Genetic and environmental controls on nitrous oxide accumulation in lakes

Significant spatiotemporal pattern of nitrous oxide emission and its influencing factors from a shallow eutropic lake in Inner Mongolia, China

Eutrophic shallow lakes are generally considered as a contributor to the emission of nitrous oxide (N2O), while regional and global estimates have remained imprecise. This due to a lack of data and insufficient understanding of the multiple contributing factors. This study characterized the spatiotemporal variability in N2O concentrations and N2O diffusive fluxes and the contributing factors in Lake Wuliangsuhai, a typical shallow eutrophic and seasonally frozen lake in Inner Mongolia with cold and arid climate. Dissolved N2O concentrations of the lake exhibited a range of 4.5 to 101.2 nmol/L, displaying significant spatiotemporal variations. The lowest and highest concentrations were measured in summer and winter, respectively. The spatial distribution of N2O flux was consistent with that of N2O concentrations. Additionally, the hotspots of N2O emissions were detected within close to the main inflow of lake. The wide spatial and temporal variation in N2O emissions indicate the complexity and its relative importance of factors influencing emissions. N2O emissions in different lake zones and seasons were regulated by diverse factors. Factors influencing the spatial and temporal distribution of N2O concentrations and fluxes were identified as WT, WD, DO, Chl-a, SD and COD. Interestingly, the same factor demonstrated opposing effects on N2O emission in various seasons or zones. This research improves our understanding of N2O emissions in shallow eutrophic lakes in cold and arid areas.

Nitrous oxide (N2O) emission characteristics of farmland (rice, wheat, and maize) based on different fertilization strategies

Fertilizer application is the basis for ensuring high yield, high quality and high efficiency of farmland. In order to meet the demand for food with the increasing of population, the application of nitrogen fertilizer will be further increased, which will lead to problems such as N2O emission and nitrogen loss from farmland, it will easily deteriorate the soil and water environment of farmland, and will not conducive to the sustainable development of modern agriculture. However, optimizing fertilizer management is an important way to solve this problem. While, due to the differences in the study conditions (geographical location, environmental conditions, experimental design, etc.), leading to the results obtained in the literatures about the N2O emission with different nitrogen fertilizer application strategies have significant differences, which requiring further comprehensive quantitative analysis. Therefore, we analyzed the effects of nitrogen fertilizer application strategies (different fertilizer types and fertilizer application rates) on N2O emissions from the fields (rice, wheat and maize) based on the Meta-analysis using 67 published studies (including 1289 comparisons). For the three crops, inorganic fertilizer application significantly increased on-farm N2O emissions by 19.7-101.05% for all three; and organic fertilizer increased N2O emissions by 28.16% and 69.44% in wheat and maize fields, respectively, but the application of organic fertilizer in rice field significantly reduced N2O emissions by 58.1%. The results showed that overall, the application of inorganic fertilizers resulted in higher N2O emissions from farmland compared to the application of organic fertilizers. In addition, in this study, the average annual temperature, annual precipitation, soil type, pH, soil total nitrogen content, soil organic carbon content, and soil bulk weight were used as the main influencing factors of N2O emission under nitrogen fertilizer strategies, and the results of the study can provide a reference for the development of integrated management measures to control greenhouse gas emissions from agricultural soils.

The imbalance between N2O production and reduction by multi-microbial communities determines sedimentary N2O emission potential in the Pearl River Estuary

Denitrification is the dominant process of nitrogen removal and nitrous oxide (N2O) emissions in estuarine ecosystems. However, little is known regarding the microbial mechanism of the production and reduction of N2O in estuaries. We investigated in situ dissolved N2O as well as potential N2O production rate (NPR), reduction rate (NRR), and emission rate (NER), and key functional genes related to N2O transformation of denitrification in the Pearl River Estuary. Higher N2O emission potential was found in the upstream and midstream regions with higher NPR and lower NRR values. In contrast, higher NRR values were detected in downstream. Notably, nirS and nirK type N2O producers dominated the upstream zone, whereas abundant N2O reducers, especially nosZ II type N2O reducers, were observed in downstream. Most importantly, the gene abundance ratio (Rnir/nosZ) was significantly correlated with the N2O emission potential (Re). Niche differentiation between N2O producers and N2O reducers from upstream to downstream affected N2O emission potential. This study highlights the N2O emission potential in estuarine sediments is determined by an imbalance between N2O production and the reduction of multi-bacterial communities.

Denitrification contributes to N2O emission in paddy soils

Denitrification is vital to nitrogen removal and N₂O release in ecosystems; in this regard, paddy soils exhibit strong denitrifying ability. However, the underlying mechanism of N₂O emission from denitrification in paddy soils is yet to be elucidated. In this study, the potential N₂O emission rate, enzymatic activity for N₂O production and reduction, gene abundance, and community composition during denitrification were investigated using the ¹⁵N isotope tracer technique combined with slurry incubation, enzymatic activity detection, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing. Results of incubation experiments showed that the average potential N₂O emission rates were 0.51 ± 0.20 μmol⋅N⋅kg^-1⋅h^-1, which constituted 2.16 ± 0.85% of the denitrification end-products. The enzymatic activity for N₂O production was 2.77-8.94 times than that for N₂O reduction, indicating an imbalance between N₂O production and reduction. The gene abundance ratio of nir to nosZ from qPCR results further supported the imbalance. Results of metagenomic analysis showed that, although Proteobacteria was the common phylum for denitrification genes, other dominant community compositions varied for different denitrification genes. Gammaproteobacteria and other phyla containing the norB gene without nosZ genes, including Actinobacteria, Planctomycetes, Desulfobacterota, Cyanobacteria, Acidobacteria, Bacteroidetes, and Myxococcus, may contribute to N₂O emission from paddy soils. Our results suggest that denitrification is highly modular, with different microbial communities collaborating to complete the denitrification process, thus resulting in an emission estimation of 13.67 ± 5.44 g N₂O⋅m^-2⋅yr^-1 in surface paddy soils.

Improved Denitrification Performance of Polybutylene Succinate/Corncob Composite Carbon Source by Proper Pretreatment: Performance, Functional Genes and Microbial Community Structure

Blending biodegradable polymers with plant materials is an effective method to improve the biodegradability of solid carbon sources and save denitrification costs, but the recalcitrant lignin in plant materials hinders the microbial decomposition of available carbon sources. In the present study, corncob pretreated by different methods was used to prepare polybutylene succinate/corncob (PBS/corncob) composites for biological denitrification. The PBS/corncob composite with alkaline pretreatment achieved the optimal NO₃^--N removal rate (0.13 kg NO₃^--N m^-3 day^-1) with less adverse effects. The pretreatment degree, temperature, and their interaction distinctly impacted the nitrogen removal performance and dissolved organic carbon (DOC) release, while the N₂O emission was mainly affected by the temperature and the interaction of temperature and pretreatment degree. Microbial community analysis showed that the bacterial community was responsible for both denitrification and lignocellulose degradation, while the fungal community was primarily in charge of lignocellulose degradation. The outcomes of this study provide an effective strategy for improving the denitrification performance of composite carbon sources.

Temperature-Related N2O Emission and Emission Potential of Freshwater Sediment

Nitrous oxide (N2O) is a major radiative forcing and stratospheric ozone-depleting gas. Among natural sources, freshwater ecosystems are significant contributors to N2O. Although temperature is a key factor determining the N2O emissions, the respective effects of temperature on emitted and dissolved N2O in the water column of freshwater ecosystems remain unclear. In this study, 48 h incubation experiments were performed at three different temperatures; 15 °C, 25 °C, and 35 °C. For each sample, N2O emission, dissolved N2O in the overlying water and denitrification rates were measured, and N2O-related functional genes were quantified at regular intervals. The highest N2O emission was observed at an incubation of 35 °C, which was 1.5 to 2.1 factors higher than samples incubated at 25 °C and 15 °C. However, the highest level of dissolved N2O and estimated exchange flux of N2O were both observed at 25 °C and were both approximately 2 factors higher than those at 35 °C and 15 °C. The denitrification rates increased significantly during the incubation period, and samples at 25 °C and 35 °C exhibited much greater rates than those at 15 °C, which is in agreement with the N2O emission of the three incubation temperatures. The NO3− decreased in relation to the increase of N2O emissions, which confirms the dominant role of denitrification in N2O generation. Indeed, the nirK type denitrifier, which constitutes part of the denitrification process, dominated the nirS type involved in N2O generation, and the nosZ II type N2O reducer was more abundant than the nosZ I type. The results of the current study indicate that higher temperatures (35 °C) result in higher N2O emissions, but incubation at moderate temperatures (25 °C) causes higher levels of dissolved N2O, which represent a potential source of N2O emissions from freshwater ecosystems.

Nitrate Addition Increases the Activity of Microbial Nitrogen Removal in Freshwater Sediment

Denitrification and anammox occur widely in aquatic ecosystems serving vital roles in nitrogen pollution removal. However, small waterbodies are sensitive to external influences; stormwater runoff carrying nutrients and oxygen, flows into waterbodies resulting in a disruption of geochemical and microbial processes. Nonetheless, little is known about how these short-term external inputs affect the microbial processes of nitrogen removal in small waterbodies. To investigate the effects of NO₃⁻, NH₄⁺, dissolved oxygen (DO) and organic C on microbial nitrogen removal in pond sediments, regulation experiments have been conducted using slurry incubation experiments and ¹⁵N tracer techniques in this study. It was demonstrated the addition of NO₃⁻ (50 to 800 μmol L⁻¹) significantly promoted denitrification rates, as expected by Michaelis-Menten kinetics. Ponds with higher NO₃⁻ concentrations in the overlying water responded more greatly to NO₃⁻ additions. Moreover, N₂O production was also promoted by such an addition of NO₃⁻. Denitrification was significantly inhibited by the elevation of DO concentration from 0 to 2 mg L⁻¹, after which no significant increase in inhibition was observed. Denitrification rates increased when organic C was introduced. Due to the abundant NH₄⁺ in pond sediments, the addition demonstrated little influence on nitrogen removal. Moreover, anammox rates showed no significant changes to any amendment.

High N2O reduction potential by denitrification in the nearshore site of a riparian zone

As a potent atmospheric greenhouse gas and a major source of ozone depletion, nitrous oxide (N₂O) emission has been given increasing attention in aquatic systems, particularly at the aquatic-terrestrial interfaces, such as riparian zones. However, the microbial mechanisms regulating N₂O emission in riparian zones remain unknown. Here, we measured the contributions of denitrification and ammonium oxidation to N₂O emission along with the abundance and community structure of nirK-, nirS-, nosZ I- and nosZ II-harbouring bacteria in both surface sediments (0-10 cm) and overlying water along a lake riparian zone (including nearshore sites and offshore sites). Overall, the nearshore sites of the riparian zones emitted less N₂O than the offshore sites. Nearshore N₂O emission was dominated by denitrification with a high N₂O reduction rate, whereas offshore N₂O emission was driven by ammonium oxidation. Furthermore, N₂O derived from ammonium oxidation was influenced by the NH₄⁺-N content, and denitrification N₂O was modulated by denitrifier communities. The N₂O-producing community was dominated by nirS-harbouring bacteria, while the N₂O-reducing community was dominated by nosZ I-harbouring bacteria. The relative abundance of Hydrogenophilales from nirS-denitrifiers and Chloroflexi unclassified from nosZ II-type communities influenced the N₂O produced by denitrification, according to high-throughput sequencing analysis. Additionally, we also found lower levels of N₂O production per unit volume in overlying water, which were 3-4 orders of magnitude less than in the surface sediment. Overall, we propose that using riparian zones can be an effective management tool for N₂O mitigation by enhancing the N₂O reduction process of denitrification and decreasing ammonium oxidation.

Submerged macrophytes regulate diurnal nitrous oxide emissions from a shallow eutrophic lake: A case study of Lake Wuliangsuhai in the temperate arid region of China

Submerged macrophytes can increase oxygen concentrations of water and promote diel oxygen fluctuations, and this phenomenon is hypothesized to play a vital role in regulating nitrous oxide (N₂O) emissions from eutrophic lakes. However, the effects of submerged macrophytes on N₂O emissions in shallow eutrophic lakes remain poorly investigated. In this study, Lake Wuliangsuhai, a typical shallow eutrophic lake, was investigated to study the role of submerged macrophytes in regulating N₂O emissions. We measured the N₂O fluxes and related parameters through continual 72-h in situ diel monitoring in two sampling sections that covered dense submerged macrophyte areas and open water. In this study, the dissolved oxygen (DO) concentration of the water in the submerged macrophyte area exhibited significant diurnal variations, with significantly higher water oxygen concentrations than the open water area during the daytime. The N₂O fluxes of Lake Wuliangsuhai ranged from 0.01 to 0.24 μmol m^-2 h^-1, with an average value of 0.11 μmol m^-2 h^-1. Moreover, significant diel variations in the N₂O flux and net N₂O production were observed in the submerged macrophyte areas, where the maximum N₂O flux occurred at midday. The molar ratios of NH₄⁺-N to oxygen (N/O ratio) of the water were responsible for the diel variations in the N₂O production in the lake. However, the high oxygen concentration of the water was the major regulator of the N₂O flux of Lake Wuliangsuhai. Therefore, submerged macrophyte restoration is significant not only for water quality improvement in shallow eutrophic lakes but also for N₂O emission mitigation by increasing the DO concentration of the water.

Microbial nitrogen loss by coupled nitrification to denitrification and anammox in a permeable subterranean estuary at Gloucester Point, Virginia

The nitrogen (N) loss processes have not been well examined in subterranean estuaries (STEs) between land and sea. We utilized a ¹⁵N isotope tracer method, q-PCR, and high-throughput sequencing to reveal the activities, abundances, and community compositions of N loss communities in a STE in Gloucester Point, Virginia, US. The highest activities, abundances and diversity of denitrifiers and anammox bacteria were detected at 50-60 cm depth in the aerobic-anaerobic transition zone (AATZ) characterized by sharp redox gradients. nirS-denitrifiers and anammox bacteria were affiliated to 10 different clusters and three genera, respectively. Denitrification and anammox played equal roles with an estimated N loss of 13.15 mmol N m^-3 day^-1. A positive correlation between ammonia oxidizing prokaryote abundances and DO as well as NO_x^- suggested that nitrification produces NO_x^- which supports the hotspot of denitrification and anammox within the AATZ. Overall, these results highlight the roles of N loss communities in STEs.

Effects of biochar on nitrification and denitrification-mediated N2O emissions and the associated microbial community in an agricultural soil

Nitrous oxide (N₂O) is a strong greenhouse gas, and it is of great significance for N₂O reduction to study the effects of biochar on its production pathway. In this research, the contributions and mechanisms of biochar on autotrophic nitrification (ANF), heterotrophic nitrification (HNF), and denitrification (DF) to N₂O emissions were studied by using ¹⁵N stable isotopes and high-throughput sequencing after laboratory incubation. The results showed that biochar addition at 2% (B2) significantly reduced the N₂O emissions from the ANF by an average of 20.6%, while adding 5% biochar (B5) had no significant effect on the ANF. Both B2 and B5 significantly reduced the N₂O emissions from the HNF by 15.7% and 13.2%, respectively, and reduced the N₂O emissions from the DF by 40.9% and 11.7%, respectively. B2 enhanced the relative contribution rate of the ANF to N₂O emissions by 6.3%, while B5 had little effect on it. Biochar addition significantly changed the copy numbers of the AOA and AOB, as well as the nirK, nirS, and nosZ genes, but it had no significant effect on the community composition of the AOA and had minimal effect on the AOB community. B2 significantly increased the abundance of the genus Rhodococcus of nirK type denitrifiers and had a significant effect on the relative abundance of Cupriavidus and Pseudomonas of the nosZ type denitrifiers. These results revealed that the inhibitory effects of biochar on N₂O emissions from nitrification might be attributed to the direct immobilization and adsorption of inorganic N by biochar and to its promotion of the genus Rhodococcus of nirK-type denitrifiers and the genera Cupriavidus and Pseudomonas of the nosZ-type denitrifiers. The soil exchangeable NH₄⁺-N and NO₃^--N concentrations were the primary factors affecting the N₂O emission rates. These results help to elucidate the effects and mechanisms of biochar on N₂O production pathways in agricultural soil.

Development of droplet digital PCR assays to quantify genes involved in nitrification and denitrification, comparison with quantitative real-time PCR and validation of assays in vineyard soil

Quantifying genes in soil is important to relate the abundance of soil bacteria to biogeochemical cycles. Quantitative real-time PCR is widely used for quantification, but its use with environmental samples is limited by poor reaction efficiencies or by PCR inhibition through co-purified soil substances. Droplet digital PCR (ddPCR) is a technology for absolute, sensitive quantification of genes. This study optimized eight ddPCR assays to quantify total bacteria and archaea as well as the nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, nosZI, nosZII) genes involved in the generation or reduction of the greenhouse gas nitrous oxide. Detection and quantification thresholds were compared with those of quantitative real-time PCR and were equal to, or improved, in ddPCR. To validate the assays using environmental samples, soil DNA was isolated from two vineyards in the Okanagan valley in British Columbia, Canada, over the 2017 growing season. Soil properties related to the observed gene abundances were determined. Total bacteria, nirK, and nosZII increased with time and the soil C/N ratio and NH₄⁺-N concentration affected total archaea and archaeal amoA negatively. The results, compared with those of other studies, showed that ddPCR is a valid alternative to qPCR to quantify genes involved in nitrification or denitrification.

Nitrate removal microbiology in woodchip bioreactors: A case-study with full-scale bioreactors treating aquaculture effluents

Woodchip bioreactors are viable low-cost nitrate (NO₃^-) removal applications for treating agricultural and aquaculture discharges. The active microbial biofilms growing on woodchips are conducting nitrogen (N) removal, reducing NO₃^- while oxidizing the carbon (C) from woodchips. However, bioreactor age, and changes in the operating conditions or in the microbial community might affect the NO₃^- removal as well as potentially promote nitrous oxide (N₂O) production through either incomplete denitrification or dissimilatory NO₃^- reduction to ammonium (DNRA). Here, we combined stable isotope approach, amplicon sequencing, and captured metagenomics for studying the potential NO₃^- removal rates, and the abundance and community composition of microbes involved in N transformation processes in the three different full-scale woodchip bioreactors treating recirculating aquaculture system (RAS) effluents. We confirmed denitrification producing di‑nitrogen gas (N₂) to be the primary NO₃^- removal pathway, but found that 6% of NO₃^- could be released as N₂O under high NO₃^- concentrations and low amounts of bioavailable C, whereas DNRA rates tend to increase with the C amount. The abundance of denitrifiers was equally high between the studied bioreactors, yet the potential NO₃^- removal rates were linked to the denitrifying community diversity. The same core proteobacterial groups were driving the denitrification, while Bacteroidetes dominated the DNRA carrying microbes in all the three bioreactors studied. Altogether, our results suggest that woodchip bioreactors have a high genetic potential for NO₃^- removal through a highly abundant and diverse denitrifying community, but that the rates and dynamics between the NO₃^- removal pathways depend on the other factors (e.g., bioreactor design, operating conditions, and the amount of bioavailable C in relation to the incoming NO₃^- concentrations).

Control of the Hydraulic Load on Nitrous Oxide Emissions from Cascade Reservoirs

Nitrous oxide (N₂O) emissions show large variability among dam reservoirs, which makes it difficult to estimate N₂O contributions to global greenhouse gases (GHGs). Because river damming alters hydraulic residence time and water depth, the hydraulic load (i.e., the ratio of the mean water depth to the residence time) was hypothesized to control N₂O emissions from dam reservoirs. To test this hypothesis, we investigated N₂O fluxes and related parameters in the cascade reservoirs along the Wujiang River in Southwest China. The N₂O fluxes showed obvious temporal and spatial variations, ranging from -7.86 to 337.22 μmol m^-2 d^-1, with an average of 12.76 μmol m^-2 d^-1. Nitrification was the main pathway of N₂O production in these reservoirs, and seasonal dissolved oxygen (DO) stratification played an important role in regulating the N₂O production. The reservoir N₂O flux had a significant negative logarithmic relationship with the hydraulic load, suggesting its control of the N₂O emission. This was because the hydraulic load was a prerequisite for regulating the nitrification-denitrification and the DO stratification in the dam reservoirs. This empirical relationship will help to estimate the contribution of reservoir N₂O emissions to global GHGs.

The DNRA-Denitrification Dichotomy Differentiates Nitrogen Transformation Pathways in Mountain Lake Benthic Habitats

Effects of nitrogen (N) deposition on microbially-driven processes in oligotrophic freshwater ecosystems are poorly understood. We quantified guilds in the main N-transformation pathways in benthic habitats of 11 mountain lakes along a dissolved inorganic nitrogen gradient. The genes involved in denitrification (nirS, nirK, nosZ), nitrification (archaeal and bacterial amoA), dissimilatory nitrate reduction to ammonium (DNRA, nrfA) and anaerobic ammonium oxidation (anammox, hdh) were quantified, and the bacterial 16S rRNA gene was sequenced. The dominant pathways and associated bacterial communities defined four main N-transforming clusters that differed across habitat types. DNRA dominated in the sediments, except in the upper layers of more productive lakes where nirS denitrifiers prevailed with potential N₂O release. Loss as N₂ was more likely in lithic biofilms, as indicated by the higher hdh and nosZ abundances. Archaeal ammonia oxidisers predominated in the isoetid rhizosphere and rocky littoral sediments, suggesting nitrifying hotspots. Overall, we observed a change in potential for reactive N recycling via DNRA to N losses via denitrification as lake productivity increases in oligotrophic mountain lakes. Thus, N deposition results in a shift in genetic potential from an internal N accumulation to an atmospheric release in the respective lake systems, with increased risk for N₂O emissions from productive lakes.

High Nitrogen Removal in a Constructed Wetland Receiving Treated Wastewater in a Cold Climate

Constructed wetlands provide cost-efficient nutrient removal, with minimal input of human labor and energy, and their number is globally increasing. However, in northern latitudes, wetlands are rarely utilized, because their nutrient removal efficiency has been questioned due to the cold climate. Here, we studied nutrient retention and nitrogen removal in a boreal constructed wetland (4-ha) receiving treated nitrogen-rich wastewater. On a yearly basis, most of the inorganic nutrients were retained by the wetland. The highest retention efficiency was found during the ice-free period, being 79% for ammonium-nitrogen (NH₄⁺-N), 71% for nitrate-nitrogen (NO₃^--N), and 88% for phosphate-phosphorus (PO₄^3--P). Wetland also acted as a buffer zone during the disturbed nitrification process of the wastewater treatment plant. Denitrification varied between 106 and 252 mg N m^-2 d^-1 during the ice-free period. During the ice-cover period, total gaseous nitrogen removal was 147 mg N m^-2 d^-1, from which 66% was removed as N₂, 28.5% as N₂O through denitrification, and 5.5% as N₂ through anammox. Nearly 2600 kg N y^-1 was estimated to be removed through microbial gaseous N-production which equaled 72% of NO₃^--N and 60% of TN yearly retention in the wetland. The wetland retained nutrients even in winter, when good oxygen conditions prevailed under ice. The results suggest that constructed wetlands are an efficient option for wastewater nitrogen removal and nutrient retention also in cold climates.

Effects of fertilizer application schemes and soil environmental factors on nitrous oxide emission fluxes in a rice-wheat cropping system, east China

Nitrous oxide (N₂O) is a potent greenhouse gas (GHG) with agricultural soils representing its largest anthropogenic source. However, the mechanisms involved in the N₂O emission and factors affecting N₂O emission fluxes in response to various nitrogenous fertilizer applications remain uncertain. We conducted a four-year (2012–2015) field experiment to assess how fertilization scheme impacts N₂O emissions from a rice-wheat cropping system in eastern China. The fertilizer treatments included Control (CK), Conventional fertilizer (CF), CF with shallow-irrigation (CF+SI), CF with deep-irrigation system (CF+DI), Optimized fertilizer (OF), OF with Urease inhibitor (OF+UI), OF with conservation tillage (OF+CT) and Slow-release fertilizer (SRF). N₂O emissions were measured by a closed static chamber method. N₂O emission fluxes ranged from 0.61 μg m^-2 h^-1 to 1707 μg m^-2 h^-1, indicating a significant impact of nitrogen fertilizer and cropping type on N₂O emissions. The highest crop yields for wheat (3515–3667 kg ha^-1) and rice (8633–8990 kg ha^-1) were observed under the SRF and OF+UI treatments with significant reduction in N₂O emissions by 16.94–21.20% and 5.55–7.93%, respectively. Our findings suggest that the SRF and OF+UI treatments can be effective in achieving maximum crop yield and lowering N₂O emissions for the rice-wheat cropping system in eastern China.

Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake

Oxygen-stratified lakes are typical for the boreal zone and also a major source of greenhouse gas emissions in the region. Due to shallow light penetration, restricting the growth of phototrophic organisms, and large allochthonous organic carbon inputs from the catchment area, the lake metabolism is expected to be dominated by heterotrophic organisms. In this study, we test this assumption and show that the potential for autotrophic carbon fixation and internal carbon cycling is high throughout the water column. Further, we show that during the summer stratification carbon fixation can exceed respiration in a boreal lake even below the euphotic zone. Metagenome-assembled genomes and 16S profiling of a vertical transect of the lake revealed multiple organisms in an oxygen-depleted compartment belonging to novel or poorly characterized phyla. Many of these organisms were chemolithotrophic, potentially deriving their energy from reactions related to sulfur, iron, and nitrogen transformations. The community, as well as the functions, was stratified along the redox gradient. The autotrophic potential in the lake metagenome below the oxygenic zone was high, pointing toward a need for revising our concepts of internal carbon cycling in boreal lakes. Further, the importance of chemolithoautotrophy for the internal carbon cycling suggests that many predicted climate change-associated fluctuations in the physical properties of the lake, such as altered mixing patterns, likely have consequences for the whole-lake metabolism even beyond the impact to the phototrophic community.

Autotrophic organisms at the base of the food web are the only life form capable of turning inorganic carbon into the organic form, facilitating the survival of all other organisms. In certain environments, the autotrophic production is limited by environmental conditions and the food web is supported by external carbon inputs. One such environment is stratified boreal lakes, which are one of the biggest natural sources of greenhouse gas emissions in the boreal region. Thus, carbon cycling in these habitats is of utmost importance for the future climate. Here, we demonstrate a high potential for internal carbon cycling via phototrophic and novel chemolithotrophic organisms in the anoxic, poorly illuminated layers of a boreal lake. Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen-depleted freshwaters and help to understand and predict how climate change-induced alterations could impact the lake carbon dynamics.

Isotope and microbiome data provide complementary information to identify natural nitrate attenuation processes in groundwater

Natural attenuation processes alleviate the impact of fertilization practices on groundwater resources. Therefore, identifying the occurrence of denitrification has become a requirement for water quality management. Several approaches are useful for this purpose, such as isotopic and microbiological methods, each of them providing distinct but complementary information about denitrification reactions, attenuation rates and their occurrence in the aquifer. In this paper, we investigate the contribution of both approaches to describe denitrification in a consolidated rock aquifer (limestone and marls), with a porosity related to fracture networks located in the northeastern sector of the Osona basin (NE Spain). Isotopic methods indicated the origin of nitrate (fertilization using manure) and that denitrification occurred, reaching a reduction of near 25% of the nitrate mass in groundwater. The studied area could be divided in two zones with distinct agricultural pressures and, consequently, nitrate concentrations in groundwater. Denitrification occurred in both zones and at different levels, indicating that attenuation processes took place all along the whole hydrogeological unit, and that the observed levels could be attributed to a larger flow path or, in a minor extent, to mixing processes that mask the actual denitrification rates. Microbiological data showed a correlation between denitrifier genes and the isotopic composition. However, the groundwater microbiome and the distribution of denitrifying bacteria did not reveal a major influence on the denitrification level observed by isotopic methods. This focuses the interest of microbiological analysis to identify functional genes within the bacteria present in the aquifer. Results indicated that isotopic methods provide information of the overall denitrification ability of the hydrogeological unit, and that genomic data represent the processes actually acting nearby the well. A combination of both approaches is advised to support induced in situ attenuation actions in polluted sites.

Denitrification and Biodiversity of Denitrifiers in a High-Mountain Mediterranean Lake

Wet deposition of reactive nitrogen (Nr) species is considered a main factor contributing to N inputs, of which nitrate ([Formula: see text]) is usually the major component in high-mountain lakes. The microbial group of denitrifiers are largely responsible for reduction of nitrate to molecular dinitrogen (N₂) in terrestrial and aquatic ecosystems, but the role of denitrification in removal of contaminant nitrates in high-mountain lakes is not well understood. We have used the oligotrophic, high-altitude La Caldera lake in the Sierra Nevada range (Spain) as a model to study the role of denitrification in nitrate removal. Dissolved inorganic Nr concentration in the water column of la Caldera, mainly nitrate, decreased over the ice-free season which was not associated with growth of microbial plankton or variations in the ultraviolet radiation. Denitrification activity, estimated as nitrous oxide (N₂O) production, was measured in the water column and in sediments of the lake, and had maximal values in the month of August. Relative abundance of denitrifying bacteria in sediments was studied by quantitative polymerase chain reaction of the 16S rRNA and the two phylogenetically distinct clades nosZI and nosZII genes encoding nitrous oxide reductases. Diversity of denitrifiers in sediments was assessed using a culture-dependent approach and after the construction of clone libraries employing the nosZI gene as a molecular marker. In addition to genera Polymorphum, Paracoccus, Azospirillum, Pseudomonas, Hyphomicrobium, Thauera, and Methylophaga, which were present in the clone libraries, Arthrobacter, Burkholderia, and Rhizobium were also detected in culture media that were not found in the clone libraries. Analysis of biological activities involved in the C, N, P, and S cycles from sediments revealed that nitrate was not a limiting nutrient in the lake, allowed N₂O production and determined denitrifiers' community structure. All these results indicate that denitrification could be a major biochemical process responsible for the N losses that occur in La Caldera lake.

Genomics and Ecology of Novel N2O-Reducing Microorganisms

Microorganisms with the capacity to reduce the greenhouse gas nitrous oxide (N₂O) to harmless dinitrogen gas are receiving increased attention due to increasing N₂O emissions (and our need to mitigate climate change) and to recent discoveries of novel N₂O-reducing bacteria and archaea. The diversity of denitrifying and nondenitrifying microorganisms with capacity for N₂O reduction was recently shown to be greater than previously expected. A formerly overlooked group (clade II) in the environment include a large fraction of nondenitrifying N₂O reducers, which could be N₂O sinks without major contribution to N₂O formation. We review the recent advances about fundamental understanding of the genomics, physiology, and ecology of N₂O reducers and the importance of these findings for curbing N₂O emissions.

Microbial Community Response on Wastewater Discharge in Boreal Lake Sediments

Despite high performance, municipal wastewater treatment plants (WWTPs) still discharge significant amounts of organic material and nitrogen and even microbes into the receiving water bodies, altering physico-chemical conditions and microbial functions. In this study, we examined how nitrified wastewater affects the microbiology of boreal lake sediments. Microbial community compositions were assessed with next generation sequencing of the 16S rRNA gene, and a more detailed view on nitrogen transformation processes was gained with qPCR targeting on functional genes (nirS, nirK, nosZ_I, nosZ_II, amoA_archaea, and amoA_bacteria). In both of the two studied lake sites, the microbial community composition differed significantly between control point and wastewater discharge point, and a gradual shift toward natural community composition was seen downstream following the wastewater gradient. SourceTracker analysis predicted that ∼2% of sediment microbes were of WWTP-origin on the study site where wastewater was freely mixed with the lake water, while when wastewater was specially discharged to the sediment surface, ∼6% of microbes originated from WWTP, but the wastewater-influenced area was more limited. In nitrogen transformation processes, the ratio between nitrifying archaea (AOA) and bacteria (AOB) was affected by wastewater effluent, as the AOA abundance decreased from the control point (AOA:AOB 28:1 in Keuruu, 11:1 in Petäjävesi) to the wastewater-influenced sampling points, where AOB dominated (AOA:AOB 1:2–1:15 in Keuruu, 1:3–1:19 in Petäjävesi). The study showed that wastewater can affect sediment microbial community through importing nutrients and organic material and altering habitat characteristics, but also through bringing wastewater-originated microbes to the sediment, and may thus have significant impact on the freshwater biogeochemistry, especially in the nutrient-poor boreal ecosystems.

Submerged macrophytes shape the abundance and diversity of bacterial denitrifiers in bacterioplankton and epiphyton in the Shallow Fresh Lake Taihu, China

nirK and nirS genes are important functional genes involved in the denitrification pathway. Recent studies about these two denitrifying genes are focusing on sediment and wastewater microbe. In this study, we conducted a comparative analysis of the abundance and diversity of denitrifiers in the epiphyton of submerged macrophytes Potamogeton malaianus and Ceratophyllum demersum as well as in bacterioplankton in the shallow fresh lake Taihu, China. Results showed that nirK and nirS genes had significant different niches in epiphyton and bacterioplankton. Bacterioplankton showed greater abundance of nirK gene in terms of copy numbers and lower abundance of nirS gene. Significant difference in the abundance of nirK and nirS genes also existed between the epiphyton from different submerged macrophytes. Similar community diversity yet different community abundance was observed between epiphytic bacteria and bacterioplankton. No apparent seasonal variation was found either in epiphytic bacteria or bacterioplankton; however, environmental parameters seemed to have direct relevancy with nirK and nirS genes. Our study suggested that submerged macrophytes have greater influence than seasonal parameters in shaping the presence and abundance of bacterial denitrifiers. Further investigation needs to focus on the potential contact and relative contribution between denitrifiers and environmental factors.

Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes

Thousands of net-heterotrophic and strongly stratifying lakes dominate the boreal landscape. Besides their central role as emitters of greenhouse gases, we have only recently begun to understand the microbial systems driving the metabolic processes and elemental cycles in these lakes. Using shotgun metagenomics, we show that the functional potential differs among lake types, with humic lakes being particularly enriched in carbon degradation genes. Most of the metabolic pathways exhibit oxygen- and temperature-dependent stratification over depth, coinciding with shifts in bacterial community composition, implying that stratification is a major factor controlling lake metabolism. In the bottom waters, rare and poorly characterized taxa, such as ε-Proteobacteria, but also autotrophs, such as photolithotrophic Chlorobia were abundant. These oxygen-depleted layers exhibited high genetic potential for mineralization, but also for fixation of carbon and nitrogen, and genetic markers for both methane production and oxidation were present. Our study provides a first glimpse of the genetic versatility of freshwater anoxic zones, and demonstrates the potential for complete turnover of carbon compounds within the water column.

Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes

Denitrification is an important microbial process in aquatic ecosystems that can reduce the effects of eutrophication. Here, quantification and pyrosequencing of nirS, nirK, and nosZ genes encoding for nitrite and nitrous oxide reductases was performed in sediment samples from four boreal lakes to determine the structure and seasonal stability of denitrifying microbial populations. Sediment quality and nitrate concentrations were linked to the quantity and diversity of denitrification genes, the abundance of denitrifying populations (nirS and nosZ genes) correlated with coupled nitrification-denitrification (Dn), and the denitrification of the overlying water NO₃^- (Dw) correlated with the nirS/nirK ratio. The number of core nirS, nirK, and nosZ operational taxonomical units (OTUs) was low (6, 7, and 3, respectively), and most of these core OTUs were shared among the lakes. Dominant nirK sequences matched best with those of the order Rhizobiales, which was one of the main bacterial orders present in the sediment microbiomes, whereas the dominant nirS sequences were affiliated with the order Burkholderiales. Over half of the nosZ sequences belonged to a single OTU of the order Burkholderiales, but coupled nitrification–denitrification rate correlated with another dominant nosZ OTU assigned to the order Rhodospirillales. The study indicates that a few core proteobacterial clusters may drive denitrification in boreal lake sediments, as the same Alpha- and Betaproteobacteria denitrifier clusters were present in different lakes and seasons.