Omics for aquatic ecotoxicology: Control of extraneous variability to enhance the analysis of environmental effects

Abstract

There are multiple sources of biological and technical variation in a typical ecotoxicology study that may not be revealed by traditional endpoints but that become apparent in an omics dataset. As researchers increasingly apply omics technologies to environmental studies, it will be necessary to understand and control the main source(s) of variability to facilitate meaningful interpretation of such data. For instance, can variability in omics studies be addressed by changing the approach to study design and data analysis? Are there statistical methods that can be employed to correctly interpret omics data and make use of unattributed, inherent variability? The present study presents a review of experimental design and statistical considerations applicable to the use of omics methods in systems toxicology studies. In addition to highlighting potential sources that contribute to experimental variability, this review suggests strategies with which to reduce and/or control such variability so as to improve reliability, reproducibility, and ultimately the application of omics data for systems toxicology.

Nonlethal laparoscopic detection of intersex (testicular oocytes) in largemouth bass (Micropterus salmoides) and smallmouth bass (Micropterus dolomieu)

“…The current direction of environmental monitoring is toward reduced lethal whole‐organism sampling and an increased reliance on molecular and cellular biomarkers. Application of “‐omics” in aquatic ecotoxicology is growing exponentially, providing mechanistic insights into biological responses to contaminants and other environmental stressors . Initially developed for laboratory screening assays, methods ranging from simple analysis of single compounds (e.g., aromatase, vitellogenin, endogenous hormones) to complex bioinformatic approaches (e.g., gene arrays, proteomics, metabolomics) are increasingly being employed in field investigations of endocrine disruption and other toxicological effects in fish .…”

In-plate toxicometabolomics of single zebrafish embryos

“…10 Furthermore, all ZF embryo toxicometabolomic studies performed to date have employed pooling approaches, extracting between 3 and 80 embryos per replicate, in order to obtain sufficient biomass for instrumental analysis. 7,8,[11][12][13] In addition to the time and costs associated with this approach, pooling decouples apical endpoints from metabolic perturbations in individual embryos. While the analysis of single ZF embryos could facilitate direct linkages between metabolic perturbation and apical endpoints, single ZF embryo metabolomics is hampered by their small size (B200 mg per individual at 120 hours post fertilization (hpf)), which makes them difficult to extract and ultimately generate sufficient quantities of extract for instrumental analysis.…”

1H NMR-based metabolomics reveals interactive effects between the carrier solvent methanol and a pharmaceutical mixture in an amphibian developmental bioassay with Limnodynastes peronii

“…The ability to simultaneously measure the end products from a wide range of cellular processes yields robust information about sub-lethal toxicological effects in response to environmental stressors (Spurgeon et al, 2010;Viant 2008;Jones et al, 2008;Bouhifd et al, 2013). Somewhat paradoxically, the same sensitivity and comprehensive scope that makes metabolite profiling so attractive may make the approach susceptible to sources of confounding that have gone unnoticed using traditional test methods (Simmons et al, 2015). Understanding such factors is critical for the future successful application of metabolomics and other omics disciplines (e.g., genomics and proteomics) towards ecotoxicology research (Simmons et…”