Impact Site Research Articles

A New Toolbox for Managing Sites Impacted by Light Non-Aqueous Phase Liquids (LNAPLs)

The Concawe LNAPL Toolbox is one of the first completely web-based tools for managing and remediating light non-aqueous phase liquids (LNAPL) impacted sites. An off-line downloadable version is also available for users who do not want to access it via the internet. LNAPLs are typically historic hydrocarbons released into soils and groundwater, such as liquid fuels, crude oil, and condensates. The toolbox was developed by Concawe, the Scientific Division of European Fuel Manufacturers Association, with the support of the engineering and environmental science-consulting agency GSI Environmental. The toolbox, written on the R-Shiny platform, was released in 2022 and includes over 20 different tools, such as, for example, infographics, nomographs, calculators, mobility models, videos, and checklists. These tools are organized into three tiers, with Tier 1 offering basic graphics and essential information, Tier 2 providing simple quantitative models and calculators, and Tier 3 featuring access and explanations of more complex tools. The toolbox is designed to address six key questions that are important for environmental consultants and regulators managing LNAPL sites, including determining the amount of LNAPL, estimating LNAPL migration and persistence, assessing LNAPL risk over time, determining the effectiveness of LNAPL recovery, and estimating Natural Source Zone Depletion (NSZD). The Concawe LNAPL Toolbox is accessible free of charge via a webpage on an internet browser or by downloading the toolbox for use on a personal computer.

The "Working Group Land of Fires" Platform for emergency management, data sharing and dissemination.

Over the last decades, the Campania Region in Italy has faced an environmental crisis due to the widespread illegal dumping and burning of waste. This has led to the area being notoriously known as the Land of Fires (Terra dei Fuochi - TdF), sparking serious concerns about public health and threatening the region's agricultural sector, one of its economic mainstays. In such a context, a timely, accurate, and reliable flow of information, aimed both at the population and at stakeholders, is crucial for establishing a proper dialogue between institutions and people, driving the empowerment of citizens. To address this crisis, the Italian Government introduced Law 6 of 2014, establishing a multidisciplinary Working Group tasked with identifying and mapping the sites affected by spills and illegal disposal in the territory. The TdF-WG defined a scientific methodology for classifying these sites in terms of prohibition on the cultivation of specific crops, consequently allowing the adoption of appropriate clean up and restoration measures for the impacted sites. This paper describes the data collection process and the IT platform commissioned by the Government to the IZS-TE and used by the TdF-WG to exchange data, knowledge, and technology, thereby fostering efficient and effective crisis management.

How restoration engineering measures can enhance the ecological value of intertidal flats

Restoration engineering measures, such as managed realignments or building groins, modify the environmental characteristics of coastal intertidal ecosystems. Creating physical modifications that are beneficial to an intertidal system's ecology necessitates an in‐depth understanding of the relationships between the abiotic and biotic components of a given intertidal habitat. In this study, we evaluate how hydrodynamics and sediment characteristics drive the development of the benthic macrofauna community during the first 5 years following engineering measures to enhance benthic macrofauna diversity at three locations. The creation of low‐energy habitats through groins (Knuitershoek and Baalhoek) and a managed realignment dike breach (Perkpolder) led to the accumulation of fine sediments in all three impact sites. Biomass of benthic macrofauna quickly increased between 2016 and 2020, with successional processes being more important in Perkpolder, where the habitat was started completely from scratch due to a managed realignment, than at Knuitershoek or Baalhoek, where habitat conditions were improved by adding groins. In addition, the density of benthos‐eating birds, especially oystercatchers, increased at some of the modified sites. While a low‐energy habitat may harbor more diverse assemblages of benthic macrofauna than a highly dynamic one, the extremely high silt content, which is typical for low‐energy habitats, may slow benthic community development. The observed increase of biomass at our impact sites highlights the value of the interventions, while the delays in the response of the benthic macrofauna community emphasizes the need for extensive monitoring both in time and space and the identification of underlying abiotic–biotic mechanisms.

Spatial and seasonal variability in benthic impact of mussel farms: Predicting and mitigating impacts using ambient oxygen conditions

Environmental impacts are a cause for concern when developing and expanding aquaculture and to be sustainable potential negative effects need to be addressed. The intensity and extent of these impacts likely vary among sites and seasons, depending on multiple factors including the physical and biological setting and operational aspects. Using a combination of sampling techniques, we investigated the spatial variability in epibenthic impacts in eleven commercial mussel farms, on the Swedish west coast. We found increased levels of organic content, changes in epibenthic macrofauna and increased cover of Beggiatoa sp., a documented indicator of hypoxia. The extent of these impacts was generally limited to the extent of the farms. Because the cover of Beggiatoa sp. was particularly clear and because oxygen conditions in the sediment is of great importance to the structure and function of these habitats, we analysed spatial patterns using an index of the benthic footprint (BFI) accounting for both intensity and extent of impacts. In the summer, the BFI varied strongly among farm-sites and subsequent analyses showed that it highly correlated with ambient bottom oxygen concentration. Repeated sampling during early spring, however, showed that impacts were quickly reversible also in the most impacted sites. Thus, we conclude that in Swedish coastal waters the benthic footprint calculated on the % cover of Beggiatoa sp. is highly dependent on ambient oxygen concentration. We suggest that knowledge about spatial and temporal patterns of oxygen in the bottom water can be used to predict the severity of impacts and provide an important criterion in a site-selection process aimed at developing a sustainable food industry.

Population structure and pathogen interaction of Escherichia coli in freshwater: Implications of land-use for water quality and public health in Aotearoa New Zealand.

Freshwater samples (n = 199) were obtained from 41 sites with contrasting land-uses (avian, low impact, dairy, urban, sheep and beef, and mixed sheep, beef and dairy) and the E. coli phylotype of 3980 isolates (20 per water sample enrichment) was determined. Eight phylotypes were identified with B1 (48.04%), B2 (14.87%) and A (14.79%) the most abundant. Escherichia marmotae (n = 22), and Escherichia ruysiae (n = 1), were rare (0.68%) suggesting that these environmental strains are unlikely to confound water quality assessments. Phylotypes A and B1 were overrepresented in dairy and urban sites (p < 0.0001), whilst B2 were overrepresented in low impact sites (p < 0.0001). Pathogens ((Salmonella, Campylobacter, Cryptosporidium or Giardia) and the presence of diarrhoeagenic E. coli-associated genes (stx and eae) were detected in 89.9% (179/199) samples, including 80.5% (33/41) of samples with putative non-recent faecal inputs. Quantitative PCR to detect microbial source tracking targets from human, ruminant and avian contamination were concordant with land-use type and E. coli phylotype abundance. This study demonstrated that a potential recreational health risk remains where pathogens occurred in water samples with low E. coli concentration, potential non-recent faecal sources, low impact sites and where human, ruminant and avian faecal sources were absent.

Mechanical properties of rubble pile asteroids (Dimorphos, Itokawa, Ryugu, and Bennu) through surface boulder morphological analysis

Planetary defense efforts rely on estimates of the mechanical properties of asteroids, which are difficult to constrain accurately from Earth. The mechanical properties of asteroid material are also important in the interpretation of the Double Asteroid Redirection Test (DART) impact. Here we perform a detailed morphological analysis of the surface boulders on Dimorphos using images, the primary data set available from the DART mission. We estimate the bulk angle of internal friction of the boulders to be 32.7 ± 2. 5° from our measurements of the roundness of the 34 best-resolved boulders ranging in size from 1.67–6.64 m. The elongated nature of the boulders around the DART impact site implies that they were likely formed through impact processing. Finally, we find striking similarities in the morphology of the boulders on Dimorphos with those on other rubble pile asteroids (Itokawa, Ryugu and Bennu). This leads to very similar internal friction angles across the four bodies and suggests that a common formation mechanism has shaped the boulders. Our results provide key inputs for understanding the DART impact and for improving our knowledge about the physical properties, the formation and the evolution of both near-Earth rubble-pile and binary asteroids.

Experimental and Numerical Simulation of Ejecta Size and Velocity of Hypervelocity Impact Rubble-Pile Asteroid

Rubble-pile asteroids may be the type of near-Earth object most likely to threaten Earth in a future collision event. Small-scale impact experiments and numerical simulations for large-scale impacts were conducted to clarify the size ratio of the boulder/projectile diameter effects on ejecta size–velocity distribution. A series of small-scale impact cratering experiments were performed on porous gypsum–basalt targets at velocities of 2.3 to 5.5 km·s−1. Three successive ejection processes were observed by high-speed and ultra-high-speed cameras. The momentum transfer coefficient and cratering size were measured. A three-dimensional numerical model reflecting the random distribution of the interior boulders of the rubble-pile structure asteroid is established. The size ratio (length to diameter) of the boulder size inside the asteroid to the projectile diameter changed from 0.25 to 1.7. We conducted a smoothed particle hydrodynamics numerical simulation in the AUTODYN software to study the boulder size effect on the ejecta size–velocity distribution. Simulation results suggest that the microscopic porosity on regolith affects the propagation of shock waves and reduces the velocity of ejecta. Experiments and numerical simulation results suggest that both excavation flow and spalling ejection mechanism can eject boulders (0.12–0.72 m) out of the rubble-pile asteroid. These experiments and simulation results help us select the potential impact site in a planetary defense scenario and reduce deflection risk. are comprised primarily of boulders of a range of sizes.

A method to describe attenuation of river contamination under peak flows: Can the public water supply from Paraopeba River finally return after the Brumadinho dam disaster?

Tailings dams' disasters begin a stage of river water contamination with no endpoint at first sight. But when the river was formerly used for public water supply and the use was suspended as consequence of a dam break, a time window for safe suspension lift must be anticipated to help water managers. The purpose of this study was to seek for that moment in the case of Brumadinho dam disaster which occurred in 2019 and injected millions of cubic meters of iron- and manganese-rich tailings into the Paraopeba River, leading to the suspension of public water supply to Belo Horizonte metropolitan region with this resource, until now. To accomplish the proposed goal, an assemblage of artificial intelligence and socio-economic development models were used to anticipate precipitation, river discharge and metal concentrations (iron, manganese) until 2033. Then, the ratios of metal concentrations between impacted and non-impacted sites were determined and values representing extreme events of river discharge were selected for further assessment. A ratio ≈1 generally indicates a similarity between impacted and non-impacted areas or, put another way, a return of impacted areas to a pre-rupture condition. Moreover, when the ratio is estimated under the influence of peak flows, then a value of ≈1 indicates a return to pre-rupture conditions under the most unfavorable hydrologic regimes, thus a safe return. So, the extreme ratios were plotted against time and fitted to a straight line with intercept-x representing the requested safe time. The results pointed to 6.57 years after the accident, while using iron as contaminant indicator, or 8.71 years when manganese was considered. Despite of being a relatively low-risk timeframe, the suspension lift should be implemented in phases and monitored for precaution of potential sporadic contamination events, while dredging of the tailings from impacted areas should continue and be accelerated.

Anisotropy component of DTI reveals long-term neuroinflammation following repetitive mild traumatic brain injury in rats

BackgroundThis study aimed to investigate the long-term effects of repetitive mild traumatic brain injury (rmTBI) with varying inter-injury intervals by measuring diffusion tensor metrics, including mean diffusivity (MD), fractional anisotropy (FA), and diffusion magnitude (L) and pure anisotropy (q).MethodsEighteen rats were randomly divided into three groups: short-interval rmTBI (n = 6), long-interval rmTBI (n = 6), and sham controls (n = 6). MD, FA, L, and q values were analyzed from longitudinal diffusion tensor imaging at days 50 and 90 after rmTBI. Immunohistochemical staining against neurons, astrocytes, microglia, and myelin was performed. Analysis of variance, Pearson correlation coefficient, and simple linear regression model were used.ResultsAt day 50 post-rmTBI, lower cortical FA and q values were shown in the short-interval group (p ≤ 0.038). In contrast, higher FA and q values were shown for the long-interval group (p ≤ 0.039) in the corpus callosum. In the ipsilesional external capsule and internal capsule, no significant changes were found in FA, while lower L and q values were shown in the short-interval group (p ≤ 0.028) at day 90. The q values in the external capsule and internal capsule were negatively correlated with the number of microglial cells and the total number of astroglial cells (p ≤ 0.035).ConclusionTensor scalar measurements, such as L and q values, are sensitive to exacerbated chronic injury induced by rmTBI with shorter inter-injury intervals and reflect long-term astrogliosis induced by the cumulative injury.Relevance statementTensor scalar measurements, including L and q values, are potential DTI metrics for detecting long-term and subtle injury following rmTBI; in particular, q values may be used for quantifying remote white matter (WM) changes following rmTBI.Key PointsThe alteration of L and q values was demonstrated after chronic repetitive mild traumatic brain injury.Changing q values were observed in the impact site and remote WM.The lower q values in the remote WM were associated with astrogliosis.Graphical

On-site and in-kind: Compensatory mitigation of California Coastal Zone habitat impacts between 2010 and 2018

Planning development while minimizing negative impacts to sensitive habitats poses a challenge for global natural resource management. After impacts from development are avoided and minimized, remaining adverse impacts may be offset using compensatory mitigation. Along the California coast, the California Coastal Commission (CCC) regulates development and subsequent mitigation for allowable impacts. We reviewed publicly available CCC staff reports for approved projects that impacted coastal habitats and required compensatory mitigation from 2010 to 2018. The median project size was approximately 728 square meters and almost all permanent impacts were mitigated at a >1:1 ratio, with regional and habitat-specific planning regulations driving some variation across the state. We found that wetlands were the most frequently impacted and had higher mitigation ratios. Temporary impacts were almost always mitigated at a 1:1 ratio. While most mitigation was on-site and in-kind, mitigation that was required off-site had a median distance of 4.7 km from the site of impact. Restoration was the most frequent mitigation action, over creation, enhancement, or preservation, but proportions of each action varied across habitat types. While our findings suggest no net loss of habitat area within the California Coastal Zone, the net change in ecosystem function is dependent on the performance of the mitigation projects. This review is only the first step in evaluating the success of compensatory mitigation along California's coast.

Pesticide occurrence and distribution in fogwater collected at four sites at Strasbourg metropolitan between 2015 and 2021

The presence of pesticides in fogwater plays a major role in accumulating relatively substantial levels of trace compounds due to their unique physico-chemical characteristics. The radiation wintertime fog in Alsace has been studied in the past few years (between 2015 and 2021) at four sites (Geispolsheim, Erstein, Strasbourg, and Cronenbourg). Fog samples are extracted using the liquid-liquid extraction (LLE) performed on the XTR Chromabond cartridge coupled with gas/liquid chromatography-tandem mass spectrometry (GC-MS/MS and LC-MS/MS). The samples are found to be contaminated by 25 semi- and non-volatile currently-used and previously-banned pesticides (like procymidone) and 16 organochlorine pesticides (OCPs) at notable levels and high detection frequency (DF). The analysis also reveals that Cronenbourg is the most contaminated site (31.5 ± 3.0 μg. L−1), followed by Erstein (23.1 ± 17.0 μg. L−1), Strasbourg (23.0 ± 3.5 μg. L−1), and Geispolsheim (22.8 ± 7.7 μg. L−1). Pearson and principal component analyses (PCA) prove the simultaneous application of fungicides, insecticides, and herbicides, and their atmospheric transport, mainly through west-southern air currents, from highly impacted sites to near-by urban and less impact sites (Strasbourg and Cronenbourg). The levels of OCPs are found at lower concentrations at all sites than other pesticides, of which dichlorodiphenyltrichloroethane (DDT) and its metabolites have the highest contribution (27%), while hexachlorobenzene (HCB) has the least contribution (3%). Ratio analysis indicates the historical emission of DDTs, whereas a recent and local input of lindane and endosulfan has been observed.

Reduced seagrass resilience due to environmental and anthropogenic effects may lead to future die-off events in Florida Bay

Coastal systems often depend on foundation species such as seagrasses that are supported by self-facilitation. Seagrass meadows, however, are threatened worldwide due to climate change and local human impact, disrupting self-facilitation leading to system instability. Florida Bay is a large seagrass dominated coastal ecosystem that suffered from multiple seagrass mortality events over the last half century driven by hypoxia, high water temperatures, hypersalinity, and high biological oxygen demand. These conditions reduce the amount of photosynthetically-derived oxygen in the plant causing sulphide intrusion into meristematic tissues. Using a bay-wide sampling design and long-term monitoring trends of seagrass condition, we investigated the current state of the meadows, sediment characteristics (e.g., organic matter, sulphide, nutrients) and discuss how climate stressors interact with plant and sediment oxygen dynamics. Our survey revealed that at sites where seagrass had been previously denuded by die-off, the dominant seagrass Thalassia testudinum had not recovered, while the pioneering seagrass Halodule wrightii recolonized the impacted areas. Organic matter and sulphide levels were higher at the impacted sites, apparently a persistent characteristic of the formerly dense T. testudinum meadows in central and western Florida Bay. These sediment conditions promote sulphide intrusion of T. testudinum belowground tissue under anoxic conditions. Plant oxidation initially buffers sulphide intrusion, but disruption of this oxidation mechanism due to changing environmental conditions results in widespread mortality and seagrass community collapse. Climate change cannot be fully mitigated by local management, however, attempts can be made to control critical salinity and oxygen levels by increasing freshwater input, reducing hypersalinity and aiming to keep the internal seagrass oxidation feedback intact. Our study shows that the Florida Bay seagrass ecosystem is still recovering four years post die-off and continues to be susceptible to future climate change and system degradation.

Numerical investigation of residual stress and strain in blades caused by foreign body impact. Comparison of impact modeling on real blade and flat surface

Damage caused by the impact of a foreign object on the turbine blades is caused by the entry of millimeter-sized foreign particles such as sand, stones, or small pieces of broken parts. Consequently, the remaining damage resulting from the impact of a foreign body on the blades is in the form of geometrical discontinuities such as craters or grooves on the blades, which create suitable conditions for the creation and growth of cracks and the complete failure of the blades. One of the most important aspects of foreign body impact damage is the study of the resulting residual stresses at the impact site, which plays a significant role in the creation and growth of cracks. In the present article, the main aim of this work was to analyze the residual stresses due to foreign object damage by expanding the simulation on the blades, considering a real blade model as well as the leading-edge curvature effect. To validate the numerical modeling, the impact of a spherical particle on a flat plate was modeled and the residual stresses and damages resulting from the modeling were compared to the experimental results available in the articles. Finally, the impact of the spherical foreign body on different places of the leading edge of a blade with different impact velocities was investigated. Moreover, the examined blade sample was replaced with a plate with the same material, and the impact of the foreign object on the flat surface was modeled for two different service temperatures. In this study, the resulting residual stresses and strains in three critical areas were compared.

Tire-derived contaminants 6PPD and 6PPD-Q: Analysis, sample handling, and reconnaissance of United States stream exposures

The environmental ubiquity of tire and road wear particles (TRWP) underscores the need to understand the occurrence, persistence, and environmental effects of tire-related chemicals in aquatic ecosystems. One such chemical is 6PPD-quinone (6PPD-Q), a transformation product of the tire antioxidant 6PPD. In urban stormwater runoff 6PPD-Q can exceed acute toxicity thresholds for several salmonid species and is being implicated in significant coho salmon losses in the Pacific Northwest. There is a critical need to understand the prevalence of 6PPD-Q across watersheds to identify habitats heavily affected by TRWPs. We conducted a reconnaissance of 6PPD and 6PPD-Q in surface waters across the United States from sites (N = 94) with varying land use (urban, agricultural, and forested) and streamflow to better understand stream exposures. A rapid, low-volume direct-inject, liquid chromatography mass spectrometry method was developed for the quantitation of 6PPD-Q and screening for 6PPD. Laboratory holding times, bottle material, headspace, and filter materials were investigated to inform best practices for 6PPD-Q sampling and analysis. Glass bottles with PTFE-lined caps minimized sorption and borosilicate glass fiber filters provided the highest recovery. 6PPD-Q was stable for at least 5 months in pure laboratory solutions and for 75 days at 5 °C with minimal headspace in the investigated surface water and stormwaters. Results also indicated samples can be frozen to extend holding times. 6PPD was not detected in any of the 526 analyzed samples and there were no detections of 6PPD-Q at agricultural or forested sites. 6PPD-Q was frequently detected in stormwater (57%, N = 90) and from urban impacted sites (45%, N = 276) with concentrations ranging from 0.002 to 0.29 μg/L. The highest concentrations, above the lethal level for coho salmon, occurred during stormwater runoff events. This highlights the importance of capturing episodic runoff events in urban areas near ecologically relevant habitat or nursery grounds for sensitive species.

SURFACTANT–POLYMER FLOODING: GEOCHEMICAL MONITORING OF THE PROPERTIES OF FORMATION FLUIDS AT THE IMPACT AREA

Chemical flooding methods improve oil extraction after standard waterflooding processes. Chemical EOR methods modify different properties of fluids and/or rock to mobilize the remaining oil. It is expected that the residual oil will be different in properties than conventional. A new technology is presented to study a surfactant–polymer flooding, based on a periodic sampling and measuring properties of oil and water during 15 months. The study area is a terrigenous reservoir with 3 chemical injection wells and 16 production wells. High-precision mass spectrometry methods were carried out on each sample, which made it possible to evaluate the effectiveness of ongoing work on chemical flooding. At each sampling date, 2D reservoir model was built to track these changes in the study area. It is shown that the composition of the water has changed - highly permeable channels were closed and formation waters were involved in the production. The properties of oil have also changed - depending on the site of impact, there are areas with more degraded oil in production after the injection of chemicals. Geochemical monitoring shows the redistribution of filtration flow directions in the reservoir volume.

Bed-scale rockweed harvest findings are not altered by study critiques, a response to Seeley et al.

Seeley et al., 2024 (Comment: A reexamination of Johnston et al., 2023, bed-scale impact and recovery of a commercially important intertidal seaweed. J. Exp. Mar. Biol. Ecol. 574) describe a number of reasons that they believe our study's experimental design was flawed and our inferential conclusions were incorrect. We believe that these claims are the result of misunderstandings of the objectives behind our sampling design and statistical analyses. Throughout this response to Seeley et al., we reiterate key objectives of our study design: examining rockweed harvest at a whole-bed scale, realistically capturing the effects of current commercial rockweed harvest methods in Maine, and using coastwide site averages to estimate effect sizes of rockweed harvest. The first claim by Seeley et al. that our study design severely undersampled rockweed beds ignores established sampling methodologies in rockweed research. The suggestion that our sampling design resulted in impact sites that were de facto control sites is not supported by our analyses that showed greater declines in mean rockweed height and biomass at impact sites relative to control sites. In response to their second claim that rockweed companies had control of key elements of our study design and execution, we detail our specific approaches to lessen any possibility for such conflicts to bias our findings. In the final section of our response, we present power analyses in support of our Before-After Control-Impact study design and we highlight the statistically significant effects of treatment on rockweed biomass that contradict Seeley et al.'s claim that we drew conclusions about biomass recovery based solely on large p-values.

Conceptualizing Controlling Factors for PFAS Salting Out in Groundwater Discharge Zones Along Sandy Beaches.

Understanding fate and transport processes for per- and poly-fluoroalkyl substances (PFAS) is critical for managing impacted sites. "PFAS Salting Out" in groundwater, defined herein, is an understudied process where PFAS in fresh groundwater mixes with saline groundwater near marine shorelines, which increases sorption of PFAS to aquifer solids. While sorption reduces PFAS mass discharge to marine surface water, the fraction that sorbs to beach sediments may be mobilized under future salinity changes. The objective of this study was to conceptually explore the potential for PFAS Salting Out in sandy beach environments and to perform a preliminary broad-scale characterization of sandy shoreline areas in the continental U.S. While no site-specific PFAS data were collected, our conceptual approach involved developing a multivariate regression model that assessed how tidal amplitude and freshwater submarine groundwater discharge affect the mixing of fresh and saline groundwater in sandy coastal aquifers. We then applied this model to 143 U.S. shoreline areas with sandy beaches (21% of total beaches in the USA), indirectly mapping potential salinity increases in shallow freshwater PFAS plumes as low (<10 ppt), medium (10-20 ppt), or high (>20 ppt) along groundwater flow paths before reaching the ocean. Higher potential salinity increases were observed in West Coast bays and the North Atlantic coastline, due to the combination of moderate to large tides and large fresh groundwater discharge rates, while lower increases occurred along the Gulf of Mexico and the southern Florida Atlantic coast. The salinity increases were used to estimate potential perfluorooctane sulfonic acid (PFOS) sorption in groundwater due to salting out processes. Low-category shorelines may see a 1- to 2.5-fold increase in sorption of PFOS, medium-category a 2.0- to 6.4-fold increase, and high-category a 3.8- to 25-fold increase in PFOS sorption. The analysis presented provides a first critical step in developing a large-scale approach to classify the PFAS Salting Out potential along shorelines and the limitations of the approach adopted highlights important areas for further research.

Splicing-specific transcriptome-wide association uncovers genetic mechanisms for schizophrenia

Recent studies have highlighted the essential role of RNA splicing, a key mechanism of alternative RNA processing, in establishing connections between genetic variations and disease. Genetic loci influencing RNA splicing variations show considerable influence on complex traits, possibly surpassing those affecting total gene expression. Dysregulated RNA splicing has emerged as a major potential contributor to neurological and psychiatric disorders, likely due to the exceptionally high prevalence of alternatively spliced genes in the human brain. Nevertheless, establishing direct associations between genetically altered splicing and complex traits has remained an enduring challenge. We introduce Spliced-Transcriptome-Wide Associations (SpliTWAS) to integrate alternative splicing information with genome-wide association studies to pinpoint genes linked to traits through exon splicing events. We applied SpliTWAS to two schizophrenia (SCZ) RNA-sequencing datasets, BrainGVEX and CommonMind, revealing 137 and 88 trait-associated exons (in 84 and 67 genes), respectively. Enriched biological functions in the associated gene sets converged on neuronal function and development, immune cell activation, and cellular transport, which are highly relevant to SCZ. SpliTWAS variants impacted RNA-binding protein binding sites, revealing potential disruption of RNA-protein interactions affecting splicing. We extended the probabilistic fine-mapping method FOCUS to the exon level, identifying 36 genes and 48 exons as putatively causal for SCZ. We highlight VPS45 and APOPT1, where splicing of specific exons was associated with disease risk, eluding detection by conventional gene expression analysis. Collectively, this study supports the substantial role of alternative splicing in shaping the genetic basis of SCZ, providing a valuable approach for future investigations in this area.

Detecting mining impacts on freshwater ecosystems using replicated sampling before and after the impact

Detecting human impact on freshwater ecosystems is problematic without rigorous assessment of temporal changes. Assessments of mining impacts are further complicated by the strong influence of local catchment geology on surface waters even in unmined environments. Such influence cannot be effectively considered by using broad-scale reference frameworks based on regionalization and stream types. Using the BACI (Before-After Control-Impact) design, we examined the impact of mining discharges on freshwater algae and macroinvertebrate communities resulting from the rerouting of treated wastewaters through a pipeline to larger water bodies in Northern and North-Eastern Finland. Impacted sites and control sites were sampled 1 to 2 years before and 1 to 3 years after the pipelines became operational. Stream diatom communities recovered from past loadings upstream of the pipeline (which was no longer impacted by wastewaters) after rerouting of the wastewaters, while no changes downstream from the pipeline were detected. Upstream from the pipeline, diatom species richness increased and changes in relative abundances of the most common diatom taxa as well as in the overall community composition were observed. The effects of the pipeline were less evident for stream macroinvertebrate communities. There was an indication that regional reference conditions used in national biomonitoring may not represent diatom communities in areas with a strong geochemical background influence. Lake profundal macroinvertebrate communities were impacted by past loadings before the construction of the pipeline, and the influence of the pipeline was observed only as changes in the abundances of a few individual species such as phantom midges (which increased in abundance in response to discharges directed through the pipeline). Our results highlight the variable influence of mining discharges on aquatic communities. Statistically strong monitoring programmes, such as BACI designs, are clearly needed to detect these influences.

Fish assemblage and functional trait responses to small‐dam removal

Abstract Dams are one of the greatest threats to freshwater biodiversity and efforts to remove dams to restore riverine systems are increasing. However, dam‐removal studies have primarily focused on taxonomic responses to large dam removals with little work on the functional trait responses of fish to small‐dam removals; such a focus limits the application of results in regions with different taxonomic compositions. We explored taxonomic and functional trait responses of fish assemblages to two small‐dam removals over 10 years using a Multiple Before After Control Impact design at a dammed and an undammed river. Eight life‐history traits were used to calculate functional diversity (RaoQ) and determine the position of each fish species within a multivariate life‐history space relative to three life‐history strategy endpoints: opportunistic, periodic, and equilibrium. The distance of each species relative to these endpoints was used to calculate community weighted means (CWM), allowing us to examine the shift in life‐history strategy of a given assemblage after dam removal. Based on life‐history theory, we predicted a decrease in the CWM of equilibrium strategists and an increase in the CWM opportunistic strategists after dam removal. For the dammed river, we observed changes in assemblage structure at both the control and impact sites driven primarily by shifts from a lentic to lotic assemblage, with the most apparent change occurring in the formerly impounded sites. These changes tended to occur within 1 year, suggesting rapid colonization by lotic species after habitat change. By contrast, no change in assemblage structure was found for the undammed river, suggesting that dam removal was the primary driver of the shifts in assemblage structure observed in the dammed river. We found no change in the CWM of periodic strategists or RaoQ of all life‐history traits at any site after dam removal. Based on CWM, life‐history strategies shifted in response to dam removal at impounded sites where equilibrium strategists decreased and opportunistic strategists tended to increase after the impounded sites changed from a stable lentic environment to an unstable lotic environment, supporting predictions made by life‐history theory. Our results suggest that small‐dam removal may provide ecological benefits by restoring fish assemblages to a more natural riverine state and reversing the negative effects of dam construction on the ecosystem. We demonstrate that combining both trait‐based and taxonomic approaches can improve our ecological understanding of the impacts of dam removal on fish assemblages and provide relevant data for local management.