Nitrogen removal through sediment denitrification in the Yangtze Estuary and its adjacent East China Sea: A nitrate limited process during summertime

Spatial distribution of potential nitrogen reduction rates and associated microbial communities revealed by metagenomic analysis in Yangtze River sediments

Understanding the intricacies of nitrogen reduction processes and the composition of associated microbial communities is crucial for illuminating the reactions of ecosystems and their functions to persistent nitrogen inputs. To enhance research on the nitrogen reduction process, we determined the potential rates, quantified the relevant genes, and analyzed the macro factors in the sediments of the Yangtze River. The results showed that dissimilatory reduction of nitrate to ammonium (DNRA) dominated the N-reduction processes in the Yangtze River sediment, with average rates of 0.89 ± 0.71 nmol N g-1 h-1. Meanwhile, denitrification and anammox rates were 0.73 ± 0.74 and 0.07 ± 0.07 nmol N g-1 h-1, respectively. The Three Gorges Dam (TGD) caused higher potential rates (nmol N g-1 h-1) of denitrification (1.38), anammox (0.12), DNRA (1.48), and N2O depletion (1.49 nmol g-1 h-1) in the Three Gorges Reservoir (TGR) compared to other river reaches. The average copy numbers (copies·g-1) of nrfA (2.96 × 106), narG (8.17 × 105), nirS (6.10 × 106), nosZ (2.77 × 106), and hzsB (3.68 × 105) in TGR sediments were higher than those in the other reaches. The TGD's interception of fine sediments and nutrients enhanced microbial gene abundance, thereby favoring N-reduction processes and resulting in N2O depletion in reservoir sediments. Moreover, the TGD caused a decreased contribution gap between DNRA and denitrification in the TGR (2%) compared with the upper (35%) and lower (18%) reaches, while causing predominant anammox (50%) in the middle reach. Metagenomic results suggested that sediment particle size, along with organic carbon and inorganic nitrogen concentrations, influenced N reduction rates by affecting narG, norB and C, nrfA and H, and hzsB and C. This study reveals the spatial pattern of the N-reduction rate in the Yangtze River sediments and quantitatively defines the intensity of dam effects on sediment N-reduction rate.

Records of biogeochemical variables for Semarang Bay, Indonesia, facing potential coastal deoxygenation

Coastal areas worldwide, including the Indonesian seas, are experiencing a decline in dissolved oxygen (DO) concentration, leading to deoxygenation. Semarang Bay, due to its semi-enclosed nature and significant terrestrial input, is particularly vulnerable to this phenomenon. We analyzed multi-annual records of biogeochemical variables, including nutrient concentrations, chlorophyll-a (Chl-a), and both surface and bottom dissolved oxygen (DO), to assess the possibility of coastal deoxygenation. The study focuses specifically on bottom DO to understand its variability and potential impact on the sediment-water interface. It aims to evaluate the potential for coastal deoxygenation in the bay region by examining sediment stable isotope signatures and biogeochemical variable records in connection with their potential influence on DO at the sediment-water interface. The analysis reveals contrasting trends in sea surface temperature, bottom temperature, and DO concentrations. Spatial analysis uncovers distinct patterns, emphasizing the influence of monsoon seasons on temperature, DO, and Chl-a concentrations. The study notes a declining trend in DO and bottom DO (i.e., -0.055 and -0.048 mmol/m3 per year, respectively), underscoring the need to monitor dissolved oxygen dynamics at the sediment-water interface. Isotope analysis of surface sediment suggests potential sediment deoxygenation at specific sampling sites, irrespective of proximity to the shoreline or bathymetric depth, with similar indications in flood channels. This research offers valuable insights into the complex dynamics of coastal biogeochemistry in Semarang Bay. The findings underscore the need for further research to refine models and explore alternative approaches to address the identified limitations, thereby contributing to enhanced environmental monitoring and assessment in the study site.

Impact of soil inorganic nitrogen on bacterial phylogeny in estuarine intertidal zones: a study of nitrogen metabolism

Here we investigated the potential impacts of soil inorganic nitrogen (SIN) content on the phylogenetic characteristics and ecological functions of soil bacterial communities in estuarine intertidal zones in China, aiming to comprehend the response mechanism of soil microorganisms to variations in SIN content within estuarine wetlands. Our results show that SIN in estuarine areas has a significant spatiotemporal variation on spatial and seasonal scales, in this study and is significantly associated with the phylogenetic diversity and phylogenetic turnover of soil bacterial communities. In addition, the results of the metagenomic analysis showed that the relative abundance of nitrogen-cycling functional genes in bacterial communities did not differ significantly in sampling sites and seasons, and weakly correlated with SIN content. Further, the results based on structural equation modeling (SEM) analysis showed that SIN directly and significantly regulated the phylogenetic characteristics of bacterial communities, thereby indirectly affecting the potential of bacterial nitrogen metabolism. This study emphasizes the key influence of SIN variations on the phylogenetic dissimilarity in soil bacterial communities. Moreover, although there was a weak direct relationship between the functional characteristics of the bacterial nitrogen metabolism and SIN content, the spatiotemporal variation of bacterial nitrogen metabolic potential may be indirectly regulated by SIN content by influencing the phylogenetic diversity in bacterial communities. Our study unravels the pivotal mechanisms through which SIN content influences bacterial communities, thereby offering novel insights into the microbial intricacies governing nitrogen metabolism within estuaries.

Regulation of potential denitrification rates in sediments by microbial-driven elemental coupled metabolisms

Microbial driven coupled processes between denitrification and methane/sulfur metabolism play a very substantial role in accelerating nitrogen removal in river sediments. Until now, little is known about how element coupling processes alter nitrogen metabolism by the microbial functional communities. The primary objective of this research was to clarify the contributory role of microbial-mediated coupled processes in controlling denitrification. Specifically, the study sought to identify the key bioindicators (or metabolic pathway) for preferably regulating and predicting potential denitrification rate (PDR). Here, a total of 40 sediment samples were collected from the inflow rivers of Chaohu Lake under nitrogen stress. The results revealed the ecological importance of methanogens and sulfate reducing bacteria in the microbial interaction network. Correlations between quantitative or predicted genes showed that the methanogenic gene (mcrA) was synergistic with denitrifying genes, further unraveling that the key role of methanogenesis in denitrification process for facilitating nitrogen removal. The PDR of sediments ranged from 0.03 to 133.21 μg N·g-1·h-1. The study uncovered specific environmental factors (NH4+ and OM) and microbial indicators (nosZ, mcrA, Paracoccus, Thauera, Methanobrevibacter and Desulfomicrobium) as potential contributors to the variations in PDR. Structural Equation Model (SEM) analysis revealed a significant direct effect of NH4+ on PDR, evidenced by a standardized coefficient (λ) of 0.77 (P < 0.001). Additionally, the findings also emphasized the salient role of methanogens (Methanobrevibacter) and methanogenic gene (mcrA) in indicating PDR. The research's aforementioned findings shed light on the substantial consequences of methanogenesis on nitrogen metabolism in coupled processes, enabling improved control of nitrogen pollution in river sediments. This study provided fresh perspectives on the effects of multiple functional taxa on denitrification, and reinforces the significance of coupling processes for nitrogen removal.

The influence of wet-to-dry season shifts on the microbial community stability and nitrogen cycle in the Poyang Lake sediment

In lake environments, seasonal changes can cause exposure of the lake sediment, leading to soil formation. Although previous studies have explored how environmental changes influence microbial functioning in the water-level-fluctuating zone, few studies have investigated how wholescale habitat changes affect microbial composition, community stability and ecological functions in lake environments. To address this issue, our study investigated the effects of sediment-to-soil conversion on microbial composition, community stability and subsequent ecological functioning in Poyang Lake, China. Our results revealed that, during sediment-to-soil conversion, the number of total and unique operational taxonomic units (OTUs) decreased by 40 % and 55 %, respectively. Moreover, sediment-to-soil conversion decreased the microbial community connectivity and complexity while significantly increasing its stability, as evidenced by increased absolute values of negative/positive cohesion. In sediment and soil, the abundance of dominant bacteria, and bacterial diversity strongly affected microbial community stability, although this phenomenon was not true in water. Furthermore, the specific microbial phyla and genes involved in the nitrogen cycle changed significantly following sediment-to-soil conversion, with the major nitrogen cycling processes altering from denitrification and dissimilatory nitrate reduction to ammonium to nitrification and assimilatory nitrate reduction to ammonia. Moreover, a compensation mechanism was observed in the functional genes related to the nitrogen cycle, such that all the processes in the nitrogen cycle were maintained following sediment-to-soil conversion. The oxidation-reduction potential strongly affected network complexity, microbial stability, and nitrogen cycling in the sediment and soil. These results aid in the understanding of responses of microorganisms to climate change and extreme drought. Our findings have considerable implications for predicting the ecological consequences of habitat conversion and for ecosystem management.

Evaluation of three prevalent global riverine nutrient transport models

Global riverine nitrogen (N) and phosphorus (P) transport models offer important insights into basin nutrient cycling. However, appropriate model selection for a given research objective remains ambiguous. This study conducted a meta-analysis to evaluate the performance and applicability of three prevalent global riverine nutrient transport models: Global NEWS, IMAGE-GNM, and WorldQual. According to performance criteria (satisfactory: R2 > 0.50 and NSE > 0.50), the Global NEWS model performs satisfactorily in simulating dissolved organic nitrogen (DON; n = 101, R2 = 0.58, NSE = 0.57) and dissolved organic phosphorus loads (DOP; n = 80, R2 = 0.59, NSE = 0.59). The model falls short in simulating dissolved inorganic nitrogen (DIN; n = 644, R2 = 0.56, NSE = - 0.80) and dissolved inorganic phosphorus loads (DIP; n = 450, R2 = 0.33, NSE = - 0.12). The IMAGE-GNM model shows satisfactory accuracies in simulating riverine total nitrogen (TN; n = 831, R2 = 0.56, NSE = 0.53) and total phosphorus (TP; n = 902, R2 = 0.59, NSE = 0.48) concentrations, particularly in European basins. The WorldQual model presented unsatisfactory performance in simulating riverine TN (n = 11, R2 = 0.76, NSE = 0.34) and TP (n = 13, R2 = 0.71, NSE = - 0.25) concentrations. Using a two-segment linear model, we recommend the Global NEWS model for basins larger than 2.2 × 104 km2 for DIN and 3.2 × 104 km2 for DIP. The IMAGE-GNM model is best suited for basins with long-term datasets and high latitudes (TN > 21 years and > 53.8 °N; TP > 22 years and > 54.5 °N). For model improvements, both the Global NEWS and WorldQual models could benefit from enhanced in-stream nutrient retention/release modules. The Global NEWS model could be further improved with a better chemical weathering module. For the IMAGE-GNM model, refining the soil erosion module is warranted to enhance model performance. Addressing legacy nutrient effects is crucial for all three models. This study provides valuable guidance for selecting and improving nutrient transport models based on specific research needs.

Response of denitrification microbiome to the nitrogen flux in three Gorges reservoir (TGR) sediments during two seasonal water fluctuation events

Three Gorges Reservoir (TGR) water fluctuation creates high water level (HWL) and low water level (LWL) condition in TGR aquatic ecosystem. HWL fluies significant nutrients, mainly introducing carbon and nitrogen into the ecosystem. The nitrogen input is a concern for water quality management of TGR since the possible eutrophication caused by nitrogen spike. Sediment denitrification is widely recognized as the dominant nitrogen removal process in freshwater ecosystem. Therefore, the response of TGR sediments microbiome to the input nitrogen flucatution is crucial for both nitrogen balance and the eutrophication status of the ecosystem. Using high throughout sequencing of 16S rRNA gene and the predicted denitrification enzyme, and qualitative PCR of denitrification functional genes, we investigated how TGR sediments denitrification microbiome respond to the input nitrogen flux during two seasonal water fluctuation events. Concomitant to expected input carbon and nitrogen, we observed distinct microbial community structure and denitrification microbiota in HWL and LWL, and also in seasonal sampling events. Sediments pH, total nitrogen and nitrate were the significant impact factors in shaping the microbial community structure. Important denitrification microbiota (e.g., Saprospiraceae, Gemmatimonadaceae, Pseudomonas) are the main taxa of the microbial community and also showed water level and seasonal variation. The relative abundance of denitrification enzyme (nar, nir, nor, nos) and function genes (nirS, nirK, nosZ) were higher in LWL than HWL. Denitrification enzyme were significantly (p < 0.05) correlated with the nitrate concentration. In addition, the relative abundance of denitrification enzyme and function genes increased during the transition from 2014 HWL to 2015 LWL. Results suggested that TGR sediments denitrification is nitrate concentration dependent. The denitrification microbiome is initially inhibited due to high nitrate input, then they developed denitrification ability in response to high nitrate concentration.

Fate of dissolved inorganic nitrogen in turbulent rivers: The critical role of dissolved oxygen levels

Dissolved inorganic nitrogen (DIN) is considered the main factor that induces eutrophication in water, and is readily influenced by hydrodynamic activities. In this study, a 4-year field investigation of nitrogen dynamics in a turbulent river was conducted, and a laboratory study was performed in the approximately homogeneous turbulence simulation system to investigate potential mechanisms involved in DIN transformation under turbulence. The field investigation revealed that, contrary to NO^-₃ dynamics, the NH⁺₄ concentrations in water were lower in flood seasons than in drought seasons. Further laboratory results demonstrated that limitation of dissolved oxygen (DO) caused inactive nitrification and active denitrification in static river sediment. In contrast, the increased DO levels in turbulent river intensified the mineralization of organic nitrogen in sediment; moreover, ammonification and nitrification were activated, while denitrification was first activated and then depressed. Turbulence therefore decreased NH⁺₄ and NO^-₂ concentrations, but increased NO^-₃ and total DIN concentrations in the overlying water, causing the total DIN to increase from 0.4 mg/L to maximum of 1.0 and 1.7 mg/L at low and high turbulence, respectively. The DIN was maintained at 0.7 and 1.0 mg/L after the 30-day incubation under low and high turbulence intensities (ε) of 3.4 × 10^-4 and 7.4 × 10^-2 m²/s³, respectively. These results highlight the critical role of DO in DIN budgets under hydrodynamic turbulence, and provide new insights into the DIN transport and transformation mechanisms in turbulent rivers.

Spatiotemporal changes of bacterial communities during a cyanobacterial bloom in a subtropical water source reservoir ecosystem in China

Cyanobacterial blooms, which not only threaten the health and stability of aquatic ecosystems but also influence the microbial community within, emerges as one of the most concerning problems in China. However, how cyanobacterial blooms affect the spatiotemporal variation of aquatic microbial communities remains relatively unclear. In this study, we used high-throughput sequencing to investigate how the cyanobacterial and bacterial community spatiotemporally vary along with main cyanobacterial bloom phases in upstream rivers of a eutrophicated water source reservoir. Both cyanobacterial and bacterial diversities in each river were significantly lower (P < 0.05) during the bloom outbreak phase, showing the apparent influence of cyanobacterial bloom. Dominant cyanobacterial taxa included Cyanobacteriales and Synechococcales, and dominant bacterial taxa comprised Acinetobacter, CL500-29, hgcI clade, Limnohabitans, Flavobacterium, Rhodoluna, Porphyrobacter, Rhodobacter, Pseudomonas, and Rhizobiales, whose changes of relative abundance along with the bloom indicated distinct community composition. Non-metric multidimensional scaling analysis proved that community composition had significant difference amongst bloom phases. Linear discriminant analysis (LDA) with LDA effect size analysis (LEfSe) identified unique dominant cyanobacterial and bacterial OTUs at different phases in each river, indicating spatiotemporal variations of communities. Canonical correlation analysis or redundancy analysis revealed that at different bloom phases communities of each river had distinct correlation patterns with the environmental parameters (temperature, ammonium, nitrate, and total phosphorus etc.), implying the spatial variations of microbial communities. Overall, these results expand current understanding on the spatiotemporal variations of microbial communities due to cyanobacterial blooms. Microbial interactions during the bloom may shed light on controlling cyanobacterial blooms in the similar aquatic ecosystems.

Allometric releases of nitrogen and phosphorus from sediments mediated by bacteria determines water eutrophication in coastal river basins of Bohai Bay

Although the Chinese government has conducted much work in recent years to reduce land-based pollutant discharge, eutrophication continues to occur frequently in many rivers, estuaries, and coastal waters. This may indicate that sediment is a major source rather than a sink for nitrogen (N) and phosphorus (P). To clarify the endogenous mechanisms of eutrophication in coastal river basins, the eutrophication status, physicochemical properties, and bacterial parameters of overlying waters and sediments in the catchment (CA), estuarine (EA), and offshore (OA) areas in the Duliujian River Basin of Bohai Bay were investigated. The results showed that the eutrophication index (EI) of CA, EA, and OA were 62.71, 57.86, and 36.51, respectively. The EI was more sensitive to increases in P (slope = 3.887) than to increases in N (slope = 0.734) of the overlying water, indicating that P is the main factor driving eutrophication in the coastal river basin. However, a nonlinear relationship was found between P in sediments and overlying waters, suggesting that bacterial mediation may occur during P release. As speculated in this study, P in the overlying water increased more quickly than N with increasing bacterial diversity and metabolic abundance, indicating that the allometric release of N and P mediated by bacteria increases the risk of eutrophication. Redundancy analysis showed that organic matter and total N in sediment have positive effects on bacterial communities, which explains 21.8% and 23.7% variation in bacterial diversity, and explains 31.3% and 7.1% variation in bacterial metabolism. This also suggests that the accumulation of N in the sediment promotes the release of P and further aggravates the eutrophication of water. Therefore, simultaneous control of N and P is necessary to control water eutrophication in coastal river basins.

Spatial and seasonal change in algal community structure and its interaction with nutrient dynamics in a gravel-bed urban river

Harmful algal blooms frequently occur in urban rivers due to intense human activities. However, little is known about the change in algal community structure and its interactions with nutrient dynamics in gravel-bed urban rivers. In present study, water samples were collected from a gravel-bed River Xin'an, China for five months over four seasons and a rainy month to measure algal community structure, dissolved nitrogen gas (N₂) and Argon (Ar) concentrations, and other water quality parameters. The results showed that the harmful Cyanophyta accounted for 31.6 ± 24.1% of the total community in the hot season while Bacillariophyta contributed more than 60% to the community in the other three seasons. The N₂ was supersaturated in the moderate and cold seasons but it was unsaturated in the hot season, along with high concentrations of nitrogen-fixing cyanobacteria (Anabaena), indicating that the nitrogen fixation capacity was strong and even stronger than denitrification and anammox in the hot season. However, nitrogen fixation was not the main source of nitrogen in the water column. The concentrations of nutrients and Chla in the downstream river were significantly higher than those in the upstream river (p < 0.001 for nutrients and p = 0.029 for Chla), suggesting that human activities along the river greatly affected nutrient concentrations, as well as algal growth. Our study provides new insights into the algal community succession in a gravel-bed urban river and puts forward effective measures such as controlling exogenous nutrient input and dredging organic sediment for mitigating the harmful algal blooms in urban rivers.