Impact of a Tropical Cyclone on Terrestrial Inputs and Bio-Optical Properties in Princess Charlotte Bay (Great Barrier Reef Lagoon)

In January 2013, tropical cyclone Oswald caused widespread flooding in the North-East coast of Australia, and large and highly episodic inputs into Princess Charlotte Bay (PCB, northern Great Barrier Reef). Freshwater outflows from the Normanby and Kennedy rivers, the two main rivers draining the adjacent catchments, resulted in drastic changes in physical, biogeochemical and optical properties within PCB. On 31 January, 2 days after the peak riverine discharge from the Normanby river, nutrients and dissolved organic matter contents peaked under the influence of large outflows from the Kennedy river into the western section of the bay (5.8 μM for dissolved inorganic nitrogen, 6.9 g m−3 for dissolved organic carbon and 6.1 m−1 for the colored dissolved organic matter absorption coefficient at 412 nm). In the eastern section of the bay, the situation appeared more ‘mixed’, with a suspended solids concentration reaching 23.1 g m−3 close to the Normanby river mouth. The main phytoplankton bloom occurred in the transition zone between the Kennedy and Normanby flood plumes, and was dominated by diatoms with a chlorophyll a concentration reaching 14.6 mg m−3. This study highlights the need to better describe the critical spatial and temporal scales of variability of key biogeochemical and optical properties after a major flood event. The data collected is key to improve the accuracy of ocean color remote sensing algorithms and regional biogeochemical budgets following highly episodic inputs

CoastColour Round Robin datasets: A data base to evaluate the performance of algorithms for the retrieval of water quality parameters in coastal waters

The use of in situ measurements is essential in the validation and evaluation of the algorithms that provide coastal water quality data products from ocean colour satellite remote sensing. Over the past decade, various types of ocean colour algorithms have been developed to deal with the optical complexity of coastal waters. Yet there is a lack of a comprehensive intercomparison due to the availability of quality checked in situ databases. The CoastColour Round Robin (CCRR) project, funded by the European Space Agency (ESA), was designed to bring together three reference data sets using these to test algorithms and to assess their accuracy for retrieving water quality parameters. This paper provides a detailed description of these reference data sets, which include the Medium Resolution Imaging Spectrometer (MERIS) level 2 match-ups, in situ reflectance measurements, and synthetic data generated by a radiative transfer model (HydroLight). These data sets, representing mainly coastal waters, are available from doi:10.1594/PANGAEA.841950. The data sets mainly consist of 6484 marine reflectance (either multispectral or hyperspectral) associated with various geometrical (sensor viewing and solar angles) and sky conditions and water constituents: total suspended matter (TSM) and chlorophyll a (CHL) concentrations, and the absorption of coloured dissolved organic matter (CDOM). Inherent optical properties are also provided in the simulated data sets (5000 simulations) and from 3054 match-up locations. The distributions of reflectance at selected MERIS bands and band ratios, CHL and TSM as a function of reflectance, from the three data sets are compared. Match-up and in situ sites where deviations occur are identified. The distributions of the three reflectance data sets are also compared to the simulated and in situ reflectances used previously by the International Ocean Colour Coordinating Group (IOCCG, 2006) for algorithm testing, showing a clear extension of the CCRR data which covers more turbid waters.JRC.H.1-Water Resource

Phytoplankton functional types from Space.

The concept of phytoplankton functional types has emerged as a useful approach to classifying phytoplankton. It finds many applications in addressing some serious contemporary issues facing science and society. Its use is not without challenges, however. As noted earlier, there is no universally-accepted set of functional types, and the types used have to be carefully selected to suit the particular problem being addressed. It is important that the sum total of all functional types matches all phytoplankton under consideration. For example, if in a biogeochemical study, we classify phytoplankton as silicifiers, calcifiers, DMS-producers and nitrogen fix- ers, then there is danger that the study may neglect phytoplankton that do not contribute in any significant way to those functions, but may nevertheless be a significant contributor to, say primary production. Such considerations often lead to the adoption of a category of “other phytoplankton” in models, with no clear defining traits assigned them, but that are nevertheless necessary to close budgets on phytoplankton processes. Since this group is a collection of all phytoplankton that defy classification according to a set of traits, it is difficult to model their physi- ological processes. Our understanding of the diverse functions of phytoplankton is still growing, and as we recognize more functions, there will be a need to balance the desire to incorporate the increasing number of functional types in models against observational challenges of identifying and mapping them adequately. Modelling approaches to dealing with increasing functional diversity have been proposed, for example, using the complex adaptive systems theory and system of infinite diversity, as in the work of Bruggemann and Kooijman (2007). But it is unlikely that remote-sensing approaches might be able to deal with anything but a few prominent functional types. As long as these challenges are explicitly addressed, the functional- type concept should continue to fill a real need to capture, in an economic fashion, the diversity in phytoplankton, and remote sensing should continue to be a useful tool to map them. Remote sensing of phytoplankton functional types is an emerging field, whose potential is not fully realised, nor its limitations clearly established. In this report, we provide an overview of progress to date, examine the advantages and limitations of various methods, and outline suggestions for further development. The overview provided in this chapter is intended to set the stage for detailed considerations of remote-sensing applications in later chapters. In the next chapter, we examine various in situ methods that exist for observing phytoplankton functional types, and how they relate to remote-sensing techniques. In the subsequent chapters, we review the theoretical and empirical bases for the existing and emerging remote-sensing approaches; assess knowledge about the limitations, assumptions, and likely accuracy or predictive skill of the approaches; provide some preliminary comparative analyses; and look towards future prospects with respect to algorithm development, validation studies, and new satellite mis- sions

CoastColour Round Robin data sets: A database to evaluate the performance of algorithms for the retrieval of water quality parameters in coastal waters

The use of in situ measurements is essential in the validation and evaluation of the algorithms that provide coastal water quality data products from ocean colour satellite remote sensing. Over the past decade, various types of ocean colour algorithms have been developed to deal with the optical complexity of coastal waters. Yet there is a lack of a comprehensive intercomparison due to the availability of quality checked in situ databases. The CoastColour Round Robin (CCRR) project, funded by the European Space Agency (ESA), was designed to bring together three reference data sets using these to test algorithms and to assess their accuracy for retrieving water quality parameters. This paper provides a detailed description of these reference data sets, which include the Medium Resolution Imaging Spectrometer (MERIS) level 2 match-ups, in situ reflectance measurements, and synthetic data generated by a radiative transfer model (HydroLight). These data sets, representing mainly coastal waters, are available from doi:10.1594/PANGAEA.841950. The data sets mainly consist of 6484 marine reflectance (either multispectral or hyperspectral) associated with various geometrical (sensor viewing and solar angles) and sky conditions and water constituents: total suspended matter (TSM) and chlorophyll a (CHL) concentrations, and the absorption of coloured dissolved organic matter (CDOM). Inherent optical properties are also provided in the simulated data sets (5000 simulations) and from 3054 match-up locations. The distributions of reflectance at selected MERIS bands and band ratios, CHL and TSM as a function of reflectance, from the three data sets are compared. Match-up and in situ sites where deviations occur are identified. The distributions of the three reflectance data sets are also compared to the simulated and in situ reflectances used previously by the International Ocean Colour Coordinating Group (IOCCG, 2006) for algorithm testing, showing a clear extension of the CCRR data which covers more turbid waters

A database of marine phytoplankton abundance, biomass and species composition in Australian waters

There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels

Distinct Peaks of UV-Absorbing Compounds in CDOM and Particulate Absorption Spectra of Near-Surface Great Barrier Reef Coastal Waters, Associated with the Presence of <i>Trichodesmium</i> spp. (NE Australia)

Distinct absorption peaks, with maxima at around 328 nm and a shoulder at 360 nm, were observed in the UV region of the absorption spectra for both the particulate and dissolved fractions of water samples collected in Keppel Bay (NE Australia) during the presence of sporadic Trichodesmium colonies. The largest absorption coefficients for these peaks were observed in samples collected in the near-surface waters (top 2–3 cm). Values approximately 3.5–6 times greater for aCDOM(328) and 13–36 times greater for ap(328) were observed in the near-surface samples compared to those collected from the top 20 cm of the water column at the same sites. Similar UV-absorption peaks observed in other studies have been attributed to the presence of mycosporine-like amino acids (MAAs). Increased UV absorption can affect both the magnitude of the absorption coefficients in the blue end of the visible region and the spectral slope of the exponential model commonly used to describe the CDOM absorption coefficient. This, in turn, can significantly affect the accuracy of satellite retrieved estimates of ocean colour products related to CDOM and particulate absorption coefficients. In tropical waters where Trichodesmium blooms are prevalent, regional ocean colour algorithms need to be developed using in situ bio-optical measurements from both the UV and visible regions of the spectra

Bio-Optical Measurements Indicative of Biogeochemical Transformations of Ocean Waters by Coral Reefs

The bio-optical properties of coral reef waters were examined across coral reef ecosystems not influenced by land-derived run-off, in the Great Barrier Reef lagoon (Heron Island) and the Coral Sea (the Coringa-Herald and Lihou Reefs). The aim was to determine whether the absorption properties, the concentration-specific absorption properties, and the phytoplankton and non-algal pigmented particle (NAP) absorption concentrations varied from the ocean waters flushing onto the reef at high tide to those waters on the reef or flushing off the reef at low tide. The optical and biogeochemical properties of on-reef waters systematically differed from the surrounding ocean waters. The chl a concentration values varied up to 7-fold and the NAP concentrations up to 29-fold; for the reef samples, the chl a values were on average 2 to 3 times lower than for the oceans whilst the NAP values were slightly higher on the reefs. The spectral absorption values of the chl a, NAP, and colored dissolved organic matter (CDOM) varied up to 6-fold for reef waters and up to 15-fold for ocean waters. The spectral absorption for chl a was up to 3-fold lower on the reef waters, the absorption by the CDOM was up to 2-fold higher and the NAP absorption was 1.6-fold higher on the reef waters. The concentration-specific absorption coefficients for chl a and NAP varied up to 9-fold in reef waters and up to 30-fold in ocean waters. In the case of Heron Island and Coringa-Herald cays, this concentration-specific absorption was on average 1.3 to 1.7-fold higher for chl a and up to 2-fold lower for NAP on the reefs. The Lihou Reef measurements were more ambiguous between the reef waters and ocean waters due to the complex nature and size of this reef. Based on our results, the assumption that the optical properties of on-reef waters and the adjacent ocean waters are the same was shown to be invalid. Ocean waters flowing on to the reef are higher in phytoplankton, whilst waters on the reef or flowing off the reefs are higher in CDOM and NAP. We found differences in the pico,- nano-, and microplankton distributions as well as in the ratios of photosynthetic to photoprotective pigments. The variability in the bio-optical properties between the reef waters and adjacent ocean waters has implications for the estimations of sunlight absorption along the water column, the UV penetration depth, the temperature distributions, and the nutrient and carbon fluxes in coral reef ecosystems. As Earth observation algorithms require proper parameterization for the water column effects when estimating benthic cover, the actual optical properties need to be used. These results will improve the use of Earth observation to systematically map the differences in the water quality between reefs and the adjacent ocean

Diel quenching of Southern Ocean phytoplankton fluorescence is related to iron limitation

Evaluation of photosynthetic competency in time and space is critical for better estimates and models of oceanic primary productivity. This is especially true for areas where the lack of iron (Fe) limits phytoplankton productivity, such as the Southern Ocean. Assessment of photosynthetic competency on large scales remains challenging, but phytoplankton chlorophyll a fluorescence (ChlF) is a signal that holds promise in this respect as it is affected by, and consequently provides information about, the photosynthetic efficiency of the organism. A second process affecting the ChlF signal is heat dissipation of absorbed light energy, referred to as non-photochemical quenching (NPQ). NPQ is triggered when excess energy is absorbed, i.e. when more light is absorbed than can be used directly for photosynthetic carbon fixation. The effect of NPQ on the ChlF signal complicates its interpretation in terms of photosynthetic efficiency, and therefore most approaches relating ChlF parameters to photosynthetic efficiency seek to minimize the influence of NPQ by working under conditions of sub-saturating irradiance. Here, we propose that NPQ itself holds potential as an easily acquired optical signal indicative of phytoplankton physiological state with respect to Fe limitation. We present data from a research voyage to the Subantarctic Zone south of Australia. Incubation experiments confirmed that resident phytoplankton were Fe-limited, as the maximum quantum yield of primary photochemistry, F-v/F-m, measured with a fast repetition rate fluorometer (FRRf), increased significantly with Fe addition. The NPQ "capacity" of the phytoplankton also showed sensitivity to Fe addition, decreasing with increased Fe availability, confirming previous work. The fortuitous presence of a remnant warm-core eddy in the vicinity of the study area allowed comparison of fluorescence behaviour between two distinct water masses, with the colder water showing significantly lower F-v/F-m than the warmer eddy waters, suggesting a difference in Fe limitation status between the two water masses. Again, NPQ capacity measured with the FRRf mirrored the behaviour observed in F-v/F-m, decreasing as F-v/F-m increased in the warmer water mass. We also analysed the diel quenching of underway fluorescence measured with a standard fluorometer, such as is frequently used to monitor ambient chlorophyll a concentrations, and found a significant difference in behaviour between the two water masses. This difference was quantified by defining an NPQ parameter akin to the Stern-Volmer parameterization of NPQ, exploiting the fluorescence quenching induced by diel fluctuations in incident irradiance. We propose that monitoring of this novel NPQ parameter may enable assessment of phytoplankton physiological status (related to Fe availability) based on measurements made with standard fluorometers, as ubiquitously used on moorings, ships, floats and gliders

Impact of wet season river flood discharge on phytoplankton absorption properties in the southern Great Barrier Reef region coastal waters

Light absorption due to particulate and dissolved material plays an important role in controlling the underwater light environment and the above water reflectance signature. Thorough understanding of absorption properties and their variability is important to estimate light propagation in the water column. However, knowledge of light absorption properties in flood impacted coastal waters is limited. To address this knowledge gap we investigated a bio-optical dataset collected during a flood (2008) in the southern Great Barrier Reef (GBR) region coastal waters. Results presented here show strong impact of river flood discharges on water column stratification, distribution of suspended substances and light absorption properties in the study area. Bio-optical analysis showed phytoplankton absorption efficiency to reduce in response to increased coloured dissolved organic matter presence in flood impacted coastal waters. Biogeophysical property ranges, relationships and parametrisation presented here will help model realistic underwater light environment and optical signature in flood impacted coastal waters

Inter-annual variability of wet season freshwater plume extent into the Great Barrier Reef lagoon based on satellite coastal ocean colour observations

Riverine freshwater plumes are the major transport mechanism for nutrients, sediments and pollutants into the Great Barrier Reef (GBR) lagoon and connect the land with the receiving coastal and marine waters. Knowledge of the variability of the freshwater extent into the GBR lagoon is relevant for marine park management to develop strategies for improving ecosystem health and risk assessments. In this study, freshwater extent has been estimated for the entire GBR lagoon area from daily satellite observations of the Moderate Resolution Imaging Spectroradiometer (MODIS) between 2002 and 2010. To enable a reliable mapping of freshwater plumes we applied a physics-based coastal ocean colour algorithm, that simultaneously retrieves chlorophyll-a, non-algal particulate matter and coloured dissolved organic matter (CDOM), from which we used CDOM as a surrogate for salinity (S) for mapping the freshwater extent