Project number: 2017-109
Project Status:
Budget expenditure: $156,370.69
Principal Investigator: Nicole Flint
Organisation: CQUniversity (CQU) Gladstone
Project start/end date: 19 Dec 2017 - 19 Dec 2018


This application answers a request for Expressions of Interest for an FRDC and GHHP project to develop a fish sampling program and fish health indicators for the Gladstone Harbour Report Card. The project will review and test approaches, drawing on earlier work commissioned by GHHP (Cowled, 2016; Kroon et al., 2016).

Fish are key biological indicators of environmental contamination, as they are continuously exposed, ubiquitous in aquatic ecosystems, and play an important ecological role (van der Oost et al., 2003). When employing fish as indicators of ecosystem health, most Australian programs consider assemblages and community structure. This approach is well-tested and simple to deploy. Its limitations are that extensive sampling can be required to ensure the monitoring program is spatially and temporally representative, avoids sampling gear bias and guarantees sufficient statistical power to detect change. The alternative approach is to measure indicators of individual fish health, such as morphometry, gross pathology, histopathology (Mishra and Mohanty, 2009), fish parasite load and diversity (Sasal et al., 2007) or chromosomal mutations (Pak et al., 2012). Other measures, such as bioaccumulation of contaminants, do not necessarily indicate poor fish health but can be useful for assessing ecosystem condition. Fish health indicators range from relatively low cost to high cost and complexity.

For this project, the preference is for testing and development of low-medium categories of indicators such as external examination, morphometry, gross pathology, parasite count and application of the health assessment index (Cowled, 2016). We will review suitable fish monitoring methods, develop and test cost-effective data collection approaches for Gladstone Harbour using adaptive sampling, evaluate the potential to transfer methods and indicators to similar areas, and produce fish indicators for inclusion in the 2017-18 Gladstone Harbour Report Card.

Future monitoring costs for 2019 are estimated at $45,324 (ex GST), not included in the budget.


1. To review and identify suitable methods to monitor fish health in the Gladstone Harbour.
2. To develop and implement a data collection approach by the end of June 2018 to monitor fish health in the Gladstone Harbour that is both cost-effective and suitable for a fish health indicator.
3. To evaluate the potential to adapt and transfer the methods and indicators developed to monitor fish health in other estuaries and ports in Northern Australia.
4. To develop fish health indicator(s) based on the data collected and apply them to the 2017-18 Gladstone Harbour Report Card.

Final report

ISBN: 13: 978-1-921047-49-7
Authors: Nicole Flint Amie Anastasi Andrew Irving Jeremy De Valck Evan Chua Adam Rose Karl French& Emma L. Jackson
Final Report • 5.90 MB


As the link between land and sea environments, estuaries are complex ecosystems vulnerable to human impacts, which directly and indirectly affect plants and animals, including fish. Fish are key biological indicators of environmental contamination, as they are water breathers, common in aquatic ecosystems, play a variety of important ecological roles, are readily identified and have high importance to the community.
Various waste water sources, of industrial, agricultural and domestic origins, can pollute downstream waterways. When fish are exposed to contaminated water, they are affected at the population level (numbers and diversity of fish species) down to biochemical impacts on single cellswithin individual fish. Fish health indicators range from relatively low to high cost and complexity.  For this project, preference was given to testing and developing low to medium cost and complexity fish health indicators such as external measurements, pathological changes that can be seen with the naked eye, parasite count, the application of an existing health assessment index, and histopathological analysis (analysis of tissue condition using a microscope by an aquatic veterinarian). 
Ultimately, the results of this project will be considered for incorporation into the Gladstone Harbour Report Card, providing stakeholders and the community with accessible information about the condition of Gladstone Harbour, with potential for application to other Northern Australian portsand estuaries. The main outcome is    an improved understanding of fish health in Gladstone Harbour (and beyond) leading to the potential for improved environmental and fisheries management practices, marketability of fisheries products and enhanced sustainability of fisheries resources. The objectives of the research project were:
  1. To review and identify suitable methods to monitor fish health in Gladstone Harbour.
  2. To develop and implement a data collection approach to monitor fish health in Gladstone Harbour that is both cost-effective and suitable for a fish health indicator.
  3. To evaluate the potential to adapt and transfer the methods and indicators developed to monitor fish health in other estuaries and ports in Northern Australia (a separate report addressing this objective is provided as Attachment B to this report). 
  4. To develop fish health indicator(s) based on the data collected.
The key steps considered in the development of fish health indicators are: indicator selection, species selection, site selection, sample size and temporal replication. The project was informed by data collected in April 2018 (Autumn, post-wet season) and September/October 2018 (Spring, pre-wet season); these dates were selected to allow for any seasonal effects on fish health.  
Three fish taxa were initially targeted for condition assessments, based on the recommendations of previous GHHP projects, and of the GHHP Independent Science Panel. The three taxa sampled in Autumn 2018 were: Barramundi (Lates calcarifer), Bream (pikey bream Acanthopagrus pacificus and Yellowfin Bream A. australis), and Mullet (Sea Mullet Mugil cephalus and Diamondscale Mullet Liza vaigiensis). In Spring 2018, an additional target species, Barred Javelin (Pomadasys kaakan) was added. An important consideration in selection of target species is their relative mobility, or how far they may travel. Fish catch and recapture tagging data was provided from the SunTag program by InfoFish Australia and was valuable in assessing the relative mobility of possible target species. Barramundi in particular are highly transient and the condition of a fish caught in a particular area may have been previously influenced by conditions many hundreds of kilometres away. 
Fish were sampled at 12 Gladstone Harbour zones and two reference sites (Stanage Bay and Baffle Creek). Reference sites were selected based on a series of selection criteria relating to their geographical location, human impacts on the local environment, accessibility, availability of habitat suitable for the target species, and their use in previous fish health studies relating to Gladstone Harbour. 
Options for suitable fish health monitoring approaches for Gladstone Harbour were identified using researcher knowledge and a range of relevant scientific literature and reports. The review of methods provided several suitable approaches to be tested in Gladstone Harbour, using an adaptive sampling technique. These included Fulton’s condition factor (K; a ratio of body weight and length), hepatosomatic index (HSI, a ratio of liver weight to body weight), gonadosomatic index (GSI, a ratio of gonad weight to body weight), health assessment index (HAI, which individually scores damage to seven organs), fluctuating asymmetry of eye diameter (differences in size of left and right eyes), prevalence of parasites and pathogens (diseases, etc), and histopathological analysis of selected fish tissues (checking organs for cell damage using a microscope). Each of these indicators has positive and negative qualities and selection depends on many factors including data availability, resource/ cost constraints, availability of expertise and equipment required for analysis, and the possible environmental impacts occurring at the study site. 
All fish were measured, weighed, checked for abnormalities and released, with the exception of target species which were humanely killed for further analysis, up to a maximum of five specimens per site. The gears and methods used were chosen to select for the target species, however additional fish species were also captured, and while most of these were released alive, any fish that died during capture were kept and returned to the laboratory for dissection and future analysis.  
Using the results obtained from sampling in 2018, several preliminary fish health measures that are particularly promising for possible inclusion in the fish health indicator for the Gladstone Harbour Report Card have been identified. The two measures that appear most useful for the Gladstone Harbour Report Card in the short term are: 
  1. Health Assessment Index (HAI):  requires a gross pathological analysis during dissection, and produces a score based on the condition of several organs and tissues. The index scores add together to reflect the acute and chronic stressors that are present in the fish’s environment. A fish with a high HAI score is less healthy than a fish with a very low score, and individual fish scores can be averaged to give a total HAI for an area.  
  2. An index of relative histopathological condition: requires microscopic study of the changes to tissues caused by disease. A draft metric is in development to compile data across four organ types, this is currently being further tested using organs collected in Spring 2018. The organs selected for this pilot project included gills, liver and a skin/muscle block. Histopathology is a useful indicator as it provides data on the medium-term responses of fish to a wide range of environmental issues. Using the draft metric, a fish with a score of 1.0 is normal, and scores below 1.0 suggest poorer health. 
Based on the results of the 2018 pilot sampling year, eight recommendations have been provided for GHHP’s consideration. 
Recommendation 1: GHHP continues to monitor HAI and histopathology in Autumn 2019, in order to calculate scores for a pilot fish health indicator using Spring 2018 and Autumn 2019 data.
Recommendation 2: GHHP considers whether to provide a wider range of fish tissues for histopathological analysis, to increase the comprehensiveness of fish health assessments.
Recommendation 3: GHHP continues to monitor Fulton’s K, HSI, GSI and fluctuating asymmetry of eye diameter to collate a dataset which may in future be used to inform the fish health indicator. 
Recommendation 4: GHHP considers testing for bioaccumulation of metals and other toxicants in collected fish tissue samples. 
Recommendation 5: GHHP considers including a hook and line fishing component in 2019 to capture more bream.
Recommendation 6: GHHP considers adding barred javelin and blue catfish as target species in 2019. 
Recommendation 7: GHHP considers targeting fish sampling at a reduced number of zones in Gladstone Harbour.
Recommendation 8: GHHP considers continuing to sample at reference sites at least once a year.

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