Elemental sulfur facilitates co-metabolism of Cr(VI) and nitrate by autotrophic denitrifiers in constructed wetlands

The antagonistic microbial reduction of chromate and nitrate poses significant challenges for their simultaneous removal in autotrophic denitrifying systems. This study explored the treatment performance and mechanisms for the simultaneous removal of chromate (0, 2, and 10 mg·L-1) and nitrate (20 mg·L-1) in constructed wetland (CW) microcosms with elemental sulfur additions at 0-, 5-, and 25-times background levels. Results showed that sulfur-amended microcosms achieved chromate and nitrate removal up to 76.46 % and 28.12 % higher, respectively, than 0S groups. Notably, the nitrate removal rate constant was higher in the presence of chromate than its absence, exclusively in the 25S groups. In a sediment core assay, the 25S groups also exhibited substantially facilitating effect of chromate removal potential in the presence of nitrate. Metagenomic analyses revealed upregulations of denitrification and sulfur oxidation-related functional genes along with sulfur supplementation. Autotrophic denitrifiers including Dechloromonas, Thiobacillus, Sulfuricella, and Sulfuritalea made significant contributions to chromate and nitrate removal rates, as well as functional genes encoding sulfur, nitrogen, and chromium transformation, in response to sulfur addition. These findings shed first light on the co-metabolism of chromate and nitrate by sulfur-based autotrophic denitrifiers, emphasizing their pivotal role in denitrification systems, e.g., CWs, with chromate inputs.

Effects of Multiscale Environmental Variables on the Taxonomic and Functional Structures of Riverine Microeukaryotic Plankton Communities: eDNA Metabarcoding and Metatranscriptomic Perspectives

Research on the impact of multiscale complex environmental variables on the structure and function of aquatic communities is currently at the forefront, yet the gene regulatory mechanisms of aquatic communities remain poorly understood. In this study, we investigated the Yongding River watershed, a model system exhibiting pronounced environmental factors across "mountain-plain-coastal" sections and three spatial scales of "basin-reach-site". Through integrated eDNA metabarcoding and metatranscriptomics, we revealed that environmental factors at different scales significantly influence riverine microeukaryotic plankton community composition and functional genes expression profiles, which may be related to basin- and reach-scale variables indirectly influencing site-scale physiochemical conditions. Under multiscale environmental gradients, community composition and functional genes expression differed across mountain-plain-coastal sections, but genes expression demonstrated remarkable spatial stability than community composition. Cross-scale environmental factors similarly impacted community composition, functional genes expression, and biogenic element metabolism, or differently influenced them in varying ways. At each scale of "basin-reach-site", the sensitivity of community composition and functional genes expression varied in their responses to different environmental factors. This decoupling of taxonomic and functional responses highlights the complexity of community-environment interactions across spatial hierarchies. This study develops a novel framework that integrates meta-omics signatures derived from environmental samples with cross-scale environmental drivers in aquatic ecosystems, effectively bridging micro-scale molecular responses with macro-scale ecosystem patterns.

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.

Nitrogen Recovery through Dissimilatory Nitrate Reduction to Ammonium: Impact of Environmental Factors

The application of the bacterial dissimilatory nitrate reduction to ammonium (DNRA) process for treating nitrate-rich wastewater offers an environmentally friendly and resource-efficient strategy with significant potential for ammonium nitrogen recovery. This study investigates the impact of carbon sources, C/N ratios, pH, and temperature on the DNRA efficiency of Pseudomonas sp. strain LZ-1 (strain LZ-1). The results revealed that sodium citrate is the most favorable carbon source among sodium formate, sodium acetate, sodium propionate, and sodium citrate for enhancing DNRA in strain LZ-1. Ammonia production by strain LZ-1 peaks at a C/N of 8 within the range of 3 to 20, increasing before and decreasing thereafter. Furthermore, neutral to alkaline conditions (pH 7-10) are favorable for the DNRA process, with an optimal initial pH of 9. Temperature studies indicate a similar trend of initial increase followed by a decline in DNRA efficiency as temperatures rise from 20 to 35 °C, with peak ammonia production at 30 °C. The presence of sulfur ions inhibits the DNRA process in the strain LZ-1. However, this inhibitory effect diminished as the S/N ratio increased from 1/4 to 1. These insights contribute to a deeper understanding of the impact of environmental factors on DNRA and serve as a valuable reference for the utilization of strain LZ-1 in nitrogen recovery from nitrate-rich wastewaters.

Nitrate reduction by salivary bacteria, glucose metabolism, and lifestyle

Background

Nitrate reductases (NR) expressed in oral bacteria reduce nitrate to nitrite. Depending on the environmental conditions and types of bacteria present nitrite can be further reduced to ammonium via Dissimilatory Nitrate Reduction to Ammonium (DNRA), or alternatively to nitric oxide (NO), which impacts cardiometabolic health.

Objective

To evaluate the associations between nitrate reduction by salivary bacteria, clinical markers of glucose metabolism, and lifestyle factors that can modulate the oral environment, potentially impacting DNRA and NR expression.

Methods

A cross-sectional study was conducted using a convenience sample of 144 participants from the San Juan Overweight Adult Longitudinal Study (SOALS), which includes data on glucose metabolism and lifestyle. DNRA and NR activities were measured in saliva under aerobic or CO2-enriched conditions.

Results

DNRA activity was inversely associated with insulin resistance (HOMA-IR) [aerobic3rd vs.1st tertile: β=-0.48 (-0.81, -0.15); CO2-enriched3rd vs.1st tertile β=-0.42 (-0.68, -0.17)], fasting blood glucose [aerobic3rd vs.1st tertile β=-0.144 (-0.268, -0.019); CO2-enriched3rd vs.1st tertile: β=-0.070 (-0.130, -0.011)], and 2-h glucose [CO2-enriched3rd vs.1st tertileβ=-0.21 (-0.37, -0.04)]. Current smokers had lower DNRA activity than non-smokers under aerobic conditions [β=-1.55 (-2.96, -0.14)], but higher under CO2-enriched conditions [β = 0.93 (0.15, 1.71)]. Toothbrushing frequency (twice/day vs. once/day) was positively associated with DNRA activity under CO2-enriched conditions [β = 4.11 (1.90, 6.32)] and with aerobic NR activity [β = 1.20, (0.14, 2.27)]. Physical activity was inversely associated with aerobic NR [β=-0.01, (-0.022, -0.003)]. Under CO2-enriched conditions NR was inversely associated with the BMI (β=-0.11, p = 0.007). Aerobic NR was higher when sucrose was added to the assays (NADP vs. sucrose β=-0.74, p = 0.02) and positively associated with salivary nitrate levels (β = 0.002, p = 0.002).

Conclusions

Nitrate reduction by salivary bacteria is inversely associated with insulin resistance and can be modulated by lifestyle factors. This knowledge could lead to the development of novel, non-invasive approaches for monitoring and preventing diabetes progression.

The interactive application and impacts of iron/nitrogen biogeochemical cycling in distributed ponds for non-point source pollution control in a watershed

The linkages of distributed ponds are utilized in conjunction with one another to remediate non-point source (NPS) pollution in a water-scarce basin. This study provides an overview of a state-of-the-art thorough evaluation of ponds, which offers insight into the majority of topics covered by the ongoing scientific studies, including their various functions and factors affecting their functioning on the hydrological, physicochemical, and biological processes, such as environmental climate factors and basin-specific landscape configuration parameters, as well as process parameters for design, operation and management aspects. The linkages of ponds provide a variety of sustainable services (6R functions), such as resources, restoration, reduction, reuse, recycling, and recovery. The significance of regional environmental geochemical substrates in the ponds, such as red soil, as a hotspot for microbial reaction is emphasized to demonstrate the significant contribution of the migration and transformation of Fe/N cycles to the pollution removal process. In this review, 178 original research publications were thoroughly analyzed to improve our knowledge of the iron-nitrogen cycle in wetlands. From a molecular biology standpoint, the identification of functional microbe species and genes linked to microbially driven iron-nitrogen cycle activities is delved. Reliable data and homogeneous datasets from 42 studies were collected. The correlation analysis results demonstrated Feammox rates contributed to the N loss amount (r = 0.871; p < 0.01), and they had a positive correlation with Fe(III) concentration (r = 0.965; p < 0.01). The proposal for the treatment of NPS pollution by large-scale linkages of ponds in a basin involves optimizing Fe/N microbial processes to promote iron crystallization and efficient circulation of Fe(II) and Fe(III). The co-benefits of geochemistry, biotechnology, and environmental science should be considered when managing contamination in engineering applications. The linkages framework for integrated ponds, which incorporates macro (watershed management) and micro (biogeochemical cycle mechanism) investigations, provides a systematic approach to the application of integrated ponds and sustainable water management for NPS pollution control.

Microbiome dynamics and functional profiles in deep-sea wood-fall micro-ecosystem: insights into drive pattern of community assembly, biogeochemical processes, and lignocellulose degradation

Wood-fall micro-ecosystems contribute to biogeochemical processes in the oligotrophic deep ocean. However, the community assembly processes and biogeochemical functions of microbiomes in wood fall remain unclear. This study investigated the diversity, community structure, assembly processes, and functional profiles of bacteria and fungi in a deep-sea wood fall from the South China Sea using physicochemical indices, amplicon sequencing, and metagenomics. The results showed that distinct wood-fall contact surfaces exhibit habitat heterogeneity. The bacterial community of all contact surfaces and the fungal community of seawater contact surface (SWCS) were affected by homogeneous selection. In SWCS and transition region (TR), bacterial communities were influenced by dispersal limitation, whereas fungal communities were affected by homogenizing dispersal. The Venn diagram visualization revealed that the shared fungal community between SWCS and TR was dominated by Aspergillaceae. Additionally, the bacterial community demonstrated a higher genetic potential for sulfur, nitrogen, and methane metabolism than fungi. The sediment contact surface enriched modules were associated with dissimilatory sulfate reduction and methanogenesis, whereas the modules related to nitrate reduction exhibited enrichment characteristics in TR. Moreover, fungi showed a stronger potential for lignocellulase production compared to bacteria, with Microascaceae and Nectriaceae identified as potential contributors to lignocellulose degradation. These results indicate that environmental filtering and organism exchange levels regulated the microbial community assembly of wood fall. The biogeochemical cycling of sulfur, nitrogen, and methane was mainly driven by the bacterial community. Nevertheless, the terrestrial fungi Microascaceae and Nectriaceae might degrade lignocellulose via the combined action of multiple lignocellulases.IMPORTANCEThe presence and activity of microbial communities may play a crucial role in the biogeochemical cycle of deep-sea wood-fall micro-ecosystems. Previous studies on wood falls have focused on the microbiome diversity, community composition, and environmental impact, while few have investigated wood-fall micro-ecosystems by distinguishing among distinct contact surfaces. Our study investigated the microbiome dynamics and functional profiles of bacteria and fungi among distinct wood-fall contact surfaces. We found that the microbiome community assembly was regulated by environmental filtering and organism exchange levels. Bacteria drive the biogeochemical cycling of sulfur, nitrogen, and methane in wood fall through diverse metabolic pathways, whereas fungi are crucial for lignocellulose degradation. Ultimately, this study provides new insights into the driving pattern of community assembly, biogeochemical processes, and lignocellulose degradation in the microbiomes of deep-sea wood-fall micro-ecosystems, enhancing our comprehension of the ecological impacts of organic falls on deep-sea oligotrophic environments.

Versatile nitrate-respiring heterotrophs are previously concealed contributors to sulfur cycle

Heterotrophic denitrifiers play crucial roles in global carbon and nitrogen cycling. However, their inability to oxidize sulfide renders them vulnerable to this toxic molecule, which inhibits the key enzymatic reaction responsible for reducing nitrous oxide (N2O), thereby raising greenhouse gas emissions. Here, we applied microcosm incubations, community-isotope-corrected DNA stable-isotope probing, and metagenomics to characterize a cohort of heterotrophic denitrifiers in estuarine sediments that thrive by coupling sulfur oxidation with denitrification through chemolithoheterotrophic metabolism. Remarkably, ecophysiology experiments from enrichments demonstrate that such heterotrophs expedite denitrification with sulfur acting as alternative electron sources and substantially curtail N2O emissions in both organic-rich and organic-limited environments. Their flexible, non-sulfur-dependent physiology may confer competitive advantages over conventional heterotrophic denitrifiers in detoxifying sulfide, adapting to organic matter fluctuations, and mitigating greenhouse gas emissions. Our study provides insights into the ecological role of heterotrophic denitrifiers in microbial communities with implications for sulfur cycling and climate change.

Nitrous oxide is the main product during nitrate reduction by a novel lithoautotrophic iron(II)-oxidizing culture from an organic-rich paddy soil

Microbial nitrate reduction coupled to iron(II) oxidation (NRFeOx) occurs in paddy soils due to high levels of dissolved iron(II) and regular application of nitrogen fertilizer. However, to date, there is no lithoautotrophic NRFeOx isolate or enrichment culture available from this soil environment. Thus, resulting impacts on greenhouse gas emissions during nitrate reduction (i.e., nitrous oxide [N2O]) and on toxic metalloid (i.e., arsenic) mobility can hardly be investigated. We enriched a lithoautotrophic NRFeOx culture, culture HP (Huilongpu paddy, named after its origin), from a paddy soil (Huilongpu Town, China), which was dominated by Gallionella (71%). The culture reduced 0.45 to 0.63 mM nitrate and oxidized 1.76 to 2.31 mM iron(II) within 4 days leading to N2O as the main N-product (62%-88% N2O-N of total reduced NO3--N). Nitrite was present as an intermediate at a maximum of 0.16 ± 0.1 mM. Cells were associated with, but mostly not encrusted by, poorly crystalline iron(III) minerals (ferrihydrite). Culture HP performed best below an iron(II) threshold of 2.5-3.5 mM and in a pH range of 6.50-7.05. In the presence of 100 µM arsenite, only 0%-18% of iron(II) was oxidized. Due to low iron(II) oxidation, arsenite was not immobilized. However, the proportion of N2O-N of total reduced NO3--N decreased from 77% to 30%. Our results indicate that lithoautotrophic NRFeOx occurs even in organic-rich paddy soils, resulting in denitrification and subsequent N2O emissions. The obtained novel enrichment culture allows us to study the impact of lithoautotrophic NRFeOx on arsenic mobility and N2O emissions in paddy soils.IMPORTANCEPaddy soils are naturally rich in iron(II) and regularly experience nitrogen inputs due to fertilization. Nitrogen fertilization increases nitrous oxide emissions as it is an intermediate product during nitrate reduction. Microorganisms can live using nitrate and iron(II) as electron acceptor and donor, respectively, but mostly require an organic co-substrate. By contrast, microorganisms that only rely on nitrate, iron(II), and CO2 could inhabit carbon-limited ecological niches. So far, no isolate or consortium of lithoautotrophic iron(II)-oxidizing, nitrate-reducing microorganisms has been obtained from paddy soil. Here, we describe a lithoautotrophic enrichment culture, dominated by a typical iron(II)-oxidizer (Gallionella), that oxidized iron(II) and reduced nitrate to nitrous oxide, negatively impacting greenhouse gas dynamics. High arsenic concentrations were toxic to the culture but decreased the proportion of nitrous oxide of the total reduced nitrate. Our results suggest that autotrophic nitrate reduction coupled with iron(II) oxidation is a relevant, previously overlooked process in paddy soils.

Plant Growth-Promoting Effect and Complete Genomic Sequence Analysis of the Beneficial Rhizosphere Streptomyces sp. GD-4 Isolated from Leymus secalinus

Plant growth-promoting rhizobacteria (PGPR) are beneficial bacteria residing in the rhizosphere and are capable of enhancing plant growth through various mechanisms. Streptomyces sp. GD-4 is a plant growth-promoting bacterium isolated from the rhizosphere soil of Leymus secalinus. To further elucidate the molecular mechanisms underlying the beneficial effects of the strain on plant growth, we evaluated the growth-promoting effects of Streptomyces sp. GD-4 on forage grasses and conducted comprehensive genome mining and comparative genomic analysis of the strain. Strain GD-4 effectively colonized the rhizosphere of three forages and significantly promoted the growth of both plant roots and leaves. Genome sequence functional annotation of GD-4 revealed lots of genes associated with nitrogen, phosphorus, and sulfur metabolism. Additionally, genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, and phosphate solubilization were annotated. Whole-genome analysis revealed that GD-4 may possess molecular mechanisms involved in soil nutrient cycling in rhizosphere soil and plant growth promotion. The bacteria also possess genes associated with adaptability to abiotic stress conditions, further supporting the ability of Streptomyces sp. GD-4 to colonize nutrient-poor soils. These findings provide a foundation for further research into soil remediation technologies in plateau regions.

Metabolic labour division trade-offs in denitrifying microbiomes

Division of metabolic labour is a defining trait of natural and engineered microbiomes. Denitrification-the stepwise reduction of nitrate and nitrite to nitrogenous gases-is inherently modular, catalysed either by a single microorganism (termed complete denitrifier) or by consortia of partial denitrifiers. Despite the pivotal role of denitrification in biogeochemical cycles and environmental biotechnologies, the ecological factors selecting for complete versus partial denitrifiers remain poorly understood. In this perspective, we critically review over 1500 published metagenome-assembled genomes of denitrifiers from diverse and globally relevant ecosystems. Our findings highlight the widespread occurrence of labour division and the dominance of partial denitrifiers in complex ecosystems, contrasting with the prevalence of complete denitrifiers only in simple laboratory cultures. We challenge current labour division theories centred around catabolic pathways, and discuss their limits in explaining the observed niche partitioning. Instead, we propose that labour division benefits partial denitrifiers by minimising resource allocation to denitrification, enabling broader metabolic adaptability to oligotrophic and dynamic environments. Conversely, stable, nutrient-rich laboratory cultures seem to favour complete denitrifiers, which maximise energy generation through denitrification. To resolve the ecological significance of metabolic trade-offs in denitrifying microbiomes, we advocate for mechanistic studies that integrate mixed-culture enrichments mimicking natural environments, multi-meta-omics, and targeted physiological characterisations. These undertakings will greatly advance our understanding of global nitrogen turnover and nitrogenous greenhouse gases emissions.

Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification

Poorly understood microorganisms "short-circuit" the nitrogen cycle via the dissimilatory nitrate reduction to ammonium to retain the element in agricultural lands and stimulate crop productivity. The prevalence of Geobacterales closely related to Trichlorobacter lovleyi in nitrate ammonification hotspots motivated us to investigate adaptive responses contributing to ammonification rates in the laboratory type strain T. lovleyi SZ. Here, we describe the identification of tightly regulated pathways for efficient nitrate foraging and respiration with acetate, an important intermediate of organic matter degradation that Geobacterales efficiently assimilate and oxidize. Challenging the established dogma that high carbon/nitrate ratios stimulate the reduction of nitrate to ammonium, T. lovleyi doubled rapidly across a wide range of ratios provided nitrate concentrations were low enough to prevent the accumulation of the toxic nitrite intermediate. Yet, excess electrons during hydrogenotrophic growth alleviated nitrite toxicity and stimulated the reduction of nitrate to ammonium even under conditions of severe acetate limitation. These findings underscore the importance of nitrite toxicity in the ammonification of nitrate by Geobacterales and provide much needed mechanistic understanding of microbial adaptations contributing to soil nitrogen conservation. This information is critical to enhance the predictive value of genomic-based traits in environmental surveys and to guide strategies for sustainable management of nitrogen fertilization as well as mitigation of green-house emissions and agrochemical leaching from agricultural lands.

Influences of fluctuating nutrient loadings on nitrate-reducing microorganisms in rivers

Rivers serve important functions for human society and are significantly impacted by anthropogenic nutrient inputs (e.g. organic and sulfur compounds). Reduced organic and sulfur compounds influence the nitrogen cycle as they are electron donors of microbial nitrate reduction. Water pollution caused by individual nutrients and the mechanisms have been studied, but how the variation in multiple nutrient loadings influences nitrate-reducing microorganisms is less understood. Two sets of microcosms were established and exposed to nitrate, along with either acetate or thiosulfate, at different times. Nutrient concentrations responded to the loading pollutant. The nutrient loading order was more important in shaping microbial community structure and microbial interactions through the exchange of growth-required substances. This indicated that upstream or historical nutrient inflows impacted current nitrate reduction by changing the seeding microbial community, highlighting the importance of river connectivity. Based on metatranscriptome analysis, although the order and type of nutrient loadings were equally important in regulating global transcriptomes, transcripts of enzymes for key metabolisms (nitrate reduction, sulfur oxidation, etc.) more actively responded to the nutrient type. The regulation of a small set of genes was sufficient to make the transition, while most transcripts were not degraded and regenerated. These insights are important for understanding the varying pollution status of rivers and for developing effective solutions, such as remediation.

Microbial community and functional shifts across agricultural and urban landscapes within a Lake Erie watershed

The role of sediment microbial communities in regulating the loss and retention of nutrients in aquatic ecosystems has been increasingly recognised. However, in the Great Lakes, where nutrient mitigation focuses on harmful algal blooms, there are limited studies examining the fundamental role of water/sediment microbes in nutrient biogeochemical cycling. Little is understood in this regard considering the increase in anthropogenic pressure on in-stream biological processes impacting nutrient flux to lakes. In this study, metagenomic and metatranscriptomic approaches were used to investigate the microbial community and gene regulation. The study focused on nitrogen (N) metabolism in a nutrient-polluted watershed of Lake Erie in southwestern Ontario, Canada. Nutrients and microbial analyses of water and sediments were collected in 2020 and 2021 from Sturgeon Creek headwaters to the nearshore of Lake Erie. Results showed no significant shifts in community structure with nutrient concentrations or land use. Metabolically, active genes involved in denitrification (consisting of 32-53% of N metabolic transcripts) showed the highest expression within agricultural and wetland dominant locations. Based on active gene expression patterns, the urbanised location coinciding with peak nitrate (NO3-) concentrations showed the greatest potential for nitrous oxide (N2O) emission and nitrogen loss along this transect. In contrast to denitrification, direct nitrification (5-21% of N metabolic transcripts) increased two-fold approaching downstream and nearshore lake locations. Across this river-lake corridor, expression of key functional genes associated with N transformation showed strong correlation with the change in concentrations of aqueous NO3- and nitrite (NO2-) and the ratio of NO2-/NO3-. Our findings demonstrated a clear link between sediment microbial metabolism and overlying water chemistry in this lotic system. We suggest that future studies assessing nutrient mitigation consider sediment biogeochemical processes and N-metabolising bacteria, and their fundamental role and cooperative relationship with nutrient and hydrological dynamics of overlying waters.

Hydrochemistry characteristics and genesis of shallow groundwater in diverse industrial agglomeration areas in typical alluvial plain of the Yellow River

The groundwater environment in the middle and upper reaches of the Yellow River in China has attracted extensive attention. But, the hydrochemistry characteristics and genesis of shallow groundwater in diverse industrial agglomeration areas in typical alluvial plain of the Yellow River are still unknown. In this study, geochemical analysis methods, the positive matrix factorisation model, and the geodetector model were used to multidimensional analyze. The results showed that 78 % of the groundwater samples had high-alkalinity-risk and high-salinity-risk, and the water quality was poor and unsuitable for irrigation. "Very poor" and "undrinkable" samples accounted for 26.31 %. The weathering of calcium magnesium minerals and the dissolution of soluble sulfate were important sources of the main chemical components of the groundwater. However, evaporation and concentration gradually dominated from the inclined plain of the piedmont to the alluvial plain of the Yellow River. Domestic and agricultural activities were important sources of nitrogen species (NO3-, NO2-, and NH4+). The presence of Al, Mn, Zn, and Pb was caused by the production activities of various enterprises. The pollution contributors of natural sources, domestic and agricultural activities, industrial production and other sources were 29.49 %, 17.05 %, 31.41 %, and 22.05 %, respectively. Groundwater velocity and enterprise type were the main factors driving groundwater pollution by these four metal substances. The interaction between enterprise type and groundwater velocity had the greatest influence on the concentrations of Al, Mn, and Zn. Moreover, the interaction between enterprise type and the distance from enterprise had the greatest influence on Pb levels. Overall, groundwater pollution in the study area was the result of both natural and human factors. The findings of this study can offer valuable insights and theoretical support for preventing groundwater pollution in other industrial agglomeration areas in the alluvial plain of the Yellow River.

Terrestrial dissolved organic matter inputs affect the nitrous oxide emission revealed by FT-ICR MS

Nitrous oxide (N2O) emission from lake systems could be affected via intrusion of terrestrial organic matter, causing impairment in biogeochemical cycling. The sources and mechanisms by which DOM (Dissolved organic matter) alters emissions of N2O are poorly understood. Here, we simulate different terrestrial DOM (anthropogenic sources, natural sources, and surface runoff) to assess the mechanisms affecting N2O emissions with variations of DOM. We used a combination of absorption spectroscopy, excitation-emission matrix fluorescence, and Fourier transform ion cyclotron resonance mass spectrometry to characterize DOM comprehensively. For the characterization of DOM, a combination of absorption spectroscopy, excitation-emission matrix fluorescence, and Fourier transform ion cyclotron resonance mass spectrometry was used. Microbial analysis was conducted to identify the potential microbial mechanisms. Different terrestrial DOM inputs primarily impact N2O emissions through the denitrification process (14.52 %, p < 0.05), with significant effects on the abundance of narG (12.97 %, p < 0.05) and nirK+S (10.13 %, p < 0.05). The biodegradable components in sediments directly promote N2O emissions, while in aquatic systems, the labile components (proteins, sugars, and lipids-like) were preferentially metabolized, producing reluctant derivatives. The biodegradable components (i.e., protein-like) from anthropogenic sources rapidly facilitate N2O production. Natural and surface runoff sources were the significant drivers for the continuous release and metabolism of DOM. N2O Loss emissions are negatively influenced by the regulation of carbon and nitrogen metabolism by nitrifiers and denitrifies in the sediment (p < 0.001). Metabolism of carbon and nitrogen regulated by nitrifier and denitrifies in the sediments negatively influences N2O flux (p < 0.001). N2O emissions were mainly influenced by bioavailability of inputs: DOM and varying terrestrial conditions. The results provide a theoretical base for the management of greenhouse gas emissions from lakes.

A multidisciplinary approach using hydrogeochemistry, δ15NNO3 isotopes, land use, and statistical tools in evaluating nitrate pollution sources and biochemical processes in Costa Rican volcanic aquifers

Nitrate pollution threatens the Barva and Colima multi-aquifer system, the primary drinking water source in the Greater Metropolitan Area of Costa Rica. In addressing nitrate contamination dynamics, this study proposes an integrated approach by combining multivariate statistical analyses, hydrochemical parameters, sewage discharge, and regional land-use and land-cover patterns to assess the extent and degree of contamination, dominant biogeochemical processes, and refine the interpretation of nitrate sources previously derived solely from δ15NNO3 information. Over seven years (2015-2022), 714 groundwater samples from 43 sites were analyzed for nitrate and major ions, including two sampling campaigns for dissolved organic and inorganic carbon, nitrite, ammonium, FeTotal, MnTotal, and δ15NNO3 analyses. The findings presented elevated nitrate concentrations in urban and agricultural/urban areas, surpassing the Maximum Concentration Levels on several occasions, and oxidizing conditions favoring mineralization and nitrification processes in unconfined Barva and locally confined Upper Colima/Lower Colima aquifers. Similar nitrate contents and spatial patterns in agricultural and urban zones in the shallow Barva aquifer suggest comparable contributions from nitrogen fertilizers and urban wastewaters despite the gradual increase in urban land cover and the reduction of agricultural areas. Isotopic analyses and dissolved organic carbon (DOC) indicate a shift in nitrate sources from agricultural to urban areas in both Barva and Colima aquifers. Principal Component and Hierarchical Cluster Analyses link land use, nitrate sources, and water quality. Three distinct sample clusters aligned with forest/grassland, agricultural/urban, and urban land use, emphasizing the impact of anthropogenic activities on groundwater quality, even in the deeper Colima aquifers. The study challenges nitrate isotope mixing models, enhancing accuracy in identifying pollution sources and assessing the spatial extent of contamination by incorporating DOC and other hydrochemical parameters. Similar outcomes, with and without the use of nitrate isotopes, reinforce the usefulness of the integrated approach, providing a practical and cost-effective alternative.

Enhancing nitrogen removal by simultaneous nitritation and denitritation in a multi-cycle SBR with supplementation of solid carbon sources

Simultaneous nitritation and denitritation have the potential to significantly improve nitrogen removal in sewage treatment processes. However, their application in low-strength sewage treatment systems presents challenges. This study explored the impact of four solid carbon sources (SCSs) on N-removal via nitrite in a multi-cycle SBR with biocarriers. Results showed that both N-removal efficiencies and nitrite accumulation rates increased with higher COD/N ratios, indicating that high COD/N ratios can improve the competition between denitrifiers and nitrite-oxidizing bacteria for nitrite, leading to stable simultaneous nitritation and denitritation. The supplementation of SCSs further enhanced this high-efficiency N-removal process, with polybutylene succinate (PBS) and polycaprolactone (PCL) showing greater increases in N-removal via nitrite than poly-hydroxybutyrate (PHB) and poly-hydroxyalkanoate (PHA). Moreover, PBS showed the most significant increase in denitrification efficiency in anoxic conditions, while PHA was the most effective external SCS at a moderate level of dissolved oxygen. These findings suggest that the incorporation of external SCSs can facilitate the simultaneous nitritation and denitrification process in multi-cycle SBRs, underscoring the importance of selecting an appropriate SCS for optimizing nitrogen removal in sewage treatment projects.

Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species

Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.

Role of biogeochemical and hydrodynamic characteristics in simulating nitrogen dynamics in river confluence

The confluence area is the link of different river systems, whose specific hydrodynamic characteristics can significantly influence mass transport and distribution, which can further make a difference to microorganism growth and biogeochemical processes. However, the specific influences of hydrodynamic characteristics in confluence on formation processes of microbial communities and the biogeochemical processes remain unclear. To this end, the present study established an indoor self-circulation confluence flume and conducted 28-day culture experiment to thoroughly investigate the characteristics of microbial communities and nitrogen dynamics in sediment of confluence area. Results illustrated that the initial homogenous microbial communities gradually emerged differences among varied hydrodynamic zones with experiment going on. Concentrations of nitrogenous materials also changed at different experiment period, NO3- concentrations peaked at day 14, and then exhibited significant downtrend. The mean NO3- concentrations decreased the most in flow separation zone, with a 62 % decrease from day 14 to day 28. A numerical model was further established following the thermodynamics of enzyme catalysis reactions to simulate nitrogen transformation rates based on abundances of associated functional genes (gene-centric model). The average relative deviation between simulated and measured N2 production rates was 32 %. To further investigate the influence of hydrodynamic characteristics on nitrogen dynamics, DamKöhler numbers were calculated as the ratio of characteristic residence time to reaction time. DamKöhler numbers were better fitted with measured N2 production rates than simulated results of gene-centric model, signifying the importance of hydrodynamic characteristics in simulating nitrogen dynamics in confluence area.

Revealing degradation pathways of soluble and dissolved organic matter in alluvial-lacustrine aquifer systems impacted by high levels of geogenic ammonium

The excessive presence of geogenic ammonium (NH4+) in groundwater poses a global environmental concern, commonly linked to the degradation of nitrogen-containing dissolved organic matter (DOM). However, there is a gap in systematic studies on the combination of soluble organic matter (SOM) in sediments and DOM in groundwater, with few indoor incubation experiments to validate their degradation pathways. This study utilized ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry to analyze the molecular characteristics of DOM and SOM in aquifer systems affected by geogenic NH4+. Subsequently, indoor incubation experiments spanning up to 140 d were conducted to verify the degradation pathways. The experimental results revealed a two-phase degradation process for both the DOM and SOM. The initial stage was characterized by the degradation of aliphatic compounds (ALC) with the production of polyphenols (PPE) and highly unsaturated compounds (HUC). The second stage was dominated by the degradation of PPE and HUC, accompanied by the re-consumption of some ALC, while more recalcitrant HUC persisted. Notably, the first stage of SOM degradation exceeded that of DOM degradation, indicating that SOM exhibited greater resistance to aging. This phenomenon may be attributed to a wider range of active enzymes in sediments, the rapid replenishment of SOM by organic matter in sediments, or the accelerated degradation of DOM. The experimental results aligned with the molecular characterization of DOM and SOM in actual aquifer systems. It is hypothesized that NH4+ produced through the direct mineralization of SOM may contribute more to the enrichment of NH4+ in groundwater than that produced through the mineralization of DOM. This study is the first to analyze DOM and SOM together in aquifer systems and validate their degradation pathways through incubation experiments, thereby providing novel insights into the enrichment of geogenic NH4+ in groundwater.

Core microbes in Cordyceps militaris sclerotia and their nitrogen metabolism-related ecological functions

Cordyceps militaris infects insects and forms sclerotia within the insect remains, establishing insect-microbe complexes. Here, C. militaris sclerotia samples from a single location in China over a 5-year period were subjected to high-throughput DNA sequencing, and the core microbes (which were stably enriched in the sclerotia over the 5 years) were identified. Next, seven bacterial strains were isolated from the C. militaris sclerotia, their biochemical characteristics were assessed, and they were co-cultured with C. militaris to study their effects on C. militaris metabolite production and biomass. Furthermore, the effects of NH4, NO3, and peptone media on C. militaris were compared. The results showed that Rhodococcus, Phyllobacterium, Pseudomonas, Achromobacter, Ensifer, Stenotrophomonas, Sphingobacterium, Variovorax, and Acinetobacter were the core microbes. Although co-culture of C. militaris with the seven bacterial strains isolated from the sclerotia did not directly increase the cordycepin level, they all had NO3 reduction ability, and four had urea decomposition ability. Meanwhile, C. militaris in NH4 medium had an increased cordycepin level compared to C. militaris in the other two media. From this, we inferred that bacteria in the sclerotia can convert NO3 to NH4, and then cordycepin is produced using NH4, which was confirmed by RNA-seq and real-time fluorescence quantitative PCR. Thus, bacteria in the sclerotia may indirectly affect the C. militaris metabolite production by regulating nitrogen metabolism. In summary, there are stable core microbes in the C. militaris sclerotia, and they may directly and indirectly affect the growth and metabolite production of C. militaris.

IMPORTANCE

The model Cordyceps species Cordyceps militaris is rich in therapeutic compounds. It has recently been demonstrated that symbiotic microbes in sclerotia affect Cordyceps' growth, development, and secondary metabolite production. In this study, core microbes were identified based on C. militaris sclerotia samples obtained from the same site over 5 years. Additionally, bacterial strains isolated from C. militaris sclerotia were found to affect metabolite production and nitrogen utilization, based on functional tests. Moreover, based on the bacterial nitrogen metabolism capacity in the sclerotia and its influence on C. militaris metabolite production, we deduced that bacteria in the sclerotia can indirectly affect C. militaris metabolite production by regulating nitrogen metabolism. This is the first report on how bacteria in the sclerotia affect C. militaris metabolite production from the perspective of the nitrogen cycle. The results increase our understanding of microbial functions in C. militaris sclerotia.

The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes

Mangrove aquatic ecosystems receive substantial nitrogen (N) inputs from both land and sea, playing critical roles in modulating coastal N fluxes. The microbially-mediated competition between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in mangrove sediments significantly impacts the N fate and transformation processes. Despite their recognized role in N loss or retention in surface sediments, how these two processes vary with sediment depths and their influential factors remain elusive. Here, we employed a comprehensive approach combining 15N isotope tracer, quantitative PCR (qPCR) and metagenomics to verify the vertical dynamics of denitrification and DNRA across five 100-cm mangrove sediment cores. Our results revealed a clear vertical partitioning, with denitrification dominated in 0-30 cm sediments, while DNRA played a greater role with increasing depths. Quantification of denitrification and DNRA functional genes further explained this phenomenon. Taxonomic analysis identified Pseudomonadota as the primary denitrification group, while Planctomycetota and Pseudomonadota exhibited high proportion in DNRA group. Furthermore, genome-resolved metagenomics revealed multiple salt-tolerance strategies and aromatic compound utilization potential in denitrification assemblages. This allowed denitrification to dominate in oxygen-fluctuating and higher-salinity surface sediments. However, the elevated C/N in anaerobic deep sediments favored DNRA, tending to generate biologically available NH4+. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems.

Evidence of Potential Anammox Activities from Rice Paddy Soils in Microaerobic and Anaerobic Conditions

Anammox, a reaction in which microorganisms oxidize ammonia under anaerobic conditions, is used in the industry to remove ammonium from wastewater in an environmentally friendly manner. This process does not produce intermediate products such as nitrite or nitrate, which can act as secondary pollutants in soil and water environments. For industrial applications, anammox bacteria should be obtained from the environment and cultivated. Anammox bacteria generally exhibit a slow growth rate and may not produce a large number of cells due to their anaerobic metabolism. Additionally, their habitats appear to be limited to specific environments, such as oxidation-reduction transition zones. Consequently, most of the anammox bacteria that are used or studied originate from marine environments. In this study, anammox bacterial evidence was found in rice paddy soil and cultured under various conditions of aerobic, microaerobic, and anaerobic batch incubations to determine whether enrichment was possible. The anammox-specific gene (hzsA) and microbial community analyses were performed on the incubated soils. Although it was not easy to enrich anammox bacteria due to co-occurrence of denitrification and nitrification based on the chemistry data, potential existence of anammox bacteria was assumed in the terrestrial paddy soil environment. For potential industrial uses, anammox bacteria could be searched for in rice paddy soils by applying optimal enrichment conditions.

Topical prebiotic nitrate: optimizing the 'hang-time', source and dose for specific oral or systemic effects

In our opinion, the 'hang-time' of nitrate-containing products discussed in the letter by Green and Green is an interesting variable that should be considered when nitrate-based treatment or prevention strategies are designed. However, due to direct nitrate recycling after nitrate intake, products with a long 'hang-time' (e.g., chewing gum) may not always have an advantage compared to products with a short 'hang-time' (e.g., vegetable juices). We argue that extending the 'hang-time' is especially relevant and potentially beneficial for different applications, such as using a low nitrate dose to stimulate the oral effects, reaching oral tissues that may otherwise not be exposed to dietary nitrate (e.g., periodontal pockets), and providing a longer nitrate exposure in individuals with an impaired salivary flow. Apart from the 'hang-time', other important variables are the nitrate dose and source (e.g., different salts and vegetable extracts), as well as the desired effect (e.g., an oral effect versus systemic effects). Finally, we believe that the alterations in salivary microbiota observed before and after chewing three nitrate-rich gums over a period of ~5 h, as reported by Green and Green, could be considered beneficial. However, the oral microbiota composition is affected by the circadian rhythm and the effect of gum mastication should be evaluated. These results should thus be confirmed by a placebo-controlled study, where these confounding factors can be accounted for.

Contrasting effects of climate change on denitrification and nitrogen load reduction in the Po River (Northern Italy)

An increase in water temperature is one of the main factors that can potentially modify biogeochemical dynamics in lowland rivers, such as the removal and recycling of nitrogen (N). This effect of climate change on N processing deserves attention, as it may have unexpected impacts on eutrophication in the coastal zones. Intact sediment cores were collected seasonally at the closing section of the Po River, the largest Italian river and one of the main N inputs to the Mediterranean Sea. Benthic oxygen fluxes, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) rates were measured using laboratory dark incubations. Different temperature treatments were set up for each season based on historical data and future predictions. Higher water temperatures enhanced sediment oxygen demand and the extent of hypoxic conditions in the benthic compartment, favoring anaerobic metabolism. Indeed, warming water temperature stimulated nitrate (NO3-) reduction processes, although NO3- and organic matter availability were found to be the main controlling factors shaping the rates between seasons. Denitrification was the main process responsible for NO3- removal, mainly supported by NO3- diffusion from the water column into the sediments, and much more important than N recycling via DNRA. The predicted increase in the water temperature of the Po River due to climate change may exert an unexpected negative feedback on eutrophication by strongly controlling denitrification and contributing to partial buffering of N export in the lagoons and coastal areas, especially in spring.

Overlooked in-situ sulfur disproportionation fuels dissimilatory nitrate reduction to ammonium in sulfur-based system: Novel insight of nitrogen recovery

Sulfur-based denitrification is a promising technology in treatments of nitrate-contaminated wastewaters. However, due to weak bioavailability and electron-donating capability of elemental sulfur, its sulfur-to-nitrate ratio has long been low, limiting the support for dissimilatory nitrate reduction to ammonium (DNRA) process. Using a long-term sulfur-packed reactor, we demonstrate here for the first time that DNRA in sulfur-based system is not negligible, but rather contributes a remarkable 40.5 %-61.1 % of the total nitrate biotransformation for ammonium production. Through combination of kinetic experiments, electron flow analysis, 16S rRNA amplicon, and microbial network succession, we unveil a cryptic in-situ sulfur disproportionation (SDP) process which significantly facilitates DNRA via enhancing mass transfer and multiplying 86.7-210.9 % of bioavailable electrons. Metagenome assembly and single-copy gene phylogenetic analysis elucidate the abundant genomes, including uc_VadinHA17, PHOS-HE36, JALNZU01, Thiobacillus, and Rubrivivax, harboring complete genes for ammonification. Notably, a unique group of self-SDP-coupled DNRA microorganism was identified. This study unravels a previously concealed fate of DNRA, which highlights the tremendous potential for ammonium recovery and greenhouse gas mitigation. Discovery of a new coupling between nitrogen and sulfur cycles underscores great revision needs of sulfur-driven denitrification technology.

Competitive partitioning of denitrification pathways during arrested methanogenesis: Implications in ammonium recovery, N2O emission, and volatile fatty acid production

The complex interaction between nitrate (NO3-) reduction and fermentation is poorly understood when high levels of NO3- are introduced into anaerobic systems. This study investigated the competitive distribution between conventional denitrification (DEN) and dissimilatory nitrate reduction to ammonium (DNRA) during simultaneous denitrification and fermentation in arrested methanogenesis. Up to 62% of initial NO3- (200 mg-N/L) was retained as ammonium through DNRA at a chemical oxygen demand (COD)/N ratio of 25. Significant N2O emission occurred (1.7 - 8.0% of the initial NO3-) with limited carbon supply (≤1600 mg COD/L) and sludge concentration (≤3000 mg COD/L). VFA composition shifted predominantly towards acetic acid (>50%) in the presence of nitrate. A novel kinetic model was developed to predict DNRA vs. DEN partitioning and NO2- accumulation. Overall, NO3- input, organic loading, and carbon source characteristics independently and collectively controlled competitive DNRA vs. DEN partitioning.

Salt marsh nitrogen cycling: where land meets sea

Salt marshes sit at the terrestrial-aquatic interface of oceans around the world. Unique features of salt marshes that differentiate them from their upland or offshore counterparts include high rates of primary production from vascular plants and saturated saline soils that lead to sharp redox gradients and a diversity of electron acceptors and donors. Moreover, the dynamic nature of root oxygen loss and tidal forcing leads to unique biogeochemical conditions that promote nitrogen cycling. Here, we highlight recent advances in our understanding of key nitrogen cycling processes in salt marshes and discuss areas where additional research is needed to better predict how salt marsh N cycling will respond to future environmental change.

Diversity and ecology of NrfA-dependent ammonifying microorganisms

Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N2O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements.

Metabolic Profiles and Microbial Synergy Mechanism of Anammox Biomass Enrichment and Membrane Fouling Alleviation in the Anammox Dynamic Membrane Bioreactor

The anammox dynamic membrane bioreactor (DMBR) is promising in applications with enhanced anammox biomass enrichment and fouling alleviation. However, the metabolic mechanism underlying the functional features of anammox sludge and the biofilm membrane is still obscure. We investigated the metabolic networks of anammox sludge and membrane biofilm in the DMBR. The cooperation between anammox and dissimilatory nitrate reduction to ammonium processes favored the robust anammox process in the DMBR. The rapid bacterial growth occurred in the DMBR sludge with 1.33 times higher biomass yield compared to the MBR sludge, linked to the higher activities of lipid metabolism, nucleotide metabolism, and B vitamin-related metabolism of the DMBR sludge. The metabolism of the DMBR biofilm microbial community benefited the fouling alleviation that the abundant fermentative bacteria and their cooperation with the anammox sludge microbial community promoted organics degradation. The intensified degradation of foulants by the DMBR biofilm community was further evidenced by the active carbohydrate metabolism and the upregulated vitamin B intermediates in the biofilms of the DMBR. Our findings provide insights into key metabolic mechanisms for enhanced biomass enrichment and fouling control of the anammox DMBR, guiding manipulations and applications for overcoming anammox biomass loss in the treatment of wastewater under detrimental environmental conditions.

Role of sulfide on DNRA distribution and the microbial community structure in a sulfide-driven nitrate reduction process

Microbial nitrate reduction processes involve two competing pathways: denitrification (DEN) and dissimilatory nitrate reduction to ammonium (DNRA). This study investigated the distribution of DNRA in a sole sulfur-driven nitrogen conversion process using a laboratory-scale sequencing biofilm batch reactor (SBBR) through a series of batch tests with varying sulfide/nitrate (S/N) ratios. The results showed that DNRA became more dominant in the sulfide-oxidizing autotrophic denitrification (SOAD) process as the S/N ratio increased to 1.5:1, 1.7:1, and 2:1, reaching a peak of 35.3% at the S/N ratio of 1.5:1. Oxidation-reduction potential (ORP) patterns demonstrated distinct inflection points for nitrate and nitrite consumption under the SOAD-only conditions, whereas these points overlapped when DNRA coexisted with SOAD. Analysis of 16S ribosomal RNA identified Ignavibacterium, Hydrogenophaga, and Geobacter as the dominant genera responsible for DNRA during autotrophic nitrate reduction. The findings of the DNRA divergence investigation provided valuable insights into enhancing biological nitrogen removal processes, particularly when coupled with the anammox.

Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures

Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance.

Review of the mechanisms involved in dissimilatory nitrate reduction to ammonium and the efficacies of these mechanisms in the environment

Dissimilatory nitrate reduction to ammonium (DNRA) is currently of great interest because it is an important method for recovering nitrogen from wastewater and offers many advantages, over other methods. A full understanding of DNRA requires the mechanisms, pathways, and functional microorganisms involved to be identified. The roles these pathways play and the effectiveness of DNRA in the environment are not well understood. The objectives of this review are to describe our current understanding of the molecular mechanisms and pathways involved in DNRA from the substrate transfer perspective and to summarize the effects of DNRA in the environment. First, the mechanisms and pathways involved in DNRA are described in detail. Second, our understanding of DNRA by actinomycetes is reviewed and gaps in our understanding are identified. Finally, the effects of DNRA in the environment are assessed. This review will help in the development of future research into DNRA to promote the use of DNRA to treat wastewater and recover nitrogen.

Role of root plasma membrane H+-ATPase in enhancing Cucumis sativus adaptation to microcystins

Microcystins (MCs) are the most widespread and hazardous cyanotoxins posing a huge threat to agro-ecosystem by irrigation. Some adaptive metabolisms can be initiated at the cellular and molecular levels of plant to survive environmental change. To find ways to improve plant tolerance to MCs after recognizing adaptive mechanism in plant, we studied effects of MCs on root morphology, mineral element contents, root activity, H+-ATPase activity, and its gene expression level in cucumber during exposure and recovery (without MCs) periods. After being exposed to MCs (1, 10, 100 and 1000 μg L-1) for 7 days, we found 1 μg L-1 MCs did not affect growth and mineral elements in cucumber. MCs at 10 μg ·L-1 increased root activity and H+-ATPase activity partly from upregulation of genes (CsHA2, CsHA3, CsHA8, and CsHA9) expression, to promote nutrient uptake. Then, the increase in NO3-, Fe, Zn, and Mn contents could contribute to maintaining root growth and morphology. Higher concentration MCs (100 or 1000 µg L-1) inhibited root activity and H+-ATPase activity by downregulating expression of genes (CsHA2, CsHA3, CsHA4, CsHA8, CsHA9, and CsHA10), decreased contents of nutrient elements except Ca largely, and caused root growing worse. After a recovery, the absorption activity and H+-ATPase activity in cucumber treated with10 μg L-1 MCs were closed to the control whereas all parameters in cucumber treated 1000 μg L-1 MCs were even worse. All results indicate that the increase in H+-ATPase activity can enhance cucumber tolerance to MC stress by regulating nutrient uptake, especially when the MCs occur at low concentrations.

Mechanism of denitrification in subsurface-dammed Ryukyu limestone aquifer, southern Okinawa Island, Japan

Denitrification crucially regulates the attenuation of groundwater nitrate and is unlikely to occur in a fast-flowing aquifer such as the Ryukyu limestone aquifer in southern Okinawa Island, Japan. However, evidences of denitrification have been observed in several wells within this region. This study analyzed environmental isotopes (δ15NNO3 and ẟ18ONO3) to derive the rationale for denitrification at this site. Additionally, the presence of two subsurface dams in the study area may influence the processes involved in nitrate attenuation. Herein, we analyzed 150 groundwater samples collected spatially and seasonally to characterize the variations in the groundwater chemistry and stable isotopes during denitrification. The values of δ15NNO3 and δ18ONO3 displayed a progressive trend up to +59.7 ‰ and + 21 ‰, respectively, whereas the concentrations of NO3--N decreased to 0.1 mg L-1. In several wells, the enrichment factors of δ15NNO3 ranged from -6.6 to -2.1, indicating rapid denitrification, and the δ15NNO3 to δ18ONO3 ratios varied from 1.3:1 to 2:1, confirming the occurrence of denitrification. Denitrification intensively proceeds under conditions of depleted dissolved oxygen concentrations (<2 mg L-1), sluggish groundwater flow with longer residence times, high concentrations of dissolved organic carbon (>1.2 mg L-1), and low groundwater levels during the dry season with precipitation rates of <100 mm per month (Jun-Sep). SF6 analysis indicated the exclusive occurrence of denitrification in specific wells with groundwater residence times exceeding 30 years. These wells are located in close proximity to the major NE-SW fault system in the Komesu area, where the hydraulic gradient was below 0.005. Detailed geological and lithological investigations based on borehole data revealed that subsurface dams did not cause denitrification while the major NE-SW fault system uplifted the impermeable basement rock of the Shimajiri Group, creating a lithological gap at an equivalent depth that ultimately formed a sluggish groundwater area, promoting denitrification.

Bioelectro-barriers prevent nitrate leaching into groundwater via nitrogen retention

Groundwater, the main freshwater resource for humans, has been widely contaminated with nitrate from fertilizers. Here, we report a new and chemical-free strategy to prevent nitrate leaching from soil based on the enrichment of electroactive bacteria, mainly of the genus Geobacter, with bioelectro-barriers, which leads to a nearly 100 % interception of nitrate and partly conserves reactive nitrogen in the form of weakly mobile ammonium by dissimilatory nitrate reduction to ammonium (DNRA). G. sulfurreducens was recognized to efficiently secrete nitrite reductase (NrfA) for rapid DNRA because it lacks nitrate reductase, which inhibits DNRA by competing with nitrite and producing toxic intracellular nitric oxide. With an increase in G. sulfurreducens abundance, near-zero nitrate leaching and 3-fold greater N retention was achieved. Periodic application of weak electricity to the bioelectro-barrier ensured the dominance of G. sulfurreducens in the microbial community and therefore its ability to consistently prevent nitrate leaching. The ability of G. sulfurreducens to intercept nitrate was further demonstrated in more diverse agricultural soils, providing a novel way to prevent nitrate leaching and conserve bioavailable nitrogen in the soil, which has broader implications for both sustainable agriculture and groundwater protection.

Anaerobic oxidation of ammonium and short-chain gaseous alkanes coupled to nitrate reduction by a bacterial consortium

The bacterial species "Candidatus Alkanivorans nitratireducens" was recently demonstrated to mediate nitrate-dependent anaerobic oxidation of short-chain gaseous alkanes (SCGAs). In previous bioreactor enrichment studies, the species appeared to reduce nitrate in two phases, switching from denitrification to dissimilatory nitrate reduction to ammonium (DNRA) in response to nitrite accumulation. The regulation of this switch or the nature of potential syntrophic partnerships with other microorganisms remains unclear. Here, we describe anaerobic multispecies cultures of bacteria that couple the oxidation of propane and butane to nitrate reduction and the oxidation of ammonium (anammox). Batch tests with 15N-isotope labelling and multi-omic analyses collectively supported a syntrophic partnership between "Ca. A. nitratireducens" and anammox bacteria, with the former species mediating nitrate-driven oxidation of SCGAs, supplying the latter with nitrite for the oxidation of ammonium. The elimination of nitrite accumulation by the anammox substantially increased SCGA and nitrate consumption rates, whereas it suppressed DNRA. Removing ammonium supply led to its eventual production, the accumulation of nitrite, and the upregulation of DNRA gene expression for the abundant "Ca. A. nitratireducens". Increasing the supply of SCGA had a similar effect in promoting DNRA. Our results suggest that "Ca. A. nitratireducens" switches to DNRA to alleviate oxidative stress caused by nitrite accumulation, giving further insight into adaptability and ecology of this microorganism. Our findings also have important implications for the understanding of the fate of nitrogen and SCGAs in anaerobic environments.

Sediment nitrates reduction processes affected by non-native Sonneratia apetala plantation in South China

Numerous studies have highlighted the importance of nitrates (NOx-) reduction processes in estuarine and coastal ecosystems over the past decades. However, the biotic and abiotic factors sediment NOx- reduction processes in mangrove of varying ages are still not fully understood. Here, we investigated the dynamics of sediment NOx- reduction processes and associated gene abundances in mangroves of different ages (including 0-year unvegetated mudflats, 10 and 20-years Sonneratia apetala, as well as >40 years of mature native Kandelia obovate) on the Qi'ao Island using 15N stable-isotope pairing techniques and quantitative PCR. The denitrification (2.64-11.30 nmol g-1 h-1), anammox (0.06-0.83 nmol g-1 h-1), and dissimilatory nitrate reduction to ammonium (DNRA, 0.58-16.34 nmol g-1 h-1) rates varied spatially and seasonally, but their contributions to the total NOx- reduction (DEN%, ANA%, and DNRA%), associated gene abundance (nirS, anammox 16S rRNA, and nrfA), and organic matter only varied spatially. Organic matter and microbial abundances are the dominating factors controlling N loss and retention. Without considering confounding factors, mangroves conservation and restoration significantly increased DNRA rates, NIRI (DNRA/(denitrification + anammox)), organic matter content, and microbial abundances (p < 0.05 for all), but reduced N loss rates. Mangroves conservation and restoration are estimated to have increased sediment N retention (~931.81 t N yr-1) and reduced N loss (~481.32 t N yr-1) in coastal wetlands of China over the past 40 years (1980-2020). Overall, our results indicate that mangrove restoration and conservation can significantly increase sediment N retention due to the rapid biomass accumulation, and it can provide more nutrients for mangrove and microorganism growth, thus creating a virtuous cycle in these N-limited ecosystems.

Field evaluation of carbon injection method for in-situ biological denitrification in groundwater using geochemical and metataxonomic analyses

This study focuses on the bioremediation of nitrate-contaminated groundwater, which has become a significant environmental problem due to the increasing usage of fertilizers and sewage disposal. The nitrate reduction efficiencies of biological denitrification by injection of carbon source in a pilot-scale treatment system setup were investigated at a groundwater contamination site. The field test was conducted using acetate as a carbon source for 22 days to assess the nitrate reduction efficiencies of in-situ treatment. Geochemical parameters and microbial community analysis using next-generation sequencing were performed before and after carbon source injection. After 12 h of reaction time, nitrate concentration decreased from 31.6 to 4.2 mg-N/L at PC-2, and then remained stable at 3.9 mg-N/L. The nitrate reduction rate when acetate was injected was 29.0 mg-N/L/day. Aquabacterium commune, pseudomonas brassicacearum, dechloromonas denitrificans, and Massilia FAOS were dominant species after acetate injection. Predictive metabolic pathway analysis indicated that nitrate reduction metabolisms during injection of acetate were denitrification and assimilatory nitrate reduction to ammonium. The evaluated hazard quotient of nitrate-contaminated groundwater significantly decreased after acetate injection (non-carcinogenic risk decreased from 1.176 to 0.134 for children). This research could provide fundamental information for decision-makers in nitrate-contaminated groundwater quality protection and management.

Implications for nitrogen and sulphur cycles: phylogeny and niche-range of Nitrospirota in terrestrial aquifers

Increasing evidence suggests Nitrospirota are important contributors to aquatic and subsurface nitrogen and sulphur cycles. We determined the phylogenetic and ecological niche associations of Nitrospirota colonizing terrestrial aquifers. Nitrospirota compositions were determined across 59 groundwater wells. Distributions were strongly influenced by oxygen availability in groundwater, marked by a trade-off between aerobic (Nitrospira, Leptospirillum) and anaerobic (Thermodesulfovibrionia, unclassified) lineages. Seven Nitrospirota metagenome-assembled genomes (MAGs), or populations, were recovered from a subset of wells, including three from the recently designated class 9FT-COMBO-42-15. Most were relatively more abundant and transcriptionally active in dysoxic groundwater. These MAGs were analysed with 743 other Nitrospirota genomes. Results illustrate the predominance of certain lineages in aquifers (e.g. non-nitrifying Nitrospiria, classes 9FT-COMBO-42-15 and UBA9217, and Thermodesulfovibrionales family UBA1546). These lineages are characterized by mechanisms for nitrate reduction and sulphur cycling, and, excluding Nitrospiria, the Wood-Ljungdahl pathway, consistent with carbon-limited, low-oxygen, and sulphur-rich aquifer conditions. Class 9FT-COMBO-42-15 is a sister clade of Nitrospiria and comprises two families spanning a transition in carbon fixation approaches: f_HDB-SIOIB13 encodes rTCA (like Nitrospiria) and f_9FT-COMBO-42-15 encodes Wood-Ljungdahl CO dehydrogenase (like Thermodesulfovibrionia and UBA9217). The 9FT-COMBO-42-15 family is further differentiated by its capacity for sulphur oxidation (via DsrABEFH and SoxXAYZB) and dissimilatory nitrate reduction to ammonium, and gene transcription indicated active coupling of nitrogen and sulphur cycles by f_9FT-COMBO-42-15 in dysoxic groundwater. Overall, results indicate that Nitrospirota are widely distributed in groundwater and that oxygen availability drives the spatial differentiation of lineages with ecologically distinct roles related to nitrogen and sulphur metabolism.

Unveiling the biogeochemical mechanism of nitrate in the vadose zone-groundwater system: Insights from integrated microbiology, isotope techniques, and hydrogeochemistry

Clarifying the biogeochemical mechanism of nitrate (NO3-) in the vadose zone-groundwater system, particularly in agricultural contexts, is crucial for mitigating groundwater NO3- pollution. However, comprehensive studies on the impacts of changes in chemical indicators and microbial communities on NO3- are still lacking. This paper aims to address this gap by employing hydrogeochemistry, stable isotopes, and microbial techniques to assess the NO3- biogeochemical processes in the vadose zone-groundwater system. The findings suggested that NO3- in upper soil layers was primarily influenced by plant root absorption, assimilation, and nitrification processes. The oxygen contents gradually decreased with the nitrification process, resulting in the occurrence of the denitrification. However, denitrification predominantly occurred in the 60-80 cm soil layer in the study area. The limited thickness of the denitrification layer results in less NO3- consumption, leading to increased NO3- leaching into groundwater. Hydrochemical and isotopic characteristics further indicated that groundwater NO3- concentrations were mainly controlled by nitrification, followed by denitrification and mixing processes. The 16S rRNA sequencing analysis revealed great influences of soil sampling depths and groundwater NO3- concentrations on the microbial community structure. Additionally, the PICRUSt2-based prediction results demonstrated a stronger potential for dissimilatory reduction of NO3- to ammonium (DNRA) in both soil and groundwater compared to the other processes, potentially due to the widespread presence of the nrfH functional genes. However, the chemical indicators and isotopes used in this study did not support the occurrence of DNRA process in the vadose zone-groundwater system. This finding highlights the importance of an integrated approach combining microbiological, isotopic, and hydrogeochemical data to comprehensive understanding biogeochemical processes. The study developed a conceptual model elucidating the NO3- biogeochemical processes in the vadose zone-groundwater system within an agricultural area, contributing to enhanced comprehension and advancement of sustainable management practices for groundwater nitrogen.

Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments

The global nitrogen (N) cycle has been strongly altered by anthropogenic activities, including increased input of bioavailable N into aquatic ecosystems. Freshwater sediments are hotspots with regards to the turnover and elimination of fixed N, yet the environmental controls on the microbial pathways involved in benthic N removal are not fully understood. Here, we analyze the abundance and expression of microbial genes involved in N transformations using metagenomics and -transcriptomics across sediments of 12 Swiss lakes that differ in sedimentation rates and trophic regimes. Our results indicate that microbial N loss in these sediments is primarily driven by nitrification coupled to denitrification. N-transformation gene compositions indicated three groups of lakes: agriculture-influenced lakes characterized by rapid depletion of oxidants in the sediment porewater, pristine-alpine lakes with relatively deep sedimentary penetration of oxygen and nitrate, and large, deep lakes with intermediate porewater hydrochemical properties. Sedimentary organic matter (OM) characteristics showed the strongest correlations with the community structure of microbial N-cycling communities. Most transformation pathways were expressed, but expression deviated from gene abundance and did not correlate with benthic geochemistry. Cryptic N-cycling may maintain transcriptional activity even when substrate levels are below detection. Sediments of large, deep lakes generally showed lower in-situ N gene expression than agriculture-influenced lakes, and half of the pristine-alpine lakes. This implies that prolonged OM mineralization in the water column can lead to the suppression of benthic N gene expression.

Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes

Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.

Metagenomics insight into the long-term effect of ferrous ions on the mainstream anammox system

Anaerobic ammonium oxidation (anammox) bacteria have a high requirement for iron for their growth and metabolism. However, it remains unclear whether iron supplementation can sustain the stability of mainstream anammox systems at varying temperatures. Here, we investigated the long-term effects of Fe2+ on the mainstream anammox systems. Our findings revealed that the nitrogen removal efficiency (NRE) of the anammox system supplemented with 5 mg/L Fe2+ decreased from 76.5 ± 0.76% at 35 °C to 39.0 ± 9.9% at 25 °C. Notably, higher dosages of Fe2+ (15 mg/L and 30 mg/L) inhibited the anammox system, resulting in NREs of 15.9 ± 8.1% and 2.5 ± 1.1% at 25 °C, respectively. The results of microbial communities and function profiles suggested that the high Fe2+ dosage seriously affected the iron assimilation and utilization in the mainstream anammox system. This was evident from the decreased abundance of genes associated with Fe(II) transport and uptake, which in turn hindered the biosynthesis of intracellular iron-cofactors, resulting in decrease in the absolute abundance of Candidatus Brocadia, a key anammox bacterium, as well as a decline in NRE. Furthermore, our results showed that the anammox process was more susceptible to iron supplementation at 25 °C compared to 35 °C, which may be due to the oxidative stress reactions induced by combined lowered temperature and a high Fe2+ dosage. Overall, these findings offer a deeper understanding of the effect of iron in mainstream anammox systems, which can contribute to improved stability maintenance and effectiveness of anammox processes.

Frequency of change determines effectiveness of microbial response strategies

Nature challenges microbes with change at different frequencies and demands an effective response for survival. Here, we used controlled laboratory experiments to investigate the effectiveness of different response strategies, such as post-translational modification, transcriptional regulation, and specialized versus adaptable metabolisms. For this, we inoculated replicated chemostats with an enrichment culture obtained from sulfidic stream microbiomes 16 weeks prior. The chemostats were submitted to alternatingly oxic and anoxic conditions at three frequencies, with periods of 1, 4 and 16 days. The microbial response was recorded with 16S rRNA gene amplicon sequencing, shotgun metagenomics, transcriptomics and proteomics. Metagenomics resolved provisional genomes of all abundant bacterial populations, mainly affiliated with Proteobacteria and Bacteroidetes. Almost all these populations maintained a steady growth rate under both redox conditions at all three frequencies of change. Our results supported three conclusions: (1) Oscillating oxic/anoxic conditions selected for generalistic species, rather than species specializing in only a single condition. (2) A high frequency of change selected for strong codon usage bias. (3) Alignment of transcriptomes and proteomes required multiple generations and was dependent on a low frequency of change.

The potential role of subseafloor fungi in driving the biogeochemical cycle of nitrogen under anaerobic conditions

Fungi represent the dominant eukaryotic group of organisms in anoxic marine sedimentary ecosystems, ranging from a few centimeters to ~ 2.5 km below seafloor. However, little is known about how fungi can colonize anaerobic subseafloor environments for tens of millions of years and whether they play a role in elemental biogeochemical cycles. Based on metabolite detection, isotope tracer and gene analysis, we examined the anaerobic nitrogen conversion pathways of 19 fungal species (40 strains) isolated from1.3 to 2.5 km coal-bearing sediments below seafloor. Our results show for the first time that almost all fungi possess anaerobic denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and nitrification pathways, but not anaerobic ammonium oxidation (anammox). Moreover, the distribution of fungi with different nitrogen-conversion abilities in subseafloor sediments was mainly determined by in situ temperature, CaCO3, and inorganic carbon contents. These findings suggest that fungi have multiple nitrogen transformation processes to cope with their requirements for a variety of nitrogen sources in nutrient deficient anaerobic subseafloor sedimentary environments.

Dynamics of Benthic Nitrate Reduction Pathways and Associated Microbial Communities Responding to the Development of Seasonal Deoxygenation in a Coastal Mariculture Zone

Intensive mariculture activities result in eutrophication and enhance coastal deoxygenation. Deoxygenation profoundly influences nitrate reduction processes and further the fate of nitrogen (N) in coastal systems. Herein, 15N isotope labeling, real-time PCR, and high-throughput sequencing techniques were jointly used to investigate the participation and seasonal dynamics of sediment nitrate reduction pathways and the succession of functional microbial communities during the development of seasonal deoxygenation in a coastal aquaculture zone. Denitrification dominated benthic nitrate reduction (46.26-80.91%). Both denitrification and dissimilatory nitrate reduction to ammonium were significantly enhanced by summer deoxygenation (dissolved oxygen levels fell to 2.94 ± 0.28 mg L-1), while anammox remained unchanged. The abundance of the nitrous oxide reductase gene nosZ increased during deoxygenation. The community of the nosZ gene was sensitive to deoxygenation, with Azospirillum and Ruegeria accounting for the majority. Pelobacter was overwhelming in the nrfA gene (encoding dissimilatory nitrite reductase) community, which was less affected by deoxygenation. The variations of benthic nitrate reduction processes were driven by bottom water oxygen combined with temperature, chlorophyll a, and microbial gene abundances and community compositions. Our results implicated that seasonal oxygen-deficient zones could be substantial N sinks of coastal ecosystems and important for N balance. Effective management measures need to be developed to avoid further exacerbation of coastal deoxygenation and maintain the sustainable development of mariculture.

The Inhibiting Effects of High-Dose Biochar Application on Soil Microbial Metagenomics and Rice (Oryza sativa L.) Production

Biochar is usually considered as an organic improver which can improve soil and increase crop yields. However, the unrestricted application of biochar to normal-fertility farmland will cause chemical stress on crops and affect agricultural production. At present, the effects and mechanisms of high-dose applications of biochar on rice (Oryza sativa L.) production and soil biological characteristics have not been fully studied. In this greenhouse pot experiment, combined with soil microbial metagenomics, three treatments in triplicates were conducted to explore the responses of rice production, soil chemical properties, and soil biological properties to high-dose applications of biochar (5%, w/w) prepared using peanut waste (peanut hulls and straw). The results show that peanut hulls, with a loose texture and pore structure, are a raw material with stronger effects for preparing biochar than peanut straw in terms of its physical structure. In a rice monoculture system, high-dose applications of biochar (5%, w/w) can slightly increase the grains per spike, while significantly inhibiting the spike number per pot and the percentage of setting. High-dose applications of biochar also have significant negative effects on the diversity and stability of soil bacterial and archaeal communities. Moreover, the microbial metabolism and nutrient cycling processes are also significantly affected by changing the soil carbon/nitrogen ratio. This study discusses the response mechanisms of rice production and soil biology to high-dose biochar applications, and complements the understanding of irrational biochar application on agricultural production and land sustainability.

Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia

Dissimilatory nitrate reduction to ammonia (DNRA) is a common biochemical process in the nitrogen cycle in natural and man-made habitats, but its significance in wastewater treatment plants is not well understood. Several ammonifying Trichlorobacter strains (former Geobacter) were previously enriched from activated sludge in nitrate-limited chemostats with acetate as electron (e) donor, demonstrating their presence in these systems. Here, we isolated and characterized the new species Trichlorobacter ammonificans strain G1 using a combination of low redox potential and copper-depleted conditions. This allowed purification of this DNRA organism from competing denitrifiers. T. ammonificans is an extremely specialized ammonifier, actively growing only with acetate as e-donor and carbon source and nitrate as e-acceptor, but H2 can be used as an additional e-donor. The genome of G1 does not encode the classical ammonifying modules NrfAH/NrfABCD. Instead, we identified a locus encoding a periplasmic nitrate reductase immediately followed by an octaheme cytochrome c that is conserved in many Geobacteraceae species. We purified this octaheme cytochrome c protein (TaNiR), which is a highly active dissimilatory ammonifying nitrite reductase loosely associated with the cytoplasmic membrane. It presumably interacts with two ferredoxin subunits (NapGH) that donate electrons from the menaquinol pool to the periplasmic nitrate reductase (NapAB) and TaNiR. Thus, the Nap-TaNiR complex represents a novel type of highly functional DNRA module. Our results indicate that DNRA catalyzed by octaheme nitrite reductases is a metabolic feature of many Geobacteraceae, representing important community members in various anaerobic systems, such as rice paddy soil and wastewater treatment facilities.