Our ability to assess the status of many important fish species is restricted by the inability to accurately estimate their biomass. In addition, the high costs of such surveys mean that they are not conducted for many species within Australia's Fisheries. Ichthyoplankton surveys to determine egg production and biomass (such as through the daily egg production method (DEPM)) offer an effective means to get this information. However, current techniques cannot be applied broadly because many fish have morphologically identical eggs and molecular sequencing is prohibitively expensive and time consuming. These issues were highlighted in the DEPM assessments for blue mackerel and red bait (FRDC 2002/061 & 2004/39) where there was poor success in morphological identification of fish eggs collected in plankton tows. These projects identified the need to develop an accurate, rapid and inexpensive technique for fish eggs identification. This project will assess the suitability of developing this technique with the ultimate aim of conducting icthyoplankton surveys to inform a DEPM for mackerel species (Qld, NT and WA), pilchard and herring species in the developing tropical small pelagics fishery(NT) and black jewfish (NT, WA, Qld). While the development is focused on tropical species the technique will have application in many southern fisheries.
This project was developed under the steerage of the Northern Research Partnership (NRP) and addresses northern Australia priorities around developing better biomass estimation methods for Spanish/grey mackerel and for the new multi-species small pelagic and Coastal Line Fisheries in the NT.
Project number:
2014-022
Project Status:
Completed
Budget expenditure:
$175,121.21
Principal Investigator:
Richard J. Saunders
Organisation:
James Cook University (JCU)
Project start/end date:
8 May 2014
-
14 Aug 2017
Contact:
FRDC
1. To develop a novel high-throughput, low cost DNA-based egg identification method for important fish species in northern Australia.
2. To assess the application of the technology developed for use in the daily egg production method (DEPM) for biomass estimation.
ISBN:
978-0-6485037-0-5
Authors:
Richard J. Saunders
Shannon Kjeldsen
Roger Huerlimann
Thor Saunders
Shane Penny
Andrew Tobin and Dean Jerry
Final Report
•
2019-12-01
•
2.27 MB
2014-022-DLD.pdf
This project aimed to develop a rapid and affordable molecular method to identify fish eggs from
plankton samples. The method selected was a multiplex bead array method where species-specific
probes are developed and bound to beads which fluoresce when passed through a flow cytometer if
bound to the target species DNA. This allows for identification of multiple species at one time as
different probe-bead combinations can be used to identify different fish species. Furthermore, as
molecular methods usually require preservation in ethanol which causes problems of egg staging, a
critical component in modelling egg mortality and thus initial egg abundance, we also considered the
impact of preservation method on egg staging and on DNA amplification.
The method was able to identify eggs of several target species from wild collected plankton samples
(confirmed by sequencing) with success rates varying between species from 50 to 100% identification
success. We identified a series of issues that potentially limit the application of this method in the
context of DEPM and egg identification. The principal issues were reliability of the chemistry and
identified false negative results resultant from preservation of DNA. DNA amplification and egg staging
were both impacted by preservation method with the best preservation method for egg staging being
5% formalin, however, this was the worst performer for DNA amplification. An ethanol based
preservation method is essential for DNA based identification and this also allows for some egg staging,
although egg staging prior to the presence of an embryo is very challenging, even for an experienced
technician.
