An integrated model for aquaculture production, pathogen interaction, and environmental effects

This work develops, applies, and tests a methodology for simulating three key determinants of aquaculture carrying capacity: production, environmental effects, and pathogen interactions. Deterministic models for simulation of biomass production and environmental effects for fish and shellfish were combined with stochastic host-pathogen models based on the Susceptible-Exposed-Infected-Recovered (SEIR) paradigm to build the Aquaculture, Biosecurity, and Carrying Capacity (ABC) platform. Individual growth models for the finfish species Atlantic salmon (Salmo salar) and gilthead bream (Sparus aurata), and the bivalve species Pacific oyster (Crassostrea gigas) and Eastern oyster (C. virginica) were integrated into an Individual Based Model (IBM) capable of scaling to any farm size; the resulting framework was coupled to host-pathogen models for: (i) salmon-Infectious Hepatopoietic Necrosis virus (IHNv); (ii) Pacific oyster-Oyster herpes virus (OsHV-1); and (iii) Pacific oyster-Vibrio aestuarianus. ABC was run for a set of scenarios both with and without pathogens, and results presented for (a) husbandry: food depletion in Eastern oyster, showing the effects of overstocking on production and water-column chlorophyll; an increase in the spacing of farm sections increases yield by 80%; (b) environmental effects: changes due to marine cage culture of gilthead sea bream, and the effect of hydrodynamics on reduction of dissolved oxygen (DO) and increase in ammonia; a farm sited in a high-dispersion area shows a variation of about 1.5 mg L−1 in DO among cages, whereas the range in a low-dispersion site can be up to 5 mg L−1; (c) three case-studies of pathogen interaction: (i) effects of a salmon-IHNv pathogen event on yield and mortality, and consequences of event timing (early- or late-stage in the culture); the late-stage event costs almost 300,000 USD more in wasted feed, and the Feed Conversion Ratio (FCR) increases from 1.5 to 2.3; (ii) consequences for a Vibrio outbreak in oysters; even though the disease event is very short, there is a 7.8% decrease in oyster harvest, and net nitrogen removal, a key regulatory ecosystem service, decreases by 10.2%; and (iii) climate change scenarios based on Representative Concentration Pathway (RCP) 8.5 and consequences for a herpes outbreak in oysters; ABC results show that the direct effect of climate change on growth, which leads to earlier harvest and less non-harvestable animals, is strongly outweighed by the indirect eff