2 results

Developing a rapid molecular identification technique to improve egg production based fish biomass assessments

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

Need

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.

Objectives

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.

Final report

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

Summary

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.

The life-cycle habitat requirements of coastal fisheries species; identifying key knowledge gaps and research needs

Project number: 2012-037
Project Status:
Completed
Budget expenditure: $57,500.00
Principal Investigator: Marcus Sheaves
Organisation: James Cook University (JCU)
Project start/end date: 30 Sep 2012 - 9 Jun 2013
Contact:
FRDC

Need

Coastal fisheries species require a series of connected habitats to complete essential life-history functions. Key habitats, like nurseries, are known for some species but the sequence of habitats used by juveniles is poorly known for most. Even where nurseries are known the relative values of alternative nurseries have not been determined, so we lack the ability to quantify the economic contributions of different habitats to fisheries production. Many habitats without apparent direct functional roles are vital as conduits between habitats critical for life-history needs. Similarly, spawning and forage sites are unknown for many species. The project provides the background to develop research detailing the life-cycle habitat and connectivity requirements of coastal fisheries species, so is the vital first step in gaining the knowledge needed by managers to understand and protect coastal habitats. It fills critical knowledge gaps identified in the DERM/QWP’s “Connectivity” project, and supports habitat classification and mapping work (e.g. QWP/DEEDI Coastal-wetlands mapping, OzCoasts). It will provide the basis for enhanced quantification of the ecological and economic importance of the chain of habitats necessary for healthy fisheries, thus addressing QFRAB 2011/12 priority 4 and priority 3. This will allow more precise management of species valuable to all fishing sectors, and provide pivotal information needed to incorporate fisheries values into impact and offset assessments for development proposals. Thus the work provides crucial information needed by Fisheries Queensland, DEEDI Fisheries Habitat Research, GBRMPA’s EC&SU and CE&WQ sections, and contributes to the long term ecological and economic health of Northern Australia’s fisheries.

Objectives

1. Review all available literature to identify key knowledge gaps and refine a potential field research program
focussing on (a) critical habitats necessary for the life-cycles of key fisheries species using estuarine and nearshore nurseries, (b) connectivities supporting that utilisation, (c) the relative importance of different nursery grounds, (d) the relative value of different habitats for life-history requirements, (e) habitat-specific food webs and trophic interactions supporting fisheries species life-cycles. The project will also develop a “business case” for future investment, considering: the risks, opportunities to protect, repair, offset etc., and developing a decision support system based on these opportunities and risks.

Final report

ISBN: 978-0-646-90839-7
Author: M. Sheaves