eDNA-based bioassessment of coastal sediments impacted by an oil spill

Exploitation of environmental DNA (eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution

The rise in worldwide population has led to a noticeable spike in the production, consumption, and transportation of energy and food, contributing to elevated environmental pollution. Marine pollution is a significant global environmental issue with ongoing challenges, including plastic waste, oil spills, chemical pollutants, and nutrient runoff, threatening marine ecosystems, biodiversity, and human health. Pollution detection and assessment are crucial to understanding the state of marine ecosystems. Conventional approaches to pollution evaluation usually represent laborious and prolonged physical and chemical assessments, constraining their efficacy and expansion. The latest advances in environmental DNA (eDNA) are valuable methods for the detection and surveillance of pollution in the environment, offering enhanced sensibility, efficacy, and involvement. Molecular approaches allow genetic information extraction from natural resources like water, soil, or air. The application of eDNA enables an expanded evaluation of the environmental condition by detecting both identified and unidentified organisms and contaminants. eDNA methods are valuable for assessing community compositions, providing indirect insights into the intensity and quality of marine pollution through their effects on ecological communities. While eDNA itself is not direct evidence of pollution, its analysis offers a sensitive tool for monitoring changes in biodiversity, serving as an indicator of environmental health and allowing for the indirect estimation of the impact and extent of marine pollution on ecosystems. This review explores the potential of eDNA metabarcoding techniques for detecting and identifying marine pollutants. This review also provides evidence for the efficacy of eDNA assessment in identifying a diverse array of marine pollution caused by oil spills, harmful algal blooms, heavy metals, ballast water, and microplastics. In this report, scientists can expand their knowledge and incorporate eDNA methodologies into ecotoxicological research.

Environmental DNA unveiling the fish community structure and diversity features in the Yangtze River basin

Fish, as top predators in aquatic ecosystems, play an important role in maintaining the structure and functioning of these ecosystems, making their diversity a topic of great interest. This study focused on the Yangtze River Basin to investigate the fish community structure and diversity using environmental DNA (eDNA) technology. The results showed that a total of 71616 fish operational taxonomic units (OTUs) and 90 fish belonging to 23 families were detected, with the Cyprinidae family being the dominant group, followed by the Cobitidae, Amblycipitidae, etc. Compared to historical traditional morphological fish surveys, the quantity of fish detected using eDNA was relatively low, but the overall distribution pattern of fish communities was generally consistent. The highest fish Shannon-Wiener diversity index in the Yangtze River Basin sites reaches 2.60 with an average value of 1.25. The fish diversity index was higher in the downstream compared to the middle and upstream regions, and there were significant differences among different sampling sites. Significant environmental factors influencing α-diversity included chlorophyll-a, chemical oxygen demand, dissolved oxygen, total nitrogen, and elevation. Non-metric multidimensional scaling (NMDS) analysis revealed significant differences in fish community composition between the upstream and middle/lower reaches of the Yangtze River, while the composition of fish communities in the middle and lower reaches was more similar. Redundancy analysis (RDA) indicated that total organic carbon (TOC) was positively correlated with fish community distribution in the upstream, while water temperature and NO3-N were negatively correlated with fish distribution in the upstream. NH3-N and CODMn were negatively correlated with fish distribution in the middle and downstream regions, indicating a relatively severe water pollution in these areas. Additionally, fish communities in the Yangtze River displayed a typical distance decay pattern.

Emerging studies on oil pollution biomonitoring: A systematic review

In the last decade, several methods were applied to monitor the impact of oil pollution on marine organisms. Recent studies showed an eminent need to standardize these methods to produce comparable results. Here we present the first thorough systematic review of the literature on oil pollution monitoring methods in the last decade. The literature search resulted on 390 selected original articles, categorized according to the analytical method employed. Except for Ecosystem-level analyses, most methods are used on short-term studies. The combination of Biomarker and Bioaccumulation analysis is the most frequently adopted strategy for oil pollution biomonitoring, followed by Omic analyses. This systematic review describes the principles of the most frequently used monitoring tools, presents their advantages, limitations, and main findings and, as such, could be used as a guideline for future researches on the field.

Environmental DNA as an emerging tool in botanical research

Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.

Assessment of biological community in riparian zone contaminated by PAHs: Linking source apportionment to biodiversity

Riparian zone, an important land-water interface, plays an essential role in maintaining the ecological health of rivers, whereas the effects of Polycyclic aromatic hydrocarbons (PAHs) on the health of biological communities in riparian groundwater remain undetermined. To understand the responses of multiple communities to environmental variables, the distribution and ecosystem risk of 16 PAHs have been investigated in the Beiluo River, China. The distribution of multiple communities in riparian groundwater was investigated by environmental DNA metabarcoding, including 16S rRNA, 18S rRNA, and COI gene sequencing for bacteria, microbial eukaryotes (including algae, fungi, and protozoa), and metazoan, respectively, followed by correlation analysis between multiple communities and PAH contamination levels. The concentration of PAHs in the Beiluo River ranged largely from 35.32 to 728.59 ng/L. Here, the Shannon's diversity index of bacteria (Firmicutes) decreased possibly due to the occurrence of Pyrene, which mainly derives from coal and biomass combustion. Furthermore, the reduced richness of fungi (Ascomycota, Basidiomycota) and algae (Chlorophyta, Chrysophyceae) can be attributed to the presence of medium molecular weight (MMW) PAHs (Pyrene, Benz(a)anthracene, Chrysene), and low molecular weight (LMW) PAHs (Naphthalene, Fluorene, Phenanthrene). The richness and Shannon's diversity index of metazoan (Arthropoda) were promoted owing to MMW PAHs (Chrysene, Fluoranthene) generated from coal and biomass combustion and traffic emission. The ecological risk of PAHs in the groundwater environment of the Beiluo River was characterized as low to medium, where LMW and MMW PAHs posed higher risk than the high molecular weight (HMW) compounds. Overall, this study provides insights into the structures of riparian multi-biological communities altered by PAHs.

Environmental DNA-based profiling of benthic bacterial and eukaryote communities along a crude oil spill gradient in a coral reef in the Persian Gulf

Coral reef ecosystems in the Persian Gulf are frequently exposed to crude oil spills. We investigated benthic bacterial and eukaryote community structures at such coral reef sites subjected to different degrees of polycyclic aromatic hydrocarbon (PAH) pollution using environmental DNA (eDNA) metabarcoding. Both bacterial and eukaryote communities responded with pronounced shifts to crude oil pollution and distinguished control sites, moderately and heavily impacted sites with significant confidentiality. The observed community patterns were predominantly driven by Alphaproteobacteria and metazoans. Among these, we identified individual genera that were previously linked to oil spill stress, but also taxa, for which a link to hydrocarbon still remains to be established. Considering the lack of an early-warning system for the environmental status of coral reef ecosystems exposed to frequent crude-oil spills, our results encourage further research towards the development of an eDNA-based biomonitoring tool that exploits benthic bacterial and eukaryote communities as bioindicators.

Environmental DNA as a tool for biodiversity monitoring in aquatic ecosystems – a review

The monitoring of changes in aquatic ecosystems due to anthropogenic activities is of utmost importance to ensure the health of aquatic biodiversity. Eutrophication in water bodies due to anthropogenic disturbances serves as one of the major sources of nutrient efflux and consequently changes the biological productivity and community structure of these ecosystems. Habitat destruction and overexploitation of natural resources are other sources that impact the equilibrium of aquatic systems. Environmental DNA (eDNA) is a tool that can help to assess and monitor aquatic biodiversity. There has been a considerable outpour of research in this area in the recent past, particularly concerning conservation and biodiversity management. This review focuses on the application of eDNA for the detection and relative quantification of threatened, endangered, invasive and elusive species. We give a special emphasis on how this technique developed in the past few years to become a tool for understanding the impact of spatial-temporal changes on ecosystems. Incorporating eDNA based biomonitoring with advances in sequencing technologies and computational abilities had an immense role in the development of different avenues of application of this tool.

Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.

Dynamics of microbiotic patterns reveal surface water groundwater interactions in intermittent and perennial streams

Exchange between groundwater (GW), hyporheic zone waters (HZ) and surface waters (SW) is critical for water quality, quantity, and the ecological health and functioning of all three ecosystems. Hydrological exchange is particularly important in intermittent creeks, such as in the Murray Darling Basin, Australia, where stream reaches shift from losing to gaining depending on the volume of surface flows. In this study we used hydrochemistry to identify SW-GW exchange and combined this with eDNA data to analyse the response of eukaryote and prokaryote communities to differing flow conditions within intermittent and perennial stream reaches. Our study suggested that SW and GW microbial communities were only around 30% similar. Differences in microbiota between SW, HZ and GW habitats were driven by changes in relative abundances of surface water dominant organisms (such as those capable of photosynthesis) as well as anaerobic taxa typical of GW environments (e.g., methanogens), with GW and HZ microbial communities becoming increasingly different to those in SW as flow ceased in intermittent creeks. Fine-scale hydrologic changes were identified through microbial communities in the perennial Maules Creek, indicating the importance of GW-SW exchange to biotic communities. This study highlights the importance of flow in shaping microbial communities and biogeochemical cycling within intermittent creeks and their connected alluvial aquifers. Our results suggest that microbiota may prove a useful indicator of SW-GW exchange, and in some circumstances, may be more sensitive in demonstrating fine-scale changes in SW-GW interactions than water chemistry. This knowledge furthers our understanding of GW-SW exchange and its impacts on ecological health.

Natural attenuation of oil in marine environments: A review

Natural attenuation is an important process for oil spill management in marine environments. Natural attenuation affects the fate of oil by physical, chemical, and biological processes, which include evaporation, dispersion, dissolution, photo-oxidation, emulsification, oil particle aggregation, and biodegradation. This review examines the cumulative knowledge regarding these natural attenuation processes as well as their simulation and prediction using modelling approaches. An in-depth discussion is provided on how oil type, microbial community and environmental factors contribute to the biodegradation process. It describes how our understanding of the structure and function of indigenous oil degrading microbial communities in the marine environment has been advanced by the application of next generation sequencing tools. The synergetic and/or antagonist effects of oil spill countermeasures such as the application of chemical dispersants, in-situ burning and nutrient enrichment on natural attenuation were explored. Several knowledge gaps were identified regarding the synergetic and/or antagonistic effects of active response countermeasures on the natural attenuation/biodegradation process. This review highlighted the need for field data on both the effectiveness and potential detrimental effects of oil spill response options to support modelling and decision-making on their selection and application.

Agricultural practices linked to shifts in groundwater microbial structure and denitrifying bacteria

Irrigation enhances the connectivity between the surface and groundwater by facilitating the transport of energy sources and oxygen. When combined with fertilisers, the impact on groundwater microbial communities and their interactions with nitrogen cycling in aquifers is poorly understood. This study examines the impact of different landuses (irrigated and non-irrigated) on groundwater microbial communities. A total of 38 wells accessing shallow aquifers in three sub-catchments of the Murray Darling Basin, Australia, were sampled for water chemistry and microbial community structure using environmental DNA (eDNA) techniques. All sub-catchments showed evidence of intense irrigation and groundwater contamination with total nitrogen, nitrates and phosphorus concentrations often well above background, with total nitrogen concentrations up to 70 mg/L and nitrate concentration up to 18 mg/L. Across sub-catchments there was high microbial diversity, with differences in community structure and function between catchments and landuses. Of the 1100 operational taxonomic units (OTUs) recorded, 47 OTUs were common across catchments with species from Woesearchaeota, Nitrospirales, Nitrosopumilales and Acidobacter taxonomic groups contributing greatly to groundwater microbial communities. Within non-irrigated sites, groundwaters contained similar proportions of nitrifying and denitrifying capable taxa, whereas irrigated sites had significantly higher abundances of microbes with nitrifying rather than denitrifying capabilities. Microbial diversity was lower in irrigated sites in the Macquarie catchment. These results indicate that irrigated landuses impact microbial community structure and diversity within groundwaters and suggest that the ratios of denitrifying to nitrifying capable microbes as well as specific orders (e.g., Nitrososphaerales) may be useful to indicate long-term nitrogen contamination of groundwaters. Such research is important for understanding the biogeochemical processes that are key predictors of redox state and contamination of groundwater by N species and other compounds. This will help to predict human impacts on groundwater microbial structure, diversity, and ecosystem functions, aiding the long-term management groundwater resources.

Insight into Bacterial Community Responses to Polycyclic Aromatic Hydrocarbons and the Degradation Potentials of Three Bacterial Isolates in Seagrass Halophila ovalis Sediments

Seagrass meadows constitute a prestigious ecosystem in the marine environment, providing valuable ecological and commercial services. Among the various causes, pollutions are considered one of the significant reasons for seagrass decline globally. This study investigates the impacts of polycyclic aromatic hydrocarbons mixture (pyrene, phenanthrene, and fluorene) on bacterial communities in Halophila ovalis sediments. The seagrass sediment bacterial microbiome was evaluated in a batch culture experiment by Illumina MiSeq sequencing. Culture-able bacterial strains were isolated and characterized by 16S rRNA gene sequencing. The results demonstrated an excellent alpha diversity in the original sediments with a Shannon index of (8.078) compared to the subsequent control group (5.908) and PAH-treated group (PAH-T) (4.916). Three phyla, Proteobacteria, Firmicutes, and Bacteroidetes, were detected in high abundance in the control and PAH-T groups. However, a significant difference (P < 0.05) was observed at the genus level between control and PAH-T group bacterial consortia. Pseudomonas, Mycobacterium, Idiomarina, Hydrogenophaga, Alteromonas, Sphingobacterium, and several others were highly abundant in PAH-T groups. Most of the culture-able isolates recovered in this study showed the closest resemblance to previously identified hydrocarbon-degrading bacteria. Among the three strains, Mix-16 (Citricoccus yambaruensis) and Mix-20 (Gordonia rubripertincta) showed a higher degradation of PAHs than Mix-19 (Isoptericola halotolerans) in the monoculture experiment. The most increased degradation of PAHs was recorded in the co-culture experiment. The present work revealed that PAHs could act as environmental stress and can influence bacterial community succession. Moreover, the co-culture strategy significantly enhanced the biodegradation of PAHs.

Environmental DNA reveals aquatic biodiversity of an urban backwater area, southeast coast of India

Strong conservation management needs comprehensive data on biodiversity. Rapid methods that document aquatic biodiversity or assess the health condition of an ecosystem remain scarce. Herein, we have performed a metagenomics study on environmental DNA (eDNA) collected from an urban backwater area - Muttukadu, located in the southeast coast of India. Shotgun metagenomics approach using Illumina®NextSeq500 sequencing yielded 88.4 million raw reads. The processed data was assigned as 80% prokaryotes, 0.4% eukaryotes, ~2% viruses, and ~17% remain unknown. This approach has the potential to identify small micro-eukaryote, unseen species from both estuarine and marine environments. We have identified 156 eukaryote organisms represented from 21 phyla and 112 families, including those that are of conservational significance and ecological importance. Furthermore, our data also demonstrated the presence of pathogenic microorganisms due to sewage mixing with the backwaters. Given its sensitivity, we suggest this approach for an initial assessment of biodiversity structure in an ecosystem for the biomonitoring program.

Biotic signals associated with benthic impacts of salmon farms from eDNA metabarcoding of sediments

Environmental DNA (eDNA) metabarcoding can rapidly characterize the composition and diversity of benthic communities, thus it has high potential utility for routine assessments of benthic impacts of marine finfish farming. In this study, 126 sediment grab samples from 42 stations were collected at six salmon farms in British Columbia, Canada. Benthic community changes were assessed by both eDNA metabarcoding of metazoans and macrofaunal polychaete surveys. The latter was done by analysing 11,466 individuals using a combination of morphology-based taxonomy and DNA barcoding. Study objectives were to: (i) compare biotic signals associated with benthic impacts of salmon farming in the two data sources, and (ii) identify potential eDNA indicators to facilitate monitoring in Canada. Alpha diversity parameters were consistently reduced near fish cage edge and negatively correlated with pore-water sulphide concentration, with coefficients ranging from -0.62 to -0.48. Although Polychaeta are a common indicator group, the negative correlation with pore-water sulphide concentration was much stronger for Nematoda OTU richness (correlation coefficient: -0.86) than for Polychaeta (correlation coefficient: -0.38). Presence/absence of Capitella generally agreed well between the two methods despite that they differed in the volume of sediments sampled and the molecular marker used. Multiple approaches were used to identify OTUs related to organic enrichment statuses. We demonstrate that eDNA metabarcoding generates biotic signals that could be leveraged for environmental assessment of benthic impacts of fish farms in multiple ways: both alpha diversity and Nematoda OTU richness could be used to assess the spatial extent of impact, and OTUs related to organic enrichment could be used to develop local biotic indices.

Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates

Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs.

Characteristics of long-term changes in microbial communities from contaminated sediments along the west coast of South Korea: Ecological assessment with eDNA and physicochemical analyses

The environmental DNA (eDNA) metabarcoding was applied to assess benthic ecological health in the west coast of South Korea by investigating a long-term microbial community change (2015-17). The ecological interaction among microorganisms, from phylum to family level, and their associations to environmental variables across the five regions were highlighted. As part of the study, the available chemistry and toxicological data in the regions during the monitoring periods were incorporated into an integrated sediment triad assessment. The bacterial communities were dominated by Proteobacteria (34.2%), Bacteroidetes (13.8%), and Firmicutes (10.8%). Proteobacteria and Bacteroidetes dominated consistently across regions and years, while Firmicutes and Cyanobacteria significantly varied by region and years (p < 0.05). The abundance of this phylum declined over time with the increasing abundance of Cyanobacteria, indicating their independent interactions to certain environmental changes. Planctomycetes and Gemmatimonadetes linked to some contaminants (ΣPAHs and Cu), implying indicator taxa. Overall, eDNA-based microbial community analysis combined with exposures of contaminants and responses of microorganisms is a promising strategy for the assessment of benthic ecological health in contaminated sediments from coastal waters.

Beyond Thresholds: A Holistic Approach to Impact Assessment Is Needed to Enable Accurate Predictions of Environmental Risk from Oil Spills

The risk assessment for the environmental impact of oil spills in Australia is often conducted in part using a combination of spill mapping and toxicological thresholds derived from laboratory studies. While this process is useful in planning operational responses, such as where to position equipment stockpiles and whether to disperse oil, and can be used to identify areas near the spill site where impacts are likely to occur, it cannot accurately predict the environmental consequences of an oil spill or the ecosystem recovery times. Evidence of this disconnect between model predictions and observed impacts is the lack of a profound effect of the Deepwater Horizon wellhead blowout on recruitment to fisheries in the northern Gulf of Mexico, contrary to the predictions made in the Natural Resources Damage Assessment and despite the occurrence of impacts of the spill on marine mammals, marshes, and deep water ecosystems. The incongruity between predictions made with the current approach using threshold monitoring and impacts measured in the field results from some of the assumptions included in the oil spill models. The incorrect assumptions include that toxicity is acute, results from dissolved phase exposure, and would be readily reversible. The toxicity tests from which threshold models are derived use members of the ecosystem that are easily studied in the lab but may not represent the ecosystem as a whole. The test species are typically highly abundant plankton or planktonic life stages, and they have life histories that account for rapid changes in environmental conditions. As a consequence, these organisms recover quickly from an oil spill. The interdependence of ecosystem components, including the reliance of organisms on their microbiomes, is often overlooked. Additional research to assess these data gaps conducted using economically and ecologically relevant species, especially in Australia and other understudied areas of the world, and the use of population dynamic models, will improve the accuracy of environmental risk assessment for oil spills. Integr Environ Assess Manag 2020;16:813-830. © 2020 SETAC.

qPCR-based assessment of microfaunal indicators of oil for monitoring benthos around oil and gas platforms

Today's benthic offshore biological monitoring of oil & gas (O&G) activities relies on macrofauna taxa enumeration. For the future, analysis of DNA isolated directly from sediments holds great potential for multi-trophic biodiversity surveys and the monitoring of a larger spectrum of benthic taxa, including micro-fauna. Here, we evaluate more specifically the potential of microfauna-specific gene quantification in relation to both petroleum-related discharge compounds and other seafloor environmental properties. We carried out this evaluation using sediment samples collected at drilling Region III on the Norwegian continental shelf where DNA metabarcoding of eukaryotic diversity was already performed. Generally, the quantification of microfauna indicator taxa related well to the gradient of contamination on the seafloor. Contrary to eukaryotic Euplotida, metabarcoding data and qPCR numbers for indicative prokaryotic taxa showed the same relationship to offshore contaminants (both showed positive relationship). We found absolute numbers of SSU rRNA gene copies of (1) Dinophyceae, Bacillariophyceae and Alcanivorax were correlated with the level of petroleum-related compounds but not with other environmental variables, (2) bacteria closely related to Shewanella were correlated with the concentration of Ba, PAH, as well to percent of gravel, (3) Desulfobacteriales correlated with petroleum-related contaminants, but as well with percent of gravel and grain size. Findings from our study suggest that biomonitoring surveys of O&G activities on benthos could benefit from quantification of specific micro-fauna indicators that is simpler and faster than the methods currently used for impact assessment of benthos.

Toward Sustainable Environmental Quality: Priority Research Questions for Asia

Environmental and human health challenges are pronounced in Asia, an exceptionally diverse and complex region where influences of global megatrends are extensive and numerous stresses to environmental quality exist. Identifying priorities necessary to engage grand challenges can be facilitated through horizon scanning exercises, and to this end we identified and examined 23 priority research questions needed to advance toward more sustainable environmental quality in Asia, as part of the Global Horizon Scanning Project. Advances in environmental toxicology, environmental chemistry, biological monitoring, and risk-assessment methodologies are necessary to address the adverse impacts of environmental stressors on ecosystem services and biodiversity, with Asia being home to numerous biodiversity hotspots. Intersections of the food-energy-water nexus are profound in Asia; innovative and aggressive technologies are necessary to provide clean water, ensure food safety, and stimulate energy efficiency, while improving ecological integrity and addressing legacy and emerging threats to public health and the environment, particularly with increased aquaculture production. Asia is the largest chemical-producing continent globally. Accordingly, sustainable and green chemistry and engineering present decided opportunities to stimulate innovation and realize a number of the United Nations Sustainable Development Goals. Engaging the priority research questions identified herein will require transdisciplinary coordination through existing and nontraditional partnerships within and among countries and sectors. Answering these questions will not be easy but is necessary to achieve more sustainable environmental quality in Asia. Environ Toxicol Chem 2020;39:1485-1505. © 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Integrated assessment of west coast of South Korea by use of benthic bacterial community structure as determined by eDNA, concentrations of contaminants, and in vitro bioassays

During the past few decades, contamination of sediments by persistent toxic substances (PTSs) has been observed in estuarine and coastal areas on the west coast of South Korea. The contaminants are suspected to cause toxicities in aquatic biota, but little is known about their ecological effects, particularly on benthic microbial communities. In this study, an eDNA-based assessment was applied along with classic assessments of exposure, such as chemistry and in vitro bioassays, to evaluate condition of benthic bacterial communities subjected to PTSs. Two strategies were adopted for the study. One was to conduct a comprehensive assessment in space (by comparing seawater and freshwater sites at five coastal regions) and in time (by following change over a 5-y period). Although we found that bacterial composition varied among and within years, some phyla, such as Proteobacteria (28.7%), Actinobacteria (13.1%), Firmicutes (12.7%), and Chloroflexi (12.5%) were consistently dominated across the study regions. Certain bacterial groups, such as Firmicutes and Verrucomicrobia have been linked to contamination at some sites in the study area and at specific points in time. Bacterial communities were not significantly correlated with salinity or AhR- and ER-mediated potencies, whereas concentrations of PAHs, APs, and certain metals (Cd and Hg) exhibited significant associations to the structure of bacterial communities at the phylum level. In fact, the relative abundance of microbes in the phylum Planctomycetes was significantly and negatively correlated with concentrations of PAHs and metals. Thus, the relative abundance of Planctomycetes could be used as an indicator of sedimentary contamination by PAHs and/or metals. Based on our correlation analyses, Cd and ER-mediated potencies were associated more with bacterial abundances at the class taxonomic level than were other PTSs and metals. Overall, the eDNA-based assessment was useful by augmenting more traditional measures of exposure and responses in a sediment triad approach and has potential as a more rapid screening tool.

Multiple evaluation of the potential toxic effects of sediments and biota collected from an oil-polluted area around Abu Ali Island, Saudi Arabia, Arabian Gulf

After the Gulf War Oil Spill, there have been many investigations about distributions of oil-derived pollutants nearby areas, but lacking in ecotoxicological assessment. We evaluated the potential toxicity of asphalt mats, sediments, and biota (polychaetes, chitons, snapping shrimps, and crabs) by combining two bioassays (H4IIE-luc and Vibrio fischeri) and in situ microbial community (eDNA). Samples were collected from Abu Ali Island, and organic extracts were bioassayed and further fractionated according to the chemical polarity using silica gel column. Great aryl hydrocarbon receptor (AhR)-mediated potencies and inhibition of bioluminescence were mainly found in aromatics (F2) and saturates (F1) fractions of asphalt mat and sediments, respectively, while great toxicological responses in biota samples were found in resins and polar (F3) fraction. We also confirmed that potential toxicities of biota were species-specific; great AhR-mediated potencies were found in polychaetes and great bioluminescence inhibitions were found in crabs. In microbial communities, most genera (up to 90%) were associated with polycyclic aromatic hydrocarbons (PAHs)-degrading bacteria, supporting that PAHs are the primary stressors of the benthic community around Abu Ali Island. The present study provides useful information on the contamination status, risk assessment of environmental matrices and benthic organisms in Abu Ali Island.

Environmental DNA: An Emerging Tool in Ecological Assessment

Environmental DNA (eDNA), as a recent research hotspot in environmental science, the use of eDNA in biological monitoring has the advantages of sensitivity and time/labor saving. The eDNA technology combined with scientific advancement has been applied in investigations of target species (such as invasive species, endangered species and other rare species), biomass, and biodiversity. In addition, ecotoxicology studies and environmental pollution impact assessments based on the development of eDNA technology have gradually emerged in recent years. In this article, we summarizes the application of eDNA in ecological assessment, include species diversity assessment and chemical contamination impacts assessment, provide guiding questions for study design. We additionally discuss current challenges associated with eDNA. Finally, looking to the future, we discuss the opportunities of eDNA technology in environmental protein, environmental sample processor and ecogenomic sensors.

Temporal variation of eukaryotic community structures in UASB reactor treating domestic sewage as revealed by 18S rRNA gene sequencing

Eukaryotes are important components of ecosystems in wastewater treatment processes. However, little is known about eukaryotic community in anaerobic wastewater treatment systems. In this study, eukaryotic communities in an up flow anaerobic sludge blanket (UASB) reactor treating domestic sewage during two years of operation were investigated using V4 and V9 regions of 18S rRNA gene for amplicon sequencing. In addition, activated sludge and influent sewage samples were also analyzed and used as the references for aerobic eukaryotic community to characterize anaerobic eukaryotes. The amplicon sequence V4 and V9 libraries detected different taxonomic groups, especially from the UASB samples, suggesting that commonly used V4 and V9 primer pairs could produce a bias for eukaryotic communities analysis. Eukaryotic community structures in the UASB reactor were influenced by the immigration of eukaryotes via influent sewage but were clearly different from the influent sewage and activated sludge. Multivariate statistics indicated that protist genera Cyclidium, Platyophrya and Subulatomonas correlated with chemical oxygen demand and suspended solid concentration, and could be used as bioindicators of treatment performance. Uncultured eukaryotes groups were dominant in the UASB reactor, and their physiological roles need to be examined to understand their contributions to anaerobic processes in future studies.

A state-of-the-art model for spatial and stochastic oil spill risk assessment: A case study of oil spill from a shipwreck

Oil spills are serious environmental issues that potentially can cause adverse effects on marine ecosystems. In some marine areas, like the Baltic Sea, there is a large number of wrecks from the first half of the 20th century, and recent monitoring and field work have revealed release of oil from some of these wrecks. The risk posed by a wreck is governed by its condition, hazardous substances contained in the wreck and the state of the surrounding environment. Therefore, there is a need for a common standard method for estimating the risks associated with different wrecks. In this work a state-of-the-art model is presented for spatial and stochastic risk assessment of oil spills from wrecks, enabling a structured approach to include the complex factors affecting the risk values. A unique feature of this model is its specific focus on uncertainty, facilitating probabilistic calculation of the total risk as the integral expected sum of many possible consequences. A case study is performed in Kattegat at the entrance region to the Baltic Sea to map the risk from a wreck near Sweden. The developed model can be used for oil spill risk assessment in the marine environment all over the world.

Ammonium loading disturbed the microbial food webs in biofilms attached to submersed macrophyte Vallisneria natans

The knowledge about the impacts of ammonium loading on microbial food webs in biofilms attached to submersed macrophytes is limited. In the present study, Illumina sequencing method was employed to investigate bacterial and eukaryotic communities in biofilms attached to leaves of Vallisneria natans (V. natans) exposed to 1-16 mg L^-1 NH₄⁺-N for 10 days, and 8 mg L^-1 NH₄⁺-N for 21 days. Ammonium loading stimulated biofilms growth, enhanced the relative abundance of nitrifying genus Nitrospira and several denitrifying genera. Eukaryotic kingdom Metazoa, Viridiplantae, Chromista, Fungi and super group SARNU (Stramenopiles, Alveolata, Rhizaria, Nucleariidae and Fonticula group and unknown eukaryotes) were obtained. Relative abundance of Metazoa decreased with the increased ammonium concentration and exposure time. Redundancy analysis revealed that ammonium, dissolved oxygen (DO) and pH had a key role in determining microbial community structure. Network analyses revealed that there were complex interactions including feeding, parasitism and predatism among organism in biofilms, and the microbial food webs were disturbed by inhibiting metazoan growth but stimulating bacteria and algae growth. These results suggest that ammonium-disturbed microbial food webs in biofilms may contribute to the growth of biofilms and algae, and thus contribute to the decline of submersed macrophyte and provide "algal seeds" for the algae burst in water column. These data will be helpful in understanding the macrophytic region transform into algal region in water column polluted by ammonium.