Over the last few years, the shellfish industry has experienced an increase in unpredictable hatchery and settlement rates of abalone and oyster larvae – batches crash for no apparent reason despite successful spawning and fertilisation. Additionally, farms experience unexplained stock losses during grow-out periods in both land and sea based culture facilities. Recently, the Australian abalone aquaculture industry ranked the ‘investigation into the causes of summer mortality and development of management protocols to minimize or prevent losses’ as one of the top three priorities for the industry (J. Fromm, pers.comm.). In oysters, farmers are looking for indicators of potential culture problems (i.e. hatchery failures) (M. Bermudes, pers.comm.).
Our ability to manage such events would be strengthened if we could determine and subsequently monitor the causative agent. There is evidence from the international literature to suggest that the cause of these events may be microbial in nature and, anecdotally, farmers believe the mortality of shellfish experienced across seasons may be a product of hydrochemistry interactions with bacteria.
Recently, CSIRO developed and adapted a suite of new cost-effective molecular tools that enable complex microbial communities in water, sediment or soil samples to be rapidly described without the need for physical culturing of the microorganisms. The identification of both commensal and harmful microorganisms which are responsive to changes in abiotic environmental parameters, as well as low abundant microbes that represent a reservoir for infection, can now be undertaken using highly sensitive and high throughput genomics techniques. Furthermore, we have developed multivariate statistical approaches capable of describing links between microbial community profiles and causative factors. We are confident that this burgeoning area of research, metagenomics, will have direct uptake and application in a wide range of aquaculture industries (including food protection and human health aspects) particularly given the increasingly cost-effectiveness of next generation sequencing.
Final report
Aquacultured species such as oysters and abalone live their entire lifecycle in seawater, and co-exist with a wide range of innocuous, pathogenic and beneficial microorganisms. Some microbes cause diseases resulting in significant losses for the farms.
This study set out to provide shellfish farms with the monitoring tools and capability to help reduce product loss and strengthen husbandry and management techniques, thereby reducing the impacts of disease and increasing farm profitability. Using state-of-the-art techniques including Next Generation Sequencing (NGS) and Automated Ribosomal Intergenic Spacer Analysis (ARISA), this report provides the first in-depth analysis of microbial communities and water chemistry associated with shellfish culture in Australia. Metagenomic analyses were effective in resolving taxonomic identity, community profile changes and assessment of microbial abundance from water samples from these shellfish farms without the need for cultivation of microbes within the laboratory.
