For more than a decade, AIMS has been sampling shallow water biodiversity from Australasia and has built up several important reference collections.

Coral Cores and Slices
AIMS has the world's largest collection of massive coral cores and small coral bommies (20 – 50cm across). Colonies were collected from a range of (~35) sites on the East coast of Australia between PNG (~10°S) and One Tree island (23°S) between 1987 and 2000. Cores were taken from a range of (~40) sites on the East coast of Australia between PNG (~5°S) and Masthead island (~23°S) between 1983 and 2007.

Slices taken from over 350 colonies and 200 cores have been analysed with x-ray and UV imagery to gain information on past climatic conditions . Many of these cores are from colonies which existed before European settlement of Australia.

Bioresources Library
The AIMS bioresources library contains almost 20,000 entities, including extracts from over 7,600 samples of marine micro-organisms, frozen material and over 9,000 cryopreserved marine-derived micro-organisms. AIMS is implementing a sophisticated system to make the bioresources library more accessible to national screening networks interested in identifying targets for biodiscovery research.

Marine Sediments
The AIMS marine and estuarine sediment sample collection has samples from more than 2,500 locations collected between 1990 and 2005. Most of the collection is from the Great Barrier Reef region, the Gulf of Papua and Australia's North West Shelf and Timor Sea.

Surface grab samples as well as core profiles were collected, and chemistry analyses of surface samples are recorded in a sediment relational database. The core profiles were analysed for chemistry, and also radionuclides by gamma spectroscopy. In collaboration with Geoscience Australia (GA), AIMS has agreed that GA will house some of the existing collections so that they can be made searchable under the national MARine Sediment (MARS) database.

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