Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience

AOP-Anchored Transcriptome Analysis Catalogue Accelerates the Discovery of Environmental Toxicants in Zebrafish

Current toxicity screening approaches to evaluate the vast number of environmental chemicals that require assessment are hampered due to their significant costs, time requirements, and reliance on live animal testing. The aim of the present study was to develop an adverse outcome pathway (AOP)-anchored transcriptome analysis (AATA) catalogue to expedite the discovery of environmental toxicants. 437 AOPs from the AOPwiki (https://aopwiki.org/) and 2280 transcriptomics data sets from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI ArrayExpress (AE) repositories were comprehensively reviewed and analyzed. By using the differentially expressed molecular key event (mKE) genes as connection nodes, we created a large-scale environmental substance─target gene (mKE)─predicted adverse outcomes (SGAs) network that included 78 substances, 1099 genes, and 354 adverse outcomes (AOs). To validate the reliability of the network, comprehensive literature verification was conducted. We demonstrated that 164 of the 354 AOs identified have been previously characterized in the literature. The results for 136 of these AOs were consistent with the predictions of the AATA catalogue, representing an accuracy rate of 82.9%. Besides, distinct patterns in molecular KEs and AOs among categories of substances, such as biocides and metals, were demonstrated. Some representative substances, including atrazine and copper, pose significant risks to fish at various levels of biological organization. Moreover, experimental verification of the AATA predictions was conducted, including exposures of zebrafish to perfluorooctanesulfonate, cresyl diphenyl phosphate, and lanthanum. Results demonstrated consistency with predictions of the AATA catalogue, with an accuracy rate of 92.3%. Collectively, the present findings support the AATA catalogue as an efficient and promising platform for identifying environmental toxicants to fish and thereby provide novel insights into the understanding of potential risks of environmental contaminants.

Metabolomic-Based Comparison of Daphnia magna and Japanese Medaka Responses After Exposure to Acetaminophen, Diclofenac, and Ibuprofen

Pharmaceuticals are found in aquatic environments due to their widespread use and environmental persistence. To date, a range of impairments to aquatic organisms has been reported with exposure to pharmaceuticals; however, further comparisons of their impacts across different species on the molecular level are needed. In the present study, the crustacean Daphnia magna and the freshwater fish Japanese medaka, common model organisms in aquatic toxicity, were exposed for 48 h to the common analgesics acetaminophen (ACT), diclofenac (DCF), and ibuprofen (IBU) at sublethal concentrations. A targeted metabolomic-based approach, using liquid chromatography-tandem mass spectrometry to quantify polar metabolites from individual daphnids and fish was used. Multivariate analyses and metabolite changes identified differences in the metabolite profile for D. magna and medaka, with more metabolic perturbations for D. magna. Pathway analyses uncovered disruptions to pathways associated with protein synthesis and amino acid metabolism with D. magna exposure to all three analgesics. In contrast, medaka exposure resulted in disrupted pathways with DCF only and not ACT and IBU. Overall, the observed perturbations in the biochemistry of both organisms were different and consistent with assessments using other endpoints reporting that D. magna is more sensitive to pollutants than medaka in short-term studies. Our findings demonstrate that molecular-level responses to analgesic exposure can reflect observations of other endpoints, such as immobilization and mortality. Thus, environmental metabolomics can be a valuable tool for selecting sentinel species for the biomonitoring of freshwater ecosystems while also uncovering mechanistic information. Environ Toxicol Chem 2024;43:1339-1351. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Metabolic disruptions and impaired reproductive fitness in wild-caught freshwater turtles (Emydura macquarii macquarii) exposed to elevated per- and polyfluoroalkyl substances (PFAS)

Per- and poly-fluoroalkyl substances (PFAS) pose a threat to organisms and ecosystems due to their persistent nature. Ecotoxicology endpoints used in regulatory guidelines may not reflect multiple, low-level but persistent stressors. This study examines the biological effects of PFAS on Eastern short-necked turtles in Queensland, Australia. In this study, blood samples were collected and analysed for PFAS, hormone levels, and functional omics endpoints. High levels of PFAS were found in turtles at the impacted site, with PFOS being the dominant constituent. The PFAS profiles of males and females differed, with males having higher PFAS concentrations. Hormone concentrations differed between impacted and reference sites in male turtles, with elevated testosterone and corticosterone indicative of stress. Further, energy utilisation, nucleotide synthesis, nitrogen metabolism, and amino acid synthesis were altered in both male and female turtles from PFAS-impacted sites. Both sexes show similar metabolic responses to environmental stressors from the PFAS-contaminated site, which may adversely affect their reproductive fitness. Purine metabolism, caffeine metabolism, and ferroptosis pathway changes in turtles can cause gout, cell death, and overall health problems. Further, the study showed that prolonged exposure to elevated PFAS levels in the wild could compromise turtle reproductive fitness by disrupting reproductive steroids and metabolic pathways.

Subtropical coastal microbiome variations due to massive river runoff after a cyclonic event

BACKGROUND

Coastal ecosystem variability at tropical latitudes is dependent on climatic conditions. During the wet, rainy season, extreme climatic events such as cyclones, precipitation, and winds can be intense over a short period and may have a significant impact on the entire land‒sea continuum. This study focused on the effect of river runoff across the southwest coral lagoon ecosystem of Grand Terre Island of New Caledonia (South Pacific) after a cyclonic event, which is considered a pulse disturbance at our study site. The variability of coastal microbiomes, studied by the metabarcoding of V4 18S (protists) and V4-V5 16S (bacteria) rDNA genes, after the cyclone passage was associated with key environmental parameters describing the runoff impact (salinity, organic matter proxies, terrestrial rock origin metals) and compared to community structures observed during the dry season.

RESULTS

Microbiome biodiversity patterns of the dry season were destructured because of the runoff impact, and land-origin taxa were observed in the coastal areas. After the rainy event, different daily community dynamics were observed locally, with specific microbial taxa explaining these variabilities. Plume dispersal modeling revealed the extent of low salinity areas up to the coral reef area (16 km offshore), but a rapid (< 6 days) recovery to typical steady conditions of the lagoon's hydrology was observed. Conversely, during the same time, some biological components (microbial communities, Chl a) and biogeochemical components (particulate nickel, terrigenous organic matter) of the ecosystem did not recover to values observed during the dry season conditions.

CONCLUSION

The ecosystem resilience of subtropical ecosystems must be evaluated from a multidisciplinary, holistic perspective and over the long term. This allows evaluating the risk associated with a potential continued and long-term disequilibrium of the ecosystem, triggered by the change in the frequency and intensity of extreme climatic events in the era of planetary climatic changes.

The road forward to incorporate seawater microbes in predictive reef monitoring

Marine bacterioplankton underpin the health and function of coral reefs and respond in a rapid and sensitive manner to environmental changes that affect reef ecosystem stability. Numerous meta-omics surveys over recent years have documented persistent associations of opportunistic seawater microbial taxa, and their associated functions, with metrics of environmental stress and poor reef health (e.g. elevated temperature, nutrient loads and macroalgae cover). Through positive feedback mechanisms, disturbance-triggered heterotrophic activity of seawater microbes is hypothesised to drive keystone benthic organisms towards the limit of their resilience and translate into shifts in biogeochemical cycles which influence marine food webs, ultimately affecting entire reef ecosystems. However, despite nearly two decades of work in this space, a major limitation to using seawater microbes in reef monitoring is a lack of a unified and focused approach that would move beyond the indicator discovery phase and towards the development of rapid microbial indicator assays for (near) real-time reef management and decision-making. By reviewing the current state of knowledge, we provide a comprehensive framework (defined as five phases of research and innovation) to catalyse a shift from fundamental to applied research, allowing us to move from descriptive to predictive reef monitoring, and from reactive to proactive reef management.

Bioaccumulation and metabolic impact of environmental PFAS residue on wild-caught urban wetland tiger snakes (Notechis scutatus)

PFAS contamination of urban waters is widespread but understanding the biological impact of its accumulation is limited to humans and common ecotoxicological model organisms. Here, we combine PFAS exposure and bioaccumulation patterns with whole organism responses and omics-based ecosurveillance methods to investigate the potential impacts of PFAS on a top predator of wetlands, the tiger snake (Notechis scutatus). Tiger snakes (18 male and 17 female) were collected from four wetlands with varying PFAS chemical profiles and concentrations in Perth, Western Australia. Tiger snake livers were tested for 28 known PFAS compounds, and Σ28PFAS in liver tissues ranged between 322 ± 193 μg/kg at the most contaminated site to 1.31 ± 0.86 μg/kg at the least contaminated site. The dominant PFAS compound detected in liver tissues was PFOS. Lower body condition was associated with higher liver PFAS, and male snakes showed signs of high bioaccumulation whereas females showed signs of maternal offloading. Biochemical profiles of snake muscle, fat (adipose tissue), and gonads were analysed using a combination of liquid chromatography triple quadrupole (QqQ) and quadrupole time-of-flight (QToF) mass spectrometry methodologies. Elevated PFAS was associated with enriched energy production and maintenance pathways in the muscle, and had weak associations with energy-related lipids in the fat tissue, and lipids associated with cellular genesis and spermatogenesis in the gonads. These findings demonstrate the bioavailability of urban wetland PFAS in higher-order reptilian predators and suggest a negative impact on snake health and metabolic processes. This research expands on omics-based ecosurveillance tools for informing mechanistic toxicology and contributes to our understanding of the impact of PFAS residue on wildlife health to improve risk management and regulation.

Multiple-biomarkers show the importance of blue carbon to commercially important fishery species

Coastal blue carbon ecosystems (BCE) support nearshore food webs and provide habitat for many commercially important fish and crustacean species. However, the complex links between catchment vegetation and the carbon food-base of estuarine systems are difficult to disern. We employed a multi-biomarker approach (stable isotope ratios - δ¹³C and δ¹⁵N, fatty acid trophic markers - FATMs and metabolomics - central carbon metabolism metabolites) to test links between estuarine vegetation and the food sources available to commercially important crabs and fish occurring within the river systems of the near-pristine eastern coastline of the Gulf of Carpentaria, Australia. Stable isotope analysis confirmed the dietary importance of fringing macrophytes to consumer diet, but showed that this is modulated by their dominance along the riverbank. FATMs indicative of specific food sources further confirmed the differences among upper intertidal macrophytes (driven by concentrations of 16: 1ω7, 18:1ω9, 18:2ω6, 18:3ω3 & 22.0) and seagrass (driven by 18:2ω6, 18:3ω3). These dietary patterns were also reflected in the concentration of central carbon metabolism metabolites. Overall, our study demonstrates the congruence of different biomarker approaches to resolve biochemical links between blue carbon ecosystems and important nekton species, and provides fresh insights into the pristine tropical estuaries of northern Australia.

The founding charter of the Omic Biodiversity Observation Network (Omic BON)

Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

A review of omics-based PFAS exposure studies reveals common biochemical response pathways

Per and Polyfluoroalkyl Substances (PFAS) are a diverse group of man-made chemicals with a range of industrial applications and which are widespread in the environment. They are structurally diverse but comprise a common chemical feature of at least one (though usually more) perfluorocarbon moiety (-C_nF_2n-) attached to a functional group such as a carboxylic or sulphonic acid. The strength of the Carbon-Fluorine bond means the compounds do not break down easily and can thus bioaccumulate. PFAS are of high concern to regulators and the public due to their potential toxicity and high persistence. At high exposure levels, PFAS have been implicated in a range of harmful effects on human and environmental health, particularly problems in/with development, cholesterol and endocrine disruption, immune system function, and oncogenesis. However, most environmental toxicology studies use far higher levels of PFAS than are generally found in the environment. Additionally, since the type of exposure, the PFAS used, and the organisms tested all vary between studies, so do the results. Traditional ecotoxicology studies may thus not identify PFAS effects at environmentally relevant exposures. Here we conduct a review of omics-based PFAS exposure studies using laboratory ecotoxicological methodologies and environmentally relevant exposure levels and show that common biochemical response pathways are identified in multiple studies. A major pathway identified was the pentose phosphate shunt pathway. Such molecular markers of sublethal PFAS exposure will greatly benefit accurate and effective risk assessments to ensure that new PFAS regulations can consider the full effects of PFAS exposure on environmental and human health receptors.

Integration of Omics Approaches Enhances the Impact of Scientific Research in Environmental Applications

In the original article [...]

How 'omics technologies can drive plant engineering, ecosystem surveillance, human and animal health

'Omics describes a broad collection of research tools and techniques that enable researchers to collect data about biological systems at a very large, or near-complete, scale. These include sequencing of individual and community genomes (genomics, metagenomics), characterization and quantification of gene expression (transcriptomics), metabolite abundance (metabolomics), protein content (proteomics) and phosphorylation (phospho-proteomics), amongst many others. Though initially exploited as tools for fundamental discovery, 'omics techniques are now used extensively in applied and translational research, for example in plant and animal breeding, biomarker development and drug discovery. In this collection of reviews, we aimed to introduce readers to current and future applications of 'omics technologies to solve real-world problems.