Global transcriptomic profiling in barramundi (Lates calcarifer) from rivers impacted by differing agricultural land uses

Abstract

Most catchments discharging into the Great Barrier Reef lagoon have elevated loads of suspended sediment, nutrients, and pesticides, including photosystem II inhibiting herbicides, associated with upstream agricultural land use. To investigate potential impacts of declining water quality on fish physiology, RNA sequencing (RNASeq) was used to characterize and compare the hepatic transcriptomes of barramundi (Lates calcarifer) captured from 2 of these tropical river catchments in Queensland, Australia. The Daintree and Tully Rivers differ in upstream land uses, as well as sediment, nutrient, and pesticide loads, with the area of agricultural land use and contaminant loads lower in the Daintree. In fish collected from the Tully River, transcripts involved in fatty acid metabolism, amino acid metabolism, and citrate cycling were also more abundant, suggesting elevated circulating cortisol concentrations, whereas transcripts involved in immune responses were less abundant. Fish from the Tully also had an increased abundance of transcripts associated with xenobiotic metabolism. Previous laboratory-based studies observed similar patterns in fish and amphibians exposed to the agricultural herbicide atrazine. If these transcriptomic patterns are manifested at the whole organism level, the differences in water quality between the 2 rivers may alter fish growth and fitness. Environ Toxicol Chem 2017;36:103-112. © 2016 SETAC.

A protocol for identifying suitable biomarkers to assess fish health: A systematic review

“…This means that RNASeq can be used to assess responses to contaminants in non-model fish species [179], such as potential suitable fish species in Gladstone Harbour like L . calcarifer [157]. Our review, however, did not identify any papers that applied RNASeq to assess effects of metals on fish health.…”

“…Our review, however, did not identify any papers that applied RNASeq to assess effects of metals on fish health. RNASeq may be a suitable biomarker for assessing fish health in Gladstone Harbour particularly given the existing knowledge of the L calcarifer transcriptome [157]. However, the application of this biomarker needs to be further development to provide clear connections between external levels of contaminant exposure, changes in transcripts abundances, and early adverse effects in organisms.…”

“…calcarifer [152–154]; (v) transcriptome for L . calcarifer [157], and (vi) various gross indices for L . calcarifer [93] and M .…”

“…In addition, our review has identified five fish species suitable for such biomarker studies, based on (i) abundance information from fisheries dependent [35–39] and independent [40–44] (S12 Table), (ii) exposure and life history information relevant to metal contamination [46–48] (http://www.fishbase.org/; http://australianmuseum.net.au/) (Table 2), and (iii) existence of suitable biomarkers [93, 152–154, 157, 181–186]. These five fish species are Acanthopagrus australis (Yellowfin Bream), Lates calcarifer (Barramundi), Mugil cephalus (Sea Mullet), Eleutheronema tetradactylum (Blue Threadfin), and Scomberomorus queenslandicus (School Mackerel).…”

Ecological Models to Infer the Quantitative Relationship between Land Use and the Aquatic Macroinvertebrate Community

“…The impact that land use poses on surface waters is not limited to river ecosystems [13,14], but also affects ponds [15] and lakes [16,17]. The change in the physico-chemical and hydromorphological characteristics of the impacted river or catchment will consequently affect the richness and abundance of aquatic organisms, such as fish [18,19], macroinvertebrates [20,21], and plants [22,23].…”