Streambed microbial communities in the transition zone between groundwater and a first-order stream as impacted by bidirectional water exchange

The input of nitrate and other agricultural pollutants in higher-order streams largely derives from first-order streams. The streambed as the transition zone between groundwater and stream water has a decisive impact on the attenuation of such pollutants. This reactivity is not yet well understood for lower-order agricultural streams, which are often anthropogenically altered and lack the streambed complexity allowing for extensive hyporheic exchange. Reactive hot spots in such streambeds have been hypothesized as a function of hydrology, which controls the local gaining (groundwater exfiltration) or losing (infiltration) of stream water. However, streambed microbial communities and activities associated with such reactive zones remain mostly uncharted. In this study, sediments of a first-order agriculturally impacted stream in southern Germany were investigated. Along with a hydraulic dissection of distinct gaining and losing reaches of the stream, community composition and the abundance of bacterial communities in the streambed were investigated using PacBio long-read sequencing of bacterial 16S rRNA gene amplicons, and qPCR of bacterial 16S rRNA and denitrification genes (nirK and nirS). We show that bidirectional water exchange between groundwater and the stream represents an important control for sediment microbiota, especially for nitrate-reducing populations. Typical heterotrophic denitrifiers were most abundant in a midstream net losing section, while up- and downstream net gaining sections were associated with an enrichment of sulfur-oxidizing potential nitrate reducers affiliated with Sulfuricurvum and Thiobacillus spp. Dispersal-based community assembly was found to dominate such spots of groundwater exfiltration. Our results indicate a coupling of N- and S-cycling processes in the streambed of an agricultural first-order stream, and a prominent control of microbiology by hydrology and hydrochemistry in situ. Such detailed local heterogeneities in exchange fluxes and streambed microbiomes have not been reported to date, but seem relevant for understanding the reactivity of lower-order streams.

Assessment of Indirect N2O Emission Factors from Agricultural River Networks Based on Long-Term Study at High Temporal Resolution

Assessment of indirect emission factors (EF_5r) of nitrous oxide (N₂O) from agricultural river networks remains challenging, and results are uncertain due to limited data availability. This study compared two methods of assessing EF_5r using data from long-term observations at high temporal resolution in a typical agricultural catchment in subtropical central China. The concentration method (method 1) and the Intergovernmental Panel on Climate Change (IPCC) 2006 method (method 2) were employed to evaluate the emission factor. EF_5r estimated using method 1 (i.e., EF_5r1) was 0.00077 ± 0.00025 (0.00038-0.00097). EF_5r calculated using method 2 (i.e., EF_5r2) was lower than EF_5r1, with a mean value of 0.00004 (0.000015-0.00012). Both EF_5r1 and EF_5r2 were significantly lower than the IPCC 2006 default value of 0.0025, suggesting that N₂O emissions from China and world river networks may be grossly overestimated. A complex N₂O production pathway and diffusion mechanism were responsible for the transfer of N₂O from the sediment to river water and then to the atmosphere. These findings provide essential data for refining national greenhouse gas inventories and contribute evidence for downward revision of indirect emission factors adopted by the IPCC.

Anthropogenic changes of nitrogen loads in a small river: external nutrient sources vs. internal turnover processes

Anthropogenic nutrient inputs increase the N-load in many aquatic systems, leading to eutrophication and potential changes of biological N-retention capacity. In this study, nitrate inputs in a small river were investigated along a gradient of anthropogenic influence. We aimed to determine changes in nitrate load and isotope signatures in the water column and to identify the anthropogenic influence on biological nitrogen assimilation and nitrification or denitrification in sediments. In seasonal sampling campaigns, we analysed dissolved inorganic nitrogen concentrations, and stable isotopes of nitrate. To differentiate rates of nitrate production and consumption in the pristine vs. agricultural river section, intact sediment cores were incubated with ¹⁵N-labelled nitrate. δ¹⁵N values of nitrate in the pristine river section were low, reflecting natural sources, but, as expected, increased with nitrate concentration in all seasons along the gradient. In general, nitrate retention and consumption were higher in the anthropogenically impacted than in the pristine river section, and nitrate consumption exceeded production. In addition to our measurements, modelled results also show that even in a small river, the anthropogenically enhanced consumption capacity is overwhelmed by surplus N-inputs, and nitrate consumption cannot increase in turn with external loads.

Assessment and identification of nitrogen pollution sources in the Cheongmi River with intensive livestock farming areas, Korea

This study aimed to develop methods for assessing and identifying nitrogen sources in the Cheongmi River, Korea, that has intensive livestock farming areas (ILFA) in its watershed. The assessment focused on the feasibility of the simultaneous use of stable isotopic compositions of ammonium (δ¹⁵N_NH4) and nitrate (δ¹⁵N_NO3) for identifying the main nitrogen pollution sources in the Cheongmi River watershed. Our results suggested that the organic nitrogen (Org-N) to total nitrogen (T-N) ratio could be used as an indicator for assessing the effect of livestock excreta on waterways in ILFA. We observed that the T-N concentration was much more strongly affected by livestock excreta than the T-P concentration in the mainstream of the Cheongmi River. The positive correlation was more significant between δ¹⁵N_NH4 and NH₄-N than that between δ¹⁵N_NO3 and NO₃-N for river water samples. Furthermore, the use of δ¹⁵N_NH4 was more effective than that of δ¹⁵N_NO3 in evaluating nitrogen variations between May and August in the Cheongmi River because the differences in δ¹⁵N_NH4 between May and August were more remarkable compared to those in δ¹⁵N_NO3. Finally, the simultaneous use of δ¹⁵N_NH4 and δ¹⁵N_NO3 showed that the dominant nitrogen source at sites M3, M4, M5, and M6, specifically in May, was livestock excreta in the Cheongmi River. The results of this study could be used for sustainable water quality management in the Cheongmi River watershed.

Biotic interactions modify multiple-stressor effects on juvenile brown trout in an experimental stream food web

Agricultural land use results in multiple stressors affecting stream ecosystems. Flow reduction due to water abstraction, elevated levels of nutrients and chemical contaminants are common agricultural stressors worldwide. Concurrently, stream ecosystems are also increasingly affected by climate change. Interactions among multiple co-occurring stressors result in biological responses that cannot be predicted from single-stressor effects (i.e. synergisms and antagonisms). At the ecosystem level, multiple-stressor effects can be further modified by biotic interactions (e.g. trophic interactions). We conducted a field experiment using 128 flow-through stream mesocosms to examine the individual and combined effects of water abstraction, nutrient enrichment and elevated levels of the nitrification inhibitor dicyandiamide (DCD) on survival, condition and gut content of juvenile brown trout and on benthic abundance of their invertebrate prey. Flow velocity reduction decreased fish survival (-12% compared to controls) and condition (-8% compared to initial condition), whereas effects of nutrient and DCD additions and interactions among these stressors were not significant. Negative effects of flow velocity reduction on fish survival and condition were consistent with effects on fish gut content (-25% compared to controls) and abundance of dominant invertebrate prey (-30% compared to controls), suggesting a negative metabolic balance driving fish mortality and condition decline, which was confirmed by structural equation modelling. Fish mortality under reduced flow velocity increased as maximal daily water temperatures approached the upper limit of their tolerance range, reflecting synergistic interactions between these stressors. Our study highlights the importance of indirect stressor effects such as those transferred through trophic interactions, which need to be considered when assessing and managing fish populations and stream food webs in multiple-stressor situations. However, in real streams, compensatory mechanisms and behavioural responses, as well as seasonal and spatial variation, may alter the intensity of stressor effects and the sensitivity of trout populations.

Temperature responses of ammonia-oxidizing prokaryotes in freshwater sediment microcosms

In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB), lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial amoA gene. The elevated temperature increased the abundance of archaeal amoA gene, whereas the abundance of bacterial amoA gene decreased. The highest diversity of bacterial amoA gene was found in the 25°C treatment sample. However, the 25°C treatment sample maintained the lowest diversity of archaeal amoA gene. Most of the archaeal amoA sequences obtained in this study affiliated with the Nitrosopumilus cluster. Two sequences obtained from the 15°C treatment samples were affiliated with the Nitrosotalea cluster. N. oligotropha lineage was the most dominant bacterial amoA gene group. Several sequences affiliated to Nitrosospira and undefined N. europaea/NC. mobilis like lineage were found in the pre-incubation and 25°C treatment groups.

Effect of eastern oysters (Crassostrea virginica) on sediment carbon and nitrogen dynamics in an urban estuary

Oyster reefs have declined globally. Interest in their restoration has motivated research into oyster-mediated ecosystem services including effects on biodiversity, filtration, and nitrogen (N) cycling. Recent evidence suggests oysters may promote denitrification, or anaerobic respiration of nitrate (NO3-) into di-nitrogen gas, via benthic deposition of carbon (C) and N-rich biodeposits. However, the mechanisms whereby biodeposits promote N transformations prerequisite to denitrification (e.g., mineralization and nitrification) are unclear. Previous research has also not measured oysters' influence on N cycling in urbanized areas. In May 2010 we deployed eastern oysters (Crassostrea virginica) in mesh cages above sand-filled boxes at four sites across a nutrient gradient in Jamaica Bay, New York City (New York, USA). Oysters were arranged at four densities: 0, 40, 85, and 150 oysters/m2. For 17 months we measured water-column nutrients and chlorophyll a, every two weeks to monthly. Every two months we measured sediment ash-free dry mass (AFDM), exchangeable ammonium (NH4+), ammonification, nitrification, denitrification potential (DNP), and NO3- and C limitation of DNP. Oysters increased sediment AFDM at three of four sites, with the greatest increase at high density. Oysters did not affect any N pools or transformations. However, variation among sites and dates illustrated environmental drivers of C and N biogeochemistry in this urban estuary. Overall, nitrification was positively related to net ammonification, water column NH4+, and sediment NH4+, but was not correlated with DNP. Denitrification was consistently and strongly NO3- limited, while C was not limiting or secondarily limiting. Therefore, the oyster-mediated increase in AFDM did not affect DNP because C was not its primary driver. Also, because DNP was unrelated to nitrification, it is unlikely that biodeposit N was converted to NO3- for use as a denitrification substrate. Predicting times or sites where denitrification is driven by the C and N species originating from oyster biodeposits remains a challenge under eutrophic conditions. Towards this goal, we synthesized our conclusions with literature predictions in a conceptual model for pathways whereby oysters might influence C and N dynamics differently in oligotrophic relative to eutrophic ecosystems.

Assessing stream restoration effectiveness at reducing nitrogen export to downstream waters

The degradation of headwater streams is common in urbanized coastal areas, and the role these streams play in contributing to downstream pollution is a concern among natural resource managers and policy makers. Thus, many urban stream restoration efforts are increasingly focused on reducing the downstream flux of pollutants. In regions that suffer from coastal eutrophication, it is unclear whether stream restoration does in fact reduce nitrogen (N) flux to downstream waters and, if so, by how much and at what cost. In this paper, we evaluate whether stream restoration implemented to improve water quality of urban and suburban streams in the Chesapeake Bay region, USA, is effective at reducing the export of N in stream flow to downstream waters. We assessed the effectiveness of restored streams positioned in the upland vs. lowland regions of Coastal Plain watershed during both average and stormflow conditions. We found that, during periods of low discharge, lowland streams that receive minor N inputs from groundwater or bank seepage reduced in-stream N fluxes. Furthermore, lowland streams with the highest N concentrations and lowest discharge were the most effective. During periods of high flow, only those restoration projects that converted lowland streams to stream-wetland complexes seemed to be effective at reducing N fluxes, presumably because the design promoted the spillover of stream flow onto adjacent floodplains and wetlands. The observed N-removal rates were relatively high for stream ecosystems, and on the order of 5% of the inputs to the watershed. The dominant forms of N entering restored reaches varied during low and high flows, indicating that N uptake and retention were controlled by distinctive processes during different hydrological conditions. Therefore, in order for stream restoration to effectively reduce N fluxes exported to downstream waters, restoration design should include features that enhance the processing and retention of different forms of N, and for a wide range of flow conditions. The use of strategic designs that match the dominant attributes of a stream such as position in the watershed, influence of groundwater, dominant flow conditions, and N concentrations is crucial to assure the success of restoration.