Metabolomics for biomonitoring: an evaluation of the metabolome as an indicator of aquatic ecosystem health

Pomfret, Sarah M.; Brua, Robert B.; Izral, Natalie M.; Yates, Adam G.

doi:10.1139/er-2019-0003

Cited by 14 publications

(27 citation statements)

References 70 publications

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“…Though many of the compounds remained unambiguously defined, integration of these approaches did reveal a network of interactive processes related to anaerobic activity and biodegradation in the presence of petroleum compounds (Bargiela et al, 2015). Overall, insights into microbial function and resilience in low-pH environments or complex hydrocarbon impacted zones have implications for predictive models of aquatic ecosystem health and sustainability, but also significant potential for resource management and biotechnological advancements such as the discovery of novel compounds (Reverter et al, 2020), as well as biomarker discovery (Pomfret et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

“…The broader field of aquatic environmental science is clearly facing the paradigm shift toward post-genomic approaches, already revealing the potential to contribute to regulatory and policy decisions. These datasets have the not over-promized ability to improved sensitivity of biomarker selection (Pomfret et al, 2019), aid in earlier and more precise detection and modeling of ecosystem perturbations (Reid et al, 2020;Hipsey et al, 2020), and improved risk assessment frameworks that includes functional characteristics of microbial behavior (Cocolin et al, 2018). This type of data also stands to revolutionize the time and expense-consuming (and oftenneglected) pursuit of microbial cultivation that is required for experimental and ecological validation of gene annotations and activities.…”

Section: Discussionmentioning

confidence: 99%

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How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes

Reid

Bergsveinson

2021

Front. Mol. Biosci.

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Culture-independent and meta-omics sequencing methods have shed considerable light on the so-called “microbial dark matter” of Earth’s environmental microbiome, improving our understanding of phylogeny, the tree of life, and the vast functional diversity of microorganisms. This influx of sequence data has led to refined and reimagined hypotheses about the role and importance of microbial biomass, that paradoxically, sequencing approaches alone are unable to effectively test. Post-genomic approaches such as metabolomics are providing more sensitive and insightful data to unravel the fundamental operations and intricacies of microbial communities within aquatic systems. We assert that the implementation of integrated post-genomic approaches, specifically metabolomics and metatranscriptomics, is the new frontier of environmental microbiology and ecology, expanding conventional assessments toward a holistic systems biology understanding. Progressing beyond siloed phylogenetic assessments and cataloging of metabolites, toward integrated analysis of expression (metatranscriptomics) and activity (metabolomics) is the most effective approach to provide true insight into microbial contributions toward local and global ecosystem functions. This data in turn creates opportunity for improved regulatory guidelines, biomarker discovery and better integration of modeling frameworks. To that end, critical aquatic environmental issues related to climate change, such as ocean warming and acidification, contamination mitigation, and macro-organism health have reasonable opportunity of being addressed through such an integrative approach. Lastly, we argue that the “post-genomics” paradigm is well served to proactively address the systemic technical issues experienced throughout the genomics revolution and focus on collaborative assessment of field-wide experimental standards of sampling, bioinformatics and statistical treatments.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes

Reid

Bergsveinson

2021

Front. Mol. Biosci.

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“…In addition, higher sensitivity of metabolomics markers than usual descriptors has been recently shown (Gauthier et al 2019;Serra-Compte et al 2018;Wang et al 2019). Also, Pomfret et al (2019) have recently highlighted that the metabolome meets many bioindicator criteria and has the potential to be a priori predictive. For instance, Taylor et al (2018) have shown that early-response metabolic biomarkers can predict chronic reproductive individual fitness and thus population response in daphnids.…”

Section: Introductionmentioning

confidence: 99%

“…To this end, beyond usual chemometric methodologies supporting the identification of relevant features (i.e., metabolites), promising approaches have been recently proposed to aggregate metabolomics fingerprints toward quantitative assessment of the dose-dependent metabolomics response to support ecological risk assessment of chemicals (Metabolic Effect Level Index, MELI; DRomics) (Larras et al 2018;Riedl et al 2015). Nevertheless, there is still an overall need for additional empirical evidence to determine the metabolic shifts that generate ecologically relevant changes and demonstrate its causal diagnostic capacity (Pomfret et al 2019). In particular, investigation of the underlying processes driving metabolome variability becomes necessary in order to develop transitive principles and enhance predictive capabilities across ecosystems (Danczak et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Metabolomics insight into the influence of environmental factors in responses of freshwater biofilms to the model herbicide diuron

Creusot

Chaumet

Éon

et al. 2021

Environ Sci Pollut Res

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Freshwater biofilms have been increasingly used during the last decade in ecotoxicology due to their ecological relevance to assess the effect(s) of environmental stress at the community level. Despite growing knowledge about the effect of various stressors on the structure and the function of these microbial communities, a strong research effort is still required to better understand their response to chemical stress and the influence of environmental stressors in this response. To tackle this challenge, untargeted metabolomics is an approach of choice because of its capacity to give an integrative picture of the exposure to multiple stress and associated effect as well as identifying the molecular pathways involved in these responses. In this context, the present study aimed to explore the use of an untargeted metabolomics approach to unravel at the molecular/ biochemical level the response of the whole biofilm to chemical stress and the influence of various environmental factors in this response. To this end, archived high-resolution mass spectrometry data from previous experiments at our laboratory on the effect of the model photosynthesis inhibitor diuron on freshwater biofilm were investigated by using innovative solutions for OMICs data (e.g., DRomics) and more usual chemometric approaches (multivariate and univariate statistical analyses). The results showed a faster (1 min) and more sensitive response of the metabolome to diuron than usual functional descriptors, including photosynthesis. Also, the metabolomics response to diuron resulted from metabolites following various trends (increasing, decreasing, U/bell shape) along increasing concentration and time. This metabolomics response was influenced by the temperature, photoperiod, and flow. A focus on a plant-specific omega-3 (eicosapentaenoic acid) playing a key role in the trophic chain highlighted the potential relevance of metabolomics approach to establish the link between molecular alteration and ecosystem structure/functioning impairment but also how complex is the response and the influence of all the tested factors on this response at the metabolomics level. Altogether, our results underline that more fundamental researches are needed to decipher the metabolomics response of freshwater biofilm to chemical stress and its link with physiological, structural, and functional responses toward the unraveling of adverse outcome pathways (AOP) for key ecosystem functions (e.g., primary production).

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“…Metabolomics could be a useful tool in elucidating thresholds at which naphthenic acids initiate biological effects that may be precursory to observable population and community level impacts ( Pomfret et al, 2020 ). Indeed, metabolomics has shown efficacy in determination of sublethal contaminant effects in various contexts and may be suitable for assessment of environmental effects of naphthenic acids ( Viant et al, 2003 ).…”

Section: Introductionmentioning

confidence: 99%

Metabolomic Analysis of Hexagenid Mayflies Exposed to Sublethal Concentrations of Naphthenic Acid

Pomfret

Brua

Milani

et al. 2021

Front. Mol. Biosci.

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The oil sands region in northeastern Alberta, Canada contain approximately 165 billion barrels of oil making it the third largest oil reserves in the world. However, processing of extracted bitumen generates vast amounts of toxic byproduct known as oil sands process waters. Naphthenic acids and associated sodium naphthenate salts are considered the primary toxic component of oil sands process waters. Although a significant body of work has been conducted on naphthenic acid toxicity at levels comparable to what is observed in current oil sands process waters, it is also important to understand any impacts of exposure to sublethal concentrations. We conducted a microcosm study using the mayfly Hexagenia spp. to identify sublethal impacts of naphthenic acid exposure on the survival, growth, and metabolome across a concentration gradient (0–100 μg L−1) of sodium naphthenate. Nuclear magnetic resonance-based metabolomic analyses were completed on both the polar and lipophilic extracted fractions of whole organism tissue. We observed a positive relationship between sodium naphthenate concentration and mean principal component score of the first axis of the polar metabolome indicating a shift in the metabolome with increasing naphthenic acid exposure. Eleven metabolites correlated with increased naphthenic acid concentration and included those involved in energy metabolism and apoptosis regulation. Survival and growth were both high and did not differ among concentrations, with the exception of a slight increase in mortality observed at the highest concentration. Although lethal concentrations of naphthenic acids in other studies are higher (150–56,200 μg L−1), our findings suggest that physiological changes in aquatic invertebrates may begin at substantially lower concentrations. These results have important implications for the release of naphthenic acids into surface waters in the Alberta oil sands region as an addition of even small volumes of oil sands process waters could initiate chronic effects in aquatic organisms. Results of this research will assist in the determination of appropriate discharge thresholds should oil sands process waters be considered for environmental release.

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Metabolomics for biomonitoring: an evaluation of the metabolome as an indicator of aquatic ecosystem health

Cited by 14 publications

References 70 publications

How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes

How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes

Metabolomics insight into the influence of environmental factors in responses of freshwater biofilms to the model herbicide diuron

Metabolomic Analysis of Hexagenid Mayflies Exposed to Sublethal Concentrations of Naphthenic Acid

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