms of number of equations and have faster computational times. Further developments of this tool should address the caveats associated with the assumptions of aggregate community models and about implementations into spatially resolved physical settings (one-dimensional and three-dimensional). With PhytoSFDM we embrace the idea of promoting open-source software and encourage scientists to build on this modelling tool to further improve our understanding of the role that biodiversity plays in shaping marine ecosystems.

Description: Diversity plays critical roles in ecosystem functioning, but it remains unclear how best to model phytoplankton diversity in order to better understand those roles and reproduce consistently observed patterns in the ocean. In contrast to the typical approach of resolving distinct species or functional groups, we present a ContInuous TRAiT-basEd phytoplankton model (CITRATE) that focuses on macroscopic properties such as total biomass, mean trait values, and trait variance. This phytoplankton component is embedded within a Nitrogen-Phytoplankton-Zooplankton-Detritus-Iron model that itself is coupled with a simplified one-dimensional ocean model. Size is used as the master trait for phytoplankton. CITRATE also incorporates trait diffusion for sustaining diversity, as well as simple representations of physiological acclimation, i.e. flexible chlorophyll-to-carbon and nitrogen-to-carbon ratios. We implemented CITRATE 1.0 at two contrasting stations in the Northwest Pacific where several years of observational data are available. The model is driven by physics forcing including vertical eddy diffusivity imported from three-dimensional ocean circulation models. One common set of model parameters for the two stations was optimized using the Delayed Rejection Adaptive Metropolis-Hasting Monte Carlo (DRAM) algorithm. The model faithfully reproduced most of the observational patterns and gave robust predictions on phytoplankton mean size and size diversity. With proper physical forcing, CITRATE 1.0 can be applied to any oceanic station where either nitrogen or iron limits phytoplankton growth.

Description: The reaction CH3C(O)O2 + HO2 → CH3C(O)OOH + O2 (Reaction R5a), CH3C(O)OH + O3 (Reaction R5b), CH3 + CO2 + OH + O2 (Reaction R5c) was studied in a series of experiments conducted at 1000 mbar and (293 ± 2) K in the HIRAC simulation chamber. For the first time, products, (CH3C(O)OOH, CH3C(O)OH, O3 and OH) from all three branching pathways of the reaction have been detected directly and simultaneously. Measurements of radical precursors (CH3OH, CH3CHO), HO2 and some secondary products HCHO and HCOOH further constrained the system. Fitting a comprehensive model to the experimental data, obtained over a range of conditions, determined the branching ratios α(R5a) = 0.37 ± 0.10, α(R5b) = 0.12 ± 0.04 and α(R5c) = 0.51 ± 0.12 (errors at 2σ level). Improved measurement/model agreement was achieved using k(R5) = (2.4 ± 0.4) × 10-11 cm3 molecule-1 s-1, which is within the large uncertainty of the current IUPAC and JPL recommended rate coefficients for the title reaction. The rate coefficient and branching ratios are in good agreement with a recent study performed by Groß et al. (2014b); taken together, these two studies show that the rate of OH regeneration through Reaction (R5) is more rapid than previously thought. GEOS-Chem has been used to assess the implications of the revised rate coefficients and branching ratios; the modelling shows an enhancement of up to 5 % in OH concentrations in tropical rainforest areas and increases of up to 10 % at altitudes of 6–8 km above the equator, compared to calculations based on the IUPAC recommended rate coefficient and yield. The enhanced rate of acetylperoxy consumption significantly reduces PAN in remote regions (up to 30 %) with commensurate reductions in background NOx.

Description: The calibration of field instruments used to measure concentrations of OH and HO2 worldwide has traditionally relied on a single method utilising the photolysis of water vapour in air in a flow tube at atmospheric pressure. Here the calibration of two FAGE (fluorescence assay by gaseous expansion) apparatuses designed for HOx (OH and HO2) measurements have been investigated as a function of external pressure using two different laser systems. The conventional method of generating known concentrations of HOx from H2O vapour photolysis in a turbulent flow tube impinging just outside the FAGE sample inlet has been used to study instrument sensitivity as a function of internal fluorescence cell pressure (1.8–3.8 mbar). An increase in the calibration constants CHO and CHO2 with pressure was observed, and an empirical linear regression of the data was used to describe the trends, with ΔCHO = (17 ± 11) % and ΔCHO2 = (31.6 ± 4.4)% increase per millibar air (uncertainties quoted to 2σ). Presented here are the first direct measurements of the FAGE calibration constants as a function of external pressure (440–1000 mbar) in a controlled environment using the University of Leeds HIRAC chamber (Highly Instrumented Reactor for Atmospheric Chemistry). Two methods were used: the temporal decay of hydrocarbons for calibration of OH, and the kinetics of the second-order recombination of HO2 for HO2 calibrations. Over comparable conditions for the FAGE cell, the two alternative methods are in good agreement with the conventional method, with the average ratio of calibration factors (conventional : alternative) across the entire pressure range, COH(conv)/COH(alt) = 1.19 ± 0.26 and CHO2(conv)/CHO2(alt) = 0.96 ± 0.18 (2σ). These alternative calibration methods currently have comparable systematic uncertainties to the conventional method: ~ 28% and ~ 41% for the alternative OH and HO2 calibration methods respectively compared to 35% for the H2O vapour photolysis method; ways in which these can be reduced in the future are discussed. The good agreement between the very different methods of calibration leads to increased confidence in HOx field measurements and particularly in aircraft-based HOx measurements, where there are substantial variations in external pressure, and assumptions are made regarding loss rates on inlets as a function of pressure.