In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments

Using ozone nanobubbles, and microalgae to promote the removal of nutrients from aquaculture wastewater: Insights from the changes of microbiomes

Integrated aquaculture wastewater treatment systems (IAWTSs) are widely used in treating aquaculture wastewater with the aeration-microalgae unit serving as an important component. In this study, we artificially constructed an IAWTS and applied two aeration-microalgae methods: ordinary aeration or ozone nanobubbles (ONBs) with microalgae (Nannochloropsis oculata). The impact of N.oculata and ONBs on the removal performance of nutrients and the underlying micro-ecological mechanisms were investigated using 16S rRNA gene amplicon sequencing. The results demonstrated that the combined use of ONBs and N.oculata exhibited superior purification effects with 78.25%, 76.59% and 86.71% removal of CODMn, TN and TP. N.oculata played a pivotal role as the primary element in wastewater purification, while ONBs influenced nutrient dynamics by affecting both N.oculata and bacterial communities. N.oculata actively shaped bacterial communities, with a specific focus on nitrogen and phosphorus cycling in the micro-environment remodeled by ONBs. Rare bacterial communities displayed heightened activity in response to the changes in N.oculata, ONBs, and nutrient levels. These findings provide a novel approach to improve the technological processes the IAWTS, contributing to the advancement of sustainable aquaculture practices by offering valuable insights into wastewater purification efficiency and micro-ecological mechanisms.

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.

How microorganisms tell the truth of potentially toxic elements pollution in environment

Potentially toxic elements (PTEs) posed a major hazard to microbial community in river sediments, but the way how different kinds of microorganisms responses to elements pollution has not been clearly understood. The target of this research was to discriminate the apposite indicators for diagnosing elements pollution based on the sensitivity of microbial abundance, biodiversity, predicted metabolic functions to PTEs (Cu, Cd, Cr, Ni, Pb, Zn, As and Hg). Considering Huaihe River Basin as the main subject, sediment samples were gathered from 135 sites. Ni, Zn and Cd significantly influenced the microbial communities and predicted functions. In general, the microbial sensitivity to PTEs was bacteria > archaea. Geo-accumulation index and potential ecological risk (PER) index suggested Hg and Cd were the significant contaminates and posed the most serious ecological risk in sediments. Structural Equation Model identified the bioindicators 1/nitrate reduction and rara taxa (Azoarcus) as reflect and speculate Hg and Cd pollution, respectively. PER was predicted by 1/nitrate reduction and rare taxa (Phaeodactylibacter and Illumatobacter). Results elucidated the rather role of rare taxa in indicating PTEs pollution. The findings contributed to provide useful reference for bioremediation of contaminated sediments under PTEs stress.

Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum

Microbial communities inhabiting soil-water-sediment continuum in coastal areas provide important ecosystem services. Their adaptation in response to environmental stressors, particularly mitigating the impact of pollutants discharged from human activities, has been considered for the development of microbial biomonitoring tools, but their use is still in the infancy. Here, chemical and molecular (16S rRNA gene metabarcoding) approaches were combined in order to determine the impact of pollutants on microbial assemblages inhabiting the aquatic network of a soil-water-sediment continuum around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected within the soil-river-lake continuum at three stations in dry (summer) and wet (winter) seasons. The contaminant pressure index (PI), which integrates Polycyclic aromatic hydrocarbons (PAHs), alkanes, Organochlorine pesticides (OCPs) and metal contents, and the microbial pressure index microgAMBI, based on bacterial community structure, showed significant correlation with contamination level and differences between seasons. The comparison of prokaryotic communities further revealed specific assemblages for soil, river and lake sediments. Correlation analyses identified potential "specialist" genera for the different compartments, whose abundances were correlated with the pollutant type found. Additionally, PICRUSt analysis revealed the metabolic potential for pollutant transformation or degradation of the identified "specialist" species, providing information to estimate the recovery capacity of the ecosystem. Such findings offer the possibility to define a relevant set of microbial indicators for assessing the effects of human activities on aquatic ecosystems. Microbial indicators, including the detection of "specialist" and sensitive taxa, and their functional capacity, might be useful, in combination with integrative microbial indices, to constitute accurate biomonitoring tools for the management and restoration of complex coastal aquatic systems.

Effects on microbiomes and resistomes and the source-specific ecological risks of heavy metals in the sediments of an urban river

This study aims to better understand the effects of heavy metal enrichment on microbiomes and resistomes and the source-specific ecological risks of metals in the sediments of an urban river. Geo-accumulation index and enrichment factor suggested the river sediments were contaminated by Cd, Cu, Pb, and Zn in varying degrees. High-throughput sequencing-based metagenomics analysis identified 430 types of antibiotic resistance genes (ARGs), dominated by the multidrug, MLS, bacitracin, quinolone, and aminoglycoside ARGs, and 52 metal resistance genes (MRGs) mainly conferring resistance to zinc, copper, cadmium, lead, mercury and multiple metals. Spearman correlation analysis and Mantel test showed the heavy metal enrichment exerted significant effects on the microbial community, ARGs and MRGs. Source apportionment using positive matrix factorization revealed that natural source (42.8%) was the largest contributor of metals in the river sediments, followed by urban activities (35.4%) and a mixed source (21.7%). However, when incorporating the apportionment results into a modified risk model to evaluate the source-specific ecological risks, results showed human activities dominated the risks of metals. Comparatively, the urban activities majorly caused moderate- and considerable- ecological risks, while the mixed source with respect to agricultural and industrial activities contributed higher percentages on high- and extremely high- ecological risks.

Divergent Patterns of Bacterial Community Structure and Function in Response to Estuarine Output in the Middle of the Bohai Sea

Understanding environment-community relationships under shifting environmental conditions helps uncover mechanisms by which environmental microbial communities manage to improve ecosystem functioning. This study investigated the microbial community and structure near the Yellow Sea River estuary in 12 stations across the middle of the Bohai Sea for over two seasons to elucidate the influence of estuarine output on them. We found that the dominant phyla in all stations were Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, and Planctomycetes. Alpha-diversity increased near the estuary and bacterial community structure differed with variation of spatiotemporal gradients. Among all the environmental factors surveyed, temperature, salinity, phosphate, silicon, nitrate, and total virioplankton abundance played crucial roles in controlling the bacterial community composition. Some inferred that community functions such as carbohydrate, lipid, amino acid metabolism, xenobiotics biodegradation, membrane transport, and environmental adaptation were much higher in winter; energy and nucleotide metabolism were lower in winter. Our results suggested that estuarine output had a great influence on the Bohai Sea environment and changes in the water environmental conditions caused by estuarine output developed distinctive microbial communities in the middle of the Bohai Sea. The distinctive microbial communities in winter demonstrated that the shifting water environment may stimulate changes in the diversity and then strengthen the predicted functions.

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.

Sediment Microbial Diversity in Urban Piedmont North Carolina Watersheds Receiving Wastewater Input

Urban streams are heavily influenced by human activity. One way that this occurs is through the reintroduction of treated effluent from wastewater treatment plants. We measured the microbial community composition of water, sediment, and soil at sites upstream and downstream from two Charlotte treatment facilities. We performed 16S rRNA gene sequencing to assay the microbial community composition at each site at four time points between the late winter and mid-summer of 2016. Despite the location of these streams in an urban area with many influences and disruptions, the streams maintain distinct water, sediment, and soil microbial profiles. While there is an overlap of microbial species in upstream and downstream sites, there are several taxa that differentiate these sites. Some taxa characteristics of human-associated microbial communities appear elevated in the downstream sediment communities. In the wastewater treatment plant and to a lesser extent in the downstream community, there are high abundance amplicon sequence variants (ASVs) which are less than 97% similar to any sequence in reference databases, suggesting that these environments contain an unexplored biological novelty. Taken together, these results suggest a need to more fully characterize the microbial communities associated with urban streams, and to integrate information about microbial community composition with mechanistic models.

Contribution of heavy metal in driving microbial distribution in a eutrophic river

Urban rivers represent an important source of freshwater. Accelerated urban development has resulted in imbalances in the water ecological environment and even eutrophication. Moreover, both natural and anthropogenic sources result in frequent heavy metal pollution in urban rivers. However, the combined impact of eutrophication and heavy metal pollution on the diversity and structure of the river microbial communities has not been adequately addressed. The microbial community distribution and predicted functions were examined in six water and sediment samples from the Laojingshui (LJS) River using metagenomic sequencing. The results showed that there were distinct differences in the microbial composition along the river. Redundancy analysis (RDA) revealed that the redox potential (Eh) was the most influential factor, explaining 76.5% of the variation (p = 0.002), and the heavy metals Zn and Cu explained 4.5 and 3.9%, respectively (p < 0.05). The results revealed that high nitrogen and phosphorus concentrations may have affected the proliferation of opportunistic plant species, such as Eichhornia crassipes, but Eh and heavy metals may have had greater impacts than N and P on the microorganisms in the water and sediment. The sensitivities of Deltaproteobacteria, Acidobacteria, Gemmatimonadetes and Nitrospira were most significant under Zn and Cu contamination when accompanied by eutrophic conditions. The expression ratio of the CYS (Cystain) gene might explain why the spatial distribution of each metal differed. This study suggests that heavy metals in eutrophication water continue to be the main factors determining the composition of microbial community, so the treatment of eutrophic water still needs to attach great importance to the complex pollution of heavy metals.

Environmental DNA Shaping a New Era of Ecotoxicological Research

Aquatic ecosystems, such as rivers and lakes, are exposed to multiple stressors from anthropogenic activity and changes in climate, which have resulted in a general decrease in biodiversity, alteration of community structures, and can ultimately result in reduction of resources provided by natural ecosystems. Adverse outcomes caused by pollutants to ecosystems are determined not only by toxic properties but also ecological contexts of ecosystems, including indigenous biodiversity and community composition. It is therefore important to identify key factors, such as diversity of species and traits that determine the vulnerability of structures and functions of ecosystems in response to toxic substances. Detection and quantification of biodiversity and its activities using environmental DNA (eDNA) is arguably one of the most important technical advances in ecology in recent years. A huge opportunity has appeared to allow more relevant approaches for assessments of risks posed to ecosystems by toxic substances. eDNA approaches provide effective and efficient tools to evaluate the effects of chemical pollutants on (1) the occurrences and population of wildlife, (2) communities, and (3) the function of ecosystem in the field. Here a conceptual framework of adverse outcome pathways to relate molecular initiating events to apical ecosystem-level responses is proposed to connecting laboratory-based prediction to observations under field conditions. Particularly, future research opportunities on effects on biodiversity, community structure, and ecosystem function by toxic substances will be discussed.

Variation in microbial community structure in surface seawater from Pearl River Delta: Discerning the influencing factors

Contamination of perfluoroalkyl acids (PFAAs) is ubiquitously detected in various environments. However, their potential effects on microbial communities remain largely unknown. In this study, surface seawater of the Pearl River Delta (PRD) is sampled to measure PFAA concentrations and profile the structure of free-living microbial community. Total PFAAs concentrations range from 131 to 1563 pg L^-1 in surface seawater. PFOS (16-470 pg L^-1), PFOA (27-272 pg L^-1), PFHpA (18-201 pg L^-1) and PFBA (25-152 pg L^-1) are the major homologues, indicating continued industrial application or release of PFOS and a gradual shift towards using shorter-chain PFAAs. Concentrations of PFAAs from this recent cruise are much lower than previous reports, which may be due to the effective management of PFAA usage around PRD region. In addition, the microbial community in PRD surface seawater is predominantly colonized by the Proteobacteria phylum (27.2 to 61.5%) and the Synechococcus genus (5.6 to 38.6%). The structure of the microbial communities varies among stations, mainly resulting from different abundances of Synechococcus, Prochlorococcus and Nitrosopumilus. Geochemical parameters (e.g., nutrients and salinity) and phytoplankton are significantly associated with the microbial community dynamics in surface seawater. In the interactive network of microbiota, a subset of bacteria (i.e., Fluviicola, Nitrosopumilus, Limnohabitans, Sediminibacterium, C39 and Polynucleobacter) shows significantly positive correlations with PFAAs (R > 0.6; P < 0.001). Overall, this study gives a timely monitoring of PFAA pollution around PRD area. Shift in environmental microbiota by geochemical factors and phytoplankton is also observed, which may affect biogeochemical cycling.

Assessing the fate of brown trout (Salmo trutta) environmental DNA in a natural stream using a sensitive and specific dual-labelled probe

Environmental DNA (eDNA) analysis in the aquatic environment has emerged as a promising tool for diagnosis of the ecological status in comprehensive monitoring strategies and might become useful in context of the European Water Framework Directive (WFD) and other legislations to derive stressor-specific indicators. Despite many studies having made significant progress for the future use of eDNA in terms of ecosystem composition and detection of invasive/rare species in inland waters, much remains unknown about the transport and fate of eDNA under natural environmental conditions. We designed a specific dual-labelled probe to detect brown trout (Salmo trutta, L.) eDNA and used the probe to describe the fate of eDNA released from an aquaculture facility into the low mountain range stream Wehebach, Germany. The probe was shown to be specific to brown trout, as ponds housing rainbow trout (Oncorhynchus mykiss) did not test positive. Even though we observed different strengths of eDNA signals for three ponds containing different brown trout quantities, no significant correlation was found between biomass (kg/L) and eDNA quantity. Our results indicate that the release of DNA from brown trout might be life stage and/or age-dependent. The effluents of the aquaculture facility were a source of high levels of eDNA which resulted in the greatest abundance of brown trout eDNA directly downstream of the facility. Despite the natural occurrence of brown trout in the Wehebach, as shown by ecological investigations conducted by authorities of the federal state of North Rhine-Westphalia (Germany) and personal observations, we observed a significant decrease of relative abundance of eDNA in the Wehebach within the first 1.5 km downstream of the aquaculture. Our results suggest that concentrations of eDNA in running waters rapidly decrease under natural conditions due to dilution and degradation processes, which might have important implications for the utility of eDNA in environmental research.

Contamination by perfluoroalkyl substances and microbial community structure in Pearl River Delta sediments

Environmental microbiota play essential roles in the maintenance of many biogeochemical processes, including nutrient cycling and pollutant degradation. They are also highly susceptible to changes in environmental stressors, with environmental pollutants being key disruptors of microbial dynamics. In the present study, a scientific cruise was launched on July 2017 around Pearl River Delta, a suitable studying site for perfluoroalkyl substances (PFASs) in the wake of the severe PFAS pollution. Surface sediment samples were collected from 18 representative stations to assess PFAS accumulation and profile microbial community. PFAS concentrations ranged from 24.2 to 181.4 pg/g dry weight in sediment, and perfluorooctanesulfonic acid (PFOS) was the dominant homologue. The concentrations of PFAS homologues in the current study were much lower than those reported in previous studies, implying effective management and control of pollution from PFAS-related industries. 16S rRNA gene amplicon sequencing revealed that Proteobacteria was the dominant phylum, while nitrogen-metabolizing Nitrosopumilus and sulfate-reducing Desulfococcus genera were the most abundant. Variations in microbial communities among sampling stations were mainly due to the differences in abundances of Escherichia, Nitrosopumilus, and Desulfococcus. The outbreak of Escherichia bacteria at specific coastal stations potentially indicated the discharge of fecal matter into the marine environment. Dissolved oxygen (DO) in bottom seawater significantly influenced the structure of microbial communities in the sediment, while current study failed to observe significant effects from PFAS pollutants. Positive correlations were found between DO and sulfate-reducing bacteria in Desulfococcus and GOUTA19 genera. Overall, this study explored relationships between environmental variables (e.g., PFAS pollutants) and sediment bacteria. Biogeochemical parameters significantly influenced the structure and composition of microbial communities in sediment.

Inherent bacterial community response to multiple heavy metals in sediment from river-lake systems in the Poyang Lake, China

Sediment is the one of most important storage of heavy metal. Microbiotas in sediment can be used as the effective indicators of heavy metals. The goal of this study was to understand the bacterial communities responding to heavy metal enrichment in sediments and prioritize some factors that affected significantly to bacterial community. Sediments were sampled from five river-lake systems in the Poyang Lake in dry season, and the bacterial community was analyzed using Illumina high-throughput sequencing. Relationships between sediment environment and the diversity and structure of bacterial communities were determined by correlation analysis and redundancy analysis (RDA). The result indicated that Cd and Sb were identified as the heavy metals of the great risk in sediments. Sediments from five river-lake systems shared 31.83% core operational taxonomic units (OTUs) of bacterial communities. Proteobacteria (33.54% of total sequences) and Actinobacteria (15.04%) were the dominant phyla across all sites. High enrichment of heavy metals (MRI and mC_d) resulted in low diversity of bacterial communities (Simpson index). The RDA revealed pH, OC, mCd, and Efs of As, Pb, Cd were major factors related to bacterial community structure changes. The dominant phylum Actinobacteria was regarded as tolerant bacteria, while the dominant phylum Proteobacteria was named as resistant bacteria in sediment with high anthropogenic Cd enrichment.

Towards a holistic and solution-oriented monitoring of chemical status of European water bodies: how to support the EU strategy for a non-toxic environment?

The definition of priority substances (PS) according to the Water Framework Directive (WFD) helped to remove many of these chemicals from the market and to reduce their concentrations in the European water bodies. However, it could not prevent that many of these chemicals have been replaced by others with similar risks. Today, monitoring of the PS-based chemical status according to WFD covers only a tiny fraction of toxic risks, extensively ignores mixture effects and lacks incentives and guidance for abatement. Thus, we suggest complement this purely status-related approach with more holistic and solution-oriented monitoring, which at the same time helps to provide links to the ecological status. Major elements include (1) advanced chemical screening techniques supporting mixture risk assessment and unraveling of source-related patterns in complex mixtures, (2) effect-based monitoring for the detection of groups of chemicals with similar effects and the establishment of toxicity fingerprints, (3) effect-directed analysis of drivers of toxicity and (4) to translate chemical and toxicological fingerprints into chemical footprints for prioritization of management measures. The requirement of more holistic and solution-oriented monitoring of chemical contamination is supported by the significant advancement of appropriate monitoring tools within the last years. Non-target screening technology, effect-based monitoring and basic understanding of mixture assessment are available conceptually and in research but also increasingly find their way into practical monitoring. Substantial progress in the development, evaluation and demonstration of these tools, for example, in the SOLUTIONS project enhanced their acceptability. Further advancement, integration and demonstration, extensive data exchange and closure of remaining knowledge gaps are suggested as high priority research needs for the next future to bridge the gap between insufficient ecological status and cost-efficient abatement measures.