Upwelling linked to warm summers and bleaching on the Great Barrier Reef

We investigate a range of indices to quantify upwelling on the central Great Barrier Reef (GBR), Australia, so that environmental and biological relationships associated with upwelling in this area can be explored. We show that "Upwelling days" (the number of days of upwelling) and diurnal variation in subsurface temperature (maximum-minimum, 20-m depth) are satisfactory metrics to describe the duration and intensity of upwelling events, respectively. We use these to examine key characteristics of shelf-break upwelling in the central GBR. Our results show, somewhat paradoxically, that although upwelling involves cold water being brought near to the surface, it is linked to positive thermal anomalies on the GBR, both locally and regionally. Summers (December to February) with strongest upwelling occurred during the GBR-wide bleaching events of 1997-1998 and 2001-2002. Upwelling in the GBR is enhanced during doldrums conditions that were a feature of these summers. During these conditions, the poleward-flowing East Australian Current flows faster, lifting the thermocline closer to the surface, spilling more sub-thermocline waters onto the shelf. Doldrums conditions also result in intense local heating, stratification of the water column, and, when severe, coral bleaching. Upwelling intrusions are spatially restricted (central GBR), generally remain subsurface, and are often intermittent, allowing GBR-wide bleaching to occur despite conditions resulting in enhanced upwelling. Intense upwelling events precede anomalous seasonal temperature maxima by up to 2 months and bleaching by 1-3 wk, leading to the prospect of using upwelling activity as a seasonal forecasting index of unusually warm summers and widespread bleaching

SWIM: A Semi-Analytical Ocean Color Inversion Algorithm for Optically Shallow Waters

Ocean color remote sensing provides synoptic-scale, near-daily observations of marine inherent optical properties (IOPs). Whilst contemporary ocean color algorithms are known to perform well in deep oceanic waters, they have difficulty operating in optically clear, shallow marine environments where light reflected from the seafloor contributes to the water-leaving radiance. The effect of benthic reflectance in optically shallow waters is known to adversely affect algorithms developed for optically deep waters [1, 2]. Whilst adapted versions of optically deep ocean color algorithms have been applied to optically shallow regions with reasonable success [3], there is presently no approach that directly corrects for bottom reflectance using existing knowledge of bathymetry and benthic albedo.To address the issue of optically shallow waters, we have developed a semi-analytical ocean color inversion algorithm: the Shallow Water Inversion Model (SWIM). SWIM uses existing bathymetry and a derived benthic albedo map to correct for bottom reflectance using the semi-analytical model of Lee et al [4]. The algorithm was incorporated into the NASA Ocean Biology Processing Groups L2GEN program and tested in optically shallow waters of the Great Barrier Reef, Australia. In-lieu of readily available in situ matchup data, we present a comparison between SWIM and two contemporary ocean color algorithms, the Generalized Inherent Optical Property Algorithm (GIOP) and the Quasi-Analytical Algorithm (QAA)

SWIM: A Semi-Analytical Ocean Color Inversion Algorithm for Optically Shallow Waters

In clear shallow waters, light that is transmitted downward through the water column can reflect off the sea floor and thereby influence the water-leaving radiance signal. This effect can confound contemporary ocean color algorithms designed for deep waters where the seafloor has little or no effect on the water-leaving radiance. Thus, inappropriate use of deep water ocean color algorithms in optically shallow regions can lead to inaccurate retrievals of inherent optical properties (IOPs) and therefore have a detrimental impact on IOP-based estimates of marine parameters, including chlorophyll-a and the diffuse attenuation coefficient. In order to improve IOP retrievals in optically shallow regions, a semi-analytical inversion algorithm, the Shallow Water Inversion Model (SWIM), has been developed. Unlike established ocean color algorithms, SWIM considers both the water column depth and the benthic albedo. A radiative transfer study was conducted that demonstrated how SWIM and two contemporary ocean color algorithms, the Generalized Inherent Optical Properties algorithm (GIOP) and Quasi-Analytical Algorithm (QAA), performed in optically deep and shallow scenarios. The results showed that SWIM performed well, whilst both GIOP and QAA showed distinct positive bias in IOP retrievals in optically shallow waters. The SWIM algorithm was also applied to a test region: the Great Barrier Reef, Australia. Using a single test scene and time series data collected by NASA's MODIS-Aqua sensor (2002-2013), a comparison of IOPs retrieved by SWIM, GIOP and QAA was conducted

Doom and Boom on a Resilient Reef: Climate Change, Algal Overgrowth and Coral Recovery

Background: Coral reefs around the world are experiencing large-scale degradation, largely due to global climate change, overfishing, diseases and eutrophication. Climate change models suggest increasing frequency and severity of warming-induced coral bleaching events, with consequent increases in coral mortality and algal overgrowth. Critically, the recovery of damaged reefs will depend on the reversibility of seaweed blooms, generally considered to depend on grazing of the seaweed, and replenishment of corals by larvae that successfully recruit to damaged reefs. These processes usually take years to decades to bring a reef back to coral dominance

Environmental Factors Controlling the Distribution of Symbiodinium Harboured by the Coral Acropora millepora on the Great Barrier Reef

Background: The Symbiodinium community associated with scleractinian corals is widely considered to be shaped by seawater temperature, as the coral's upper temperature tolerance is largely contingent on the Symbiodinium types harboured. Few studies have challenged this paradigm as knowledge of other environmental drivers on the distribution of Symbiodinium is limited. Here, we examine the influence of a range of environmental variables on the distribution of Symbiodinium associated with Acropora millepora collected from 47 coral reefs spanning 1,400 km on the Great Barrier Reef (GBR), Australia

The variability and potential for prediction of harmful algal blooms in the southern Benguela ecosystem

Harmful Algal Blooms (HABs) in the southern Benguela are usually attributed to dinoflagellate species, which constitute a regular component of normal phytoplankton populations. Fundamental to the success of HAB predictive systems is a sound knowledge of their variability. Although the Benguela remains poorly explored in terms of phytoplankton distribution, important biogeographic differences between the northern and southern Benguela, and the West Coast and Western Agulhas Bank have been reported and are reflected in the composition of HABs. The southern Benguela is characterized by clear seasonal trends, and high phytoplankton biomass and productivity during the latter months of the upwelling season can be attributed largely to dinoflagellate populations. Superimposed on the seasonal trend of increasing dinoflagellates and phytoplankton biomass are shorter successional patterns associated with spatial and temporal transitions in water column stratification driven by wind cycles and coastal topography. Understanding the mechanisms that control the transport, concentration and dissipation of dinoflagellate blooms is critical in predicting their coastal impact. For this purpose models of coastal wind-driven upwelling are required to reproduce both across-shelf and alongshore dynamics. Such information stands us in good stead in attempts to predict high biomass dinoflagellate blooms which impact the Benguela through low oxyten and hydrogen sulphide events. Less progress has been made on species-specific prediction fundamental to the prediction of toxin related events

Satellite monitoring of the evolution of a Coccolithophorid bloom in the Southern Benguela upwelling system

Upwelling systems are thought to be characterized by the dominance of chain-forming diatoms, and the large fisheries typical of coastal upwelling systems are considered to be based on the classical food chain of “diatoms - copepods - fish” (Cushing, 1989). Little consideration has been given to the contribution of coccolithophorids to the phytoplankton communities in upwelling systems. The coccolithophorids belong to the Prymnesiophyceae and are able to synthesize external calcium carbonate platelets, or coccoliths, which cover the outer surface of the cell. Coccolithophorids are globally cosmopolitan (Brown and Yoder, 1994) and known to form near mono-specific blooms that can extend over large areas of the ocean surface (Holligan et al., 1983, 1993). Such blooms provide a milky turquoise colour to the ocean, owing to the scattering properties of the coccoliths (Balch et al., 1996a)

Thermal applications

Coral reef scientists and managers are increasingly relying on remote sensing data to provide information on biophysical processes of reefs and to help identify optimum management strategies for reef resources. For these users, we provide some guidelines to identify which remote sensing tools and data should be used to address coral reef research and management questions. We additionally discuss: opportunities to reconcile the sometimes conflicting needs of producers and users of coral reef information; data requirements and limitations for specific coral reef management applications; and trade-offs between production costs and accuracy of coral reef remote sensing data products. Finally, we provide several in-depth examples of current uses of remote sensing data to: provide resources inventories for prioritizing areas for management; develop spatially explicit models of reef fish assemblage characteristics; and monitor and respond to threats (e.g., from terrestrial runoff, crown-of-thorns outbreaks, oil spills and ship groundings). Throughout, we emphasize ways that remote sensing can be cost-effectively integrated within coral reef management programs to improve the quality of information on which management decisions are based

Upwelling linked to warm summers and bleaching on the Great Barrier Reef

Abstract We investigate a range of indices to quantify upwelling on the central Great Barrier Reef (GBR), Australia, so that environmental and biological relationships associated with upwelling in this area can be explored. We show that ''Upwelling days'' (the number of days of upwelling) and diurnal variation in subsurface temperature (maximum-minimum, 20-m depth) are satisfactory metrics to describe the duration and intensity of upwelling events, respectively. We use these to examine key characteristics of shelf-break upwelling in the central GBR. Our results show, somewhat paradoxically, that although upwelling involves cold water being brought near to the surface, it is linked to positive thermal anomalies on the GBR, both locally and regionally. Summers (December to February) with strongest upwelling occurred during the GBR-wide bleaching events of 1997-1998 and 2001-2002. Upwelling in the GBR is enhanced during doldrums conditions that were a feature of these summers. During these conditions, the poleward-flowing East Australian Current flows faster, lifting the thermocline closer to the surface, spilling more sub-thermocline waters onto the shelf. Doldrums conditions also result in intense local heating, stratification of the water column, and, when severe, coral bleaching. Upwelling intrusions are spatially restricted (central GBR), generally remain subsurface, and are often intermittent, allowing GBR-wide bleaching to occur despite conditions resulting in enhanced upwelling. Intense upwelling events precede anomalous seasonal temperature maxima by up to 2 months and bleaching by 1-3 wk, leading to the prospect of using upwelling activity as a seasonal forecasting index of unusually warm summers and widespread bleaching