Coupling between Nitrification and Denitrification as well as Its Effect on Phosphorus Release in Sediments of Chinese Shallow Lakes

Microbial mechanisms of C/N/S geochemical cycling during low-water-level sediment remediation in urban rivers

Low-water-level regulation has been effectively implemented in the restoration of urban river sediments in Guangzhou City, China. Further investigation is needed to understand the microbial mechanisms involved in pollutant degradation in low-water-level environments. This study examined sediment samples from nine rivers, including low-water-level rivers (LW), tidal waterways (TW), and enclosed rivers (ER). Metagenomic high-throughput sequencing and the Diting pipeline were utilized to investigate the microbial mechanisms involved in sediment C/N/S geochemical cycling during low-water-level regulation. The results reveal that the degree of pollution in LW sediment is lower compared to TW and ER sediment. LW sediment exhibits a higher capacity for pollutant degradation and elimination of black, odorous substances due to its stronger microbial methane oxidation, nitrification, denitrification, anammox, and oxidation of sulfide, sulfite, and thiosulfate. Conversely, TW and ER sediment showcase greater microbial methanogenesis, anaerobic fermentation, and sulfide generation abilities, leading to the persistence of black, odorous substances. Factors such as grit and silt content, nitrate, and ammonia concentrations impacted microbial metabolic pathways. Low-water-level regulation improved the micro-environment for functional microbes, facilitating pollutant removal and preventing black odorous substance accumulation. These findings provide insights into the microbial mechanisms underlying low-water-level regulation technology for sediment restoration in urban rivers.

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.

A novel sulfur autotrophic denitrification in-situ coupled sequencing batch reactor system to treat low carbon to nitrogen ratio municipal wastewater: Performance, niche equilibrium and pollutant removal mechanisms

A novel integrated sulfur fixed-film activated sludge in SBR system (IS0FAS-SBR) was proposed to treat the low C/N ratio municipal wastewater. The effluent total inorganic nitrogen (TIN) and PO43--P decreased from 17 mg/L and 3.5 mg/L to 8.5 mg/L and 0.5 mg/L, and higher nitrogen removal efficiency was contributed by the autotrophic denitrification. Microbial response characteristics showed that catalase (CAT), reduced nicotinamide adenine dinucleotide (NADH) and extracellular polymeric substance (EPS) alleviated the oxidative stress of sulfur carrier to maintain cell activity, while metabolic activity analysis indicated that the electron transfer rate was enhanced to improve mixotrophic denitrification efficiency. Meanwhile, the increased key enzyme activities further facilitated nitrogen removal and sulfur oxidation process. Additionally, the microbial community, functional proteins and genes revealed a niche equilibrium of C, N, S metabolic bacteria. Sulfur autotrophic in-situ coupled SBR system enlarged a promising strategy for treatment of low C/N ratio municipal wastewater.

Soil pH management for mitigating N2O emissions through nosZ (Clade I and II) gene abundance in rice paddy system

Soil nitrous oxide (N₂O) is produced by abiotic and biotic processes, but it is solely consumed by denitrifying microbes-encoded by nosZ genes. The nosZ gene includes two groups i.e. Clade I and Clade II, which are highly sensitive to pH. Managing pH of acidic soils can substantially influence soil N₂O production or consumption through nosZ gene abundance. Nevertheless, the response of nosZ (Clade I and Clade II) to pH management needs elucidation in acidic soils. To clarify this research question, a pot experiment growing rice crop was conducted with three treatments: control (only soil), low dose of dolomite (LDD), and high dose of dolomite (HDD). The soil pH increased from 5.41 to 6.23 in the control, 6.5 in LDD and 6.8 in HDD treatment under flooded condition. The NH₄⁺ and NO₃^- contents increased and reached the maximum at 30.4 and 21.5 mg kg^-1, respectively, in HDD treatment under flooding condition. The contents of dissolved organic carbon and microbial biomass carbon showed a swift rise at midseason aeration and reached maximum at 30.7 and 101 mg kg^-1 in the HDD treatment. Clade I, Clade II and 16S rRNA genes abundance increased with the onset of flooding, and occurred maximum in the HDD treatment. A peak in N₂O emissions (5.96 μg kg^-1 h^-1) occurred at midseason events in the control when no dolomite was added. Dolomite application significantly (p ≤ 0.001) suppressed N₂O emissions, and HDD treatment was more effective in reducing emissions. Pearson correlation, linear regressions and principal component analysis displayed that increased soil pH and Clade I and Clade II were the main controlling factors for N₂O emission mitigation in acidic soil. This research demonstrates that ameliorating soil acidity with dolomite application is a potential option for the mitigation of N₂O emissions.

Community Structure of Nitrifying and Denitrifying Bacteria from Effluents Discharged into Lake Victoria, Kenya

An active microbial community of nitrifying and denitrifying bacteria is needed for efficient utilization of nitrogenous compounds from wastewater. In this study, we explored the bacterial community diversity and structure within rivers, treated and untreated wastewater treatment plants (WWTPs) discharging into Lake Victoria. Water samples were collected from rivers and WWTPs that drain into Lake Victoria. Physicochemical analysis was done to determine the level of nutrients or pollutant loading in the samples. Total community DNA was extracted, followed by Illumina high throughput sequencing to determine the total microbial community and abundance. Enrichment and isolation were then done to recover potential nitrifiers and denitrifiers. Physicochemical analysis pointed to high levels total nitrogen and ammonia in both treated and untreated WWTPs as compared to the samples from the lake and rivers. A total of 1,763 operational taxonomic units (OTUs) spread across 26 bacterial phyla were observed with the most dominant phylum being Proteobacteria. We observed a decreasing trend in diversity from the lake, rivers to WWTPs. The genus Planktothrix constituted 19% of the sequence reads in sample J2 collected from the lagoon. All the isolates recovered in this study were affiliated to three genera: Pseudomonas, Klebsiella and Enterobacter in the phylum Proteobacteria. A combination of metagenomic analysis and a culture-dependent approach helped us understand the relative abundance as well as potential nitrifiers and denitrifiers present in different samples. The recovered isolates could be used for in situ removal of nitrogenous compounds from contaminated wastewater.

Deciphering waste bound nitrogen by employing psychrophillic Aporrectodea caliginosa and priming of coprolites by associated heterotrophic nitrifiers under high altitude Himalayas

Himalayan ecosystem is characterized by its fragile climate with rich repositories of biodiversity. Waste collection and disposal are becoming increasingly difficult due to topographical variations. Aporrectodea caligenosa, a versatile psychrophillic soil dweller, is a useful biocatalyst with potent bio-augmented capability for waste treatment at low temperatures. Microcosm experiments were conducted to elucidate the comprehensive nature of biogenic nitrogen transformation to NH₄⁺ and NO₃⁻ produced by coupling of earthworm-microbes. Higher biogenic recovery of NH₄⁺-N from coprolites of garden soil (47.73 ± 1.16%) and Himalayan goat manure (86.32 ± 0.92%) with an increment of 14.12 and 47.21% respectively over their respective control (without earthworms) with a linear decline beyond 4th week of incubation was reported. NO₃^–-N recovery progressively sustained in garden soil and goat manure coprolites during entire incubation with highest 81.81 ± 0.45 and 87.20 ± 1.08 µg-N g⁻¹dry weight recorded in 6th and 5th week of incubation respectively and peak increments as 38.58 and 53.71% relative to respective control (without earthworms). Declined NH₄⁺–N in coprolites at low temperature (15.0 ± 2.0 °C) evidenced increased nitrification rates by taking over the process by abundant nitrifying microbes. Steady de-nitrification with progressive incubation on an average was 16.95 ± 0.46 ng-N g⁻¹ per week and 21.08 ± 0.87 ng-N g⁻¹ per week compared to 14.03 ± 0.58 ng-N g⁻¹ per week and 4.50 ± 0.31 ng-N g⁻¹ per week in respective control treatments. Simultaneous heterotrophic nitrification and aerobic denitrification (SHNAD) was found to be a prominent bioprocess at low temperature that resulted in high and stable total nitrogen and nitrate accumulation from garden soil and goat manure with relative recovery efficiency of 11.12%, 14.97% and 14.20%; 19.34%. A. caligenosa shows promising prospects for mass applicability in biogenic N removal from manure of Himalayan goat.

Soil moisture determines nitrous oxide emission and uptake

Soils are major sources and sinks of nitrous oxide (N₂O). The main pathway of N₂O emission is performed through soil denitrification; however, the uptake phenomenon in denitrification is overlooked, leading to an underestimation of N₂O production. Soil moisture strongly influences denitrification rates, but exact quantifications coupled with nosZ, nirK, and nirS gene analysis remain inadequately unaccounted for. In this study, a ¹⁵N-N₂O pool dilution (¹⁵N₂OPD) method was used to measure N₂O production rates under different soil moisture levels. Therefore, 20%, 40%, 60%, 80% and 100% soil water holding capacity (WHC) were used. The results revealed that N₂O uptake rates increased proportionally with soil moisture content and peaked at 80% WHC with 4.17 ± 2.74 μg N kg^-1 soil h^-1. The N₂O production and net emission rates similarly peaked at 80% WHC, reading at 32.50 ± 4.86 and 27.63 ± 3.09 μg N kg^-1 soil h^-1 during the incubation period (18 days). Soil moisture content increased the gene copy number of the nosZ, NH₄⁺ content, and denitrification potential in soil. N₂O uptake at WHC 80-100% was significantly greater than that at WHC 20-60%. It was attributed to a decrease in O₂ and the high NO₃^- concentration inhibition (> 50 mg N kg^-1 of soil NO₃^--N content). Principal components analysis (PCA) indicated that the number of nosZ genes was the major driver of N₂O uptake, especially nosZ clade II. Thus, the results of this study deepen our understanding of the mechanisms underpinning N₂O sources and sinks in soils and provide a useful gene-based indicator to estimate N₂O uptake.

Effects of antibiotics and heavy metals on denitrification in shallow eutrophic lakes

Antibiotic and heavy metal residues in shallow lakes caused by aquaculture and human activities such as sewage discharge have attracted much attention and public concern. However, mechanisms by which these environmental pollutants affect the microorganism-mediated biogeochemical cycle are unknown. This study focused on the effects of antibiotics, heavy metal, and antibiotic resistance genes (ARGs) on denitrification in shallow lakes. The results showed that antibiotics and metal elements had inhibitory effects on denitrification, whereas AGRs exhibited stimulating effects. Specifically, the enrofloxacin concentration showed a significant negative correlation with the copy number of denitrifying bacteria, whereas the copy number of the ARGs sulI, sulII, and tetG showed significant positive correlations. In addition, tetG was closely related to the community structure of nirS-type denitrifiers, and nirS-type denitrifiers were significantly correlated with the potential denitrification rate (PDR). Furthermore, the ARGs sulI, sulII, and tetG were positively correlated with PDR (P < 0.05). By contrast, the metal elements arsenic, manganese, cobalt, and antimony were negatively correlated with the copy number of denitrifying bacteria. Arsenic was significantly correlated with the community composition of nirK-type denitrifiers, but nirK-type denitrifiers did not show a significant correlation with the PDR. This work extends our understanding of the effects of antibiotics and heavy metals on denitrification, but further studies are needed to determine the interaction effects of pollutants.

Comparative genome analysis of the genus Hydrotalea and proposal of the novel species Hydrotalea lipotrueae sp. nov., isolated from a groundwater aquifer in the south of Mallorca Island, Spain

From a collection of > 140 strains isolated from groundwater with thermal anomalies for the purpose of obtaining good candidates with applications in the cosmetic industry, two strains were selected because of their taxonomic novelty. Among the isolates, strains TMF_100^T and TFM_099 stood out for their potential biotechnological relevance, and a comparative analysis of 16S rRNA gene sequences indicated that these strains represented a new species of the genus Hydrotalea. In addition, from the public genomic databases, metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) could be retrieved that affiliated with this genus. These MAGs and SAGs had been obtained from different environmental samples, such as acid mine drainage or marine sediments. In addition to the description of the new species, the ecological relevance of the members of this genus was demonstrated by means of denitrification, CRISPR-Cas system diversity and heavy metal resistance, as well as their wide geographical distribution and environmental versatility. Supported by the taxonomic study, together with physiological and morphological differences and ecological features, we concluded that strain TMF_100^T represented a novel species within the genus Hydrotalea, for which we propose the name Hydrotalea lipotrueae sp. nov.

Determination of Changes in the Quality of Surface Water in the River—Reservoir System

Assessing the changing parameters of water quality at different points in the river–reservoir system can help prevent river pollution and implement remedial policies. It is also crucial in modeling water resources. Multivariate statistical analysis is useful for the analysis of changes in surface water quality. It helps to identify indicators that may be responsible for the eutrophication process of a reservoir. Additionally, the analysis of the water quality profile and the water quality index (WQI) is useful in assessing water pollution. These tools can support and verify the results of a multivariate statistical analysis. In this study, changes in water quality parameters of the Turawa reservoir (TR), and the Mała Panew river at the point below the Turawa reservoir (bTR) and above the Turawa reservoir (aTR), were analyzed. The analyzed period was from 2019 to 2020 (360 samples were analyzed). It was found that TN, NO2-N, and NO3-N decreased after passing through the Turawa reservoir. Nevertheless, principal component analysis (PCA) and redundancy analysis (RDA) showed that NO2-N and NO3-N contribute to the observed variability of the water quality in the river-reservoir system. PCA showed that pH and PO4-P had a lower impact on the water quality in the reservoir than nitrogen compounds. Additionally, RDA proved that the values of the NO3-N and NO2-N indicators obtained the highest values at the aTR point, PO4-P at the bTR, and pH at the TR. This allows the conclusion that the Turawa reservoir reduced the concentration of NO2-N and NO3-N in comparison with the concentration of these compounds flowing into the reservoir. PCA and RDA showed that both parameters (NO2-N and NO3-N) may be responsible for the eutrophication process of the Turawa reservoir. The analysis of short-term changes in water quality data may reveal additional sources of water pollution. High temperatures and alkaline reaction may cause the release of nitrogen and phosphorus compounds from sediments, which indicates an increased concentration of TP, PO4-P, and Norg in the waters at the TR point, and TP, PO4-P, and NH4-N concentrations at the bTR point. The water quality profile combined with PCA and RDA allows more effective monitoring for the needs of water management in the reservoir catchment area. The analyzed WQI for water below the reservoir (bTR) was lower than that of the reservoir water (TR), which indicates an improvement in water after passing through the reservoir.

Comparison of Community and Function of Dissimilatory Nitrate Reduction to Ammonium (DNRA) Bacteria in Chinese Shallow Lakes with Different Eutrophication Degrees

Dissimilatory nitrate reduction to ammonium (DNRA) plays an important role in controlling nitrogen (N) loading in lake ecosystems. However, studies on the linkage between DNRA bacterial community structure and lake eutrophication remain unclear. We examined the community and abundance of DNRA bacteria at six basins of four shallow lakes with different degrees of eutrophication in China. Measurements of the different forms of N and phosphorus (P) in the water column and interstitial water as well as total organic carbon (TOC) and sulfide in the sediments in summer (July 2016) were performed. The nutritional status of Lake Chaohu was more serious than that of the lakes in Wuhan, including Lake Qingling, Lake Houguan, and Lake Zhiyin by comparing geochemical and physical parameters. We found a higher abundance of the nrfA gene, which is a function gene of DNRA bacteria in sediments with higher contents of TOC and sulfide. Moreover, nitrate was a significant factor influencing the DNRA bacterial community structure. A significant difference of the DNRA bacterial community structure between Lake Chaohu and the lakes in Wuhan was discovered. Furthermore, DNRA bacterial abundance and community positively correlated with NH4+ and Chl a concentrations in Lake Chaohu, in which a percent abundance of dominant populations varied along eutrophication gradients. Overall, the abundance and community structure of the DNRA bacteria might be important regulators of eutrophication and cyanobacteria bloom in Lake Chaohu.