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Malerba M.E.,James Cook University | Malerba M.E.,Australian Institute of Marine Science | Heimann K.,James Cook University | Heimann K.,Center for Sustainable Tropical Fisheries and Aquaculture | Connolly S.R.,James Cook University
Journal of Theoretical Biology

Ecologists have often used indirect proxies to represent variables that are difficult or impossible to measure directly. In phytoplankton, the internal concentration of the most limiting nutrient in a cell determines its growth rate. However, directly measuring the concentration of nutrients within cells is inaccurate, expensive, destructive, and time-consuming, substantially impairing our ability to model growth rates in nutrient-limited phytoplankton populations. The red chlorophyll autofluorescence (hereafter "red fluorescence") signal emitted by a cell is highly correlated with nitrogen quota in nitrogen-limited phytoplankton species. The aim of this study was to evaluate the reliability of including flow cytometric red fluorescence as a proxy for internal nitrogen status to model phytoplankton growth rates. To this end, we used the classic Quota model and designed three approaches to calibrate its model parameters to data: where empirical observations on cell internal nitrogen quota were used to fit the model ("Nitrogen-Quota approach"), where quota dynamics were inferred only from changes in medium nutrient depletion and population density ("Virtual-Quota approach"), or where red fluorescence emission of a cell was used as an indirect proxy for its internal nitrogen quota ("Fluorescence-Quota approach"). Two separate analyses were carried out. In the first analysis, stochastic model simulations were parameterized from published empirical relationships and used to generate dynamics of phytoplankton communities reared under nitrogen-limited conditions. Quota models were fitted to the dynamics of each simulated species with the three different approaches and the performance of each model was compared. In the second analysis, we fit Quota models to laboratory time-series and we calculate the ability of each calibration approach to describe the observed trajectories of internal nitrogen quota in the culture. Results from both analyses concluded that the Fluorescence-Quota approach including per-cell red fluorescence as a proxy of internal nitrogen substantially improved the ability of Quota models to describe phytoplankton dynamics, while still accounting for the biologically important process of cell nitrogen storage. More broadly, many population models in ecology implicitly recognize the importance of accounting for storage mechanisms to describe the dynamics of individual organisms. Hence, the approach documented here with phytoplankton dynamics may also be useful for evaluating the potential of indirect proxies in other ecological systems. © 2016 Elsevier Ltd. Source

Steinig E.J.,James Cook University | Neuditschko M.,University of Sydney | Khatkar M.S.,University of Sydney | Khatkar M.S.,Center for Sustainable Tropical Fisheries and Aquaculture | And 5 more authors.
Molecular Ecology Resources

Network-based approaches are emerging as valuable tools for the analysis of complex genetic structure in wild and captive populations. netview p combines data quality control with the construction of population networks through mutual k-nearest neighbours thresholds applied to genome-wide SNPs. The program is cross-platform compatible, open-source and efficiently operates on data ranging from hundreds to hundreds of thousands of SNPs. The pipeline was used for the analysis of pedigree data from simulated (n = 750, SNPs = 1279) and captive silver-lipped pearl oysters (n = 415, SNPs = 1107), wild populations of the European hake from the Atlantic and Mediterranean (n = 834, SNPs = 380) and grey wolves from North America (n = 239, SNPs = 78 255). The population networks effectively visualize large- and fine-scale genetic structure within and between populations, including family-level structure and relationships. netview p comprises a network-based addition to other population analysis tools and provides user-friendly access to a complex network analysis pipeline through implementation in PYTHON. © 2016 John Wiley & Sons Ltd. Source

Malerba M.E.,James Cook University | Malerba M.E.,Australian Institute of Marine Science | Malerba M.E.,Center for Sustainable Tropical Fisheries and Aquaculture | Connolly S.R.,James Cook University | And 2 more authors.
Ecological Modelling

Nitrate and ammonium are the two most important ionic forms of inorganic nitrogen driving biomass production in marine and freshwater aquatic systems. The performance of plants and algae often changes when reared with either of these two forms of nitrogen individually, as well as when they are both present, or when cells have experienced previous periods of nitrogen starvation. Current functional responses quantifying how ambient nitrogen drives changes in population density are unable to capture interacting and transient effects of nitrate and ammonium. Hence, in this paper we formulate, calibrate, and test a new nitrate-ammonium quota model that accounts for nitrate and ammonium uptake, as well as the effects of nitrogen starvation length and ammonium-induced nitrate uptake inhibition. We fit the model with several time-series from the green alga Chlorella sp. reared in laboratory batch cultures under multiple initial conditions. We show that a single set of calibrated model parameters can capture time-series collected from experiments inoculated at 12 different initial concentrations of nitrate, ammonium, and biomass. The model also performed well when validated against time-series from two novel initial conditions withheld from model calibration. Our model therefore provides a framework for evaluating the potential broader ecological and environmental consequences of ambient nitrate and ammonium regimes for phytoplankton communities in nature and aquaculture. © 2015 Elsevier B.V. Source

Huerlimann R.,James Cook University | Huerlimann R.,Center for Sustainable Tropical Fisheries and Aquaculture | Steinig E.J.,James Cook University | Loxton H.,James Cook University | And 6 more authors.

Very long-chain polyunsaturated fatty acids (VLC-PUFAs) are important dietary requirements for maintaining human health. Many marine microalgae are naturally high in ω-3 VLC-PUFAs, however, the molecular mechanisms underpinning fatty acid (FA) desaturation and elongation in algae are poorly understood. An advanced molecular understanding would facilitate improvements of this nascent industry. We aimed to investigate expression responses of four front-end fatty acid desaturase genes and downstream effects on FA profiles to nitrogen limitation and cultivation growth stage in Isochrysis aff. galbana (TISO). Cultures were grown in nitrogen-replete and -deplete medium; samples were harvested during logarithmic, late logarithmic and stationary growth phases to analyse FA content/composition and gene expression of {increment}6-, {increment}8-, {increment}5- and {increment}4-desaturases (d6FAD (putative), d8FAD, d5FAD and d4FAD, respectively). d6FAD (putative) exhibited no differential expression, while d8FAD, d5FAD and d4FAD were significantly upregulated during logarithmic growth of nutrient-replete cultures, coinciding with rapid cell division. In conclusion, it is demonstrated that expression of some FADs in I. aff. galbana varies with culture age and nitrogen status which has downstream consequences on FA desaturation levels. This has implications for the commercial production of VLC-PUFAs where a trade-off between total lipid yield and VLC-PUFAs has to be made. © 2014 Elsevier B.V. Source

Huerlimann R.,James Cook University | Huerlimann R.,Center for Sustainable Tropical Fisheries and Aquaculture | Steinig E.J.,James Cook University | Loxton H.,James Cook University | And 6 more authors.

Lipids from microalgae have become a valuable product with applications ranging from biofuels to human nutrition. While changes in fatty acid (FA) content and composition under nitrogen limitation are well documented, the involved molecular mechanisms are poorly understood. Acetyl-CoA carboxylase (ACCase) is a key enzyme in the FA synthesis and elongation pathway. Plastidial and cytosolic ACCases provide malonyl-CoA for de novo FA synthesis in the plastid and FA elongation in the endoplasmic reticulum, respectively. The present study aimed at investigating the expression of plastidial and cytosolic ACCase in Chromera velia and Isochrysis aff. galbana (TISO) and their impact on FA content and elongation level when grown under nitrogen-deplete conditions. In C. velia, plastidial ACCase was significantly upregulated during nitrogen starvation and with culture age, strongly correlating with increased FA content. Conversely, plastidial ACCase of I. aff. galbana was not differentially expressed in nitrogen-deplete cultures, but upregulated during the logarithmic phase of nitrogen-replete cultures. In contrast to plastidial ACCase, the cytosolic ACCase of C. velia was downregulated with culture age and nitrogen-starvation, strongly correlating with an increase in medium-chain FAs. In conclusion, the expression of plastidial and cytosolic ACCase changed with growth phase and nutrient status in a species-specific manner and nitrogen limitation did not always result in FA accumulation. © 2014 Elsevier B.V. Source

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