Algae biotechnologies offer one possible path to addressing the forecast challenges of human society which are the increased demands of food, fuel and water due to population growth and large scale lifestyle change. The development of renewable algae production technologies helps to establish a basis for sustainable development and provide options to decrease CO2 emissions to address climate change. Algae are increasingly recognised as a promising bioresource and the range of cultivated species and their products is expanding. Compared to terrestrial crops, microalgae are highly biodiverse and offer considerable versatility for a range of biotechnological applications including the production of animal feeds, fuels, high value products and waste-water treatment. Despite their versatility and capacity for high biomass productivity microalgae represent a relatively unexplored bioresource both for native and engineered strains. Success in this area requires (1) appropriate methods to source and isolate microalgae strains, (2) efficient maintenance and preservation of parental stocks, (3) rapid strain characterisation and correct matching of strains to applications, (4) ensuring productive and stable cultivation at scale, and (5) ongoing strain development (breeding, adaptation and engineering). In chapter 2 a streamlined process was developed for the isolation, identification and maintenance of over 150 local microalgae strains as a bioresource for ongoing strain development and biotechnological applications. 121 algal strains could be purified to the axenic level, whereas the rest were maintained as unialgal, non-axenic cultures. All algae used in the large scale trials were obtained as axenic cultures. A range of isolating techniques were explored. Fluorescence activated cell sorting (FACS) proved to be a useful method for high throughput isolation and purification of physically robust algal species, while micromanipulation was most beneficial to obtain a high species diversity. A separate survey by Wolf et al (2014) optimised the nutrient requirements and identified the highest biomass producing strains. Eight algae isolates identified as high production strains based on lab experiments, as well as an isolated invasive algal species and a polyculture of five morphological different strains were tested outdoors to identify key variables limiting optimised production at pilot-scale. The results showed that based on the maximum specific growth rates achieved in sterile laboratory systems, exposed pond systems achieved ~30-50%, indicating limitations imposed by environmental and biological iii factors. Highest daily growth rates in open pond trials single strain trials were obtained for M. pusillum (5_H4) (0.959 d-1), Chlorella sp. (11_H5) (0.719 d-1), Chlorococcum sp. (12_02) (0.755 d- 1), and the polyculture (0.743 d-1). M. pusillum (5_H4), Scenedesmus sp. (Pinjarra001). The polyculture trials achieved the highest optical densities (up to OD750=4). In addition to fast growth, other variables influencing performance included the ability to grow to high densities, autoflocculation, and resistance to predators proved important. Polyculture trials achieved the highest maximum areal and volumetric productivity (24.3 g m-2 day and 266.7 g m-3 day). However the polyculture productivity values are only about 6-10 % higher than those of the highest single strain cultivations and may have resulted from the different cultivation timings. The polyculture growth during spring was favoured by higher mean solar energy, higher absolute temperatures and greater temperature flux than cultivations during autumn and winter. Nevertheless the polyculture trials are considered to be a potential alternative to single species cultivation due to their increased robustness against invasive predatory influences. Contamination by invasive organisms is expected and observations revealed that their impact on the algal culture is dependent both on the cultivated species and the predatory organism. Grazing and competition for nutrients had negative impacts on algal growth and change of algal morphology (e.g. spines and flocculation). Positive impacts of certain grazers included reductions in bacterial and protozoa load, providing opportunities to use “predators” as a tool to sustain algal cultures and optimise the culture production. The flocculation of C. sorokiniana (8_C4) in the presence of a Tetrahymena like ciliate was one of the most promising leads for the optimisation of algae production systems in the form of a novel harvesting technology. Chapter 4 focused on the characterisation and optimisation of a novel bioflocculation method using the native isolated ciliate Tetrahymena. Tetrahymena is a common invader of microalgae cultures, typically feeding on bacteria rather than on the microalgae themselves. Tetrahymena thermophilia, a freshwater ciliate, is well studied for its ability of undergoing dramatic metabolic changes during starvation, its secretory granule biogenesis and exocytosis. Here a locally isolated and identified Tetrahymena culture was used as a controllable bioflocculation agent for the microalgae Chlorella sorokiniana (8_C4). The process was triggered by adding chemical substances to the starved ciliate leading to exocytosis of extracellular polymeric substances (EPS) which functioned as a binding substance between the algae cells. The ratio of ciliate to algae could be reduced to as little as 1:400 cells to initiate rapid bioflocculation. Furthermore stimulators of ryanodine receptors (caffeine and p-chlorocresol) were identified as useful triggers for exocytosis. Future experiments at larger scale iv can prove that the protocol is transferable to greater volumes which could have significant potential for industrial scale application. The work described in this chapter has been the basis for a patent application and has been included in a manuscript published in the journal Algal Research [1]. In conclusion, 150 native microalgae were successfully isolated, cryo-preservation applied (Bui et al., 2013) and their nutrient media optimised (Wolf et al., 2014). The performance of 9 strains was analysed in high rate ponds both in mono and polyculture and a novel Tetrahymena based harvesting system identified (paper published and patent filing submitted).