Nitrogen Metabolic Pathways Research Articles

Analysis of Relative Expression of Key Enzyme Genes and Enzyme Activity in Nitrogen Metabolic Pathway of Two Genotypes of Potato (Solanum tuberosum L.) under Different Nitrogen Supply Levels

Nitrogen (N) plays an important role in the growth cycle of the potato, and is an important guarantee of yield and quality. Rational N application is one of the key ways to improve a crop’s high and stable yield and economic and environmental benefits. The N nutrition level of potato regulates the gene expression of enzymes related to the N metabolism pathway, which shows the change of the activity of key enzymes in N metabolism, and finally realizes the regulation of N absorption and utilization. In this study, the key enzyme genes and enzyme activity of different genotypes of potato under different N supply treatments were identified, which laid a foundation for further exploration of the functions of each gene in the potato N metabolism pathway and provided theoretical basis for rational N application. The results showed that the relative expression levels of StNRT1.5, StNR, StNiR in leaves, StNRT2.5, StNRT2.4, StGS1-2 in roots and StNRT2.7, StGS1-3, StGS2, StGS1-4, StFd-GOGAT in leaves and roots showed that the levels of N-inefficient potato Atlantic (A) were higher than the N-efficient potato Yanshu 4 (Y), while the relative expression levels of StNRT2.5, StGS1-2 in leaves, StNRT1.5StNR, StNiR in roots and StGDH, StNADH-GOGAT in leaves and roots showed that levels in Yanshu 4 (Y) were higher than in Atlantic (A). At the same time, we especially found that the GDH activity in the leaves of the two genotypes of potato were higher at low N levels. Additionally, the activity of NR and NiR, and the activity of GS and GOGAT were correlated. In addition, the changes of key enzymes in different N metabolism showed a certain continuity with the advancement of growth and development, and some gene expression rules and enzyme activity changes also showed a certain consistency.

Rapid start-up and stable operation of an aerobic/oxic/anoxic simultaneous nitrification, denitrification, and phosphorus removal reactor with no sludge discharge

An anaerobic/aerobic/anoxic mode simultaneous nitrification, denitrification, and phosphorus removal system was visited for enhanced low-strength wastewater treatment and dramatic in situ sludge reduction. Results showed that rapid start-up was achieved with conventional activated sludge after 15 days, with effluent ammonia nitrogen, total nitrogen, total phosphorus, and chemical oxygen demand being 0.25, 7.89, 0.12, 24.37 mg/L, respectively. A two-stage biomass growth rate was observed with the sludge yield of 0.285 (day 1–50) and 0.017 g MLSS/g COD (day 51–110) without sludge discharge. Dynamics of bacterial community has been identified with outstanding accumulation of Candidatus_Competibacter up to 29.06 %, which contributed to both simultaneous nutrients removal and sludge reduction. Further analysis via PICRUSt2 revealed the main pathway of nitrogen metabolism, while proposed mechanism for phosphorus removal with no sludge discharge was analyzed from the intracellular and extracellular perspectives. Overall, this study provided guidance and reference for the development and application of A/O/A-SNDPR technology.

The fecal microbiota of gravidas with fetal growth restriction newborns characterized by metagenomic sequencing

BackgroundFetal growth restriction (FGR) is a complex obstetric complication with various causes and of great harm. However, the specific pathogenesis of FGR is unclear, which limits its effective treatment. Gut microbiota dysbiosis was found to be important in pathogenesis of various diseases. However, its role in FGR development remains unclear and needs to be clarified. MethodsIn our case-control study, we recruited eight FGR and eight control female participants and collected their fecal samples in third trimester before delivery. We performed metagenomic sequencing and bioinformatic analysis to compare the gut microbiota composition and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways between the two groups. ResultsOur results showed that totally 20 gut microbes were significantly different between two groups (p<0•05), and the correlation analysis found that g__Roseomonas and g__unclassified_f__Propionibacteriaceae were significantly positive correlated with both maternal body mass index (BMI) before delivery, placental weight, and neonatal birth weight (BW) percentile (all p<0•05), while g__Marinisporobacter and g__Sphingomonas were significantly negative correlated with both neonatal BMI and neonatal BW percentile (all p<0•05). Through KEGG pathway analysis, we found that the abundance of the Nitrogen metabolism pathway decreased significantly (p<0•05) whereas the abundance of the Amoebiasis pathway increased significantly in the FGR group (p<0•05). ConclusionIn this study, we demonstrated that the occurrence of FGR is associated with the change of gut microbiota of pregnant women.

Sugarcane Genotypes with Contrasting Biological Nitrogen Fixation Efficiencies Differentially Modulate Nitrogen Metabolism, Auxin Signaling, and Microorganism Perception Pathways.

Sugarcane is an economically important crop that is used for the production of fuel ethanol. Diazotrophic bacteria have been isolated from sugarcane tissues, without causing visible plant anatomical changes or disease symptoms. These bacteria can be beneficial to the plant by promoting root growth and an increase in plant yield. Different rates of Biological Nitrogen Fixation (BNF) were observed in different genotypes. The aim of this work was to conduct a comprehensive molecular and physiological analysis of two model genotypes for contrasting BNF efficiency in order to unravel plant genes that are differentially regulated during a natural association with diazotrophic bacteria. A next-generation sequencing of RNA samples from the genotypes SP70-1143 (high-BNF) and Chunee (low-BNF) was performed. A differential transcriptome analysis showed that several pathways were differentially regulated among the two BNF-contrasting genotypes, including nitrogen metabolism, hormone regulation and bacteria recognition. Physiological analyses, such as nitrogenase and GS activity quantification, bacterial colonization, auxin response and root architecture evaluation, supported the transcriptome expression analyses. The differences observed between the genotypes may explain, at least in part, the differences in BNF contributions. Some of the identified genes might be involved in key regulatory processes for a beneficial association and could be further used as tools for obtaining more efficient BNF genotypes.

Genome sequencing and oenologically relevant traits of the Uruguayan native yeast &lt;i&gt;Issatchenkia terricola&lt;/i&gt;

Issatchenkia terricola 0621 is a non-Saccharomyces yeast strain isolated from Tannat grapes from Uruguayan vineyards; it stands out for its ability to produce high levels of β-glucosidase activity, which contributes to the aromatic complexity of wines. To delve into the potential oenological applications of this strain, its high-quality genome was obtained and explored, allowing the main central carbon and nitrogen metabolic pathways to be reconstructed. I. terricola is able to utilise glycerol as the sole carbon source in a way that has not previously been described for yeasts. The genes of the fermentome and those involved in stress resistance during winemaking were also identified, and differences were found when compared to S. cerevisiae, which may explain why I. terricola is unable to complete fermentation. The pathways responsible for natural aroma synthesis were also reconstructed, and the production of aromatic acids, alcohols, esters, acetates and lactones was verified experimentally. Finally, sequences encoding for β-glucosidases, in addition to the previously characterised one, were identified in the genome. The work presented here lays the groundwork for experimental research focused on the dissection of the metabolism of a native non-Saccharomyces strain and its application for oenological and biotechnological purposes.

Transcriptome analysis and phenotyping of walnut seedling roots under nitrogen stresses

Nitrogen is an essential core element in walnut seedling growth and development. However, nitrogen starvation and excessive nitrogen stress can cause stunted growth and development of walnut seedlings, and environmental pollution is also of concern. Therefore, it is necessary to study the mechanism of walnut seedling resistance to nitrogen stress. In this study, morphological and physiological observations and transcriptome sequencing of walnut seedlings under nitrogen starvation and excess nitrogen stress were performed. The results showed that walnut seedlings under nitrogen starvation and excess stress could adapt to the changes in the nitrogen environment by changing the coordination of their root morphology and physiological indexes. Based on an analysis of transcriptome data, 4911 differential genes (DEGs) were obtained (2180 were upregulated and 2731 were downregulated) in a comparison of nitrogen starvation and control groups. A total of 9497 DEGs (5091 upregulated and 4406 downregulated) were obtained in the comparison between the nitrogen overdose and control groups. When these DEGs were analysed, the differential genes in both groups were found to be significantly enriched in the plant’s circadian pathway. Therefore, we selected the circadian rhythm as the focus for further analysis. We made some discoveries by analysing the gene co-expression network of nitrogen metabolism, circadian rhythm, and hormone signal transduction. (a) Nitrite nitrogen (NO2−) or Glu may act as a nitrogen signal to the circadian clock. (b) Nitrogen signalling may be input into the circadian clock by regulating changes in the abundance of the CRY1 gene. (c) After the nitrogen signal enters the circadian clock, the expression of the LHY gene is upregulated, which causes a phase shift in the circadian clock. (d) The RVE protein may send information about the circadian clock’s response to nitrogen stress back to the nitrogen metabolic pathway via the hormone transduction pathway. In conclusion, various metabolic pathways in the roots of walnut seedlings coordinated with one another to resist the ill effects of nitrogen stress on the root cells, and these coordination relationships were regulated by the circadian clock. This study is expected to provide valuable information on the circadian clock regulation of plant resistance to nitrogen stress.

Melatonin Mediates Axillary Bud Outgrowth by Improving Nitrogen Assimilation and Transport in Rice.

Melatonin plays an important role in plant resistance to biotic and abiotic stresses. However, whether melatonin is involved in the regulation of plant architecture, such as the formation of axillary bud outgrowth or tillering, in rice remains unknown. Here, we found that different concentrations of melatonin influenced axillary bud outgrowth in rice, and moderate melatonin concentrations also alleviated the inhibition of axillary bud outgrowth in the presence of high concentrations of basic amino acids lysine and arginine. Furthermore, transcriptome analysis demonstrated that genes involved in nitrogen metabolism and phytohormone signal transduction pathways may affect axillary bud outgrowth, which is regulated by melatonin. We determined that the differentially expressed genes glutamine synthetase OsGS2 and amino acid transporter OsAAP14, which are involved in nitrogen metabolism and are regulated by melatonin and basic amino acids, were the key regulators of axillary bud outgrowth in rice. In addition, we validated the functions of OsGS2 and OsAAP14 using rice transgenic plants with altered axillary bud outgrowth and tillers. Taken together, these results suggest that melatonin mediates axillary bud outgrowth by improving nitrogen assimilation and transport in rice.

Effect of UV irradiation on microbial structure, metabolic pathways and functional genes of nitrogen metabolism in highland wastewater

&lt;p&gt;In this experiment, in the background of the plateau environment, the effects of ultraviolet irradiation on the microbial community structure, metabolic pathways and nitrogen metabolism function genes of sewage were studied at 0 (control group), 5, 10, 30, and 180 min. The results showed that the increase of UV irradiation time promoted the microbial richness of sewage, but decreased the microbial diversity. In terms of community structure, the increase of ultraviolet irradiation time will inhibit or promote some bacterial genera, for example, it has a promoting effect on Bacteroidota, norank_f_ Saprospiraceae, etc., and an inhibitory effect on Phreatobacter. The relative abundance of metabolic pathways changed significantly with the increase of UV irradiation time, and the change trends at different metabolic levels were the same. In nitrogen metabolism pathways, the relative abundance of genes involved in nitrification and denitrification functions was inhibited by the duration of UV irradiation.&lt;/p&gt;&#x0D;

Socializing Models During Lactation Alter Colonic Mucosal Gene Expression and Fecal Microbiota of Growing Piglets.

The enrichment of the social environment during lactation alleviates the stress of weaned piglets. It is significant to understand how the enriched social environment improves the weaning stress of piglets. RNA sequencing (RNA-seq) of colonic mucosa, 16S rRNA sequencing of feces, and short-chain fatty acids (SCFAs) of colonic content were used to determine the effects of social contact during lactation. In this study, thirty litter lactating piglets were divided into intermittent social contact (ISC) group that contacted with neighbors intermittently, continuous social contact (CSC) group that contacted with neighbors starting at day (D) 14 after birth, and control (CON) group in which piglets were kept in their original litter. The piglets were weaned at D35 and regrouped at D36. The colonic mucosal RNA-seq, fecal microbes, and SCFAs of colonic contents of 63-day-old piglets were analyzed. The results of RNA-seq showed that compared with the CON group, the pathways of digestion and absorption of minerals, protein, and vitamins of piglets were changed in the ISC group, whereas the pathways of retinol metabolism and nitrogen metabolism in the colonic mucosal were affected and stimulated the immune response in the CSC group. Compared with the CON group, the abundances of pernicious microorganisms (Desulfovibrio, Pseudomonas, Brevundimonas, etc.) in the CSC group and pernicious microorganisms (Desulfovibrio, Neisseria, Sutterella, etc.) and beneficial bacteria (Bifidobacterium, Megamonas, and Prevotella_9) in the ISC group were significantly higher (p < 0.05). The abundances of proinflammatory bacteria (Coriobacteriaceae_unclassified, Coprococcus_3, and Ruminococcus_2) in the CSC group were significantly increased (p < 0.05), but the abundances of SCFAs producing bacteria (Lachnospiraceae_UCG-010, Parabacteroides, Anaerotruncus, etc.) and those of anti-inflammatory bacteria (Eubacterium, Parabacteroides, Ruminiclostridium_9, and Alloprevotella) were significantly reduced (p < 0.05) in the CSC group. Compared with the CON group, the concentrations of microbial metabolites, acetate, and propionate in the colonic contents were reduced (p < 0.05) in the ISC group, whereas the concentration of acetate was reduced (p < 0.05) in the CSC group. Therefore, both ISC and CSC during lactation affected the composition of fecal microbes and changed the expression of intestinal mucosal genes related to nutrient metabolism and absorption of piglets.

Synchronised interaction of carbon and nitrogen provides drought tolerance in Cyamopsis tetragonoloba

Drought is a major adverse environmental factor that limits plant productivity. Concomitant assimilation of carbon (C) and nitrogen (N) in illuminated leaves requires the regulated partitioning of reductant and photosynthate to sustain the demands of amino acid and carbohydrate biosynthesis. The short-term exposure to drought and its responses of photosynthesis and photosynthate partitioning to N enrichment was studied in Cyamopsis tetragonoloba (L.) Taub (guar). Four contrasting varieties of guar, HG-563, RGC-986 (drought-tolerant) and RGC-471, Varsha (drought-sensitive) were subjected to 15 days water stress and leaf tissues were studied in order to contemplate the counter strategy engaged under drought conditions. In guar plants, sensors trigger a signalling cascade that activates numerous proteins to induce the expression of certain genes involved in carbon and nitrogen metabolism.The levels of glucose, starch, and Glutamate dehydrogenase (GDH), Aspartate aminotransferase (AspAT), isocitrate dehydrogenase (ICDH), Nitrate Reductase (NR), and Nitrite reductase (NiR) activities were determined biochemically during 15 days drought treatment, at three stages. Further, the carbon (oxidative phosphorylation and TCA cycle) - nitrogen metabolic pathway interaction was studied at the molecular level. The respiratory pathway genes were upregulated, while the nitrogen metabolic pathway genes were downregulated under all stages of drought in guar plants. The physiological, biochemical and molecular data suggests that the high rates of dark respiration was insufficient to provide extra carbon required to assist amino acid synthesis but rather sufficed by a rapid metamorphosis in the photosynthetic carbon partitioning to amino acid metabolism via the nitrogen metabolism. • Drought causes NADH DEHYDROGENASE gene to escalate dark respiration. • Nitrogen assimilation reduces under drought in leguminous Cyamopsis tetragonoloba. • Drought triggers protein kinase cascade signalling in guar plants. • Drought regulates nitrogen metabolic genes in guar. • Drought triggers increase in sugar content at the cost of amino acids.

Metagenomic analyses reveal nitrogen metabolism responses to copper and chromium contamination in sludge-based microbial communities

In this study, we used metagenomic sequencing to explore the effects of chromium (Cr) and copper (Cu) on microbial communities and function by analyzing pathway of nitrogen metabolism based on KEGG annotation. High concentrations of Cr (VI) and Cu (II) reduced the removal efficiency of total nitrogen and ammonium in the system. Metagenomic analyses showed that the taxonomic composition of nitrogen metabolism-associated microorganisms (NMAM) was mainly composed of Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Sphingobacteria, Deltaproteobacteria, Flavobacteria and Nitrospira. Different concentrations of Cr (VI) and Cu (II) led to great changes in NMAM in activated sludge and enriched dominant microbes, respectively, suggesting specific response strategies in microbial communities. NMDS (Non-metric multidimensional scaling) analyses revealed the impact of different Cr (VI) and Cu (II) concentrations on NMAM β diversity, and indicated that Cr (VI) treatment induced greater variations in NMAM communities than Cu (II). We also identified a significant association (p < 0.05) between enzymes of nitrogen metabolism pathway and corresponding NMAM. This study revealed that under Cu (II) and Cr (VI) stress, the sludge nitrification pathway was inhibited, especially for ammonia monooxygenase and hydroxylamine dehydrogenase. These combined effects led to a decrease in sludge efficiency for nitrogen removal. These findings underscore the influence of heavy metals in water treatment.

Co-impacts of the microplastic polyamide and sertraline on the denitrification function and microbial community structure in SBRs

The co-impacts of microplastics (MPs) and organic pollutants on activated sludge have attracted extensive attention. In this study, microplastic polyamide (PA) and sertraline (SER) were respectively or simultaneously added to sequencing batch reactors (SBRs), and the impacts of these pollutants on activated sludge were investigated. The results showed that NH4+-N and TN removal efficiencies significantly decreased with the simultaneous adding of the two pollutants. The coexistence of PA and SER could observably decrease the settling ability of activated sludge, and more proteins and polysaccharides were generated to reduce the combined toxicity. The microbial diversity, especially the denitrification microorganism, was restrained and the metabolic function and the key enzyme involved in nitrogen metabolism pathways were observably decreased, due to the combined toxicity of this two pollutants. Furthermore, the effective SER interception by PA in SBR could induce the SER enrichment in activated sludge and enhance the biotoxicity toward sludge microorganisms.

The relationship analysis and reaction mechanism of carbon, nitrogen, and phosphorus metabolism in sewage treatment in plateau habitat.

The efficiency of pollutant removal in sewage is mainly determined by the structure and abundance of microbial flora, which is essentially represented by the type and abundance of genes and enzymes, and the reaction mechanism is the abundance and degree of reaction of metabolic pathways and metabolic modules. In order to study the mechanism of carbon, nitrogen, and phosphorus metabolism of activated sludge microflora in the A2O process at high altitudes at different temperatures, so as to improve the removal rate of pollutants and reduce the discharge concentration of pollutants. Based on the research environment of high-altitude environmental research, the author used the A2O system as the treatment process and put Illumina MiSeq high-through sequencing technology to comprehensively dissect the reaction relationship of carbon, nitrogen and phosphorus metabolic pathways, and derived the main functional genes and enzymes of carbon, nitrogen, and phosphorus metabolism. It was demonstrated that the abundance of the most metabolic modules and functional genes tended to increase and then decrease with increasing temperature. In particular, the highest abundance and activity and the best pollutant removal efficiency were observed at 20°C. This study will provide a valuable reference for the study of carbon metabolism, nitrogen metabolism, and phosphorus metabolism of microbial flora in sewage treatment under plateau habitats.

Mechanisms of Pine Disease Susceptibility Under Experimental Climate Change

Climate change (CC) conditions projected for many temperate areas of the world, expressed by way of excessive temperatures and low water availability, will impact forest health directly by means of abiotic stress but also by predisposing trees to pathogenic attack. However, we do not yet know how such environmental conditions alter the physiology and metabolism of trees to render them more susceptible to pathogens. To explore these mechanisms, we conditioned 3-year-old Austrian pine saplings to a simulated CC environment (combined drought and elevated temperatures), followed by pathogenic inoculation with two sister fungal species characterized by contrasting aggressiveness, Diplodia sapinea (aggressive) and D. scrobiculata (less aggressive). Lesion lengths resulting from infection were measured after 3 weeks to determine phenotypes, while dual transcriptomics analysis was conducted on tissues collected from the margins of developing lesions on separate branches 72 h post inoculation. As expected, climate change conditions enhanced host susceptibility to the less aggressive pathogen, D. scrobiculata, to a level that was not statistically different from the more aggressive D. sapinea. Under controlled climate conditions, D. sapinea induced suppression of critical pathways associated with host nitrogen and carbon metabolism, while enhancing its own carbon assimilation. This was accompanied by suppression of host defense-associated pathways. In contrast, D. scrobiculata infection induced host nitrogen and fatty acid metabolism as well as host defense response. The CC treatment, on the other hand, was associated with suppression of critical host carbon and nitrogen metabolic pathways, alongside defense associated pathways, in response to either pathogen. We propose a new working model integrating concurrent host and pathogen responses, connecting the weakened host phenotype under CC treatment with specific metabolic compartments. Our results contribute to a richer understanding of the mechanisms underlying the oft-observed increased susceptibility to fungal infection in trees under conditions of low water availability and open new areas of investigation to further integrate our knowledge in this critical aspect of tree physiology and ecology.

Metagenomics Unveils Microbial Diversity and Their Biogeochemical Roles in Water and Sediment of Thermokarst Lakes in the Yellow River Source Area.

Thermokarst lakes have long been recognized as biogeochemical hotspots, especially as sources of greenhouse gases. On the Qinghai-Tibet Plateau, thermokarst lakes are experiencing extensive changes due to faster warming. For a deep understanding of internal lake biogeochemical processes, we applied metagenomic analyses to investigate the microbial diversity and their biogeochemical roles in sediment and water of thermokarst lakes in the Yellow River Source Area (YRSA). Sediment microbial communities (SMCs) had lower species and gene richness than water microbial communities (WMCs). Bacteria were the most abundant component in both SMCs and WMCs with significantly different abundant genera. The functional analyses showed that both SMCs and WMCs had low potential in methanogenesis but strong in aerobic respiration, nitrogen assimilation, exopolyphosphatase, glycerophosphodiester phosphodiesterases, and polyphosphate kinase. Moreover, SMCs were enriched in genes involved in anaerobic carbon fixation, aerobic carbon fixation, fermentation, most nitrogen metabolism pathways, dissimilatory sulfate reduction, sulfide oxidation, polysulfide reduction, 2-phosphonopropionate transporter, and phosphate regulation. WMCs were enriched in genes involved in assimilatory sulfate reduction, sulfur mineralization, phosphonoacetate hydrolase, and phosphonate transport. Functional potentials suggest the differences of greenhouse gas emission, nutrient cycling, and living strategies between SMCs and WMCs. This study provides insight into the main biogeochemical processes and their properties in thermokarst lakes in YRSA, improving our understanding of the roles and fates of these lakes in a warming world.

Nitrate Removal from Groundwater by Heterotrophic and Electro-Autotrophic Denitrification

A heterotrophic and autotrophic denitrification (HAD) system shows satisfactory performance for groundwater with nitrate contamination. In this study, an HAD system combining solid-phase heterotrophic denitrification and electrochemical hydrogen autotrophic denitrification (SHD-EHD) was developed for the treatment of nitrate-contaminated groundwater, in which polycaprolactone (PCL) was used as the carbon source to enhance the nitrate removal performance and prevent secondary pollution of the electrochemical hydrogen autotrophic denitrification (EHD) system. The denitrification performance, microbial community structure and nitrogen metabolism were investigated. The results showed that a high nitrate removal rate of 99.04% was achieved with an influent nitrate concentration of 40 mg/L, a current of 40 mA and a hydraulic retention time (HRT) of 4 h. By comparing the performance with the EHD system, it was found that the HAD system with PCL promoted the complete denitrification and reduced the accumulation of NO2−-N. Analysis of the microbial community structure identified the key denitrifying bacteria: Dechloromonas, Thauera and Hydrogenophaga. A comparison of microbial communities from SHD-EHD and solid-phase heterotrophic denitrification (SHD) demonstrated that electrical stimulation promoted the abundance of the dominant denitrifying bacteria and the electroactive bacteria. Analysis of the nitrogen metabolic pathway revealed that the conversion of NO to N2O was the rate-limiting step in the overall denitrification pathway. The SHD-EHD developed in this study showed great potential for groundwater nitrate removal.

Complete genome sequence of Pseudomonas stutzeri S116 owning bifunctional catalysis provides insights into affecting performance of microbial fuel cells

BackgroundPseudomonas stutzeri S116 is a sulfur-oxidizing bacteria isolated from marine sludge. It exhibited excellent electricity generation as bioanode and biocathode applied in microbial fuel cells (MFCs). Complete genome sequencing of P. stutzeri and cyclic voltammetry method were performed to reveal its mechanism in microbial fuel cells system.ResultsThis study indicated that the MFCs generated a maximum output voltage of 254.2 mV and 226.0 mV, and maximum power density of 765 mW/m2 and 656.6 mW/m2 respectively. Complete genome sequencing of P. stutzeri S116 was performed to indicate that most function genes showed high similarities with P. stutzeri, and its primary annotations were associated with energy production and conversion (6.84%), amino acid transport and metabolism (6.82%) and inorganic ion transport and metabolism (6.77%). Homology of 36 genes involved in oxidative phosphorylation was detected, which suggests the strain S116 possesses an integrated electron transport chain. Additionally, many genes encoding pilus-assembly proteins and redox mediators (riboflavin and phenazine) were detected in the databases. Thiosulfate oxidization and dissimilatory nitrate reduction were annotated in the sulfur metabolism pathway and nitrogen metabolism pathway, respectively. Gene function analysis and cyclic voltammetry indicated that P. stutzeri probably possesses cellular machinery such as cytochrome c and redox mediators and can perform extracellular electron transfer and produce electricity in MFCs.ConclusionThe redox mediators secreted by P. stutzeri S116 were probably responsible for performance of MFCs. The critical genes and metabolic pathways involved in thiosulfate oxide and nitrate reduction were detected, which indicated that the strain can treat wastewater containing sulfide and nitrite efficiently.

Nitrite Generating and Depleting Capacity of the Oral Microbiome and Cardiometabolic Risk: Results from ORIGINS.

BackgroundThe enterosalivary nitrate–nitrite–nitric oxide (NO3–NO2–NO) pathway generates NO following oral microbiota‐mediated production of salivary nitrite, potentially linking the oral microbiota to reduced cardiometabolic risk. Nitrite depletion by oral bacteria may also be important for determining the net nitrite available systemically. We examine if higher abundance of oral microbial genes favoring increased oral nitrite generation and decreased nitrite depletion is associated with a better cardiometabolic profile cross‐sectionally.Methods and ResultsThis study includes 764 adults (mean [SD] age 32 [9] years, 71% women) enrolled in ORIGINS (Oral Infections, Glucose Intolerance, and Insulin Resistance Study). Microbial DNA from subgingival dental plaques underwent 16S rRNA gene sequencing; PICRUSt2 was used to estimate functional gene profiles. To represent the different components and pathways of nitrogen metabolism in bacteria, predicted gene abundances were operationalized to create summary scores by (1) bacterial nitrogen metabolic pathway or (2) biochemical product (NO2, NO, or ammonia [NH3]) formed by the action of the bacterial reductases encoded. Finally, nitrite generation‐to‐depletion ratios of gene abundances were created from the above summary scores. A composite cardiometabolic Z score was created from cardiometabolic risk variables, with higher scores associated with worse cardiometabolic health. We performed multivariable linear regression analysis with cardiometabolic Z score as the outcome and the gene abundance summary scores and ratios as predictor variables, adjusting for sex, age, race, and ethnicity in the simple adjusted model. A 1 SD higher NO versus NH3 summary ratio was inversely associated with a −0.10 (false discovery rate q=0.003) lower composite cardiometabolic Z score in simple adjusted models. Higher NH3 summary score (suggestive of nitrite depletion) was associated with higher cardiometabolic risk, with a 0.06 (false discovery rate q=0.04) higher composite cardiometabolic Z score.ConclusionsIncreased net capacity for nitrite generation versus depletion by oral bacteria, assessed through a metagenome estimation approach, is associated with lower levels of cardiometabolic risk.

An Integrated Regulatory Network of mRNAs, microRNAs, and lncRNAs Involved in Nitrogen Metabolism of Moso Bamboo.

Nitrogen is a key macronutrient essential for plant growth and development, and its availability has a strong influence on biological processes. Nitrogen fertilizer has been widely applied in bamboo forests in recent decades; however, the mechanism of nitrogen metabolism in bamboo is not fully elucidated. Here, we characterized the morphological, physiological, and transcriptome changes of moso bamboo in response to different schemes for nitrogen addition to illuminate the regulation mechanism of nitrogen metabolism. The appropriate addition of nitrogen improved the chlorophyll content and Pn (net photosynthetic rate) of leaves, the nitrogen and ammonium contents of the seedling roots, the biomass of the whole seedling, the number of lateral roots, and the activity of enzymes involved in nitrogen metabolism in the roots. Based on the whole transcriptome data of the roots, a total of 8,632 differentially expressed mRNAs (DEGs) were identified under different nitrogen additions, such as 52 nitrate transporter genes, 6 nitrate reductase genes, 2 nitrite reductase genes, 2 glutamine synthase genes, 2 glutamate synthase genes (GOGAT), 3 glutamate dehydrogenase genes, and 431 TFs belonging to 23 families. Meanwhile, 123 differentially expressed miRNAs (DEMs) and 396 differentially expressed lncRNAs (DELs) were characterized as nitrogen responsive, respectively. Furthermore, 94 DEM-DEG pairs and 23 DEL-DEG pairs involved in nitrogen metabolism were identified. Finally, a predicted regulatory network of nitrogen metabolism was initially constructed, which included 17 nitrogen metabolic pathway genes, 15 TFs, 4 miRNAs, and 10 lncRNAs by conjoint analysis of DEGs, DEMs, and DELs and their regulatory relationships, which was supported by RNA-seq data and qPCR results. The lncRNA-miRNA-mRNA network provides new insights into the regulation mechanism of nitrogen metabolism in bamboo, which facilitates further genetic improvement for bamboo to adapt to the fluctuating nitrogen environment.

Microbiomes and Planctomycete diversity in large-scale aquaria habitats.

In commercial large-scale aquaria, controlling levels of nitrogenous compounds is essential for macrofauna health. Naturally occurring bacteria are capable of transforming toxic nitrogen species into their more benign counterparts and play important roles in maintaining aquaria health. Nitrification, the microbially-mediated transformation of ammonium and nitrite to nitrate, is a common and encouraged process for management of both commercial and home aquaria. A potentially competing microbial process that transforms ammonium and nitrite to dinitrogen gas (anaerobic ammonium oxidation [anammox]) is mediated by some bacteria within the phylum Planctomycetes. Anammox has been harnessed for nitrogen removal during wastewater treatment, as the nitrogenous end product is released into the atmosphere rather than in aqueous discharge. Whether anammox bacteria could be similarly utilized in commercial aquaria is an open question. As a first step in assessing the viability of this practice, we (i) characterized microbial communities from water and sand filtration systems for four habitats at the Tennessee Aquarium and (ii) examined the abundance and anammox potential of Planctomycetes using culture-independent approaches. 16S rRNA gene amplicon sequencing revealed distinct, yet stable, microbial communities and the presence of Planctomycetes (~1–15% of library reads) in all sampled habitats. Preliminary metagenomic analyses identified the genetic potential for multiple complete nitrogen metabolism pathways. However, no known genes diagnostic for the anammox reaction were found in this survey. To better understand the diversity of this group of bacteria in these systems, a targeted Planctomycete-specific 16S rRNA gene-based PCR approach was used. This effort recovered amplicons that share <95% 16S rRNA gene sequence identity to previously characterized Planctomycetes, suggesting novel strains within this phylum reside within aquaria.