Additionally, a project with James Cook University funded by Nufarm Limited, the world’s ninth largest agrichemical company, advanced discoveries of a novel herbicide to the glasshouse testing stage, thus achieving a milestone in the transfer of Intellectual Property to industry. Nufarm reported in 2001: "Preliminary results are very encouraging. The most promising candidate molecules so far identified are in synthesis development at Nufarm’s French laboratories and indicate that these organisms could be a rich source of novel crop protection products."

AIMS continues to host the Australian Research Network for Algal Toxins (ARNAT) which brings together more than 100 researchers in Australia, New Zealand, Canada and the US.

Genetics is used at AIMS to understand the evolution and maintenance of marine biodiversity. In the project Genetics for Bioresource Management and Ecology, a range of DNA traits were studied in 2001-02 to understand reproductive connections between populations, genetic diversity within marine populations, and the processes leading to this diversity. The use of biotechnology in this manner aids the design and management of Marine Protected Areas. For example, genetic data reveals that cross-fertilisation between coral species is important on an evolutionary timescale, but occurs infrequently in common corals of the genus Acropora. Hence, the effects of this cross-fertilisation are negligible and most species are distinct genetic entities. Population studies on commercially fished holothurians (sea cucumbers or bęche-de-mer) highlighted the need to consider gene flow (genetic exchange between populations) in planning biodiversity protection. Research found that one species with unrestricted gene flow between populations can be managed over large scales, whereas another species with a restricted gene flow requires protection of local populations. A forensic method was developed for identification of specimens to determine growth and migration rates, and this technique is amenable to other species for future conservation planning.

Scientists at AIMS are also using molecular indicators to quantify variations in heat stress responses of coral species during bleaching episodes on the Great Barrier Reef. Like other organisms, corals produce heat shock proteins for protection, and these proteins indicate to scientists the degree of heat stress experienced. In 2001-02, scientists discovered that Acropora millepora coral from an inshore reef was more able to produce these protective proteins and can withstand heat stress more than specimens living on an offshore reef. This thermal tolerance is also correlated with the strain of symbiotic algae or zooxanthellae living in the coral tissue. Results suggest the ability of corals to associate with different strains of symbiotic algae may contribute to their susceptibility to coral bleaching.

Marine bacteria isolated from the mucus of shallow-water corals have a biochemical adaptation that enhances the recycling of coenzyme Q (CoQ) in their metabolism. In human health, CoQ is vital to energy production and antioxidant balance. AIMS research into CoQ production by marine bacteria won support from the Australian Academy of Science and the Japan Society for the Promotion of Science. The Institute is now collaborating with the University of Tokyo and the Osaka City University Medical School to take this research to the next level.

In a similar vein, collaboration with the University of Canterbury and logistic support from Antarctica New Zealand underpinned AIMS research into human impacts on Antarctic sponges. The seabed environment of the Antarctic shelf under ice is dominated by sponges which filter hundreds of litres of seawater per hour, making them ideal bio-indicators of pollution near areas of human occupation. Additionally, these animals harbour bacteria with potential to act as indicators of metabolic stress. AIMS researchers examined the effects of pollution on the sponges’ biochemistry and the bacteria they host. This collaboration succeeded in gaining second-year funding from Antarctica New Zealand and is now attracting the interest of environmental management agencies. It provides a novel opportunity to examine tropical-polar extremes in comparative physiology, environmental biochemistry and the functional ecology of marine sponges.