In Response: Integration of ‘omics to larger‐scale watershed assessments: A mixed government/academic perspective

The proliferation of different ‘omics (genomics, proteomics, and metabolomics) approaches over the past decade has provided a means of characterizing the subcellular biological processes underlying higher-order responses to stressors, allowing for an unparalleled evaluation of the molecular and biochemical status of organisms [1]. Platforms supporting ‘omics-based studies have matured such that they are technically reliable. This has allowed them to be applied to a number of long-standing issues within aquatic ecotoxicology and has opened up the possibility of combining these new lines of evidence with more established approaches that aim to identify chemicals in the water or target effects at higher biological levels. Perhaps the greatest advantage over traditional assessment approaches is the ability to mechanistically assess the sublethal effects of environmental contaminants. Generally, these approaches have been applied in controlled laboratory chemical exposures, where ‘omics technologies have been shown to be particularly useful in identifying toxic pathway responses to a single compound or to classes of compounds, and in the identification of modes of action in screening and prioritization programs, primarily within the pharmaceutical industry [2]. Importantly, they have provided valuable insight into the molecular pathways that may be altered by a given stressor, which can be potentially useful for determining risk for new or poorly characterized chemicals. Transcriptomic approaches have also been utilized to create so-called molecular fingerprints for chemicals with known phenotypic toxic outcomes such as cancer [3] or endocrine disruption [4]. When such fingerprints are compared with ‘omic responses of previously untested compounds, they may act as valuable predictive tools that help link an initiating event or an altered pathway with useful regulatory endpoints such as swimming performance, growth, or reproduction, aiding chemical prioritization and driving further risk-assessment decisions. The use of fingerprinting is confounded by impacts of multiple stressors, resulting in a somewhat limited field application; however, it is a valuable tool in the assessment of effect-based responses that may be indicative of the overall health status of an organism [5] or the determination of contaminant sources [6], thus assessing risks associated with exposure and location within a watershed. Despite their potential, obstacles remain in the use of ‘omics for determining chemical impacts on organism or community health in complex aquatic ecosystems. This is not to say that there have not been successes in the assessment of changes in the expression of single-gene biomarkers elicited by chemical exposure. For example, the well-characterized biomarker vitellogenin is a widely accepted indicator of exposure to endocrine disrupting compounds, with predictive value for reproductive impacts and potential population status in fish. Vitellogenin, however, is somewhat of an exception in that there is a considerable body of work underlying its linkage to estrogenic exposure and detailing its performance. Though vitellogenin may be useful for identifying estrogenic exposures, field-based exposures will likely involve complex mixtures and require multiple biomarkers. In addition, global transcriptional platforms (i.e., microarrays) have been applied to selected species in field settings to generate site-specific signatures used to characterize location differences that, in some cases, can be attributed to particular contaminant classes [7,8] or sources of contamination along a chemical gradient [6,9–11]. These In This Issue: