Australian aquatic bio-optical dataset with applications for satellite calibration, algorithm development and validation.

The authors present bio-optical data spanning 316 sets of observations made at 34 inland waterbodies in Australia. The data was collected over the period 2013-2021 and comprise radiometric measurements of remote sensing reflectance (Rrs), diffuse attenuation extinction coefficient (Kd); optical backscattering; absorption of coloured dissolved organic matter (aCDOM), phytoplankton (aph) and non-algal particles (aNAP); HPLC analysis of algal pigments including chlorophyll-a (CHL-a); organic and inorganic total suspended solids (TSS); and total and dissolved organic carbon concentration. Data collection has been timed to coincide with either Landsat 8 or Sentinel-2 overpasses. The dataset covers a diverse range of optical water types and is suitable for algorithm development, satellite calibration and validation as well as machine learning applications.

A database of zooplankton biomass in Australian marine waters.

Zooplankton biomass data have been collected in Australian waters since the 1930s, yet most datasets have been unavailable to the research community. We have searched archives, scanned the primary and grey literature, and contacted researchers, to collate 49187 records of marine zooplankton biomass from waters around Australia (0-60°S, 110-160°E). Many of these datasets are relatively small, but when combined, they provide >85 years of zooplankton biomass data for Australian waters from 1932 to the present. Data have been standardised and all available metadata included. We have lodged this dataset with the Australian Ocean Data Network, allowing full public access. The Australian Zooplankton Biomass Database will be valuable for global change studies, research assessing trophic linkages, and for initialising and assessing biogeochemical and ecosystem models of lower trophic levels.

Dataset on the in vivo absorption characteristics and pigment composition of various phytoplankton species.

This paper contains data on the absorption spectra and pigment composition and concentration of 22 phytoplankton species. All phytoplankton cultures were taken from the Australian National Algae Culture Collection. Each absorption spectrum is accompanied by the pigment composition quantified using High Performance Liquid Chromatography (HPLC).

Dataset on the absorption characteristics of extracted phytoplankton pigments.

This article presents the raw and analysed data on the absorption features of 30 pigments commonly occurring in phytoplankton. All unprocessed absorption spectra are given between 350 and 800 nm. The presented data also gives information on the wavelength of the main absorption peaks together with associated magnitudes of the concentration-specific absorption coefficient.

The golden paradox - a new heterokont lineage with chloroplasts surrounded by two membranes.

A marine, sand-dwelling, golden-brown alga is described from clonal cultures established from a high intertidal pool in southeastern Australia. This tiny, unicellular species, which we call the "golden paradox" (Chrysoparadoxa australica gen. et sp. nov.), is benthic, surrounded by a multilayered cell wall and attached to the substratum by a complex adhesive plug. Each vegetative cell gives rise to a single, naked zoospore with heterokont flagella that settles and may become briefly amoeboid prior to dividing. Daughter cells are initially amoeboid, then either permanently attach and return to the benthic stage or become motile again prior to final settlement. Two deeply lobed chloroplasts occupy opposite ends of the cell and are surrounded by only two membranes. The outer chloroplast membrane is continuous between the two chloroplasts via the outer membrane of the nuclear envelope. Only two membranes occupy the chloroplast-nucleus interface, the inner membrane of the nuclear envelope and the inner chloroplast membrane. A small pyrenoid is found in each chloroplast and closely abuts the nucleus or protrudes into it. It contains an unusual, membrane-bound inclusion that stains with SYBR green but is unlikely to be a nucleomorph. Phylogenies inferred from a 10-gene concatenated alignment show an early-branching position within the PX clade. The unusual morphological features and phylogenetic position indicate C. australica should be classified as a new class, Chrysoparadoxophyceae. Despite an atypical plastid, exploration of the C. australica transcriptome revealed typical heterokont protein targeting to the plastid.

A database of chlorophyll a in Australian waters.

Chlorophyll a is the most commonly used indicator of phytoplankton biomass in the marine environment. It is relatively simple and cost effective to measure when compared to phytoplankton abundance and is thus routinely included in many surveys. Here we collate 173, 333 records of chlorophyll a collected since 1965 from Australian waters gathered from researchers on regular coastal monitoring surveys and ocean voyages into a single repository. This dataset includes the chlorophyll a values as measured from samples analysed using spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). The Australian Chlorophyll a database is freely available through the Australian Ocean Data Network portal (https://portal.aodn.org.au/). These data can be used in isolation as an index of phytoplankton biomass or in combination with other data to provide insight into water quality, ecosystem state, and relationships with other trophic levels such as zooplankton or fish.

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.

Response of phytoplankton photophysiology to varying environmental conditions in the Sub-Antarctic and Polar Frontal Zone.

Climate-driven changes are expected to alter the hydrography of the Sub-Antarctic Zone (SAZ) and Polar Frontal Zone (PFZ) south of Australia, in which distinct regional environments are believed to be responsible for the differences in phytoplankton biomass in these regions. Here, we report how the dynamic influences of light, iron and temperature, which are responsible for the photophysiological differences between phytoplankton in the SAZ and PFZ, contribute to the biomass differences in these regions. High effective photochemical efficiency of photosystem II (F'(q)/F'(m)0.4), maximum photosynthesis rate (P(B)(max)), light-saturation intensity (E(k)), maximum rate of photosynthetic electron transport (1/[Symbol: see text]PSII), and low photoprotective pigment concentrations observed in the SAZ correspond to high chlorophyll a and iron concentrations. In contrast, phytoplankton in the PFZ exhibits low F'(q)/F'(M) (~ 0.2) and high concentrations of photoprotective pigments under low light environment. Strong negative relationships between iron, temperature, and photoprotective pigments demonstrate that cells were producing more photoprotective pigments under low temperature and iron conditions, and are responsible for the low biomass and low productivity measured in the PFZ. As warming and enhanced iron input is expected in this region, this could probably increase phytoplankton photosynthesis in this region. However, complex interactions between the biogeochemical processes (e.g. stratification caused by warming could prevent mixing of nutrients), which control phytoplankton biomass and productivity, remain uncertain.

Evaluation of growth, nutrient utilization and production of bioproducts by a wastewater-isolated microalga.

Treatment of wastewater while producing microalgal biomass is receiving ever-increasing attention, particularly in the biofuels arena. In this study, a wastewater chlorophyte isolate, Kirchneriella sp., was tested for its ability to be mass cultivated, utilize nutrients from defined media and wastewater, and produce bioproducts of commercial interest. Growth studies were carried out in various systems at scales up to 60L, with Kirchneriella sp. showing an excellent amenability to being cultured. Biomass concentrations of greater than 1gL(-1) were consistently achieved, nitrogen and phosphorus uptake was rapid, and stable medium-term cultures were maintained. Nitrogen limitation affected biomass yield, fatty acid methyl ester (FAME) yield, and cetane index. In contrast, a low phosphorus condition had no effect. Kirchneriella sp. showed an ability to produce several products of commercial value, including carbohydrate-rich biomass, FAME/biodiesel and the pigments ß,ß-carotene and lutein.

Exploring the Link between Micronutrients and Phytoplankton in the Southern Ocean during the 2007 Austral Summer.

Bottle assays and large-scale fertilization experiments have demonstrated that, in the Southern Ocean, iron often controls the biomass and the biodiversity of primary producers. To grow, phytoplankton need numerous other trace metals (micronutrients) required for the activity of key enzymes and other intracellular functions. However, little is known of the potential these other trace elements have to limit the growth of phytoplankton in the Southern Ocean. This study, investigates whether micronutrients other than iron (Zn, Co, Cu, Cd, Ni) need to be considered as parameters for controlling the phytoplankton growth from the Australian Subantarctic to the Polar Frontal Zones during the austral summer 2007. Analysis of nutrient disappearance ratios, suggested differential zones in phytoplankton growth control in the study region with a most intense phytoplankton growth limitation between 49 and 50°S. Comparison of micronutrient disappearance ratios, metal distribution, and biomarker pigments used to identify dominating phytoplankton groups, demonstrated that a complex interaction between Fe, Zn, and Co might exist in the study region. Although iron remains the pivotal micronutrient for phytoplankton growth and community structure, Zn and Co are also important for the nutrition and the growth of most of the dominating phytoplankton groups in the Subantarctic Zone region. Understanding of the parameters controlling phytoplankton is paramount, as it affects the functioning of the Southern Ocean, its marine resources and ultimately the global carbon cycle.

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.

Biodiscovery of new Australian thraustochytrids for production of biodiesel and long-chain omega-3 oils.

Heterotrophic growth of thraustochytrids has potential in co-producing a feedstock for biodiesel and long-chain (LC, ≥C(20)) omega-3 oils. Biodiscovery of thraustochytrids from Tasmania (temperate) and Queensland (tropical), Australia, covered a biogeographic range of habitats including fresh, brackish, and marine waters. A total of 36 thraustochytrid strains were isolated and separated into eight chemotaxonomic groups (A-H) based on fatty acid (FA) and sterol composition which clustered closely with four different genera obtained by 18S rDNA molecular identification. Differences in the relative proportions (%FA) of long-chain C(20), C(22), omega-3, and omega-6 polyunsaturated fatty acids (PUFA), including docosahexaenoic acid (DHA), docosapentaenoic acid, arachidonic acid, eicosapentaenoic acid (EPA), and saturated FA, as well as the presence of odd-chain PUFA (OC-PUFA) were the major factors influencing the separation of these groups. OC-PUFA were detected in temperate strains of groups A, B, and C (Schizochytrium and Thraustochytrium). Group D (Ulkenia) had high omega-3 LC-PUFA (53% total fatty acids (TFA)) and EPA up to 11.2% TFA. Strains from groups E and F (Aurantiochytrium) contained DHA levels of 50-61% TFA after 7 days of growth in basal medium at 20 °C. Groups G and H (Aurantiochytrium) strains had high levels of 15:0 (20-30% TFA) and the sum of saturated FA was in the range of 32-51%. ß,ß-Carotene, canthaxanthin, and astaxanthin were identified in selected strains. Phylogenetic and chemotaxonomic groupings demonstrated similar patterns for the majority of strains. Our results demonstrate the potential of these new Australian thraustochytrids for the production of biodiesel in addition to omega-3 LC-PUFA-rich oils.

Review of fluorescent standards for calibration of in situ fluorometers: recommendations applied in coastal and ocean observing programs.

Fluorometers are widely used in ecosystem observing to monitor fluorescence signals from organic compounds, as well as to infer geophysical parameters such as chlorophyll or CDOM concentration, but measurements are susceptible to variation caused by biofouling, instrument design, sensor drift, operating environment, and calibration rigor. To collect high quality data, such sensors need frequent checking and regular calibration. In this study, a wide variety of both liquid and solid fluorescent materials were trialed to assess their suitability as reference standards for performance assessment of in situ fluorometers. Criteria used to evaluate the standards included the spectral excitation/emission responses of the materials relative to fluorescence sensors and to targeted ocean properties, the linearity of the fluorometer's optical response with increasing concentration, stability and consistency, availability and ease of use, as well as cost. Findings are summarized as a series of recommended reference standards for sensors deployed on stationary and mobile platforms, to suit a variety of in situ coastal to ocean sensor configurations. Repeated determinations of chlorophyll scale factor using the recommended liquid standard, Fluorescein, achieved an accuracy of 2.5%. Repeated measurements with the recommended solid standard, Plexiglas Satinice® plum 4H01 DC (polymethylmethacrylate), over an 18 day period varied from the mean value by 1.0% for chlorophyll sensors and 3.3% for CDOM sensors.

Oceanographic basis of the global surface distribution of Prochlorococcus ecotypes.

By using data collected during a continuous circumnavigation of the Southern Hemisphere, we observed clear patterns in the population-genetic structure of Prochlorococcus, the most abundant photosynthetic organism on Earth, between and within the three Southern Subtropical Gyres. The same mechanisms that were previously invoked to account for the vertical distribution of ecotypes at local scales accounted for the global (horizontal) patterns we observed. Basin-scale and seasonal variations in the structure and strength of vertical stratification provide a basis for understanding large-scale horizontal distribution in genetic and physiological traits of Prochlorococcus, and perhaps of marine microbial communities in general.

Flow-injection analysis with fluorescence detection for the determination of trace levels of ammonium in seawater.

A method using flow-injection, gas-diffusion, derivatisation and then fluorescent detection has been established for ammonium ion determination in seawater. The fluorescent derivative formed by reacting ortho-phthaldialdehyde (OPA) and sulfite with ammonia gives high sensitivity while removing potential interferences. This is required to measure the low concentrations of ammonium often seen in the open ocean. The experimental conditions (flow-rate, reagent concentrations, membrane configurations, etc.) were manipulated to improve performance. For a sample throughput of 30 samples h(-1), the limit of detection was 7 nM, the coefficient of variation was 5.7% at 800 nM, and the calibration curve was linear to at least 4 micromol L(-1). Interferences were minimised by a gaseous diffusion step. Volatile small molecular-weight amines as interferents were discriminated against by this method. They neither passed through the membrane as efficiently as ammonia, nor reacted as readily with OPA when sulfite was the reductant. Contamination by ammonia from laboratory and shipboard sources complicates application of the method to natural waters, especially measurement of low concentrations (<100 nM) in open-ocean waters. Steps to overcome contamination are described in detail. Some results are presented for ammonium determination in Southern Ocean and Huon Estuary (Tasmania) waters.