Hypoxia and salinity constrain the sediment microbiota-mediated N removal potential in an estuary: A multi-trophic interrelationship perspective

Reactive nitrogen (N) enrichment is a common environmental problem in estuarine ecosystems, while the microbial-mediated N removal process is complicated for other multi-environmental factors. Therefore, A systematic investigation is necessary to understand the multi-trophic microbiota-mediated N removal characteristics under various environmental factors in estuaries. Here, we studied how multiple factors affect the multi-trophic microbiota-mediated N removal potential (denitrification and anammox) and N2O emission along a river-estuary-bay continuum in southeastern China using the environmental DNA (eDNA) approach. Results suggested that hypoxia and salinity were the dominant environmental factors affecting multi-trophic microbiota-mediated N removal in the estuary. The synergistic effect of hypoxia and salinity contributed to the loss of taxonomic (MultiTaxa) and phylogenetic (MultiPhyl) diversity across multi-trophic microbiota and enhanced the interdependence among multi-trophic microbiota in the estuary. The N removal potential calculated as the activities of key N removal enzymes was also significantly constrained in the estuary (0.011), compared with the river (0.257) and bay (0.461). Structural equation modeling illustrated that metazoans were central to all sediment N removal potential regulatory pathways. The top-down forces (predation by metazoans) restrained the growth of heterotrophic bacteria, which may affect microbial N removal processes in the sediment. Furthermore, we found that the hypoxia and salinity exacerbated the N2O emission in the estuary. This study clarifies that hypoxia and salinity constrain estuarine multi-trophic microbiota-mediated N removal potential and highlights the important role of multi-trophic interactions in estuarine N removal, providing a new perspective on mitigating estuarine N accumulation.

Hydro-bio-geo-socio-chemical interactions and the sustainability of residential landscapes

Residential landscapes are essential to the sustainability of large areas of the United States. However, spatial and temporal variation across multiple domains complicates developing policies to balance these systems' environmental, economic, and equity dimensions. We conducted multidisciplinary studies in the Baltimore, MD, USA, metropolitan area to identify locations (hotspots) or times (hot moments) with a disproportionate influence on nitrogen export, a widespread environmental concern. Results showed high variation in the inherent vulnerability/sensitivity of individual parcels to cause environmental damage and in the knowledge and practices of individual managers. To the extent that hotspots are the result of management choices by homeowners, there are straightforward approaches to improve outcomes, e.g. fertilizer restrictions and incentives to reduce fertilizer use. If, however, hotspots arise from the configuration and inherent characteristics of parcels and neighborhoods, efforts to improve outcomes may involve more intensive and complex interventions, such as conversion to alternative ecosystem types.

Urbanization and fragmentation have opposing effects on soil nitrogen availability in temperate forest ecosystems

Nitrogen (N) availability relative to plant demand has been declining in recent years in terrestrial ecosystems throughout the world, a phenomenon known as N oligotrophication. The temperate forests of the northeastern U.S. have experienced a particularly steep decline in bioavailable N, which is expected to be exacerbated by climate change. This region has also experienced rapid urban expansion in recent decades that leads to forest fragmentation, and it is unknown whether and how these changes affect N availability and uptake by forest trees. Many studies have examined the impact of either urbanization or forest fragmentation on nitrogen (N) cycling, but none to our knowledge have focused on the combined effects of these co-occurring environmental changes. We examined the effects of urbanization and fragmentation on oak-dominated (Quercus spp.) forests along an urban to rural gradient from Boston to central Massachusetts (MA). At eight study sites along the urbanization gradient, plant and soil measurements were made along a 90 m transect from a developed edge to an intact forest interior. Rates of net ammonification, net mineralization, and foliar N concentrations were significantly higher in urban than rural sites, while net nitrification and foliar C:N were not different between urban and rural forests. At urban sites, foliar N and net ammonification and mineralization were higher at forest interiors compared to edges, while net nitrification and foliar C:N were higher at rural forest edges than interiors. These results indicate that urban forests in the northeastern U.S. have greater soil N availability and N uptake by trees compared to rural forests, counteracting the trend for widespread N oligotrophication in temperate forests around the globe. Such increases in available N are diminished at forest edges, however, demonstrating that forest fragmentation has the opposite effect of urbanization on coupled N availability and demand by trees.

Land-Water Transport and Sources of Nitrogen Pollution Affecting the Structure and Function of Riverine Microbial Communities

The characterization of variations in riverine microbiota that stem from contaminant sources and transport modes is important for understanding biogeochemical processes. However, the association between complex anthropogenic nitrogen pollution and bacteria has not been extensively investigated owing to the difficulties faced while determining the distribution of nitrogen contaminants in watersheds. Here, we employed the Soil and Water Assessment Tool alongside microbiological analysis to explore microbial characteristics and their responses to complex nitrogen pollution patterns. Significant variations in microbial communities were observed in sub-basins with distinct land-water pollution transport modes. Point source-dominated areas (PSDAs) exhibited reduced microbial diversity, high number of denitrification groups, and increased nitrogen cycling compared with others. The negative relative deviations (-3.38) between the measured and simulated nitrate concentrations in PSDAs indicated that nitrate removal was more effective in PSDAs. Pollution sources were also closely associated with microbiota. Effluents from concentrated animal feeding operations were the primary factors relating to the microbiota compositions in PSDAs and balanced areas. In nonpoint source-dominated areas, contaminants from septic tanks become the most relevant sources to microbial community structures. Overall, this study expands our knowledge regarding microbial biogeochemistry in catchments and beyond by linking specific nitrogen pollution scenarios to microorganisms.

Cross-media transfer of nitrogen pollution in the fast-urbanized Greater Bay Area of China: Trends and essential control paths

For urban agglomerations in the bay area, which concentrate multiple environmental elements and intense anthropogenic activities, comprehensive control of nitrogen pollution is particularly challenging due to diverse cross-media migration and transformation forms of nitrogen pollutants. Existing studies on urban nitrogen metabolism mainly focused on quantification of nitrogen flux, without systematic consideration of physiochemical changes of nitrogen between environmental media. This study conducted a dynamic simulation of nitrogen cross-media metabolism in urban agglomeration over 30 consecutive years, and recognized the types, quantities, and trends of cross-media transfer of nitrogen pollution as well as pollution control paths based on ecological network analysis and scenario analysis. Taking the Guangdong-Hong Kong-Macao Greater Bay Area as the case, results show that during its fast-urbanized stage in 1989-2018, more than 25% of the total nitrogen pollution emissions were transferred from other media. The higher degree of imbalance between the socioeconomic system and the soil in the nitrogen metabolic network emphasizes the increased pressure and necessity of pollution control of nitrogen in the solid state with urban development. Promoting fertilizer reduction and sludge land use are priority paths for collaborative control of cross-media nitrogen pollution. The study provides methods to systematically analyze the features of cross-media transfer of nitrogen pollution at the city level, and accordingly propose paths aiming at sustainable urban nitrogen management with multi-media integrity and synergy.

Slight flow volume rises increase nitrogen loading to nitrogen-rich river, while dramatic flow volume rises promote nitrogen consumption

Concentrated rainfall and water transfer projects result in slight and dramatic increases in flow volume over short periods of time, causing nitrogen recontamination in the water-receiving areas of nitrogen-rich rivers. This study coupled hydrodynamic and biochemical reaction models to construct a model for quantifying diffusive transport and transformation fluxes of nitrogen across the water-sediment interface and analysed possible changes in the relative abundance of microbial functional genes using high-throughput sequencing techniques. In this study, the processes of ammonium (NH₄⁺-N) and nitrate (NO₃^--N) nitrogen release and sedimentation with resuspended particles, as well as mineralisation, nitrification, and denitrification processes were investigated at the water-sediment interface in the Fu River during slight and dramatic increases in flow volume caused by concentrated rainfall and water diversion projects. Specifically, a slight flow volume rise increased the release of NH₄⁺-N from the sediment, inhibited sedimentation of NO₃^--N, decreased the mineralisation rate, increased the nitrification rate, and had little effect on the denitrification process, ultimately increasing the nitrogen load to the river water. A dramatic increase in flow volume simultaneously increased NH₄⁺-N and NO₃^--N exchange fluxes, inhibited the mineralisation process, promoted nitrification-denitrification processes, and increased inorganic nitrogen consumption in the river. This study provides a solution for the re-pollution of rivers that occurs during the implementation of reservoir management and water diversion projects. Furthermore, these results indicate a potential global nitrogen sink that may have been overlooked.

New insights into nitrogen removal potential in urban river by revealing the importance of microbial community succession on suspended particulate matter

The importance of suspended particulate matter (SPM) in nitrogen removal from aquatic environments has been acknowledged in recent years by recognizing the role of attached microbes. However, the succession of attached microbes on suspended particles and their role in nitrogen removal under specific surface microenvironment are still unknown. In this study, the causation among characteristics of SPM, composition and diversity of particle-attached microbial communities, and abundances of nitrogen-related genes in urban rivers was firstly quantitatively established by combing spectroscopy, 16 S rRNA amplicon sequencing, absolute gene quantification and supervised integrated machine learning. SPM in urban rivers, coated with organic layers, was mainly composed of silt and clay (87.59-96.87%) with D50 (medium particle size) of 8.636-30.130 μm. In terms of material composition of SPM, primary mineral was quartz and the four most abundant elements were O, Si, C, Al. The principal functional groups on SPM were hydroxyl and amide. Furthermore, samples with low, medium and high levels of ammoxidation potential were classified into three groups, among which significant differences of microbial communities were found. Samples were also separated into three groups with low, medium and high levels of denitrification potential and significant differences occurred among groups. The particle size, content of functional groups and concentration of SPM were identified as the most significant factors related with microbial communities, playing an important role in succession of particle-attached microbes. In addition, the path model revealed the significantly positive effect of organic matter and particle size on the microbial communities and potential nitrogen removal. The content of hydroxyl and temperature were identified as the most effective predicting factors for ammoxidation potential and denitrification potential respectively by Random Forests Regression models, which had good predictive performances for potential of ammoxidation (R² = 0.71) and denitrification (R² = 0.61). These results provide a basis for quickly assessing the ability of nitrogen removal in urban rivers.

Unconventional microbial mechanisms for the key factors influencing inorganic nitrogen removal in stormwater bioretention columns

Bioretention systems are environmentally friendly measures to control the amount of water and pollutants in urban stormwater runoff, and their treatment performance for inorganic N strongly depends on various microbial processes. However, microbial responses to variations of N mass reduction in bioretention systems are complex and poorly understood, which is not conducive to management designs. In the present study, a series of bioretention columns were established to monitor their fate performance for inorganic N (NH4+and NO3-) by using different configurations and by dosing with simulated stormwater events. The results showed that NH4+ was efficiently oxidized to NO3-, mainly by ammonia- and nitrite-oxidizing bacteria in the oxic media, regardless of the configurations of the bioretention systems or stormwater conditions. In contrast, NO3- removal pathways varied greatly in different columns. The presence of vegetation efficiently improved NO3-mass reduction through root assimilation and enhancement of microbial NO3- reduction in the rhizosphere. The construction of an organic-rich saturation zone can make the redox potential too low for heterotrophic denitrification to occur, so as to ensure high NO3- mass reduction mainly via stimulating chemolithotrophic NO3- reduction coupled with oxidation of reductive sulfur compounds derived from the bio-reduction of sulfate. In contrast, in the organic-poor saturation zone, multiple oligotrophic NO3- reduction pathways may be responsible for the high NO3- mass reduction. These findings highlight the necessity of considering the variation of N bio-transformation pathways for inorganic N removal in the configuration of bioretention systems.

Denitrifying bioreactor microbiome: Understanding pollution swapping and potential for improved performance

Denitrifying woodchip bioreactors are a best management practice to reduce nitrate-nitrogen (NO₃ -N) loading to surface waters from agricultural subsurface drainage. Their effectiveness has been proven in many studies, although variable results with respect to performance indicators have been observed. This paper serves the purpose of synthesizing the current state of the science in terms of the microbial community, its impact on the consistency of bioreactor performance, and its role in the production of potential harmful by-products including greenhouse gases, sulfate reduction, and methylmercury. Microbial processes other than denitrification have been observed in these bioreactor systems, including dissimilatory nitrate reduction to ammonia (DNRA) and anaerobic ammonium oxidation (anammox). Specific gene targets for denitrification, DNRA, anammox, and the production of harmful by-products are identified from bioreactor studies and other environmentally relevant systems for application in bioreactor studies. Lastly, cellulose depletion has been observed over time via increasing ligno-cellulose indices, therefore, the microbial metabolism of cellulose is an important function for bioreactor performance and management. Future work should draw from the knowledge of soil and wetland ecology to inform the study of bioreactor microbiomes.

Photosynthesis, fluorescence, and biomass responses of white oak seedlings to urban soil and air temperature effects

Urban forest patches can provide critical ecosystem services and their ability to regenerate native tree species is critical to their sustainability. Little is known about native tree seedling establishment and physiological function in urban ecosystems. This growth chamber study examined the effects of urban soil and air temperatures on white oak (Quercus alba L.) germination, seedling growth, and leaf-level physiology. A split-plot design tested effects of field collected soils from urban and reference forest sites in Baltimore, Maryland, and warm (urban) versus cool (rural) growth chamber temperature regimes. Seedlings were harvested at the end of the 23-week experiment to assess foliar chemistry and biomass allocation. Seed germination was unaffected by treatments and was high in both soil types and temperature regimes. Urban soils supported significantly higher total seedling biomass and had a significant effect on leaf-level physiological parameters, with seedlings grown in urban soils having greater A_net , V_cmax , ETR_max , J_max , PNUE, g_s , A_net /R_d , and PI_abs (an integrated chlorophyll fluorescence parameter). PI_abs measurements taken throughout the experiment revealed a significant time × temperature interaction effect. Baltimore urban forest patch soils were higher in nutrients than reference soils, but also higher in heavy metals. Despite higher levels of heavy metals, these results demonstrate that urban forest patch soils are able to support robust white oak seedling growth and enhanced seedling physiological parameters. However, interactions with temperature suggest that warming air temperatures may cause seedling stress and reduced growth.

Water-Quality Data Imputation with a High Percentage of Missing Values: A Machine Learning Approach

The monitoring of surface-water quality followed by water-quality modeling and analysis are essential for generating effective strategies in surface-water-resource management. However, worldwide, particularly in developing countries, water-quality studies are limited due to the lack of a complete and reliable dataset of surface-water-quality variables. In this context, several statistical and machine-learning models were assessed for imputing water-quality data at six monitoring stations located in the Santa Lucía Chico river (Uruguay), a mixed lotic and lentic river system. The challenge of this study is represented by the high percentage of missing data (between 50% and 70%) and the high temporal and spatial variability that characterizes the water-quality variables. The competing algorithms implement univariate and multivariate imputation methods (inverse distance weighting (IDW), Random Forest Regressor (RFR), Ridge (R), Bayesian Ridge (BR), AdaBoost (AB), Hubber Regressor (HR), Support Vector Regressor (SVR) and K-nearest neighbors Regressor (KNNR)). According to the results, more than 76% of the imputation outcomes are considered “satisfactory” (NSE > 0.45). The imputation performance shows better results at the monitoring stations located inside the reservoir than those positioned along the mainstream. IDW was the model with the best imputation results, followed by RFR, HR and SVR. The approach proposed in this study is expected to aid water-resource researchers and managers in augmenting water-quality datasets and overcoming the missing data issue to increase the number of future studies related to the water-quality matter.

Coupling Genomics and Hydraulic Information to Predict the Nitrogen Dynamics in a Channel Confluence

The simulation of nitrogen dynamics in urban channel confluences is essential for the evaluation and improvement of water quality. The omics-based modeling approaches that have been rapidly developed have been increasingly applied to characterize metabolisms of the microbial community and transformation of the associated materials. However, the transport of microorganisms and chemicals within and among different phases, which could be the rate-limiting step for the nitrogen dynamics, are always neglected or oversimplified in omics-based models. Therefore, this study proposes a novel simulation system coupling genomic and hydraulic information to simulate transport and transformation processes and provide predictions of nitrogen dynamics in a confluence. The proposed model was able to capture multiphase mass transport, microbial population dynamics, and nitrogen transformation and accurately predict gene abundances and nitrogen concentrations in both water and sediment; the mean relative errors were all lower than 40%. The model emphasized the importance of transport processes, which contributed more than 90% to gene abundances and chemical concentrations. Moreover, the simulation of reaction rates exhibited the specific nitrogen transformation processes in the confluence. The sulfide oxidation and the nitrate reduction and anaerobic ammonium oxidation, with the participation of the genes nap and hzo, respectively, were promoted as the main processes of nitrate and nitrite reduction.

Land use in urban areas impacts the composition of soil bacterial communities involved in nitrogen cycling. A case study from Lefkosia (Nicosia) Cyprus

The different types of land-use and soil lithology in urban and peri-urban areas of modern cities compose a complex mosaic of soil ecosystems. It is largely unknown how these differences result in changes in bacterial community composition and structure as well as in functional guilds involved in N cycling. To investigate the bacterial composition and the proportion of denitrifiers in agricultural, forested, schoolyard and industrial areas, 24 samples were collected from urban and peri-urban sites of Lefkosia. Bacterial diversity and the proportion of denitrifiers were assessed by NGS and qPCR, respectively. Proteobacteria, Actinobacteria, Bacteriodetes, Chloroflexi, Acidobacteria and Planctomycetes were identified as the most dominant phyla across all sites, while agricultural sites exhibited the highest bacterial diversity. Heavy metals such as Co, Pb, V and Al were identified as key factors shaping bacterial composition in industrial and schoolyard sites, while the bacterial assemblages in agricultural and forested sites were associated with Ca. Variance partitioning analysis showed that 10.2% of the bacterial community variation was explained by land use management, 5.1% by chemical elements due to soil lithology, and 1.4% by sampling location. The proportion of denitrifiers varied with land use management. In industrial and schoolyard sites, the abundance of the nosZII bacterial community increased while nirK abundance declined. Our data showed that land use and lithology have a moderate impact on the bacterial assemblages in urban and peri-urban areas of Lefkosia. As the nosZII bacterial community is important to the N₂O sink capacity of soils, it would be interesting to elucidate the factors contributing to the proliferation of the nosZII clade in these soils.

Net anthropogenic nitrogen and phosphorus inputs in Pearl River Delta region (2008-2016)

Excess inputs of nitrogen (N) and phosphorus (P) are the main contributors of aquatic environmental deterioration. Due to the agricultural and industrial activities in the rapidly urbanized basin, the anthropogenic N and P cycle are significantly different from other regions. In this study, we took the Pearl River Delta as an example and introduced the budget list of N and P in the five survey years, including the net anthropogenic N inputs (NANI) and net anthropogenic P inputs (NAPI). The results revealed that the intensities of NANI and NAPI in this area increased from 2008 to 2010 and then decreased after 2010. The peak values were 21001 kg N km^-2yr^-1 and 4515 kg P km^-2yr^-1 for the intensities of NNAI and NAPI, respectively, while the lowest values decreased to 19186 kg N km^-2yr^-1 and 4103 kg P km^-2yr^-1 in 2016. The most important contribution of NANI and NAPI sources in this area were net N and P inputs for human food and animal feed with an average contribution of 61.41% and 76.83%, which indicated that large amounts of N and P were introduced into the environment through the food system. This study expanded the knowledge on regional environmental management from human dietary consumption, human life consumption, animal consumption and fertilizer consumption. Its reuse will be put into practice by understanding the driving factors of N and P inputs in each region of the basin, combining the urbanization characteristics.

Nitrate removal uncertainty in stormwater control measures: Is the design or climate a culprit?

Eutrophication is caused by excess nitrate and other nutrient exported via stormwater runoff to surface waters, which is projected to increase as a result of climate change. Despite recent increases in the implementation of stormwater control measures (SCM), nutrient export has not abated, indicating poor or inconsistent removal capacities of SCM for nitrate. However, the cause of the variability is unclear. We show that both design and local climate can explain nitrate removal variability by critically analyzing data reported on the international BMP database for nitrate removal by four common types of SCM: bioretention cells, grass swales, media filters, and retention ponds. The relative importance of climate or design on nitrate removal depends on the SCM type. Nitrate removal in grass swales and bioretention systems is more sensitive to local climate than design specifications, whereas nitrate removal in the retention ponds is less sensitive to climate and more sensitive to design features such as vegetation and pond volume. Media filters without amendment have the least capacity compared to other SCM types surveyed, and their removal capacity was independent of the local climate. Adding amendments made up of carbon biomass, iron-based media, or a mixture of these amendments can significantly improve nitrate removal. The type of carbon biomass is also a factor since biochar does not appear to affect nitrate removal. This analysis can help inform the selection of SCM and modification of their design based on local and projected climate to maximize nitrate removal and minimize eutrophication.

Chlorophyll fluorescence parameters, leaf traits and foliar chemistry of white oak and red maple trees in urban forest patches

The provisioning of critical ecosystem services to cities of the eastern USA depends on the health and physiological function of trees in urban areas. Although we know that the urban environment may be stressful for trees planted in highly developed areas, it is not clear that trees in urban forest patches experience the same stressful environmental impacts. In this study, we examine chlorophyll fluorescence parameters, leaf traits, foliar nutrients and stable isotope signatures of urban forest patch trees compared with trees growing at reference forest sites, in order to characterize physiological response of these native tree species to the urban environment of three major cities arranged along a latitudinal gradient (New York, NY; Philadelphia, PA; Baltimore, MD). Overall, white oaks (Quercus alba L.) show more differences in chlorophyll fluorescence parameters and leaf traits by city and site type (urban vs reference) than red maples (Acer rubrum L.). The exceptions were δ13C and δ15N, which did not vary in white oak foliage but were significantly depleted (δ13C) and enriched (δ15N) in urban red maple foliage. Across all sites, red maples had higher thermal tolerance of photosynthesis (Tcrit) than white oaks, suggesting a greater ability to withstand temperature stress from the urban heat island effect and climate change. However, the highest average values of Tcrit were found in the Baltimore urban white oaks, suggesting that species suitability and response to the urban environment varies across a latitudinal gradient. Stomatal pore index (SPI) showed inter-specific differences, with red maple SPI being higher in urban trees, whereas white oak SPI was lower in urban trees. These results demonstrate that differences in native tree physiology occur between urban and reference forest patches, but they are site- and species-specific. Data on local site characteristics and tree species performance over time remain necessary to gain insight about urban woodland ecosystem function.

Long-term sulfide input enhances chemoautotrophic denitrification rather than DNRA in freshwater lake sediments

Partitioning between nitrate reduction pathways, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) determines the fate of nitrate removal and thus it is of great ecological importance. Sulfide (S^2-) is a potentially important factor that influences the role of denitrification and DNRA. However, information on the impact of microbial mechanisms for S^2- on the partitioning of nitrate reduction pathways in freshwater environments is still lacking. This study investigated the effects of long-term (108 d) S^2- addition on nitrate reduction pathways and microbial communities in the sediments of two different freshwater lakes. The results show that the increasing S^2- addition enhanced the coupling of S^2- oxidation with denitrification instead of DNRA. The sulfide-oxidizing denitrifier, Thiobacillus, was significantly enriched in the incubations of both lake samples with S^2- addition, which indicates that it may be the key genus driving sulfide-oxidizing denitrification in the lake sediments. During S^2- incubation of the Hongze Lake sample, which had lower inherent organic carbon (C) and sulfate (SO₄^2-), Thiobacillus was more enriched and played a dominant role in the microbial community; while during that of the Nansi Lake sample, which had higher inherent organic C and SO₄^2-, Thiobacillus was less enriched, but increasing abundances of sulfate reducing bacteria (Desulfomicrobium, Desulfatitalea and Geothermobacter) were observed. Moreover, sulfide-oxidizing denitrifiers and sulfate reducers were enriched in the Nansi Lake control treatment without external S^2- input, which suggests that internal sulfate release may promote the cooperation between sulfide-oxidizing denitrifiers and sulfate reducers. This study highlights the importance of sulfide-driven denitrification and the close coupling between the N and S cycles in freshwater environments, which are factors that have often been overlooked.

Metagenomic Sequencing and Quantitative Real-Time PCR for Fecal Pollution Assessment in an Urban Watershed

Microbial contamination of recreation waters is a major concern globally, with pollutants originating from many sources, including human and other animal wastes often introduced during storm events. Fecal contamination is traditionally monitored by employing culture methods targeting fecal indicator bacteria (FIB), namely E. coli and enterococci, which provides only limited information of a few microbial taxa and no information on their sources. Host-associated qPCR and metagenomic DNA sequencing are complementary methods for FIB monitoring that can provide enhanced understanding of microbial communities and sources of fecal pollution. Whole metagenome sequencing (WMS), quantitative real-time PCR (qPCR), and culture-based FIB tests were performed in an urban watershed before and after a rainfall event to determine the feasibility and application of employing a multi-assay approach for examining microbial content of ambient source waters. Cultivated E. coli and enterococci enumeration confirmed presence of fecal contamination in all samples exceeding local single sample recreational water quality thresholds (E. coli, 410 MPN/100 mL; enterococci, 107 MPN/100 mL) following a rainfall. Test results obtained with qPCR showed concentrations of E. coli, enterococci, and human-associated genetic markers increased after rainfall by 1.52-, 1.26-, and 1.11-fold log₁₀ copies per 100 mL, respectively. Taxonomic analysis of the surface water microbiome and detection of antibiotic resistance genes, general FIB, and human-associated microorganisms were also employed. Results showed that fecal contamination from multiple sources (human, avian, dog, and ruminant), as well as FIB, enteric microorganisms, and antibiotic resistance genes increased demonstrably after a storm event. In summary, the addition of qPCR and WMS to traditional surrogate techniques may provide enhanced characterization and improved understanding of microbial pollution sources in ambient waters.

Integrating Microbial Community Assembly and Fluid Kinetics to Decouple Nitrogen Dynamics in an Urban Channel Confluence

Understanding the characteristics of biogeochemical processes in urban channel confluences is essential for the evaluation and improvement of water environmental capacity. However, influences of biogeochemical processes in confluence were always overlooked or simply parametrized since the transformation processes controlled by microbial community assembly were hard to quantify. To address this knowledge gap, the present study proposed a novel mathematical modeling system, based on microbial community assembly theory and fluid kinetics, to decouple nitrogen dynamics into flow-induced transport and microorganism-induced transformation processes, and quantified their contributions to nitrogen concentrations. Results revealed that variable selection processes (including hydrodynamic conditions) contributed to significant difference in microbial communities among different hydraulic regions. Variation in microbial communities further shifted transformation processes. Rhodobacterales and Sphingomonadales, which were reported to be vital participants in denitrification process, were enriched in flow separation region, and promoted it as a hotspot for nitrogen removal. In the flow separation region, microorganism-induced transformation processes accounted for 56% of total nitrogen removal, which was significantly higher than that in other regions (12% on average; p < 0.01). Results and findings could provide useful information for the improvement of water environmental capacity.

Influence of Land Use/Land Cover on Surface-Water Quality of Santa Lucía River, Uruguay

Land use/land cover is one of the critical factors that affects surface-water quality at catchment scale. Effective mitigation strategies require an in-depth understanding of the leading causes of water pollution to improve community well-being and ecosystem health. The main aim of this study is to assess the relationship between land use/land cover and biophysical and chemical water-quality parameters in the Santa Lucía catchment (Uruguay, South America). The Santa Lucía river is the primary potable source of the country and, in the last few years, has had eutrophication issues. Several multivariate statistical analyses were adopted to accomplish the specific objectives of this study. The principal component analysis (PCA), coupled with k-means cluster analysis (CA), helped to identify a seasonal variation (fall/winter and spring/summer) of the water quality. The hierarchical cluster analysis (HCA) allowed one to classify the water-quality monitoring stations in three groups in the fall/winter season. The factor analysis (FA) with a rotation of the axis (varimax) was adopted to identify the most significant water-quality variables of the system (turbidity and flow). Finally, another PCA was run to link water-quality variables to the dominant land uses of the watershed. Strong correlations between TP and agriculture-land use, TP and livestock farming, NT and urban areas arose. It was found that these multivariate exploratory tools can provide a proper overview of the water-quality behavior in space and time and the correlations between water-quality variables and land use.

Stormwater ponds: An overlooked but plentiful urban designer ecosystem provides invasive plant habitat in a subtropical region (Florida, USA)

Designed ecosystems are built as part of ongoing urban expansion, providing a suite of valued ecosystem services. However, these new ecosystems could also promote disservices by facilitating the colonization and spread of invasive species. We conduct the first assessment of the quantity and invasion of an overlooked designed ecosystem: stormwater ponds. These ponds are commonly recommended for managing urban hydrology, but little is known about their ecology or extent of proliferation. Using a broad-scale survey of pond coverage in Florida, USA, we found that over 76,000 stormwater ponds have been built just in this state, forming 2.7% of total urban land cover. This extensive pondscape of manufactured habitats could facilitate species spread throughout urban areas and into nearby natural waterbodies. We also conducted a survey of the severity of plant invasion in 30 ponds in Gainesville, FL, US across two pond types (dry vs. wet), and a gradient of management intensities (low, medium, high) and pond ages. We unexpectedly found a high number of invasive plant species (28 in just 30 ponds). Ninety-six percent of surveyed ponds contained from one to ten of these species, with ponds exhibiting high turnover in invader composition (i.e., high beta diversity). The bank sections of dry unmanaged ponds exhibited the highest mean invasive species richness (5.8 ± 1.3) and the inundated centers of wet medium managed ponds exhibited the highest mean invasive species cover (34 ± 12%). Invasive plant richness and cover also tended to be greater in dry ponds with higher soil nutrient levels, and in older wet ponds. Therefore, we found that highly maintained and younger wet ponds were the least invaded. Nevertheless, common management practices that limit plant invasions may also limit native species establishment and invasion may increase in the decades following pond construction.

Bend-induced sediment redistribution regulates deterministic processes and stimulates microbial nitrogen removal in coarse sediment regions of river

Understanding the differences of biogeochemical processes between straight and bent channel is important for weighting them in urban river planning and reconstruction. Shifts in the assembly of the sediment microbial community of bent channels are key, but understudied, component of bend-induced increases in biogeochemical reaction rates. Here, the assembly of microbial community and its feedback to nitrogen transformation in urban river bends were firstly studied by coupling ecological theory, aqueous biogeochemistry, DNA sequencing, and hydrodynamic profiling. It was found that the sediment particle size was the main driving force for producing the significant difference of microbial community structure in river bends. Homogeneous selection, quantified by β-nearest taxon index (βNTI), emerged in the urban river bends and accounted for 79.2% of all ecological processes. Moreover, a significant positive relationship between βNTI and the sediment particle size indicated that shifts in particle size were associated with shifts in deterministic selective pressures, which govern the composition of the microbial community. The significant correlation between the βNTI and changes in nitrate concentration also indicated that nitrate leads to deterministic processes, which select microbial taxa. These microbial taxa which are governed by deterministic processes show specific nitrogen transformation traits, and react on the nitrate concentration. A multiphase transport model allowed the separation of the effects of deterministic processes on nitrogen concentration from measured concentration influenced by complex biogeochemical processes. The results indicated that both the ammonia transformation and microbial nitrogen removal were stimulated in coarse sediment regions of the river bends, and were confirmed by abundant differences of microbial taxa that could promote ammoxidation and denitrification. The coarse sediment benefits microbial nitrogen removal in urban river bends, a discovery that should inform urban river reconstruction designs and the efforts to assess the environmental water capacity of urban rivers.

Metagenomics Reveals Bacterial and Archaeal Adaptation to Urban Land-Use: N Catabolism, Methanogenesis, and Nutrient Acquisition

Urbanization results in the systemic conversion of land-use, driving habitat and biodiversity loss. The "urban convergence hypothesis" posits that urbanization represents a merging of habitat characteristics, in turn driving physiological and functional responses within the biotic community. To test this hypothesis, we sampled five cities (Baltimore, MD, United States; Helsinki and Lahti, Finland; Budapest, Hungary; Potchefstroom, South Africa) across four different biomes. Within each city, we sampled four land-use categories that represented a gradient of increasing disturbance and management (from least intervention to highest disturbance: reference, remnant, turf/lawn, and ruderal). Previously, we used amplicon sequencing that targeted bacteria/archaea (16S rRNA) and fungi (ITS) and reported convergence in the archaeal community. Here, we applied shotgun metagenomic sequencing and QPCR of functional genes to the same soil DNA extracts to test convergence in microbial function. Our results suggest that urban land-use drives changes in gene abundance related to both the soil N and C metabolism. Our updated analysis found taxonomic convergence in both the archaeal and bacterial community (16S amplicon data). Convergence of the archaea was driven by increased abundance of ammonia oxidizing archaea and genes for ammonia oxidation (QPCR and shotgun metagenomics). The proliferation of ammonia-oxidizers under turf and ruderal land-use likely also contributes to the previously documented convergence of soil mineral N pools. We also found a higher relative abundance of methanogens (amplicon sequencing), a higher relative abundance of gene sequences putatively identified as Ni-Fe hydrogenase and nickel uptake (shotgun metagenomics) under urban land-use; and a convergence of gene sequences putatively identified as contributing to the nickel transport function under urban turf sites. High levels of disturbance lead to a higher relative abundance of gene sequences putatively identified as multiple antibiotic resistance protein marA and multidrug efflux pump mexD, but did not lead to an overall convergence in antibiotic resistance gene sequences.

Seeing the light: urban stream restoration affects stream metabolism and nitrate uptake via changes in canopy cover

The continually increasing global population residing in urban landscapes impacts numerous ecosystem functions and services provided by urban streams. Urban stream restoration is often employed to offset these impacts and conserve or enhance the various functions and services these streams provide. Despite the assumption that "if you build it, [the function] will come," current understanding of the effects of urban stream restoration on stream ecosystem functions are based on short term studies that may not capture variation in restoration effectiveness over time. We quantified the impact of stream restoration on nutrient and energy dynamics of urban streams by studying 10 urban stream reaches (five restored, five unrestored) in the Baltimore, Maryland, USA, region over a two-year period. We measured gross primary production (GPP) and ecosystem respiration (ER) at the whole-stream scale continuously throughout the study and nitrate (NO₃^- -N) spiraling rates seasonally (spring, summer, autumn) across all reaches. There was no significant restoration effect on NO₃^- -N spiraling across reaches. However, there was a significant canopy cover effect on NO₃^- -N spiraling, and directly comparing paired sets of unrestored-restored reaches showed that restoration does affect NO₃^- -N spiraling after accounting for other environmental variation. Furthermore, there was a change in GPP : ER seasonality, with restored and open-canopied reaches exhibiting higher GPP : ER during summer. The restoration effect, though, appears contingent upon altered canopy cover, which is likely to be a temporary effect of restoration and is a driver of multiple ecosystem services, e.g., habitat, riparian nutrient processing. Our results suggest that decision-making about stream restoration, including evaluations of nutrient benefits, clearly needs to consider spatial and temporal dynamics of canopy cover and trade-offs among multiple ecosystem services.

Environmental diagnosis of an urban basin from a social-ecological perspective

The critical factor in restoration and conservation of urban streams and their catchments is the human population, however the most of studies of urban ecosystems do not present social descriptors as concrete variables of analysis. The objective of this study is to perform an environmental diagnosis from a social-ecological perspective by considering both ecological and urban development descriptors of an urban basin. We selected 12 sampling sites of the Langueyú upper basin where social and ecological descriptors were determined. We arranged sampling sites according to their physicochemical characteristics (pre-urban, urban and post-urban sites). An ecological index was defined from habitat and biological descriptors: vegetation cover, richness and total density of invertebrates and organic matter. The index determined that urban and post-urban sites showed similar characteristics, and pre-urban sites presented the best habitat and biological conditions. An urbanisation index was defined from urban development descriptors: distance to the stormwater drainage network, number of industries, distance to a house without sewage, impervious surface and housing density. The results showed that the pre-urban and post-urban sites share a greater similarity in relation to the urban descriptors but with different impact in ecological quality. The headwaters in the hills (pre-urban zone) still presents a very good ecological condition (although threatened by urbanisation and tourism); however, once it crosses the dense urban area, no >5 km distance, the environmental degradation is alarming. We were able to determine that the structural measures associated with greater urbanisation, added to illegally connected sewer pipes and illegally industrial connections, produce the ecological degradation of the stream. This environmental diagnosis allowed us a deep understanding of the urbanisation impact on the ecological integrity of an urban stream in a developing country which, like many others, doesn't have monitoring programs or an integrated vision of water resources.

Influence of urban river restoration on nitrogen dynamics at the sediment-water interface

River restoration projects focused on altering flow regimes through use of in-channel structures can facilitate ecosystem services, such as promoting nitrogen (N) storage to reduce eutrophication. In this study we use small flux chambers to examine ammonium (NH₄⁺) and nitrate (NO₃^-) cycling across the sediment-water interface. Paired restored and unrestored study sites in 5 urban tributaries of the River Thames in Greater London were used to examine N dynamics following physical disturbances (0–3 min exposures) and subsequent biogeochemical activity (3–10 min exposures). Average ambient NH₄⁺ concentrations were significantly different amongst all sites and ranged from 28.0 to 731.7 μg L^-1, with the highest concentrations measured at restored sites. Average NO₃^- concentrations ranged from 9.6 to 26.4 mg L^-1, but did not significantly differ between restored and unrestored sites. Average NH₄⁺ fluxes at restored sites ranged from -8.9 to 5.0 μg N m^-2 sec^-1, however restoration did not significantly influence NH₄⁺ uptake or regeneration (i.e., a measure of release to surface water) between 0–3 minutes and 3–10 minutes. Further, average NO₃^- fluxes amongst sites responded significantly between 0–3 minutes ranging from -33.6 to 97.7 μg N m^-2 sec^-1. Neither NH₄⁺ nor NO₃^- fluxes correlated to sediment chlorophyll-a, total organic matter, or grain size. We attributed variations in overall N fluxes to N-specific sediment storage capacity, biogeochemical transformations, potential legacy effects associated with urban pollution, and variations in river-specific restoration actions.

Anthropogenic nutrient inputs in the NW Iberian Peninsula estuaries determined by nitrogen and carbon isotopic signatures of Zostera noltei seagrass meadows

Coastal watersheds of the NW Iberian Peninsula have undergone increases in population densities and urbanization over the past decades. However, the effect of altered nutrient inputs to estuarine Zostera noltei ecosystems associated to these anthropogenic pressures remains largely unknown. Eleven Zostera noltei meadows located in the NW Iberian Peninsula were studied to assess the relationship between the anthropogenic pressure over coastal watersheds and the nitrogen and carbon isotopic signatures of Z. noltei meadows. Anthropogenic pressure on the watersheds was estimated from human population data and land cover classes. Carbon and nitrogen stable isotopic analyses were performed on Z. noltei leaves and in the sediments surrounding the rhizospheres. Our results indicate that the N and C isotopic signatures of Z. noltei meadows from the NW Iberian Peninsula reflect the impact of anthropogenic pressures. Nevertheless, these relationships are complex due to several processes acting simultaneously altering the expected isotopic responses.

Effects of Urban Stormwater Control Measures on Denitrification in Receiving Streams

Urban areas are increasingly adopting the use of ecologically-based technologies for stormwater management to mitigate the effects of impervious surface runoff on receiving water bodies. While stormwater control measures (SCMs) reduce runoff, their ability to influence ecosystem function in receiving streams is not well known. To understand the effect of SCMs on net ecosystem function in stream networks, we measured sediment denitrification in four streams across a gradient of urban and suburban residential development in Charlotte, NC. We evaluated the influence of SCM inputs on actual (DNF) and potential (DEA) denitrification activity in stream sediments at the SCM-stream confluence to quantify microbial processes and the environmental factors that control them. DNF was variable across sites, ranging from 0–6.60 mg-N·m−2·h−1 and highly correlated with in-stream nitrate (NO3-N) concentrations. Sites with a greater impervious area showed a pattern of significantly higher DEA rates upstream of the SCM compared to downstream, while sites with less imperviousness showed the opposite trend. We hypothesize that this is because of elevated concentrations of carbon and nitrogen provided by pond and wetland outflows, and stabilization of the benthic habitat by lower peak discharge. These results suggest that SCMs integrated into the watershed have the potential to create cascading positive effects on in-stream nutrient processing and thereby improve water quality; however, at higher levels of imperviousness, the capacity for SCMs to match the scale of the impacts of urbanization likely diminishes.