Unraveling microbial processes involved in carbon and nitrogen cycling and greenhouse gas emissions in rewetted peatlands by molecular biology.

Restoration of drained peatlands through rewetting has recently emerged as a prevailing strategy to mitigate excessive greenhouse gas emissions and re-establish the vital carbon sequestration capacity of peatlands. Rewetting can help to restore vegetation communities and biodiversity, while still allowing for extensive agricultural management such as paludiculture. Belowground processes governing carbon fluxes and greenhouse gas dynamics are mediated by a complex network of microbial communities and processes. Our understanding of this complexity and its multi-factorial controls in rewetted peatlands is limited. Here, we summarize the research regarding the role of soil microbial communities and functions in driving carbon and nutrient cycling in rewetted peatlands including the use of molecular biology techniques in understanding biogeochemical processes linked to greenhouse gas fluxes. We emphasize that rapidly advancing molecular biology approaches, such as high-throughput sequencing, are powerful tools helping to elucidate the dynamics of key biogeochemical processes when combined with isotope tracing and greenhouse gas measuring techniques. Insights gained from the gathered studies can help inform efficient monitoring practices for rewetted peatlands and the development of climate-smart restoration and management strategies. Supplementary Information: The online version contains supplementary material available at 10.1007/s10533-024-01122-6.

Non-negligible N2O emission hotspots: Rivers impacted by ion-adsorption rare earth mining.

Rare earth mining causes severe riverine nitrogen pollution, but its effect on nitrous oxide (N2O) emissions and the associated nitrogen transformation processes remain unclear. Here, we characterized N2O fluxes from China's largest ion-adsorption rare earth mining watershed and elucidated the mechanisms that drove N2O production and consumption using advanced isotope mapping and molecular biology techniques. Compared to the undisturbed river, the mining-affected river exhibited higher N2O fluxes (7.96 ± 10.18 mmol m-2d-1 vs. 2.88 ± 8.27 mmol m-2d-1, P = 0.002), confirming that mining-affected rivers are N2O emission hotspots. Flux variations scaled with high nitrogen supply (resulting from mining activities), and were mainly attributed to changes in water chemistry (i.e., pH, and metal concentrations), sediment property (i.e., particle size), and hydrogeomorphic factors (e.g., river order and slope). Coupled nitrification-denitrification and N2O reduction were the dominant processes controlling the N2O dynamics. Of these, the contribution of incomplete denitrification to N2O production was greater than that of nitrification, especially in the heavily mining-affected reaches. Co-occurrence network analysis identified Thiomonas and Rhodanobacter as the key genus closely associated with N2O production, suggesting their potential roles for denitrification. This is the first study to elucidate N2O emission and influential mechanisms in mining-affected rivers using combined isotopic and molecular techniques. The discovery of this study enhances our understanding of the distinctive processes driving N2O production and consumption in highly anthropogenically disturbed aquatic systems, and also provides the foundation for accurate assessment of N2O emissions from mining-affected rivers on regional and global scales.

Cost effectiveness, nitrogen, and phosphorus removal in field-based woodchip bioreactors treating agricultural drainage water.

Nitrogen (N) and phosphorus (P) losses to surface and coastal waters are still critically high across Europe and globally. Measures to mitigate and reduce these losses are being implemented both at the cultivated land surface and at the edge-of-fields. Woodchip bioreactors represent a new alternative in Denmark for treating agricultural drainage water, and the present study-based on two years of data from five Danish field-based bioreactors-determined N removal rates varying from 1.49 to 5.37 g N m-3 d-1 and a mean across all bioreactors and years of 2.90 g N m-3 d-1. The loss of phosphorus was relatively high the first year after bioreactor establishment with rates varying from 298.4 to 890.8 mg P m-3 d-1, but in the second year, the rates ranged from 12.2 to 77.2 mg P m-3 d-1. The investments and the costs of the bioreactors were larger than expected based on Danish standard investments. The cost efficiency analysis found the key issues to be the need for larger investments in the bioreactor itself combined with higher advisory costs. For the four woodchip bioreactors considered in the cost efficiency analysis, the N removal cost was around DKK 350 per kg N ($50 per kg N), which is ca. 50% higher than the standard costs defined by the Danish authorities. Based on the estimated costs of the four bioreactor facilities included in this analysis, a bioreactor is one of the most expensive nitrogen reduction measures compared to other mitigation tools.

Pollution caused by mining reshaped the structure and function of bacterial communities in China's largest ion-adsorption rare earth mine watershed.

Ion-adsorption rare earth mining results in the production of high levels of nitrogen, multiple metals, and strong acidic mine drainage (AMD), the impacts of which on microbial assembly and ecological functions remain unclear. To address this knowledge gap, we collected river sediments from the watershed of China's largest ion-adsorption rare earth mine and analyzed the bacterial community's structure, function, and assembly mechanisms. Results showed that bacterial community assembly was weakly affected by spatial dispersion, and dispersal limitation and homogeneous selection were the dominant ecological processes, with the latter increasing with pollution gradients. Bacterial alpha diversity decreased with pollution, which was mainly influenced by lead (Pb), pH, rare earth elements (REEs), and electrical conductivity (EC). However, bacteria developed survival strategies (i.e., enhanced acid tolerance and interspecific competition) to adapt to extreme environments, sustaining species diversity and community stability. Community structure and function showed a consistent response to the polluted environment (r = 0.662, P = 0.001). Enhanced environmental selection reshaped key microbial-mediated biogeochemical processes in the mining area, in particular weakening the potential for microbial denitrification. These findings provide new insights into the ecological response of microbes to compound pollution and offer theoretical support for proposing effective remediation and management strategies for polluted areas.

Microbiome Structure and Function in Woodchip Bioreactors for Nitrate Removal in Agricultural Drainage Water.

Woodchip bioreactors are increasingly used to remove nitrate (NO3 -) from agricultural drainage water in order to protect aquatic ecosystems from excess nitrogen. Nitrate removal in woodchip bioreactors is based on microbial processes, but the microbiomes and their role in bioreactor efficiency are generally poorly characterized. Using metagenomic analyses, we characterized the microbiomes from 3 full-scale bioreactors in Denmark, which had been operating for 4-7 years. The microbiomes were dominated by Proteobacteria and especially the genus Pseudomonas, which is consistent with heterotrophic denitrification as the main pathway of NO3 - reduction. This was supported by functional gene analyses, showing the presence of the full suite of denitrification genes from NO3 - reductases to nitrous oxide reductases. Genes encoding for dissimilatory NO3 - reduction to ammonium were found only in minor proportions. In addition to NO3 - reducers, the bioreactors harbored distinct functional groups, such as lignocellulose degrading fungi and bacteria, dissimilatory sulfate reducers and methanogens. Further, all bioreactors harbored genera of heterotrophic iron reducers and anaerobic iron oxidizers (Acidovorax) indicating a potential for iron-mediated denitrification. Ecological indices of species diversity showed high similarity between the bioreactors and between the different positions along the flow path, indicating that the woodchip resource niche was important in shaping the microbiome. This trait may be favorable for the development of common microbiological strategies to increase the NO3 - removal from agricultural drainage water.

Nitrogen removal and greenhouse gas fluxes from integrated buffer zones treating agricultural drainage water.

Integrated buffer zones (IBZ) are novel mitigation measures designed to decrease the loading of nitrogen (N) transported by subsurface drainage systems from agricultural fields to streams. In IBZ, drainage water flows into a pond with free water surface followed by an inundated, vegetated filterbed. This design provides an environment favorable for denitrification and thus a decrease in nitrate concentration is expected as water flow through the IBZ. However, due to the establishment of anaerobic conditions, there is a risk for increasing emissions of the greenhouse gases nitrous oxide (N2O) and methane (CH4). In this year-long study, we evaluated the N removal efficiency along with the risk of N2O and CH4 emissions from two pilot-scale IBZs (IBZ1 and 2). The two IBZs had very different yearly removal efficiencies, amounting to 29% and 71% of the total N load at IBZ1 and 2, respectively. This was probably due to differences in infiltration rates to the filterbed, which was 22% and 81% of the incoming water at IBZ1 and 2, respectively. The site (IBZ2) with the highest removal efficiency was a net N2O sink, while 0.9% of the removed nitrate was emitted as N2O at IBZ1. Both IBZs were net sources of CH4 but with different pathways of emission. In IBZ1 CH4 was mainly lost directly to the atmosphere, while waterborne losses dominated in IBZ2. In conclusion, the IBZs were effective in removing N three years after establishment, and although the IBZs acted as greenhouse gas sources, especially due to CH4, the emissions were comparable to those of natural wetlands and other drainage transport mitigation measures.

Influence of plant habitats on denitrification in lowland agricultural streams.

The aim of this study was to assess potential differences in denitrification in contrasting stream habitats in agricultural lowland streams located in Denmark. The study focused on three types of habitats i) vegetated habitats with emergent plants, ii) vegetated habitats with submerged plants, iii) bare sediments. Denitrification rates were measured in situ using denitrification chambers and nitrogen isotope pairing technique three times during a growing season. Denitrification rates across all habitats and samplings were 73 ± 116 µmol N m-2 h-1 (mean ± sd) with greater denitrification rates in vegetated habitats compared to bare sediments. Habitats with emergent plants had significantly higher denitrification rates than habitats with submerged plants. The habitats exhibited differences in oxygen and carbon availability probably connected to differences in flow velocity and physical effect of the vegetation (if present) which likely acted as a trap for finer organic-rich particles. Placing these results in the context of stream and river restoration highlights the potential of in-stream vegetation to mitigate nitrogen pollution, especially by restoring plant habitats in degraded and channelized streams to sustain vegetation promoting higher denitrification rates.

Warming and eutrophication interactively drive changes in the methane-oxidizing community of shallow lakes.

Freshwater ecosystems are the largest natural source of the greenhouse gas methane (CH4), with shallow lakes a particular hot spot. Eutrophication and warming generally increase lake CH4 emissions but their impacts on the sole biological methane sink-methane oxidation-and methane-oxidizer community dynamics are poorly understood. We used the world's longest-running freshwater climate-change mesocosm experiment to determine how methane-oxidizing bacterial (MOB) abundance and composition, and methane oxidation potential in the sediment respond to eutrophication, short-term nitrogen addition and warming. After nitrogen addition, MOB abundance and methane oxidation potential increased, while warming increased MOB abundance without altering methane oxidation potential. MOB community composition was driven by both temperature and nutrient availability. Eutrophication increased relative abundance of type I MOB Methyloparacoccus. Warming favoured type II MOB Methylocystis over type I MOB Methylomonadaceae, shifting the MOB community from type I dominance to type I and II co-dominance, thereby altering MOB community traits involved in growth and stress-responses. This shift to slower-growing MOB may explain why higher MOB abundance in warmed mesocosms did not coincide with higher methane oxidation potential. Overall, we show that eutrophication and warming differentially change the MOB community, resulting in an altered ability to mitigate CH4 emissions from shallow lakes.

Efficiency of mitigation measures targeting nutrient losses from agricultural drainage systems: A review.

Diffusive losses of nitrogen and phosphorus from agricultural areas have detrimental effects on freshwater and marine ecosystems. Mitigation measures treating drainage water before it enters streams hold a high potential for reducing nitrogen and phosphorus losses from agricultural areas. To achieve a better understanding of the opportunities and challenges characterising current and new drainage mitigation measures in oceanic and continental climates, we reviewed the nitrate and total phosphorus removal efficiency of: (i) free water surface constructed wetlands, (ii) denitrifying bioreactors, (iii) controlled drainage, (iv) saturated buffer zones and (v) integrated buffer zones. Our data analysis showed that the load of nitrate was substantially reduced by all five drainage mitigation measures, while they mainly acted as sinks of total phosphorus, but occasionally, also as sources. The various factors influencing performance, such as design, runoff characteristics and hydrology, differed in the studies, resulting in large variation in the reported removal efficiencies.

Wetland buffer zones for nitrogen and phosphorus retention: Impacts of soil type, hydrology and vegetation.

Wetland buffer zones (WBZs) are riparian areas that form a transition between terrestrial and aquatic environments and are well-known to remove agricultural water pollutants such as nitrogen (N) and phosphorus (P). This review attempts to merge and compare data on the nutrient load, nutrient loss and nutrient removal and/or retention from multiple studies of various WBZs termed as riparian mineral soil wetlands, groundwater-charged peatlands (i.e. fens) and floodplains. Two different soil types ('organic' and 'mineral'), four different main water sources ('groundwater', 'precipitation', 'surface runoff/drain discharge', and 'river inundation') and three different vegetation classes ('arboraceous', 'herbaceous' and 'aerenchymous') were considered separately for data analysis. The studied WBZs are situated within the temperate and continental climatic regions that are commonly found in northern-central Europe, northern USA and Canada. Surprisingly, only weak differences for the nutrient removal/retention capability were found if the three WBZ types were directly compared. The results of our study reveal that for example the nitrate retention efficiency of organic soils (53 ± 28%; mean ± sd) is only slightly higher than that of mineral soils (50 ± 32%). Variance in load had a stronger influence than soil type on the N retention in WBZs. However, organic soils in fens tend to be sources of dissolved organic N and soluble reactive P, particularly when the fens have become degraded due to drainage and past agricultural usage. The detailed consideration of water sources indicated that average nitrate removal efficiencies were highest for ground water (76 ± 25%) and lowest for river water (35 ± 24%). No significant pattern for P retention emerged; however, the highest absolute removal appeared if the P source was river water. The harvesting of vegetation will minimise potential P loss from rewetted WBZs and plant biomass yield may promote circular economy value chains and provide compensation to land owners for restored land now unsuitable for conventional farming.

Nitrogen and phosphorus retention in Danish restored wetlands.

Wetland restoration is considered an effective mitigation method for decreasing nitrogen (N) losses from agricultural land. However, when former cropland becomes rewetted, there is a risk that phosphorus (P) accumulated in soils will be released downstream. Here, we evaluate N and P retention in eight restored wetlands in Denmark monitored for 1 year using a mass balance approach. The wetlands represented different types, for instance, lakes and wet meadows, and ages (3-13 years). We also show the results from a long-term monitoring station established in 1973, located downstream a lake that was re-established in 2006. All restored wetlands removed total N (42-305 kg N ha-1 year-1), while some wetlands acted as source of total P and others as a sink (- 2.8 to 10 kg P ha-1 year-1). Our study confirms that restored wetlands are effective at removing N, whereas P can be released for several years after restoration.

Forest streams are important sources for nitrous oxide emissions.

Streams and river networks are increasingly recognized as significant sources for the greenhouse gas nitrous oxide (N2 O). N2 O is a transformation product of nitrogenous compounds in soil, sediment and water. Agricultural areas are considered a particular hotspot for emissions because of the large input of nitrogen (N) fertilizers applied on arable land. However, there is little information on N2 O emissions from forest streams although they constitute a major part of the total stream network globally. Here, we compiled N2 O concentration data from low-order streams (~1,000 observations from 172 stream sites) covering a large geographical gradient in Sweden from the temperate to the boreal zone and representing catchments with various degrees of agriculture and forest coverage. Our results showed that agricultural and forest streams had comparable N2 O concentrations of 1.6 ± 2.1 and 1.3 ± 1.8 µg N/L, respectively (mean ± SD) despite higher total N (TN) concentrations in agricultural streams (1,520 ± 1,640 vs. 780 ± 600 µg N/L). Although clear patterns linking N2 O concentrations and environmental variables were difficult to discern, the percent saturation of N2 O in the streams was positively correlated with stream concentration of TN and negatively correlated with pH. We speculate that the apparent contradiction between lower TN concentration but similar N2 O concentrations in forest streams than in agricultural streams is due to the low pH (<6) in forest soils and streams which affects denitrification and yields higher N2 O emissions. An estimate of the N2 O emission from low-order streams at the national scale revealed that ~1.8 × 109  g N2 O-N are emitted annually in Sweden, with forest streams contributing about 80% of the total stream emission. Hence, our results provide evidence that forest streams can act as substantial N2 O sources in the landscape with 800 × 109  g CO2 -eq emitted annually in Sweden, equivalent to 25% of the total N2 O emissions from the Swedish agricultural sector.

An Assessment of the Multifunctionality of Integrated Buffer Zones in Northwestern Europe.

Integrated buffer zones (IBZs) have recently been introduced in the Northwestern Europe temperate zone to improve delivery of ecosystem services compared with the services associated with long-established vegetated buffer zones. A common feature of all the studied IBZ sites is that tile drainage, which previously discharged directly into the streams, is now intercepted within the IBZ. Specifically, the design of IBZs combines a pond, where soil particles present in drain water or surface runoff can be deposited, and a planted subsurface flow infiltration zone. Together, these two components should provide an optimum environment for microbial processes and plant uptake of nutrients. Nutrient reduction capacities, biodiversity enhancement, and biomass production functions were assessed with different emphasis across 11 IBZ sites located in Denmark, Great Britain, and Sweden. Despite the small size of the buffer zones (250-800 m) and thus the small proportion of the drained catchment (mostly <1%), these studies cumulatively suggest that IBZs are effective enhancements to traditional buffer zones, as they (i) reduce total N and P loads to small streams and rivers, (ii) act as valuable improved habitats for aquatic and amphibian species, and (iii) offer economic benefits by producing fast-growing wetland plant biomass. Based on our assessment of the pilot sites, guidance is provided on the implementation and management of IBZs within agricultural landscapes.

The interplay between total mercury, methylmercury and dissolved organic matter in fluvial systems: A latitudinal study across Europe.

Large-scale studies are needed to identify the drivers of total mercury (THg) and monomethyl-mercury (MeHg) concentrations in aquatic ecosystems. Studies attempting to link dissolved organic matter (DOM) to levels of THg or MeHg are few and geographically constrained. Additionally, stream and river systems have been understudied as compared to lakes. Hence, the aim of this study was to examine the influence of DOM concentration and composition, morphological descriptors, land uses and water chemistry on THg and MeHg concentrations and the percentage of THg as MeHg (%MeHg) in 29 streams across Europe spanning from 41°N to 64 °N. THg concentrations (0.06-2.78 ng L-1) were highest in streams characterized by DOM with a high terrestrial soil signature and low nutrient content. MeHg concentrations (7.8-159 pg L-1) varied non-systematically across systems. Relationships between DOM bulk characteristics and THg and MeHg suggest that while soil derived DOM inputs control THg concentrations, autochthonous DOM (aquatically produced) and the availability of electron acceptors for Hg methylating microorganisms (e.g. sulfate) drive %MeHg and potentially MeHg concentration. Overall, these results highlight the large spatial variability in THg and MeHg concentrations at the European scale, and underscore the importance of DOM composition on mercury cycling in fluvial systems.

Nitrogen and Phosphorus Removal from Agricultural Runoff in Integrated Buffer Zones.

Integrated buffer zones (IBZs) represent a novel form of edge-of-field technology in Northwest Europe. Contrary to the common riparian buffer strips, IBZs collect tile drainage water from agricultural fields by combining a ditch-like pond (POND), where soil particles can settle, and a flow-through filter bed (FILTERBED) planted with Alnus glutinosa (L.), a European alder (black alder). The first experimental IBZ facility was constructed and thoroughly tested in Denmark for its capability to retain various nitrogen (N) and phosphorus (P) species within the first three years after construction. We calculated the water and nutrient budget for the total IBZ and for the two compartments, POND and FILTERBED, separately. Furthermore, a tracer experiment using sodium bromide was conducted in order to trace the water flow and estimate the hydraulic residence time in the FILTERBEDs. The monthly average removal efficiency amounted to 10-67% for total N and 31-69% for total P, with performance being highest during the warm season. Accordingly, we suggest that IBZs may be a valuable modification of dry buffer strips in order to mitigate the adverse impacts of high nutrient loading from agricultural fields on the aquatic environment.

Eutrophication effects on greenhouse gas fluxes from shallow-lake mesocosms override those of climate warming.

Fresh waters make a disproportionately large contribution to greenhouse gas (GHG) emissions, with shallow lakes being particular hot spots. Given their global prevalence, how GHG fluxes from shallow lakes are altered by climate change may have profound implications for the global carbon cycle. Empirical evidence for the temperature dependence of the processes controlling GHG production in natural systems is largely based on the correlation between seasonal temperature variation and seasonal change in GHG fluxes. However, ecosystem-level GHG fluxes could be influenced by factors, which while varying seasonally with temperature are actually either indirectly related (e.g. primary producer biomass) or largely unrelated to temperature, for instance nutrient loading. Here, we present results from the longest running shallow-lake mesocosm experiment which demonstrate that nutrient concentrations override temperature as a control of both the total and individual GHG flux. Furthermore, testing for temperature treatment effects at low and high nutrient levels separately showed only one, rather weak, positive effect of temperature (CH4 flux at high nutrients). In contrast, at low nutrients, the CO2 efflux was lower in the elevated temperature treatments, with no significant effect on CH4 or N2 O fluxes. Further analysis identified possible indirect effects of temperature treatment. For example, at low nutrient levels, increased macrophyte abundance was associated with significantly reduced fluxes of both CH4 and CO2 for both total annual flux and monthly observation data. As macrophyte abundance was positively related to temperature treatment, this suggests the possibility of indirect temperature effects, via macrophyte abundance, on CH4 and CO2 flux. These findings indicate that fluxes of GHGs from shallow lakes may be controlled more by factors indirectly related to temperature, in this case nutrient concentration and the abundance of primary producers. Thus, at ecosystem scale, response to climate change may not follow predictions based on the temperature dependence of metabolic processes.

Phosphorus load to surface water from bank erosion in a Danish lowland river basin.

Phosphorus loss from bank erosion was studied in the catchment of River Odense, a lowland Danish river basin, with the aim of testing the hypothesis of whether stream banks act as major diffuse phosphorus (P) sources at catchment scale. Furthermore, the study aimed at analyzing the impact of different factors influencing bank erosion and P loss such as stream order, anthropogenic disturbances, width of uncultivated buffer strips, and the vegetation of buffer strips. A random stratified procedure in geographical information system (GIS) was used to select two replicate stream reaches covering different stream orders, channelized vs. naturally meandering channels, width of uncultivated buffer strips (≤ 2 m and ≥ 10 m), and buffer strips with different vegetation types. Thirty-six 100-m stream reaches with 180 bank plots and a total of 3000 erosion pins were established in autumn 2006, and readings were conducted during a 3-yr period (2006-2009). The results show that neither stream size nor stream disturbance measured as channelization of channel or the width of uncultivated buffer strip had any significant ( < 0.05) influence on bank erosion and P losses during each of the 3 yr studied. In buffer strips with natural trees bank erosion was significantly ( < 0.05) lower than in buffer strips dominated by grass and herbs. Gross and net P input from bank erosion amounted to 13.8 to 16.5 and 2.4 to 6.3 t P, respectively, in the River Odense catchment during the three study years. The net P input from bank erosion equaled 17 to 29% of the annual total P export and 21 to 62% of the annual export of P from diffuse sources from the River Odense catchment. Most of the exported total P was found to be bioavailable (71.7%) based on a P speciation of monthly suspended sediment samples collected at the outlet of the river basin. The results found in this study have a great importance for managers working with P mitigation and modeling at catchment scale.