Ecogenomic responses of benthic communities under multiple stressors along the marine and adjacent riverine areas of northern Bohai Sea, China

Deciphering the spatial distribution and function profiles of soil bacterial community in Liao River estuarine wetland, Northeast China

Soil microbes play vital roles in estuarine wetlands. Understanding the soil bacterial community structure and function profiles is essential to reveal the ecological functions of microbes in estuarine wetlands. Herein, soil samples were collected from Liao River estuarine wetland, Northeast China, along the river to the estuarine mouth, and soil bacterial communities were explored. Results showed that soil physiochemical properties, bacterial community structure and functions exhibited distinct variations influenced by geographical location. Bacterial phyla in soils were dominated by Proteobacteria and Bacteroidetes, while Gillisia and Woeseia were the predominant genera. Soil pH, electrical conductivity and nitrogen-related nutrients were the important factors affecting bacterial community structure. Based on PICRUSt prediction, the genes related to metabolism of nitrogen, sulfur and methane showed spatial distribution patterns, and the abundances of most biomarker genes increased as the distance from estuarine mouth extended. These findings could enrich the understanding of soil microbiome in estuarine wetlands.

Occurrence of OCPs & PCBs and their effects on multitrophic biological communities in riparian groundwater of the Beiluo River, China

Persistent Organic Pollutants (POPs) may exert adverse effects on human and ecosystem health. However, as an ecologically fragile zone with strong interaction between river and groundwater, the POPs pollution in the riparian zone has received little attention. The goal of this research is to examine the concentrations, spatial distribution, potential ecological risks, and biological effects of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in the riparian groundwater of the Beiluo River, China. The results showed that the pollution level and ecological risk of OCPs in riparian groundwater of the Beiluo River were higher than PCBs. The presence of PCBs (Penta-CBs, Hexa-CBs) and CHLs, respectively, may have reduced the richness of bacteria (Firmicutes) and fungi (Ascomycota). Furthermore, the richness and Shannon's diversity index of algae (Chrysophyceae and Bacillariophyta) decreased, which could be linked to the presence of OCPs (DDTs, CHLs, DRINs), and PCBs (Penta-CBs, Hepta-CBs), while for metazoans (Arthropoda) the tendency was reversed, presumably as a result of SULPHs pollution. In the network analysis, core species belonging to bacteria (Proteobacteria), fungi (Ascomycota), and algae (Bacillariophyta) played essential roles in maintaining community function. Burkholderiaceae and Bradyrhizobium can be considered biological indicators of PCBs pollution in the Beiluo River. Note that the core species of interaction network, playing a fundamental role in community interactions, are strongly affected by POPs pollutants. This work provides insights into the functions of multitrophic biological communities in maintaining the stability of riparian ecosystems through the response of core species to riparian groundwater POPs contamination.

Evidence that offshore wind farms might affect marine sediment quality and microbial communities

Offshore wind power is a typical example of clean energy production and plays a critical role in achieving carbon neutrality. Offshore wind farms can have an impact on the marine environment, especially sedimentary environments, but their influence on sediments remain largely unknown. This study, which uses the control-impact principle to define different areas, investigated the characteristics of marine sediments under the Putidao offshore wind farm in Bohai Bay, China. We used chemical and microbiological observations to evaluate sediment quality and microbial community structure. According to both the geo-accumulation index (I_geo) and contamination factor (CF) indexes, copper, chromium and zinc were the major contaminants in the offshore wind farm sediments. The pollution load index (PLI) index showed that the various sites on the wind farm were only lightly polluted compared with baseline values. Closer to the wind farm's center, the metal concentrations started to rise. The physicochemical features of the sediments could better explain changes in the microorganisms present, and screening the microbiomes showed a correlation with heavy metal levels, linking the relative abundance of microorganisms to the sediment quality index. This comprehensive study fills a knowledge gap in China and adds to our understanding of how to assess the sedimentary environments of offshore wind farms.

eDNA metabarcoding revealed differential structures of aquatic communities in a dynamic freshwater ecosystem shaped by habitat heterogeneity

Freshwater ecosystems have been threatened by complicated disturbances from both natural and anthropogenic variables, especially in dynamic and complex river basins. The environmental DNA (eDNA)-based approach provides a broader spectrum and higher throughput way of biomonitoring for biodiversity assessment compared with traditional morphological survey. Most eDNA metabarcoding studies have been limited to a few specific taxa/groups and habitat scopes. Here we applied the eDNA metabarcoding to characterize the structures and spatial variations of zooplankton and fish communities among different habitat types in a highly dynamic and complex freshwater ecosystem of the Daqing River basin (DRB). The results showed that varied species spectra of zooplankton and fish communities were identified and unique dominant species occurred across habitats. Additionally, markedly spatial distributions of biotic community structures were observed in areas with different habitat characteristics. Natural variables, including geographic distances and gradient ratio, as well as anthropogenic factors of chemical oxygen demand (COD) and organic chemicals demonstrated significant effects but different outcomes on the structures of zooplankton and fish communities. Moreover, the relative abundances of specific aquatic taxa were associated with the gradient of particular environmental variables. This case study verified the distribution patterns and differentiation mechanisms of biotic communities under habitat heterogeneity could be captured by application of eDNA biomonitoring. And habitat-specific and even species-specific environmental stressors would be diagnosed for improving management of complex river basins.

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.

Seasonal variations of soil bacterial communities in Suaeda wetland of Shuangtaizi River estuary, Northeast China

Estuarine wetland is the transitional interface linking terrestrial with marine ecosystems, and wetland microbes are crucial to the biogeochemical cycles of nutrients. The soil samples were collected in four seasons (spring, S1; summer, S2; autumn, S3; and winter, S4) from Suaeda wetland of Shuangtaizi River estuary, Northeast China, and the variations of bacterial community were evaluated by high-throughput sequencing. Soil properties presented a significant seasonal change, including pH, carbon (C) and total nitrogen (TN), and the microbial diversity, richness and structure also differed with seasons. Canonical correspondence analysis (CCA) and Mantel tests implied that soil pH, C and TN were the key factors structuring the microbial community. Gillisia (belonging to Bacteroidetes) and Woeseia (affiliating with Gammaproteobacteria) were the two primary components in the rhizosphere soils, displaying opposite variations with seasons. Based on PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) prediction, the xenobiotics biodegradation related genes exhibited a seasonal decline, while the majority of biomarker genes involved in nitrogen cycle showed an ascending trend. These findings could advance the understanding of rhizosphere microbiota of Suaeda in estuarine wetland.

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.

Development of the transcriptome for a sediment ecotoxicological model species, Chironomus dilutus

Chironomus dilutus is a prominent model species in conventional sediment toxicity testing and sediment contamination diagnosis. However, lack of genomic data significantly limited its application in identifying toxicological mode of action (MOA) and molecular biomarkers of toxicants. Here the transcriptome of C. dilutus in full life span and both sexes (1st, 2nd, 3rd and 4th instar larvae, pupae, and adults) were developed and temporal gene expression across adjacent life stages were investigated to understand the regulation of development. Furthermore, transcriptional response of Midges (the 4th instar larvae) exposed to chemicals of different MOAs (CdCl₂, nonylphenol and triclosan) were profiled based on the reference transcriptome. Consequently, a complete transcriptome of 31132 unigenes with N50 of 3117bp, covering 98.8% of the arthropod single-copy orthologs were assembled. While 364 genes were differentially expressed among adjacent larval stages, 7142 and 2127 of transcripts were significantly changed for the transition of larvae-pupae and pupae-adults, respectively. Finally, chemical-specific gene expression profile were identified in the midges, showed its potential in classifying distinct contaminants. Overall, the comprehensive transcriptome of C. dilutus developed here could not only facilitate the mechanistic understanding of environmental toxicants during critical life stage of aquatic insects, but also provide molecular diagnostic tools in sediment ecotoxicology.

Changes in Microbial Community Structures under Reclaimed Water Replenishment Conditions

Using reclaimed water as a resource for landscape water replenishment may alleviate the major problems of water resource shortages and water environment pollution. However, the safety of the reclaimed water and the risk of eutrophication caused by the reclaimed water replenishment are unclear to the public and to the research community. This study aimed to reveal the differences between natural water and reclaimed water and to discuss the rationality of reclaimed water replenishment from the perspective of microorganisms. The microbial community structures in natural water, reclaimed water and natural biofilms were analyzed, and the community succession was clarified along the ecological niches, water resources, fluidity and time using 16S rRNA gene amplicon sequencing. Primary biofilms without the original community were added to study the formation of microbial community structures under reclaimed water acclimation. The results showed that the difference caused by ecological niches was more than those caused by the fluidity of water and different water resources. No significant difference caused by the addition of reclaimed water was found in the microbial diversity and community structure. Based on the results of microbial analysis, reclaimed water replenishment is a feasible solution that can be used for supplying river water.

Bacterial community structure and function in soils from tidal freshwater wetlands in a Chinese delta: Potential impacts of salinity and nutrient

Microorganisms in tidal freshwater wetlands affect biogeochemical cycling of nutrients, but the structures and functions of the wetland communities change due to natural and anthropogenic stresses. Soil samples were collected along a 350-m sampling belt in typical tidal freshwater wetlands of Yellow River Delta to investigate nutrient distributions, bacterial community structures and potential metabolic functions under tide and runoff stress by high-throughput sequencing and PICRUSt analysis. The total nitrogen (TN) contents varied greatly while total phosphorous (TP) contents were relatively stable. The bacterial community structures and predicted functions varied along a 350-m sampling belt. Some sulfate-reducing bacteria, nitrifying bacteria, Marmoricola, unclassified_f_Salinisphaeraceae and Oceanococcus exhibited a decreased trend with increasing distances far away from the river bank (B-0m). However, Salinisphaera was more dominant far away from the river bank (B-350m), indicating the stronger tolerance degree under salt stress. Marinobacterium and Marinobacter could be widely detected from B-0m to B-350m, demonstrating that those bacteria could tolerate a broad range of salinity and have its exceptional adaptation capacities. Redundancy analysis (RDA) indicated that nutrient and salinity played an important role in shaping bacterial community composition. NH₄⁺-N and AP were the key factors in explaining the variance of the genus level. Predicted by PICRUSt analysis, nitrogen fixation (NF), nitrogen mineralization (NM), denitrification and dissimilatory nitrate reduction to ammonium (DNRA) might be the dominant processes of nitrogen metabolism and related genes abundance were abundant in tidal freshwater wetland soils. These findings could provide new insights into the prevention and control of potential nutrient pollution in tidal freshwater wetlands under the dual stress of tide and runoff.

Nutrients and heavy metals mediate the distribution of microbial community in the marine sediments of the Bohai Sea, China

The Bohai Sea, one of the largest marginal seas in China, is extensively influenced by human and industrial activities. The pollutant loads from anthropogenic activities have induced severe ecological problems. The study investigates the physicochemical characteristics of seawater and sediments in Bohai Bay and Laizhou Bay of the Bohai Sea. The diversity and composition of microbial community in sediments are analyzed by 16S rRNA gene amplicon sequencing. The sequencing results present 16 phyla and 31 classes from the samples. Proteobacteria constituted a dominant phylum, of which the classes of Gamma-, Delta-, and Epsilon-are predominant sub-divisions. Nitrogen, phosphorus, and sulfur cycling related microbes present high abundance in both bays. The metabolism of organic matters is the main factor that influences the distribution of microbial communities in Bohai Bay, while the inflow of Yellow River is the dominant factor that influences the distribution of microbial communities in Laizhou Bay. Sulfur oxidizing process is expected to be positively influenced by heavy metals, while ammonia (NH₄⁺) oxidizing process is prone to be negatively affected by heavy metals in both bays. Microbial communities in the offshore sediments of Laizhou Bay and the majority microbial communities in Bohai Bay sediments are subject to similar predominant controlling factors. This phenomenon is likely ascribed to ocean circulation. The results of this study can provide constructive guidelines on ecosystem management of marginal seas in Bohai and elsewhere.

Culture-Dependent and -Independent Analyses Reveal the Diversity, Structure, and Assembly Mechanism of Benthic Bacterial Community in the Ross Sea, Antarctica

The benthic bacterial community in Antarctic continental shelf ecosystems are not well-documented. We collected 13 surface sediments from the Ross Sea, a biological hotspot in high-latitude maritime Antarctica undergoing rapid climate change and possible microflora shift, and aimed to study the diversity, structure and assembly mechanism of benthic bacterial community using both culture-dependent and -independent approaches. High-throughput sequencing of 16S rRNA gene amplicons revealed 370 OTUs distributed in 21 phyla and 284 genera. The bacterial community was dominated by Bacteroidetes, Gamma- and Alphaproteobacteria, and constituted by a compact, conserved and positively-correlated group of anaerobes and other competitive aerobic chemoheterotrophs. Null-model test based on βNTI and RCBray indicated that stochastic processes, including dispersal limitation and undominated fractions, were the main forces driving community assembly. On the other hand, environmental factors, mainly temperature, organic matter and chlorophyll, were significantly correlated with bacterial richness, diversity and community structure. Moreover, metabolic and physiological features of the prokaryotic taxa were mapped to evaluate the adaptive mechanisms and functional composition of the benthic bacterial community. Our study is helpful to understand the structural and functional aspects, as well as the ecological and biogeochemical role of the benthic bacterial community in the Ross Sea.

Anthropogenic pollutant-driven geographical distribution of mesozooplankton communities in estuarine areas of the Bohai Sea, China

Mesozooplankton communities in marine ecosystems are mainly influenced by both anthropogenic pollutants (e.g. nutrients and heavy metals) and natural variables (e.g. temperature, salinity and geographic distance). To achieve a deeper understanding of the effects of anthropogenic pollutants on mesozooplankton communities, we analyzed the community structure of mesozooplankton from 91 stations representing five typical estuarine regions in the Bohai Sea and assessed the relative importance of anthropogenic pollutants and natural variables by using multiple statistical approaches. Cd was identified as the leading pollutant for observed community variation among the five regions, followed by NH₄-N and COD. Redundancy analysis (RDA) model demonstrated that mesozooplankton communities were largely determined by both anthropogenic pollutants and natural variables, and the indicator species of mesozooplankton also varied when responding to different factors. Variance partitioning analysis showed both anthropogenic pollutants and natural variables posed significant influences (ANOVA, P < 0.05) on the mesozooplankton community structure, but the explanatory power of anthropogenic pollutants overrode the natural variables. These observations highlighted the importance of anthropogenic pollutants in the shifts of zooplankton structures among different regions. Our results obtained in this study provided new insights into the mechanism of the influence of anthropogenic pollutants on mesozooplankton communities in estuarine areas.

Chemical-, site-, and taxa-dependent benthic community health in coastal areas of the Bohai Sea and northern Yellow Sea: A sediment quality triad approach

To investigate benthic ecological quality associated with coastal pollution in the Bohai Sea and northern Yellow Sea, a sediment quality triad (SQT) approach was applied. Chemical (six groups of persistent toxic substances (PTSs) and 8 metals and metalloids), toxicological (AhR-mediated potency), and ecological (bacterial and meiofaunal communities) elements were selected and used in an integrated sediment assessment. The benthic meiofaunal community was newly analyzed and used as an additional component of the infaunal community during the SQT. Concentrations of chemicals and potential toxicity in sediments both indicated moderate to severe pollution in the study area, characterized by site-specific and land-uses. In particular, As, DDTs, and bioassay-derived dioxin equivalents exceeded corresponding sediment quality guidelines at nearly all locations. Limited occurrences of meiofaunal taxa (mean = 5.2) and relatively low species diversity, mainly comprised of nematodes (75.3%) and copepods (14.6%), among locations was generally consistent with pollution. The benthic community was consistent with compound-specific responses to gradients of contamination, particularly for As. Densities of two taxa, Nematoda and Nemertea exhibited strong negative correlations with concentrations of As. Compound-, site-, and taxa-specific variability of pollution of sediments was further supported by results of cluster analysis (CA) and nonmetric multidimensional scaling (NMDS). Finally, assessment integrating five benthic quality elements, including: 1) PTSs; 2) metals and metalloids; 3) sediment toxicity; 4) sediment microbiome; and 5) benthic meiofaunal community, explained contamination of sediments associated with land-uses, locality, or habitat. Status of the benthic community could not be explained by single component and their associations were not quantitative. Results of the integrated assessment, considering multiple benthic quality elements were useful to address overall quality of sediment, and were consistent with chemical-, species-, or site-dependent pollution of sediments in the Bohai and Yellow Seas.

Effects of secondary salinisation on macroinvertebrate functional traits in surface mining-contaminated streams, and recovery potential

Secondary salinisation has become a hot spot internationally due to its adverse effects on freshwater ecosystems. Although its effects on ecosystem patterns has been broadly studied, its potential effect on ecosystem functions, in particular on the functional traits of freshwater organisms, and functional trait recovery are largely unknown. In this study, we conducted a field investigation at 405 sample sites from May 2009 to July 2016 in surface mining-contaminated streams, in order to evaluate the influence of secondary salinisation on macroinvertebrate functional traits and the recovery potential of dominant functional traits. Results of univariate models showed that sensitive, very tolerant, gill-breathers, cutaneous-breathers, shredders, predators and gatherers were the most responsive indicators to enhanced specific conductivity and sulfate loadings with sensitive, gill-breathers, shredders and predators demonstrating a reduction in abundance, whereas cutaneous-breathers and gatherers exhibiting an increase. Complicated relationships among different species indicated that co-exclusions would not occur because all macroinvertebrate taxa exhibited positive correlations. Results of relative recovery potential showed that omnivores and gatherers recovered quickly following improvements in water quality, whereas gill-breathers, pneumostome-breathers, filterers and scrapers would be expected to recover slowly due to their sensitivity to both specific conductivity and sulfate and low drift propensity. Overall, secondary salinisation has posed severely ecological risks to macroinvertebrate functional attributes in surface mining-contaminated streams, and their effects should be considered in future conservation plans.

Application of Environmental DNA Metabarcoding for Predicting Anthropogenic Pollution in Rivers

Rivers are among the most threatened freshwater ecosystems, and anthropogenic activities are affecting both river structures and water quality. While assessing the organisms can provide a comprehensive measure of a river's ecological status, it is limited by the traditional morphotaxonomy-based biomonitoring. Recent advances in environmental DNA (eDNA) metabarcoding allow to identify prokaryotes and eukaryotes in one sequencing run, and could thus allow unprecedented resolution. Whether such eDNA-based data can be used directly to predict the pollution status of rivers as a complementation of environmental data remains unknown. Here we used eDNA metabarcoding to explore the main stressors of rivers along which community structure changes, and to identify the method's potential for predicting pollution status based on eDNA data. We showed that a broad range of taxa in bacterial, protistan, and metazoan communities could be profiled with eDNA. Nutrients were the main driving stressor affecting communities' structure, alpha diversity, and the ecological network. We specifically observed that the relative abundance of indicative OTUs was significantly correlated with nutrient levels. These OTUs data could be used to predict the nutrient status up to 79% accuracy on testing data sets. Thus, our study gives a novel approach to predicting the pollution status of rivers by eDNA data.

Interactive effects of multiple stressors revealed by sequencing total (DNA) and active (RNA) components of experimental sediment microbial communities

Coastal waterways are increasingly exposed to multiple stressors, e.g. contaminants that can be delivered via pulse or press exposures. Therefore, it is crucial that ecological impacts can be differentiated among stressors to manage ecosystem threats. We investigated microbial community development in sediments exposed to press and pulse stressors. Press exposures were created with in situ mesocosm sediments containing a range of 'metal' concentrations (sediment contaminated with multiple metal(loid)s) and organic enrichment (fertiliser), while the pulse exposure was simulated by a single dose of organic fertiliser. All treatments and exposure concentrations were crossed in a fully factorial field experiment. We used amplicon sequencing to compare the sensitivity of the 1) total (DNA) and active (RNA) component of 2) bacterial (16S rRNA) and eukaryotic (18S rRNA) communities to contaminant exposures. Overall microbial community change was greater when exposed to press than pulse stressors, with the bacterial community responding more strongly than the eukaryotes. The total bacterial community represents a more time-integrated measure of change and proved to be more sensitive to multiple stressors than the active community. Metals and organic enrichment treatments interacted such that the effect of metals was weaker when the sediment was organically enriched. Taxa-level analyses revealed that press enrichment resulted in potential functional changes, mainly involving nitrogen cycling. Furthermore, enrichment generally reduced the abundance of active eukaryotes in the sediment. As well as demonstrating interactive impacts of metals and organic enrichment, this study highlights the sensitivity of next-generation sequencing for ecosystem biomonitoring of interacting stressors and identifies opportunities for more targeted application.

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

Oil spills offshore can cause long-term ecological effects on coastal marine ecosystems. Despite their important ecological roles in the cycling of energy and nutrients in food webs, effects on bacteria, protists or arthropods are often neglected. Environmental DNA (eDNA) metabarcoding was applied to characterize changes in the structure of micro- and macro-biota communities of surface sediments over a 7-year period since the occurrence of Hebei Spirit oil spill on December 7, 2007. Alterations in diversities and structures of micro- and macro-biota were observed in the contaminated area where concentrations of polycyclic aromatic hydrocarbons were greater. Successions of bacterial, protists and metazoan communities revealed long-term ecological effects of residual oil. Residual oil dominated the largest cluster of the community-environment association network. Presence of bacterial families (Aerococcaceae and Carnobacteriaceae) and the protozoan family (Platyophryidae) might have conferred sensitivity of communities to oil pollution. Hydrocarbon-degrading bacterial families (Anaerolinaceae, Desulfobacteraceae, Helicobacteraceae and Piscirickettsiaceae) and algal family (Araphid pennate) were resistant to adverse effects of spilt oil. The protistan family (Subulatomonas) and arthropod families (Folsomia, Sarcophagidae Opomyzoidea, and Anomura) appeared to be positively associated with residual oil pollution. eDNA metabarcoding can provide a powerful tool for assessing effects of anthropogenic pollution, such as oil spills on sediment communities and its long-term trends in coastal marine environments.

Omics Advances in Ecotoxicology

Toxic substances in the environment generate adverse effects at all levels of biological organization from the molecular level to community and ecosystem. Given this complexity, it is not surprising that ecotoxicologists have struggled to address the full consequences of toxic substance release at ecosystem level, due to the limits of observational and experimental tools to reveal the changes in deep structure at different levels of organization. -Omics technologies, consisting of genomics and ecogenomics, have the power to reveal, in unprecedented detail, the cellular processes of an individual or biodiversity of a community in response to environmental change with high sample/observation throughput. This represents a historic opportunity to transform the way we study toxic substances in ecosystems, through direct linkage of ecological effects with the systems biology of organisms. Three recent examples of -omics advance in the assessment of toxic substances are explored here: (1) the use of functional genomics in the discovery of novel molecular mechanisms of toxicity of chemicals in the environment; (2) the development of laboratory pipelines of dose-dependent, reduced transcriptomics to support high-throughput chemical testing at the biological pathway level; and (3) the use of eDNA metabarcoding approaches for assessing chemical effects on biological communities in mesocosm experiments and through direct observation in field monitoring. -Omics advances in ecotoxicological studies not only generate new knowledge regarding mechanisms of toxicity and environmental effect, improving the relevance and immediacy of laboratory toxicological assessment, but can provide a wholly new paradigm for ecotoxicology by linking ecological models to mechanism-based, systems biology approaches.

The impact of artificial surfaces on marine bacterial and eukaryotic biofouling assemblages: A high-throughput sequencing analysis

Vessel hulls and underwater infrastructure can be severely impacted by marine biofouling. Knowledge on which abiotic conditions of artificial structures influence bacterial and eukaryotic community composition is limited. In this study, settlement plates with differing surface texture, orientation and copper-based anti-fouling coatings were deployed in a marina. After three months, biofouling samples were collected and bacterial and eukaryotic communities characterised using DNA metabarcoding. The copper anti-fouling coating treatments incurred the most significant compositional changes (p ≤ 0.001) within both domains. Bacterial diversity decreased, with Gammaproteobacteria becoming the dominant phylum. In contrast, protist diversity increased as well as opportunist nematodes and bryozoans; urochordates and molluscs became less abundant. Network analyses displayed complex relationships on untreated plates, while revealing a simpler, but disturbed and unstable community composition on the anti-fouling coated plates. These networks of copper treatments displayed opportunist taxa that appeared as key organisms in structuring the bacterial and eukaryotic communities.

Aerobic degradation of crude oil by microorganisms in soils from four geographic regions of China

A microcosm experiment was conducted for 112 d by spiking petroleum hydrocarbons into soils from four regions of China. Molecular analyses of soils from microcosms revealed changes in taxonomic diversity and oil catabolic genes of microbial communities. Degradation of total petroleum hydrocarbons (TPHs) in Sand from the Bohai Sea (SS) and Northeast China (NE) exhibited greater microbial mineralization than those of the Dagang Oilfield (DG) and Xiamen (XM). High-throughput sequencing and denaturing gradient gel electrophoresis (DGGE) profiles demonstrated an obvious reconstruction of the bacterial community in all soils. The dominant phylum of the XM with clay soil texture was Firmicutes instead of Proteobacteria in others (DG, SS, and NE) with silty or sandy soil texture. Abundances of alkane monooxygenase gene AlkB increased by 10- to 1000-fold, relative to initial values, and were positively correlated with rates of degradation of TPHs and n-alkanes C13-C30. Abundances of naphthalene dioxygenase gene Nah were positively correlated with degradation of naphthalene and total tricyclic PAHs. Redundancy analysis (RDA) showed that abiotic process derived from geographical heterogeneity was the primary effect on bioremediation of soils contaminated with oil. The optimization of abiotic and biotic factors should be the focus of future bioremediation of oil contaminated soil.