title: A protocol for identifying suitable biomarkers to assess fish health: A systematic review.
abstract: BACKGROUND
  Biomarkers have been used extensively to provide the connection between external levels of contaminant exposure, internal levels of tissue contamination, and early adverse effects in organisms.
  
  
  OBJECTIVE
  To present a three-step protocol for identifying suitable biomarkers to assess fish health in coastal and marine ecosystems, using Gladstone Harbour (Australia) as a case study.
  
  
  METHODS
  Prior to applying our protocol, clear working definitions for biomarkers were developed to ensure consistency with the global literature on fish health assessment. First, contaminants of concern were identified based on the presence of point and diffuse sources of pollution and available monitoring data for the ecosystem of interest. Second, suitable fish species were identified using fisheries dependent and independent data, and prioritised based on potential pathways of exposure to the contaminants of concern. Finally, a systematic and critical literature review was conducted on the use of biomarkers to assess the health of fish exposed to the contaminants of concern.
  
  
  CONCLUSIONS
  We present clear working definitions for bioaccumulation markers, biomarkers of exposure, biomarkers of effect and biomarkers of susceptibility. Based on emission and concentration information, seven metals were identified as contaminants of concern for Gladstone Harbour. Twenty out of 232 fish species were abundant enough to be potentially suitable for biomarker studies; five of these were prioritised based on potential pathways of exposure and susceptibility to metals. The literature search on biomarkers yielded 5,035 articles, of which 151met the inclusion criteria. Based on our review, the most suitable biomarkers include bioaccumulation markers, biomarkers of exposure (CYP1A, EROD, SOD, LPOX, HSP, MT, DNA strand breaks, micronuclei, apoptosis), and biomarkers of effect (histopathology, TAG:ST).
  
  
  CONCLUSIONS
  Our protocol outlines a clear pathway to identify suitable biomarkers to assess fish health in coastal and marine ecosystems, which can be applied to biomarker studies in aquatic ecosystems around the world.
authors.affiliation: Australian Institute of Marine Science, Townsville, Queensland, Australia.
authors.forename: Frederieke
authors.identifier: http://orcid.org/0000-0001-8771-6543
authors.initials: F
authors.lastname: Kroon
authors.affiliation: Australian Institute of Marine Science, Arafura Timor Research Facility, Brinkin, Northern Territory, Australia.
authors.forename: Claire
authors.initials: C
authors.lastname: Streten
authors.affiliation: Australian Institute of Marine Science, Arafura Timor Research Facility, Brinkin, Northern Territory, Australia.
authors.forename: Simon
authors.initials: S
authors.lastname: Harries
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000378:metabolism; D005393:Fish Diseases / Q000175:diagnosis* / Q000378:metabolism*; D029941:Fish Proteins / Q000378:metabolism; D005399:Fishes; D018384:Oxidative Stress; D000078202:Systematic Reviews as Topic; D014874:Water Pollutants, Chemical / Q000378:metabolism / Q000633:toxicity*; D060753:Water Quality
chemical_list: D015415:Biomarkers; D029941:Fish Proteins; D014874:Water Pollutants, Chemical