Denitrification Research Articles

Exploring oral bacterial compositional network in two oral disease groups using a convergent approach of NGS-molecular diagnostics.

Since most of the commonly known oral diseases are explained in link with balance of microbial community, an accurate bacterial taxonomy profiling for determining bacterial compositional network is essential. However, compared to intestinal microbiome, research data pool related to oral microbiome is small, and general 16S rRNA screening method has a taxonomy misclassification issue in confirming complex bacterial composition at the species level. Present study aimed to explore bacterial compositional networks at the species level within saliva of 39 oral disease patients (Dental Caries group: n = 26 and Periodontitis group: n = 13) through comparison with public Korean-specific healthy oral microbiome data. Here, we applied comprehensive molecular diagnostics based on qRT-PCR and Sanger sequencing methods to complement the technical limitations of NGS-based 16S V3-V4 amplicon sequencing technology. As a result of microbiome profiling at the genus level, relative frequencies of many nitrate-reducing bacteria within each oral disease group were found to be significantly low compared to the healthy group. In addition, the molecular diagnostics-based bacterial identification method allowed the determination of the correct taxonomy of screened primary colonizers (Streptococcus and Actinomyces unclassification clusters) for each oral disease. Finally, as with the results of microbiome profiling at the genus level, many core-species classified within the saliva of each oral disease group were also related to nitrate-reduction, and it was estimated that various pathogens associated with each disease formed a bacterial network with the core-species. Our study introduced a novel approach that can compensate for the difficulty of identifying an accurate bacterial compositional network at the species level due to unclear taxonomy classification by using the convergent approach of NGS-molecular diagnostics. Ultimately, we suggest that our experimental approach and results could be potential reference materials for researchers who intend to prevent oral disease by determining the correlation between oral health and bacterial compositional network according to the changes in the relative frequency for nitrate-reducing species.

Bacteria-photocatalyst biohybrid system for sustainable ammonium production

Although the Haber–Bosch process supports the growth of modern agriculture with abundant ammonia and fertilizer production, substantial energy consumption and enormous greenhouse emissions demand an alternative and sustainable approach. Here, we report a novel approach that combines the non-photosynthetic bacterium Shewanella oneidensis MR-1 (S. oneidensis MR-1) with cadmium sulfide nanoparticles (CdS NPs) to enable the photosynthesis of ammonium (NH4+) from nitrate (NO3−) using photoexcited electrons as donors. The NO3− reduction efficiency reached almost 100%, with an NH4+ production selectivity of over 90%. The maximum instantaneous quantum efficiency was 3.01% under light irradiation. The reverse metal-reducing (Mtr) pathway is responsible for the transfer of photoexcited electrons to intracellular compartments. Parallel reaction monitoring analysis illustrated that NO3− to NH4+ was produced via the dissimilatory nitrate reduction to ammonium (DNRA) pathway in S. oneidensis MR-1. This study provides a facile strategy for light-driven ambient NH4+ synthesis and solar-to-chemical conversion.

Nitrate promotes the growth and the production of short-chain fatty acids and tryptophan from commensal anaerobe Veillonella dispar in the lactate-deficient environment by facilitating the catabolism of glutamate and aspartate.

Veillonella spp. are nitrate-reducing bacteria with anaerobic respiratory activity that reduce nitrate to nitrite. They are obligate anaerobic, Gram-negative cocci that ferment lactate as the main carbon source and produce short-chain fatty acids (SCFAs). Commensal Veillonella reside in the human body site where lactate level is, however, limited for Veillonella growth. In this study, nitrate was shown to promote the anaerobic growth of Veillonella in the lactate-deficient media. We aimed to investigate the underlying mechanisms and the metabolism involved in nitrate respiration. Nitrate (15 mM) was demonstrated to promote Veillonella dispar growth and viability in the tryptone-yeast extract medium containing 0.5 mM L-lactate. Metabolite and transcriptomic analyses revealed nitrate enabled V. dispar to actively utilize glutamate and aspartate from the medium and secrete tryptophan. Glutamate or aspartate was further supplemented to a medium to investigate individual catabolism during nitrate respiration. Notably, nitrate was demonstrated to elevate SCFA production in the glutamate-supplemented medium, and further increase tryptophan production in the aspartate-supplemented medium. We proposed that the increased consumption of glutamate provided reducing power for nitrate respiration and aspartate served as a substrate for fumarate formation. Both glutamate and aspartate were incorporated into the central metabolic pathways via reverse tricarboxylic acid cycle and were linked with the increased production of acetate, propionate, and tryptophan. This study provides further understanding of the promoted growth and metabolic mechanisms by commensal V. dispar utilizing nitrate and specific amino acids to adapt to the lactate-deficient environment.IMPORTANCENitrate is a pivotal ecological factor influencing microbial community and metabolism. Dietary nitrate provides health benefits including anti-diabetic and anti-hypertensive effects via microbial-derived metabolites such as nitrite. Unraveling the impacts of nitrate on the growth and metabolism of human commensal bacteria is imperative to comprehend the intricate roles of nitrate in regulating microbial metabolism, community, and human health. Veillonella are lactate-utilizing, nitrate-reducing bacteria that are frequently found in the human body site where lactate levels are low and nitrate is at millimolar levels. Here, we comprehensively described the metabolic strategies employed by V. dispar to thrive in the lactate-deficient environment using nitrate respiration and catabolism of specific amino acids. The elevated production of SCFAs and tryptophan from amino acids during nitrate respiration of V. dispar further suggested the potential roles of nitrate and Veillonella in the promotion of human health.

Insights into nitrogen biogeochemical cycling in mangrove wetland from Genome-Resolved metagenomic sequencing

The critical role of nitrogen (N) in sustaining the vitality of mangrove wetlands is widely recognized, yet research elucidating complex microbiome structures and functional genes driving N biogeochemical cycles are markedly limited. This study leverages high-throughput and metagenomic sequencing to investigate N biogeochemical cycling from the Dongzhai Harbor mangrove wetland. Results reveal that Proteobacteria (29.95–49.26%), Chloroflexi (15.68–35.33%), and Acidobacteria (5.18–12.46%) are the predominant phyla, with Deltaproteobacteria (3.71–7.95%), Gammaproteobacteria (0.83–8.73%), and Alphaproteobacteria (1.73–14.13%) leading at the order level. Microbial diversity and the prevalence of functional genes diminish with increasing sediment depth, indicating that N transformation predominantly occurs in surface sediments. The identified N metabolic pathways in mangrove sediments encompass N fixation (nifD, nifK, nifH genes), nitrification (amoA, amoB, amoC, hao, nxrA and nxrB genes), denitrification (narG, nirK, nirS, norB and nosZ genes), dissimilatory nitrate reduction to ammonium (hzo、hzsA and hzsB genes), and organic N mineralization (gdhA and ureC genes). Organic N mineralization and N fixation are most pronounced in mangrove sediments, with N fixation exhibiting greater intensity in the mangrove than mudflat zone. Salinity, TOC, TN, and SO42- predominantly foster N cycling facilitated by microbial activities, while Fe appears to impede it. These insights offer a scientific foundation for the ecological restoration and conservation of mangrove wetlands.

Feasibility and mechanism exploration of enhancing short chain fatty acid production assisted by nitrate photolysis during sludge fermentation

Seeking for the eco-friendly and low-cost pretreatment technology has become the prerequisite for the efficient release of the embedded organics in waste activated sludge (WAS), further for the higher production of short chain fatty acids (SCFAs) via anaerobic fermentation. Nitrate, which can produce reactive oxygen species (ROS) and reactive nitrogen species (RNS) during photolysis, may have the positive effect on WAS disintegration and organics degradation, while its performance and mechanism for WAS treatment is still unknown. This study investigated the feasibility of the nitrate photolysis on WAS disintegration and SCFAs production, and elucidated the underlying mechanism. Results showed that the highest acidification rate (26.6 h−1) and short-chain fatty acid (SCFAs) production (5370.6 mg COD/L) were achieved at 8 d in the nitrate photolysis group (Nitrate-UV) during the anaerobic fermentation, significantly promoted by 2.3 and 12.7 folds than that of Control (raw WAS). Acetic acid (HAc) and propionic acid (HPr) accounted for 89.1 % and 90.1 % in Nitrate-UV and Nitrate group (sole nitrate addition), which were much higher than that obtained in UV and Control. HO• and O2•− were the main contributors compared with NO2•, ONOO– and NO• on the release and bioconversion of the soluble organics. Microbial community and metagenomics revealed the promotion of nitrate photolysis on anaerobic fermentation bacteria (AFB) and nitrate reducing bacteria (NRB), as well as the gene abundance related to the metabolic pathways of glycolysis, amino acid, acetate and nitrogen metabolism, which jointly devoted to the SCFAs enhancement during the anaerobic fermentation.

Enhancing simultaneous nitrification and denitrification in a plant-scale integrated fixed-film activated sludge system: Focusing on the cooperation between activated sludge and biofilm

To further remove nutrients through simultaneous nitrification and denitrification (SND), the integrated fixed-film activated sludge (IFAS) system has become one of the most efficient pathways for modifying the existing wastewater treatment plants. This study investigated the cooperation between suspended activated sludge and carrier-attached biofilm for promoting SND in different seasons in a plant-scale IFAS system. The results showed that the involvement of biofilm could stimulate SND, removing 23.9 % of influent total nitrogen (TN) in the aerobic IFAS system. The nitrification rate and the SND ratio were much influenced by the temperature, resulting in higher TN removal efficiency in summer (90.3 %) than that in winter (86.4 %). The highest SND ratio of 67 % could be achieved at the temperature of 23 °C. Additionally, the SND ratio also depended on a variety of operational parameters (such as dissolved oxygen (DO), COD/NH4+-N, and mixed liquor suspended solids (MLSS)). High-throughput sequencing technology further confirmed that the composition of the functional bacterial communities in activated sludge significantly differed from that in biofilm. Nitrifying bacteria were mostly detected in biofilm samples, while more denitrifying bacteria existed in activated sludge, thus resulting in the enhancement of synergic nitrogen removal via SND in the IFAS system.

Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling

Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R2 = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R2 = 0.076 ~ R2 = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.

Community Composition and Functional Characterization of Microorganisms in Surface Sediment of the New Britain Trench.

The deep-sea harbors abundant prokaryotic biomass is a major site of organic carbon remineralization and long-term carbon burial in the ocean. Deep-sea trenches are the deepest part of the ocean, and their special geological and morphological features promoting the accumulation of organic matter and active organic carbon turnover. Despite the expanding reports about the organic matter inputs, limited information is known regarding microbial processes in deep-sea trenches. In this study, we investigated the species composition and metabolic potential in surface sediment of the New Britain Trench (NBT), using a metagenomic approach. The predominant microbial taxa in NBT sediment include Proteobacteria, Acidobacteria, Planctomycetes, Actinobacteria and Chloroflexota. The microbial communities showed highly diverse metabolic potentials. Particularly, genes encoding enzymes for degradation of aromatic compounds, as well as those encoding haloalkane dehalogenase and haloacetate dehalogenase were annotated in the NBT surface sediment, which indicate the potential of microorganisms to degrade different types of refractory organic matter. The functional genes encoding enzymes for dissimilatory nitrate reduction, denitrification, and nitrification were also represented in the NBT metagenome. Overall, the microbial communities show high diversity of heterotrophic lineages and metabolic features, supporting their potential contributions in organic carbon metabolism. Meanwhile, Nitrosopumilus, a dominant genus in the surface sediment of the NBT, is a typical ammonia-oxidizing archaea (AOA), with autotrophic CO2 fixation pathways including the 3-hydroxypropionate/4-hydroxybutylate (3HP/4HB) cycle, the reductive TCA (rTCA) cycle. The results demonstrate that autotrophic metabolic processes also play an important role in the surface sediment, by providing newly synthesized organic matter.

Groundwater flow regime shapes nitrogen functional traits by affecting microbial community assembly processes in the subsurface

The complex nitrogen (N) cycle in groundwater systems is affected by both biological and environmental factors. The interactions between hydrogeological conditions and the microbial community assembly processes that impact N-cycling processes remain poorly understood. We explored the assembly patterns of N-cycling microbial communities along the groundwater flow path. The environmental heterogeneity in different hydrological phases increased along the flow path (mean Ed: 0.16–0.49), accompanied by different microbial community assembly patterns. The assembly patterns that engaged in dissimilatory nitrate reduction to ammonium (DNRA) and denitrification changed across the water-sediment phases. Nitrifying microorganisms in the discharge area were mainly influenced by heterogeneous selection (41–69 %), and were closely correlated with dissolved oxygen (DO) concentrations. Homogeneity along flow-through increased stochastic assemblies, such as downstream drift of anammox bacterial (AnAOB) communities. Thus, the N removal pathway changed from “nitrification-denitrification” in the recharge area to “partial nitrification-anammox” in the discharge area. The increasing environmental heterogeneity brought more deterministic assembly patterns of N-cycling communities, linked to higher community turnover along the groundwater flow path. This study indicated that groundwater flow regime determined microbial community assembly patterns, providing valuable insight into the response of N transitions to environmental variations in groundwater systems.

Enhancing total nitrogen removal in constructed wetlands: A Comparative study of iron ore and biochar amendments

Efficient nitrogen removal in constructed wetlands (CWs) remains challenging when treating agricultural runoff with a low carbon-to-nitrogen ratio (C/N). However, using biochar, iron ore, and FeCl3-modified biochar (Fe-BC) as amendments could potentially improve total nitrogen (TN) removal efficiency in CWs, but the underlying mechanisms associated with adding these substrates are unclear. In this study, five CWs: quartz sand constructed wetland (Control), biochar constructed wetland, Fe-BC constructed wetland, iron ore constructed wetland, and iron ore + biochar constructed wetland, were built to compare their treatment performance. The rhizosphere microbial community compositions and their co-occurrence networks were analyzed to reveal the underlying mechanisms driving their treatment performance. The results showed that iron ore was the most efficient amendment, although all treatments increased TN removal efficiency in the CWs. Ammonia-oxidizing, heterotrophic denitrifying, nitrate-dependent anaerobic ferrous oxidizing (NAFO), and Feammox bacteria abundance was higher in the iron ore system and led to the simultaneous removal of NH4+-N, NO3−-N, and NO2−-N. Visual representations of the co-occurrence networks further revealed that there was an increase in cooperative mutualism (the high proportion of positive links) and more complex interactions among genera related to the nitrogen and iron cycle (especially ammonia-oxidizing bacteria, heterotrophic denitrifying bacteria, NAFO bacteria, and Feammox bacteria) in the iron ore system, which ultimately contributed to the highest TN removal efficiency. This study provides critical insights into how different iron ore or biochar substrates could be used to treat agricultural runoff in CWs.

Interplay between denitrifying and sulfate-reducing bacterial communities under acid mine drainage stress

Acid mine drainage (AMD) pollution leads to the enrichment of sulfate in paddy soil. The interplay between denitrifying and sulfate-reducing bacteria across varying soil depths, and their response to AMD pollution is not yet fully understood. The responses of denitrifying and sulfate-reducing bacteria(SRB) to AMD pollution were analyzed by collecting soil samples at four depths (0–10 cm, 10–20 cm, 20–40 cm, 40–60 cm) under two treatments (AMD-polluted and control soil). AMD pollution resulted in a significant decrease in pH value, elevated SO42- and metal concentrations. Compared to the control soil, denitrifying and sulfate-reducing bacteria in AMD-polluted soils were more sensitive to environmental fluctuations. Co-occurrence analysis revealed that there were more microbiological linkages and nodes in control soil than in polluted soil. Denitrifying and sulfate-reducing bacteria can maintain part of N and S cycle under long-term AMD pollution by increasing the negative correlation in ecological network. Desulfobacca exhibited a positive correlation with nitrate and held a significant position in the symbiotic network, suggesting its potential important role in inhibiting nitrogen loss. This study revealed the intricate ecological network of functional communities, which could have important implications for environmental management and the development of sustainable agricultural practices in areas affected by AMD pollution.

Association between oral microbial nitrate metabolism and poor prognosis in acute ischemic stroke patients with a history of hypertension

ABSTRACT Background Oral microbes mediate the production of nitric oxide (NO) through the denitrification pathway. This study aimed to investigate the association between oral microbial nitrate metabolism and prognosis in acute ischemic stroke (AIS) patients. Methods This prospective, observational, single-center cohort study included 124 AIS patients admitted within 24 hours of symptom onset, with 24-hour ambulatory blood pressure data. Oral swabs were collected within 24 hours. Hypertensive AIS patients were stratified by the coefficient of variation (CV) of 24-hour systolic blood pressure. Microbial composition was analyzed using LEfSe and PICRUSt2 for bacterial and functional pathway identification. Results Significant differences in oral microbiota composition were observed between hypertensive AIS patients with varying CVs. Lower CV groups showed enrichment of nitrate-reducing bacteria and “Denitrification, nitrate => nitrogen” pathways. The TAX score of oral nitrate-reducing bacteria, derived from LASSO modeling, independently correlated with 90-day modified Rankin Scale scores, serving as an independent risk factor for poor prognosis. Mediation analyses suggested indirect that the TAX score not only directly influences outcomes but also indirectly affects them by modulating 24-hour systolic blood pressure CV. Conclusions AIS patients with comorbid hypertension and higher systolic blood pressure CV exhibited reduced oral nitrate-reducing bacteria, potentially worsening outcomes.

Arcobacteraceae are ubiquitous mixotrophic bacteria playing important roles in carbon, nitrogen, and sulfur cycling in global oceans.

Mixotrophy is an important trophic strategy for bacterial survival in the ocean. However, the global relevance and identity of the major mixotrophic taxa remain largely elusive. Here, we combined phylogenetic, metagenomic, and metatranscriptomic analyses to characterize ubiquitous Arcobacteraceae based on our deep-sea in situ incubations and the global data. The phylogenomic tree of Arcobacteraceae is divided into three large clades, among which members of clades A and B are almost all from terrestrial environments, while those of clade C are widely distributed in various marine habitats in addition to some terrestrial origins. All clades harbor genes putatively involved in chitin degradation, sulfide oxidation, hydrogen oxidation, thiosulfate oxidation, denitrification, dissimilatory nitrate reduction to ammonium, microaerophilic respiration, and metal (iron/manganese) reduction. Additionally, in clade C, more unique pathways were retrieved, including thiosulfate disproportionation, ethanol fermentation, methane oxidation, fatty acid oxidation, cobalamin synthesis, and dissimilatory reductions of sulfate, perchlorate, and arsenate. Within this clade, two mixotrophic Candidatus genera represented by UBA6211 and CAIJNA01 harbor genes putatively involved in the reverse tricarboxylic acid pathway for carbon fixation. Moreover, the metatranscriptomic data in deep-sea in situ incubations indicated that the latter genus is a mixotroph that conducts carbon fixation by coupling sulfur oxidation and denitrification and metabolizing organic matter. Furthermore, global metatranscriptomic data confirmed the ubiquitous distribution and global relevance of Arcobacteraceae in the expression of those corresponding genes across all oceanic regions and depths. Overall, these results highlight the contribution of previously unrecognized Arcobacteraceae to carbon, nitrogen, and sulfur cycling in global oceans.IMPORTANCEMarine microorganisms exert a profound influence on global carbon cycling and ecological relationships. Mixotrophy, characterized by the simultaneous utilization of both autotrophic and heterotrophic nutrition, has a significant impact on the global carbon cycling. This report characterizes a group of uncultivated bacteria Arcobacteraceae that thrived on the "hot time" of bulky particulate organic matter and exhibited mixotrophic strategy during the in situ organic mineralization. Compared with clades A and B, more unique metabolic pathways were retrieved in clade C, including the reverse tricarboxylic acid pathway for carbon fixation, thiosulfate disproportionation, methane oxidation, and fatty acid oxidation. Global metatranscriptomic data from the Tara Oceans expeditions confirmed the ubiquitous distribution and extensive transcriptional activity of Arcobacteraceae with the expression of genes putatively involved in carbon fixation, methane oxidation, multiple sulfur compound oxidation, and denitrification across all oceanic regions and depths.

Survival Strategy, Metabolic Potential and Taxonomic Reframe of Kocuria polaris

Antarctica is renowned as the most inhospitable environment where microorganisms are thriving in the frontiers of life. In the past few years, many novel bacterial species have been reported from the Antarctic environment. During taxonomic re-evaluation of novel bacterial species from Antarctica, it was noticed that Kocuria polaris shared high 16S rRNA gene sequence similarity with Kocuria rosea. In the present study, the taxonomic position, metabolic potentials, and stress survival strategy of K. polaris were evaluated through genome analysis. K. polaris encodes genes for glycolysis, citrate cycle, pentose phosphate pathway, dissimilatory nitrate reduction, assimilatory sulfate reduction, etc. In addition, K. polaris also encodes genes for cold and salt stress. The 16S rRNA gene sequence extracted from K. polaris and K. rosea genomes showed 99.7% similarity. In the phylogenomic tree, K. polaris and K. rosea clustered together. The average nucleotide identity and digital DNA–DNA hybridization values between K. polaris and K. rosea exceeded the threshold (95-96% for ANI and 70% for dDDH) value for distinguishing species, showing that they are similar species. The present study shed light on K. polaris survival strategy in extreme conditions. We further propose to reclassify Kocuria polaris as a later heterotypic synonym of Kocuria rosea.

Enhanced degradation of polylactic acid microplastics in acidic soils: Does the application of biochar matter?

Biodegradable plastics, as an alternative to petroleum plastics, are fiercely increasing, but their incomplete degradation under natural conditions may lead to the breakdown into microplastics (MPs). Here, we explored the impacts of chicken manure-derived (MBC) and wood waste-derived biochar (WBC) on the degradation of polylactic acid microplastics (PLA-MPs) during soil incubation for one year. Both biochars induced more pronounced degradation characteristics in PLA-MPs, including enhanced surface roughness, the proportion of MPs < 100 µm by 12.89 %−25.67 %, oxygen loading and O/C ratio to 71.74 %−75.87 % and 1.70–1.76, as well as accelerated carbon loss and the cleavage of ester group and C-C bond. Also, biochar increased soil pH, depleted inorganic nitrogen and available phosphorus, and changed enzymic activity in PLA-MP-polluted soils. We proposed that both biochars accelerated the PLA-MP degradation by inducing alkaline, aminolysis/ammonolysis, oxidative, and microbial degradation. Among these, MBC induced aminolysis/ammonolysis by NH4+ via Fe2+-driven NO3-/NO2- reduction and microbial nitrogen fixation, and oxidative degradation by radicals generated through Fenton/Fenton-like reaction. WBC caused aminolysis/ammonolysis and oxidative degradation mainly through dissimilatory nitrate reduction to ammonium and surface free radicals on biochar. These findings indicate that biochar has the potential to accelerate PLA-MP degradation, and its regulatory mechanism depends on the type of biochar.

Geographical factor dominates spatial patterns of potential nitrate reduction rates in coastal wetland sediments in Fujian Province, China

Nitrate (NO3−) reduction is a key process governing the nitrogen (N) dynamics of coastal wetland sediments. Although the effects of environmental factors on the NO3− reduction mechanism in coastal wetland sediments have been examined in various studies, the effects of spatial variation in potential NO3− reduction processes in coastal wetland sediments and the factors driving geographical variation in these processes have not been widely examined. Here, we conducted research on surface sediment samples from four different vegetation types at six coastal wetland sites across two regions. We characterized potential rates of NO3− reduction processes (including denitrification (DF), anammox (ANA), and dissimilatory nitrate reduction to ammonium (DNRA)) using a15N tracer method. Additionally, we assessed the abundances of functional genes, and microbial community structure using high-throughput sequencing, and metagenomic sequencing. In six wetland sites, the contribution ranges of DF, ANA, and DNRA to NO3− reduction were 38.43%–55.69%, 31.33%–45.65%, and 5.26%–17.11%, respectively, and potential NO3− reduction was mainly driven by N removal via gaseous N (DF+ANA). Significant spatial differences were observed in the structure of bacterial and fungal microbial communities, suggesting that geographical distance has a major effect on microbial community structure. Environmental factors and Functional gene abundances were significantly related to potential NO3− reduction processes, and physicochemical properties had a stronger effect on potential NO3− reduction processes than gene abundances. Factors showing significant differences across regions were the main drivers of variation in potential NO3− reduction processes. Overall, our study showed that sediment substrates and geographical environmental factors rather than the abundance of functional genes and vegetation types were the main indicators of potential NO3− reduction activities in coastal wetlands.

Transcriptome analysis of the degradation process of organic nitrogen by two heterotrophic nitrifying and aerobic denitrifying bacteria.

The heterotrophic nitrification aerobic denitrification bacteria (HNDS) can perform nitrification and denitrification at the same time. Two HNDS strains, Achromobacter sp. HNDS-1 and Enterobacter sp. HNDS-6 which exhibited an amazing ability to solution nitrogen (N) removal have been successfully isolated from paddy soil in our lab. When peptone or ammonium sulfate as sole N source, no significant difference in gene expression related to nitrification and denitrification of the strains was found according to the transcriptome analysis. The expression of phosphomethylpyrimidine synthase (thiC), ABC transporter substrate-binding protein, branched-chain amino acid ABC transporter substrate-binding protein, and RNA polymerase (rpoE) in HNDS-1 were significantly upregulated when used peptone as N source, while the expression of exopolysaccharide production protein (yjbE), RNA polymerase (rpoC), glutamate synthase (gltD) and ABC-type branched-chain amino acid transport systems in HNDS-6 were significantly upregulated. This indicated that these two strains are capable of using organic N and converting it into NH4+-N, then utilizing NH4+-N to synthesize amino acids and proteins for their own growth, and strain HNDS-6 can also remove NH4+-N through nitrification and denitrification.

Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau

Permafrost, characterized by its frozen soil, serves as a unique habitat for diverse microorganisms. Understanding these microbial communities is crucial for predicting the response of permafrost ecosystems to climate change. However, large-scale evidence regarding stratigraphic variations in microbial profiles remains limited. Here, we analyze microbial community structure and functional potential based on 16S rRNA gene amplicon sequencing and metagenomic data obtained from an ∼1000 km permafrost transect on the Tibetan Plateau. We find that microbial alpha diversity declines but beta diversity increases down the soil profile. Microbial assemblages are primarily governed by dispersal limitation and drift, with the importance of drift decreasing but that of dispersal limitation increasing with soil depth. Moreover, genes related to reduction reactions (e.g., ferric iron reduction, dissimilatory nitrate reduction, and denitrification) are enriched in the subsurface and permafrost layers. In addition, microbial groups involved in alternative electron accepting processes are more diverse and contribute highly to community-level metabolic profiles in the subsurface and permafrost layers, likely reflecting the lower redox potential and more complicated trophic strategies for microorganisms in deeper soils. Overall, these findings provide comprehensive insights into large-scale stratigraphic profiles of microbial community structure and functional potentials in permafrost regions.

Metagenomic insights into microbial metabolic mechanisms of a combined solid-phase denitrification and anammox process for nitrogen removal in mainstream wastewater treatment

To overcome the significant challenges associated with nitrite supply and nitrate residues in mainstream anaerobic ammonium oxidation (anammox)-based processes, this study developed a combined solid-phase denitrification (SPD) and anammox process for low-strength nitrogen removal without the addition of nitrite. The SPD step was performed in a packed-bed reactor containing poly-3-hydroxybutyrate-co-3-hyroxyvelate (PHBV) prior to employing the anammox granular sludge reactor in the continuous-flow mode. The removal efficiency of total inorganic nitrogen reached 95.7 ± 1.2% under a nitrogen loading rate of 0.18 ± 0.01 kg N·m3·d−1, and it required 1.02 mol of nitrate to remove 1 mol of ammonium nitrogen. The PHBV particles not only served as biofilm carriers for the symbiosis of hydrolytic bacteria (HB) and denitrifying bacteria (DB), but also carbon sources that facilitated the coupling of partial denitrification and anammox in the granules. Metagenomic sequencing analysis indicated that Burkholderiales was the most abundant HB genus in SPD. The metabolic correlations between DB (Betaproteobacteria, Rhodocyclaceae, and Anaerolineae) and anammox bacteria (Candidatus Brocadiac and Kuenenia) in the granules were confirmed through microbial co-occurrence networks analysis and functional gene annotations. Additionally, the genes encoding nitrate reductase (Nap) and nitrite reductase (Nir) in DB primarily facilitated nitrate reduction, thereby supplying nitric oxide to anammox bacteria for subsequent nitrogen removal with hydrazine synthase (Hzs) and hydrazine dehydrogenase (Hdh). The findings provide insights into microbial metabolism within combined SPD and anammox processes, thus advancing the development of mainstream anammox-based processes in engineering applications.

Long-term operation and dynamic response of dissimilatory nitrate reduction to ammonium process under low-frequency infrared electromagnetic field

Dissimilatory nitrate reduction to ammonium (DNRA) received more attention for its ability to recover ammonium. This study investigated the possibility of low-frequency infrared electromagnetic field (IR-EMF) to improve DNRA. The optimal IR-EMF intensity of 0.04 μT could effectively improve DNRA activity of nonwoven fabric membrane bioreactors. In the long-term operation, the average ammonium conversion efficiency was enhanced by 117.7% and 62.5% under 0.04 μT and 0.06 μT IR-EMF, respectively. The highest nrfA-gene abundance and potential DNRA rate were obtained under 0.04 μT IR-EMF exposure. Bacteroidetes fragilis, Shewanelle oneidensis MR-1, and Thauera sp. RT1901 were selected to investigate the dynamic response of nitrogen transformation and energy metabolism to IR-EMF. The transcriptome sequencing and RT-qPCR results suggested that IR-EMF could enhance both denitrification and DNRA process, mainly by improving ATP synthesis to boost metabolic activity. This study provided an efficient method for the nitrogen recovery via DNRA process by applying IR-EMF.