Nutrient loading is a major threat to estuaries and coastal environments worldwide, therefore, it is critical that we have good monitoring tools to detect early signs of degradation in these ecologically important and vulnerable ecosystems. Traditionally, bottom-dwelling macroinvertebrates have been used for ecological health assessment but recent advances in environmental genomics mean we can now characterize less visible forms of biodiversity, offering a more holistic view of the ecosystem and potentially providing early warning signals of disturbance. We carried out a manipulative nutrient enrichment experiment (0, 150 and 600 g N fertilizer m⁻²) in two estuaries in New Zealand to assess the effects of nutrient loading on benthic communities. After seven months of enrichment, environmental DNA (eDNA) metabarcoding was used to examine the response of eukaryotic (18S rRNA), diatom only (rbcL) and bacterial (16S rRNA) communities. Multivariate analyses demonstrated changes in eukaryotic, diatom and bacterial communities in response to nutrient enrichment at both sites, despite differing environmental conditions. These patterns aligned with changes in macrofaunal communities identified using traditional morphological techniques, confirming concordance between disturbance indicators detected by eDNA and current monitoring approaches. Clear shifts in eukaryotic and bacterial indicator taxa were seen in response to nutrient loading while changes in diatom only communities were more subtle. Community changes were discernible between 0 and 150 g N m⁻² treatments, suggesting that estuary health assessment tools could be developed to detect early signs of degradation. Increasing variation in community structure associated with nutrient loading could also be used as an indicator of stress or approaching tipping points. This work represents a first step towards the development of molecular-based estuary monitoring tools, which could provide a more holistic and standardized approach to ecosystem health assessment with faster turn-around times and lower costs.

Large benthic foraminifers (LBFs) are significant contributors to coral island formation in the Pacific Ocean. In recent years, the population of LBFs has decreased because of the increase in anthropogenic influences, such as wastewater (WW) discharge. To implement efficient mitigation measures, pollution tolerance in LBFs should be understood. However, the effects of WW on LBFs and their symbionts have not yet been demonstrated. This study examined the changes in the photosynthetic efficiency (Y[II]) of Calcarina gaudichaudii and Baculogypsina sphaerulata in response to WW by using a pulse-amplitude-modulation fluorometer. These LBFs were exposed to WW with different dilution levels for 22 days. The Y(II) values of the LBFs were found to deteriorate within 1–2 days. However, the Y(II) values both deteriorated and were enhanced in the experiments, thus indicating that WW contains both harmful and beneficial components. Baculogypsina sphaerulata showed an earlier response and greater sensitivity to WW and a higher epibiont infestation than C. gaudichaudii. This result can be attributed to the differences in the physiological and morphological responses of distinct LBFs. A sequencing analysis of 18S rDNA confirmed that the dominant eukaryotic symbionts in the two LBFs studied were Ochrophyta and Labyrinthulomycetes. These eukaryotic symbionts were released and attached as epibionts onto LBFs that were exposed to WW, thus leading to an increase in inactive LBFs. The Shannon–Weaver and Simpson diversity indices revealed that eukaryotic symbiont communities decreased in biodiversity after exposure to WW because of the abundance of algal symbionts. On the basis of these results, we conclude that WW, even with 10,000 × dilution, causes a decrease in active LBF populations owing to the release of eukaryotic symbionts, the decrease in biodiversity, and the infestation of epibionts even though Y(II) is temporarily enhanced. These responses are more significant in B. sphaerulata than in C. gaudichaudii.

The hydro-acoustic noise radiating from underwater tunnels during vehicle passage may be harmful to aquatic fauna, and this is a particular concern for endangered species. Therefore, the effects of underwater noise radiation and propagation on aquatic biodiversity must be investigated. In this study, the dynamic response of the sediment and tunnel structure in the Yangtze River in China was explored by conducting a field test, and the associated noise radiation from the tunnel was recorded and investigated. A three-dimensional numerical model was then developed to simulate the vibration of the tunnel-sediment coupling system induced by random traffic-flow models. Next, a modal acoustic transfer vector-based method was used to predict underwater noise radiation by use of a three-dimensional finite-element acoustic model. Finally, the accuracy of the simulated results was verified by comparison with measurements. The results showed that the noise radiation induced by passing vehicles was approximately 14 dB greater than the background noise, with a main frequency range of 12–25 Hz. The random traffic-flow model had obvious influence of the simulated noise level above 20 Hz. Vehicle-induced underwater noise may thus have a direct effect on fish species that can perceive low-frequency sound pressure. The proposed method can be used for further investigation of methods to reduce the effect of underwater noise on aquatic fauna, especially endangered species.

Nitrogen (N) deposition in China may increase due to urbanization and economic growth. Current research has considered the ecological significance under the assumption of increasing N deposition. Atmospheric N deposition tending toward levelling or declining has been observed in China. Such potential recovery and responses of high N loads ecosystems under decreasing atmospheric N deposition scenarios have yet to be adequately investigated. This work reviews existing literature to consider possible responses of carbon (C) sequestration, biodiversity and species composition, soil acidification, and greenhouse emissions in ecosystems responding to recent patterns of N deposition. Potential effects of N composition and internal ratios may be further explored through state-of-the-art N addition experiments and model development.

Plant species occurrence in Europe is affected by changes in nitrogen deposition and climate. Insight into potential future effects of those changes can be derived by a model approach based on field-based empirical evidence on a continental scale. In this paper, we present a newly developed empirical model PROPS, predicting the occurrence probabilities of plant species in response to a combination of climatic factors, nitrogen deposition and soil properties. Parameters included were temperature, precipitation, nitrogen deposition, soil pH and soil C/N ratio. The PROPS model was fitted to plant species occurrence data of about 800,000 European relevés with estimated values for pH and soil C/N ratio and interpolated climate and modelled N deposition data obtained from the Ensemble meteo data set and EMEP model results, respectively. The model was validated on an independent data set. The test of ten species against field data gave an average Pearson’s r-value of 0.79.PROPS was applied to a grassland and a heathland site to evaluate the effect of scenarios for nitrogen deposition and climate change on the Habitat Suitability Index (HSI), being the average of the relative probabilities, compared to the maximum probability, of all target species in a habitat. Results for the period 1930–2050 showed that an initial increase and later decrease in nitrogen deposition led to a pronounced decrease in HSI, and with dropping nitrogen deposition to an increase of the HSI. The effect of climate change appeared to be limited, resulting in a slight increase in HSI.

Large amounts of non-biodegradable plastics are currently deposited on beach-dune systems, and biodegradable plastics could enter these already declining habitats in coming years. Yet, the impacts of plastics on vegetative recruitment, a plant strategy playing a key role in dune stabilization, are unknown. Whether these pollutants interact with increased atmospheric nitrogen (N) deposition, a major global driver of plant biodiversity loss, in affecting plant communities of such nutrient-poor habitats, and how plant-plant interactions mediate their effects need to be explored. In a one-year field experiments, we examined individual and combined effects of plastic (non-biodegradable, biodegradable), N deposition (ambient, elevated) and biotic condition (no interaction, interaction with a conspecific or with a hetero-specific) on the colonization success and growth of vegetative propagules of dune plants. Thinopyrum junceum and Sporobolus pumilus were chosen as models because they co-occur along Mediterranean dunes and differ in ecological role (dune- vs. non dune-building) and photosynthetic pathway (C3 vs. C4). For both species, survival probability was reduced by non-biodegradable plastic and elevated N by up to 100%. Thinopyrum junceum survival was also reduced by S. pumilus presence. Elevated N and biodegradable plastic reduced T. junceum shoot biomass when grown alone and with a conspecific, respectively; these factors in combination mitigated their negative individual effects on root biomass. Biodegradable plastic increased S. pumilus shoot and root biomass, and in combination with elevated N caused a greater biomass investment in belowground (root plus rhizome) than aboveground organs. Non-biodegradable plastic may be a further threat to dune habitats by reducing plant colonization. Biodegradable plastic and increased N deposition could favour the generalist S. pumilus and hinder the dune-building T. junceum. These findings highlight the urgency of implementing measures for preventing plastic deposition on beaches and reducing N input.

Wastewater discharges from dairy industries can cause a range of harmful effects in aquatic ecosystems, including a decline in biodiversity due to species evasion. Therefore, it is important to know the purification potential of rivers for the removal of pollutants released in dairy wastewater (DWW). The hypothesis adopted in this work was that the release of DWW into stretches of the Ribeirão dos Pombos River (São Paulo State, Brazil) might trigger an avoidance response, resulting in fish migrating to other regions, with the response being greater when the self-cleaning potential of the river is smaller. Therefore, the goals of the present study were to: (i) investigate how land use and seasonality of the rainfall regime influence the quality of the water in different areas of the river (P1: river source; P2: urban region; P3: rural region); (ii) assess the potential of the river to purify DWW; and (iii) evaluate the potential toxicity and repellency of DWW to the freshwater fish Danio rerio, using acute toxicity (mortality) and non-forced avoidance tests, respectively. P1 was shown to be the most preserved area. The chemical composition of the river varied seasonally, with higher concentrations of Cl⁻ and SO₄²⁻ at P3 during the rainy period. The river purification potential for DWW was higher at P2, due to greater microbiological activity (associated with higher BOD). The DWW was more acutely toxic in water from P2. The avoidance response was strongly determined by the concentration of DWW, especially for water from P2. The high capacity for self-cleaning at P2 did not seem sufficient to maintain the stability of the ecosystem. Finally, the non-forced exposure system proved to be a suitable approach that can assist in predicting how contaminants may affect the spatial distributions of organisms.

Nutrient effluents from urban and agricultural inputs have resulted in high concentrations of nitrate in freshwater ecosystems. Exposure to nitrate can be particularly threatening to aquatic organisms, but a quantitative synthesis of the overall effects on amphibians, amphipods and fish is currently unavailable. Moreover, in disturbed ecosystems, organisms are unlikely to face a single stressor in isolation, and interactions among environmental stressors can enhance the negative effects of nitrate on organisms. Here, the effects of elevated nitrate on activity level, deformity rates, hatching success, growth and survival of three taxonomic groups of aquatically respiring organisms are documented. Effect sizes were extracted from 68 studies and analysed using meta-analytical techniques. The influence of nitrate on life-stages was also assessed. A factorial meta-analysis was conducted to examine the effect of nitrate and its interaction with other ecological stressors on organismal survival. Overall, the impacts of nitrate are biased towards amphibians (46 studies) and fish (13 studies), and less is known about amphipods (five studies). We found that exposure to nitrate translates to a 79% decrease in activity, a 29% decrease in growth, and reduces survival by 62%. Nitrate exposure also increases developmental deformities but does not affect hatching success. Nitrate exposure was found to influence all life-stages except embryos. Differences in the sensitivity of nitrate among taxonomic groups tended to be negligible. The factorial meta-analysis (14 amphibians and two amphipod studies) showed that nitrate in combination with other stressors affects survival in a non-additive manner. Our results indicate that nitrate can have strong effects on aquatic organisms and can interact with other environmental stressors which compound the negative effects on survival. Overall, the impacts of nitrate and additional stressors are complex requiring a holistic approach to better conserve freshwater biodiversity in the face of ongoing global change.

The presence of Eschericia coli O157:H7 in the natural environment is a serious threat to human health. The native microbial community in soil plays an important role in resisting E. coli O157:H7 invasion. This study examined the responses of soil microbial community to E. coli O157:H7 invasion during a 32-day incubation. The E. coli O157:H7 persisted longer in γ-irradiated soil than non-irradiated soil while glucose addition decreased its persistence in the irradiated soil which was associated with an increasing recovery of the native community. The invasion of E. coli O157:H7 increased soil organic carbon mineralization, an indicator of microbial activity, in both non-irradiated and irradiated soils, while glucose addition significantly promoted the carbon mineralization process. The 16S rRNA sequencing data showed the gradual recovery of the native bacterial population including specific taxa such as proteobacteria and actinobacteria following irradiation. It is concluded that soil microbial function and structure can affect persistence of E. coli O157:H7 and that lower biodiversity of the native community favors its persistence.

The Atrato watershed is a rainforest that supports exceptional wildlife species and is considered one of the most biodiversity-rich areas on the planet, currently threatened by massive gold mining. Aimed to protect this natural resource, the Constitutional Court of Colombia declared the river subject to rights. The objective of this study was to quantify trace elements in sediments and fish from Atrato watershed, assessing their environmental and human health risk. Forty-two trace elements were quantified using ICP-MS. Thirty-one elements increased their concentration downstream the river. Concentration Factors (CF) suggest sediments were moderately polluted by Cr, Cu, Cd, and strongly polluted by As. Most stations had Cr (98%) and Ni (78%) concentrations greater than the Probable Effect Concentration (PEC) criteria. Together, toxic elements generate a Pollution Load Index (PLI) and a Potential Ecological Risk Index (RI) that categorized 54% of the sediments as polluted, and 90% as moderate polluted, respectively. Hemiancistrus wilsoni, a low trophic guild fish species, had the greater average levels for Ni, Cu, As and Cd, among other elements. Rubidium and Cs showed a positive correlation with fish trophic level, suggesting these two metals biomagnify in the food chain. The Hazard Quotient (HQ) for As was greater than 1 for several species, indicating a potential risk to human health. Collectively, data suggest gold mining carried out in this biodiversity hotspot releases toxic elements that have abrogated sediment quality in Atrato River, and their incorporation in the trophic chain constitutes a large threat on environmental and human health due to fish consumption. Urgent legal and civil actions should be implemented to halt massive mining-driven deforestation to enforce Atrato River rights.