Genomic approaches in the identification of hypoxia biomarkers in model fish species

Abstract

Eutrophication leading to hypoxic water conditions has become a major problem in aquatic systems worldwide. Monitoring the levels and biological effects of lowered oxygen levels in aquatic systems may provide data useful in management of natural aquatic environments. Fishes represent an economically important resource that is subject to hypoxia exposure effects. Due to the extreme diversity of fish species and their habitats, fishes in general have evolved unique capabilities to modulate gene expression patterns in response to hypoxic stress. Recent studies have attempted to document quantitative changes in gene expression patterns induced in various fish species in response to reduced dissolved oxygen levels. From a management perspective, the goal of these studies is to provide a more complete characterization of hypoxia responsive genes in fish, as molecular indicators (biomarkers) of ecosystem hypoxic stress.The molecular genetic response to hypoxia is highly complex and overlaps with other stress responses making it difficult to identify hypoxia specific responses using traditional single gene or low throughput approaches. Therefore, recent approaches have been aimed at developing functional genomic (e.g. high density microarray and real-time PCR) and proteomic (two-dimensional fluorescence difference in gel electrophoresis coupled with mass spectrometry based peptide identification) technologies that employ fish species. Many of the fish species utilized in these studies do not have the advantages of underlying genome resources (i.e., genome or transcriptome sequences). Efforts have attempted to establish correlations between discreet molecular responses elicited by fish in response to hypoxia and changes in the genetic profiles of stressed organs or tissues. Notable progress in these areas has been made using several different versions of either cDNA or oligonucleotide based microarrays to profile changes in gene expression patterns in response to hypoxic stress.Due to these efforts, hundreds of hypoxia responsive genes have been identified both from laboratory reared aquaria fish and from feral fish derived from both fresh and saltwater habitats. Herein, we review these reports and the emergence of hypoxia biomarker development in aquatic species. We also include some of our own recent results using the medaka (Oryzias latipes) as a model to define genetic profiles of hypoxia exposure.

Figure 1

Dissolved oxygen changes in hypoxia tank and control tank during medaka hypoxia experiments. Two 20 gal aquaria were programmed to become hypoxic and one 20 gal control aquarium was immediately adjacent to the others. Each tank was monitored and maintained under pre-set oxygen level profiles using an OxyCycler oxygen control system (Model F84DO, BioSpherix, NY, USA) specifically designed for aquaria. The control tank (blue line) was maintained at 7.3–8.0 mg l⁻¹ DO throughout the experiment by bubbling compressed air through air stones into the tank water. The oxygen level in the hypoxic tanks (pink line) was slowly (over 5 h) brought to 2.5 mg l⁻¹ by bubbling compressed air or nitrogen through air stones, then dropped to 2.0, 1.5 and finally 0.8 mg l⁻¹ over each day and held at 0.8 mg l⁻¹ for 5 d when the fish were sacrificed for experimental analyses.