Nitrogen Metabolic Pathways Research Articles

Transcriptome and Metabolome Reveal the Molecular Mechanism of Barley Genotypes Underlying the Response to Low Nitrogen and Resupply.

Nitrogen is one of the most important mineral elements for plant growth and development. Excessive nitrogen application not only pollutes the environment, but also reduces the quality of crops. However, are few studies on the mechanism of barley tolerance to low nitrogen at both the transcriptome and metabolomics levels. In this study, the nitrogen-efficient genotype (W26) and the nitrogen-sensitive genotype (W20) of barley were treated with low nitrogen (LN) for 3 days and 18 days, then treated with resupplied nitrogen (RN) from 18 to 21 days. Later, the biomass and the nitrogen content were measured, and RNA-seq and metabolites were analyzed. The nitrogen use efficiency (NUE) of W26 and W20 treated with LN for 21 days was estimated by nitrogen content and dry weight, and the values were 87.54% and 61.74%, respectively. It turned out to have a significant difference in the two genotypes under the LN condition. According to the transcriptome analysis, 7926 differentially expressed genes (DEGs) and 7537 DEGs were identified in the leaves of W26 and W20, respectively, and 6579 DEGs and 7128 DEGs were found in the roots of W26 and W20, respectively. After analysis of the metabolites, 458 differentially expressed metabolites (DAMs) and 425 DAMs were found in the leaves of W26 and W20, respectively, and 486 DAMs and 368 DAMs were found in the roots of W26 and W20, respectively. According to the KEGG joint analysis of DEGs and DAMs, it was discovered that glutathione (GSH) metabolism was the pathway of significant enrichment in the leaves of both W26 and W20. In this study, the metabolic pathways of nitrogen metabolism and GSH metabolism of barley under nitrogen were constructed based on the related DAMs and DEGs. In leaves, GSH, amino acids, and amides were the main identified DAMs, while in roots, GSH, amino acids, and phenylpropanes were mainly found DAMs. Finally, some nitrogen-efficient candidate genes and metabolites were selected based on the results of this study. The responses of W26 and W20 to low nitrogen stress were significantly different at the transcriptional and metabolic levels. The candidate genes that have been screened will be verified in future. These data not only provide new insights into how barley responds to LN, but also provide new directions for studying the molecular mechanisms of barley under abiotic stress.

Impact of tropospheric ozone on root proteomes of two soybean genotypes with contrasting sensitivity to ozone

Tropospheric ozone (O3), a critically harmful greenhouse gas, has steadily increased over the last several decades, leading to significant soybean (Glycine max) yield loses worldwide. However, substantial efforts have focused on the effect of elevated O3 concentration (eOZ) on shoots rather than the roots that support plant fitness and directly interact with soil ecosystems. To better assess the impact of eOZ on roots, this study investigated morphological and proteomic profiles of two soybean genotypes from the same genetic background, but with contrasting O3 resilience, Fiskeby III (O3-tolerant) and Fiskeby 840–7–3 (O3-sensitive). Plants were treated either with sub-ambient O3 or eOZ in a field-based air exclusion system (AES) and harvested at flowering and pod-filling stages. Our results established that the effect of eOZ on decreasing root biomass initiated at the flowering stage, while above-ground biomass was not altered. However, O3-caused biomass reduction was observed in both, roots and shoots, at the pod-filling stage. Season-long eOZ ultimately caused a 29 % seed yield reduction in Fiskeby III, and 50 % in Fiskeby 840–7–3. Root proteome analysis showed that the effect of O3 in roots is complex, and distinct between flowering and pod-filling stages. Changes in the abundance of proteins correspond to glycolysis, TCA cycle, nitrogen metabolism, secondary metabolites, antioxidant, and stress response pathway, and differed between genotypes. Some of these changes may be in response to eOZ as an attempt to mitigate the effects of a challenging environment, and others are likely due to genetic differences that confer an adaptative advantage to the O3 resilient genotype. These findings provide further knowledge of proteins and pathways that may confer O3-tolerance, which can be applied to develop O3-resistant, high-yielding soybean.

Transcriptomics analysis and fed-batch regulation of high astaxanthin producing Phaffia rhodozyma/Xanthophyllomyces dendrorhous obtained through adaptive laboratory evolution.

Astaxanthin has high utilization value in functional food because of its strong antioxidant capacity. However, the astaxanthin content of Phaffia rhodozyma is relatively low. Adaptive laboratory evolution is an excellent method to obtain high-yield strains. TiO2 is a good inducer of oxidative stress. In this study, different concentrations of TiO2 were used to domesticate P. rhodozyma. Results showed that the optimal astaxanthin-producing P. rhodozyma JMU-ALE105 was obtained under domestication with 1000mg/L TiO2 concentration on the 105th day. After fermentation, the astaxanthin content reached 6.50mg/g, which was 41.61% higher than that of the original strain. The ALE105 strain was fermented by batch and fed-batch, and the astaxanthin content reached 6.81mg/g. Transcriptomics analysis showed that astaxanthin synthesis pathway, fatty acid, pyruvate and nitrogen metabolism pathway of ALE105 strain were significantly up-regulated. Based on the nitrogen metabolism pathway, the nitrogen source was adjusted by ammonium sulphate fed-batch fermentation, which increased the astaxanthin content reached 8.36mg/g. This study provides technical basis and theoretical research for promoting industrialization of astaxanthin production of P. rhodozyma.

A novel aerobic denitrifying phosphate-accumulating bacterium efficiently removes phthalic acid ester, total nitrogen and phosphate from municipal wastewater

Simultaneous removal of nitrogen, phosphate and emerging pollutants are critical for safe reuse of wastewater, but research in this field is limited. In the present study, a novel aerobic denitrifying phosphate-accumulating bacterial strain RL-GZ01 was found to be able to utilize phthalic acid esters (PAEs) as carbon resource for cell growth. Based on 16S rRNA gene analysis, physiological and biochemical characterization, and genome-based average nucleotide identity calculation, RL-GZ01 was identified as Rhodococcus pyridinivorans. Strain RL-GZ01 showed high DEHP degradation in alkaline conditions and good tolerance of salinity and organic solvents. The degradation of DEHP by RL-GZ01 fitted well with a modified Gompertz model (R2 = 0.9985). Metabolic intermediates of DEHP were identified via UHPLC-MS/MS analysis and the catabolic pathway was proposed thereafter. Genes and gene clusters contributed to the utilization of DEHP were analyzed through genomic analysis. Analysis of KEGG nitrogen metabolism pathway indicated that nitrate and nitrite were further transformed into ammonium which was further used for the biosynthesis of l-glutamine and L-glutamate. Strain RL-GZ01 was further identified as a denitrifying phosphate accumulating organism which can accumulate phosphate by generating polyphosphate. Finally, strain RL-GZ01 was applied to municipal wastewater treatment for simultaneous removal of nitrogen, phosphate and DEHP. The removal percentages of DEHP (5 mg/L), TN (71.2 mg/L), NH4+-N (70.9 mg/L), PO43−-P (10.89 mg/L) and COD (622.4 mg/L) by strain RL-GZ01 were 89.94 %, 64.45 %, 64.94 %, 76.30 % and 63.23 % within 84 h, respectively. These demonstrated the capability of strain RL-GZ01 for the biological treatment of wastewater containing PAEs.

Platymonas helgolandica-driven nitrogen removal from mariculture wastewater under different photoperiods: Performance evaluation, enzyme activity and transcriptional response

The nitrogen removal performance and biological mechanism of Platymonas helgolandica var. Tsingtaoensis (P. helgolandica) were investigated in treating mariculture wastewater under different light: dark (L:D) photoperiods. The growth of P. helgolandica was positively correlated with the photoperiods from 6L:18D to 15L:9D, and the highest photosynthetic activity appeared under 6L:18D photoperiod on day 3. P. helgolandica exhibited the highest removal efficiencies of total nitrogen and COD at 89 % and 93 % under 15L:9D photoperiod, respectively. NH4+-N assimilation was proportional to the photoperiods from 6L:18D to 15L:9D and longer illumination promoted NO2−-N removal. However, the highest NO3−-N reduction rate was achieved under 12L:12D photoperiod. The different nitrogen-transformed enzymatic activities were affected by photoperiod. Transcriptome revealed that unigenes were enriched in nitrogen metabolism and photosynthesis pathways, of which the functional gene expression was up-regulated significantly. This study provides insights into the optimization of photoperiod for mariculture wastewater treatment by P. helgolandica.

Impacts of dibutyl phthalate on bacterial community composition and carbon and nitrogen metabolic pathways in a municipal wastewater treatment system

Dibutyl phthalate (DBP) is a typical toxic and hazardous pollutant in pharmaceutical wastewater, affecting the metabolism of microbial flora, leading to decreased treatment efficiency, and deteriorated effluent quality in municipal wastewater treatment plants (WWTPs). This study conducted a long-term experiment with 6 operational stages in a pilot-scale A2O-MBR system, analyzing the effect of DBP on the bacterial community and their carbon and nitrogen metabolic pathways. 16S rRNA gene amplicon sequencing analysis and principal components analysis (PCA) showed that DBP at 8 mg/L significantly influenced the structure of bacterial community (P < 0.05), resulting in reduced bacterial community diversity. Metagenomic analysis was used to explore the embedded carbon and nitrogen metabolic pathways. At the presence of DBP, the metabolism of saccharides, lipids, and aromatic compounds were blocked owing to the vanishment of key enzyme (such as acetylaminohexosyltransferase (EC 2.4.1.92) and UDP-sugar pyro phosphorylase (EC 2.7.7.64)) encoding genes, resulting in weakened carbon metabolism, and thus reduced COD removal performance. The resultant deficiency of the genes such as those encoding hydroxyproline dehydrogenase (EC 1.5.5.3) gave rise to interrupted metabolic pathways of amino acid (arginine, proline, tyrosine, and tryptophan), resulting in declined function of nitrogen metabolism and thus reduced TN removal efficiency. The uncovery of the mechanisms by which DBP affects wastewater treatment system efficiency and microbial metabolism is of theoretical importance for the efficient operation of municipal and pharmaceutical wastewater treatment systems.

Limited dissolved oxygen facilitated nitrogen removal at biocathode during the hydrogenotrophic denitrification process using bioelectrochemical system

Effects of limited dissolved oxygen (DO) on hydrogenotrophic denitrification at biocathode was investigated using bioelectrochemical system. It was found that total nitrogen removal increased by 5.9%, as DO reached about 0.24 mg/L with the cathodic chamber unplugged (group R_Exposure). With the presence of limited DO, not only the nitrogen metabolic pathway was influenced, but the composition of microbial communities of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were enriched accordingly. After metagenomic analysis, enriched genes in R_Exposure were found to be associated with nearly each of nitrogen removal steps as denitrification, nitrification, DNRA, nitrate assimilation and even nitrogen fixation. Moreover, genes encoding both Complexes III and IV constituted the electron transfer chain were significantly enriched, indicating that more electrons would be orientated to the reduction of NO2–-N, NO-N and oxygen. Therefore, enhanced nitrogen removal could be attained through the co-respiration of nitrate and oxygen by means of NH4+-N oxidation.

Transcriptome analysis and identification of genes associated with leaf crude protein content in foxtail millet [Setaria italica (L.) P. Beauv.

Introduction: Spruce spider mite is a primary insect pest of Chinese chestnut in China and seriously influences its yield and quality. However, the current management against this mite is costly and poorly effective. In previous research, we bred several foxtail millet materials for interplanting with chestnut tree, and found that they had high levels of crude protein (CP) in leaves and attracted spruce spider mite to feed on the leaves, thereby reducing chestnut damage. Methods: In this study, four foxtail millet varieties with significant differences in leaf crude protein content were used for high-throughput sequencing and identification of genes associated with leaf crude protein content. Gene enrichment analyses were carried out to comprehend the functions of these genes and the biological processes in which they are involved. In addition, transcription factors (TFs) were evaluated. Results: 435 differentially expressed genes (DEGs) were identified, suggesting their potential role in crude protein accumulation. Some differentially expressed genes were found to be associated with nitrogen metabolism and ubiquitin-mediated proteolysis pathways. Moreover, we identified 40 TF genes categorized into 11 transcription factor families. Discussion: Our findings represent an important resource that clarifies the mechanisms of accumulation and control of leaf crude protein in foxtail millet, and provide an opportunity for suppression of spruce spider mite attack on Chinese chestnut by interplanting with foxtail millet varieties with high concentrations of leaf crude protein.

Treatment of nitrogen-rich wastewater by mixed aeration combined with bioaugmentation in a sequencing batch biofilm reactor: Biofilm formation and nitrogen-removal capacity analysis

The mixed aerated and bioaugmented sequencing batch biofilm reactor (SBBR) was developed to improve the efficiency of nitrogen-rich wastewater treatment, and the mechanism of biofilm formation and nitrogen removal was analyzed. The results showed that the addition of aerobic denitrifiers could shorten the start-up time and significantly improve the biofilm formation ability of SBBRs. The presence of nanobubbles could make the biofilm more compact and secrete more EPS, which promoted the activity and stability of the biofilm. During the stable operation stage, the bioaugmented SBBR under mixed aeration mode showed the best nitrogen removal performance and the removal rates of NH4+-N (95.65) and TN (94.88%） were increased by 19.86% and 14.36% compared with the control group, respectively. Microbial community structure and nitrogen metabolism pathway analysis revealed that strain ZS1 colonized the reactor. Hyphomonas, Defluviicoccus and Hydrogenophaga played important roles in N removal in the mixed aerated and bioaugmented SBBR. Meanwhile, the suitable oxidative environment created by mixed aeration made autotrophic nitrifiers（mainly Nitrospira and Nitrosomonas）and aerobic denitrifiers (mainly Hydrogenophaga, Hyphomonas and Pseudofulvimonas) coexist successfully, increasing the relative abundance of the key functional genes (amoABC, hao, napAB genes) in nitrification and denitrification processes to improve the N removal performance. Furthermore, mixed aeration combined with bioaugmented stimulated the nirA, gltBD and GLUD genes, thus promoting the process of nitrogen assimilation and providing a pathway of the direct removal of NH4+-N.

Foliar Selenium Nanoparticles Application Promotes the Growth of Maize (Zea mays L.) Seedlings by Regulating Carbon, Nitrogen and Oxidative Stress Metabolism

Current understanding of selenium (Se) nanoparticles (SeNPs) effects on growth of C4 cereals is deeply scarce, and thus a hydroponic experiment was conducted to explore the physiological, biochemical, and metabolites variations in maize following foliar application of SeO32- and SeNPs each at 2 and 20 mg/L. The results demonstrated that fresh weight of Se foliar-applied leaves (Se-leaves) significantly increased by 27% after foliar application of SeNPs at 20 mg/L, which was mainly attributed to the improved photosynthetic efficiency (50%–78%) and stomatal conductance (46%–60%) of Se-leaves. Foliar-applied SeNPs and SeO32- both increased the Se concentration of each part of maize, while SeNPs was more efficient in improving the Se concentration, and Se was mainly accumulated in the cell wall. Significant increase was observed in GSH (14%–64%), POD (6%–24%), SOD (2%–11%), CAT (55%–73%), APX (50%–90%) at SeNPs application in comparison with control. Metabolomic results indicated that foliar application of 20 mg/L SeNPs significantly up-regulated 42 metabolites, which were mainly carbohydrates, amino acids, ketone and phenol, vitamin, and ten metabolic pathways (2 metabolic pathways related with carbon metabolism, 5 related with nitrogen metabolism, and 1 related with oxidative stress metabolism) was improved. Therefore, SeNPs mainly enhanced the antioxidant capacity by improving metabolic pathways of glutathione metabolism, carbon metabolism, and nitrogen metabolism and finally improved various physiological indexes of maize to boost the growth of maize.

Survival mechanisms of microorganisms occurring in acid mine drainage: sulfur, iron, carbon, and nitrogen metabolic pathways

Survival mechanisms of microorganisms occurring in acid mine drainage: sulfur, iron, carbon, and nitrogen metabolic pathways

Metabolite profiling of leaves of three &lt;i&gt;Epilobium&lt;/i&gt; species

BACKGROUND: The ability of plants to adapt to oxygen deficiency is associated with the presence of various adaptations, many of which are mediated by significant changes of metabolism. These changes allow resistant wetland plants to grow even in oxygen-deficient environment.&#x0D; AIM: The aim of the study was to carry out metabolic profiling of the leaves of the wetland species Epilobium palustre and Epilobium hirsutum, and the mesophyte species Epilobium angustifolium in order to identify the most characteristic metabolome traits of hypoxia-resistant plants.&#x0D; MATERIALS AND METHODS: Metabolite profiling was performed by GC-MS. Statistical analysis of metabolomics data was processed using R 4.2.1 Funny-Looking Kid.&#x0D; RESULTS: The resulting profile included about 360 compounds. 70 of these were identified and 50 compounds were determined to a class. Sugars (64) were the most widely represented in the obtained profiles. 16 amino and 20 carboxylic acids, lipids and secondary compounds have been identified. Significant differences were revealed between the profiles of leaf metabolomes of mesophyte E. angustifolium and hydrophytes E. hirsutum and E. palustre. The mesophyte was characterized by high levels of sugars. The metabolomes of wetland Epilobium species practically did not differ from each other and were characterized by the accumulation of amino acids, including GABA shunt intermediates, dicarboxylic acids of the Krebs cycle, and metabolites of glycolysis and lactic acid fermentation, which reflects the stimulation of anaerobic respiration, nitrogen metabolism, and alternative pathways of NAD(P)H reoxidation in wetland plants.&#x0D; CONCLUSIONS: Traits of metabolic profiles detected in hydrophyte Epilobium species can be used to assess the degree of plant resistance to oxygen deficiency.

Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism.

Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.

Simultaneous nitrification and denitrification in a novel rotating self-aerated biofilm reactor for decentralized wastewater treatment

Decentralized wastewater pollution in rural areas has become a serious problem for the rural environment. In this study, a novel rotating self-aerated biofilm reactor was developed for decentralized wastewater treatment without any aeration equipment. After the long-term operation of 110 days, the removal efficiency reached to 96.06 % (COD), 98.06 % (NH4+-N), and 62.58 % (TN) in the last phase. Under high dissolved oxygen level, the simultaneous nitrification–denitrification (SND) maintained at a stable ratio of 62.53 % and the denitrification rates reached over 28.37 mg/L/h. With the organic loading rate increased, key nitrogen functional bacterial communities such as anoxic denitrifiers (Thiothrix, Flavobacterium, Pseudoxanthomonas, Aquimonas and Azoarcus) and aerobic denitrifiers (Hydrogenophaga, Zoogloea and Terrimonas) increased obviously. Overall, microbial analysis and nitrogen metabolism pathway indicated that an integration of SND process was achieved in this single reactor by the combined action of nitrification, denitrification and comammox without any aeration equipment.

Fungus Pichia kudriavzevii XTY1 and heterotrophic nitrifying bacterium Enterobacter asburiae GS2 cannot efficiently transform organic nitrogen via hydroxylamine and nitrite.

Heterotrophic nitrification is a process of organic nitrogen degradation completed by the participation of heterotrophic nitrifying microorganisms, which can accelerate the nitrogen transformation process. However, the current research mainly focuses on heterotrophic nitrifying bacteria and their ammonium degradation capacities. And there is little accumulation of research on fungi, the main force of heterotrophic nitrification, and their capacities to transform organic nitrogen. In this study, novel heterotrophic nitrifying fungus (XTY1) and bacterium (GS2) were screened and isolated from upland soil, and the strains were identified and registered through GenBank comparison. After 24 h single nitrogen source tests and 15N labeling tests, we compared and preliminarily determined the heterotrophic nitrification capacities and pathways of the two strains. The results showed that XTY1 and GS2 had different transformation capacities to different nitrogen substrates and could efficiently transform organic nitrogen. However, the transformation capacity of XTY1 to ammonium was much lower than that of GS2. The two strains did not pass through NH2OH and NO2 - during the heterotrophic nitrification of organic nitrogen, and mainly generated intracellular nitrogen and low N2O. Other novel organic nitrogen metabolism pathways may be existed, but they remain to be further validated.

Nitrogen removal and metabolic pathways of nitrifying coal ash propelled by temperature change under high nitrogen loading

Coal ash, owing to its cost-effectiveness and greater adhesion with nitrifiers, has been used as a carrier for immobilizing nitrifiers when treating wastewater with a low C/N ratio and high nitrogen loading. Various environmental conditions significantly affect the nitrogen metabolic pathways of nitrifying coal ash. In this study, the nitrogen metabolic pathways of nitrifying coal ash propelled at different temperatures were investigated to evaluate the impact of seasonal variation on nitrifying coal ash. Results showed average NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;-N effluent concentrations increased with temperature, and reached 3.37, 5.16, and 76.06 mg N/L with 1158 mg N/L influent under 15 ℃, 25 ℃, and 35 ℃ systems. The total nitrogen removal rate at a cooling temperature of 15 ℃ was higher than that at 25 ℃ and 35 ℃. Further analysis showed &lt;i&gt;Nitrosomonas&lt;/i&gt; and &lt;i&gt;Nitrobacter&lt;/i&gt; were enhanced, whereas a significant evolution of autotrophic denitrifiers, &lt;i&gt;Acidovorax&lt;/i&gt;, was enriched at 15 ℃. An in-depth investigation of N-metabolism pathways suggested higher temperatures of 25 ℃ and 35 ℃ reduced the abundance of key genes involved in ammonia oxidation (amoABC, &lt;i&gt;hao&lt;/i&gt;) and nitrite oxidation (&lt;i&gt;nar&lt;/i&gt;GH). Network analysis between N-metabolic functional genes and genera presented stronger relevance and richer sources between nitrifiers/denitrifiers and nitrification/denitrification-associated genes under cooler temperatures.

Characteristics of bacterial communities in a rural river water restored by ecological floating beds with Oenathe javanica

Ecological floating beds (EFB) can efficiently remove nitrogen and phosphorus from eutrophic water. However, there are significant gaps in our understanding of bacterial community characteristics in water in rural rivers that have been restored by EFBs. In this study, we applied EFBs using Oenathe Javanica to restore a eutrophic rural river in southeast China from March to May in 2018. We then conducted high-throughput sequencing of 16S rRNA from river water samples to develop a comprehensive profile of the bacterial community structure in the river. The richness indices of the bacterial community were higher in the planted area than the open area (the CK area) on March 29 and April 20, as were the Shannon indices on April 20 and May 18. The proportions of Betaproteobacteria, Actinobacteria, Cyanobacteria, Sphingobacteriia, Verrucomicrobiae and Cytophagia were significantly higher in the planted area than the CK area on April 20, when plants on the EFBs were growing rapidly. Root length had stronger relationships with OTUs than plant length, Spad and dry biomass weight in the planted area, while TN, TP, SS, pH and DO had stronger relationships with OTUs than other water quality indexes in the whole river segment. The average relative abundance of genes associated with nitrogen metabolism, methane metabolism and carbon fixation pathways in the planted areas were higher than in the CK area. These findings suggest that use of ecological floating beds (EFB) with Oenathe Javanica under the relatively lower temperatures that occur during early spring has a positive impact on microbial communities that might contribute to the growth and metabolism of microorganisms and help to promote nitrogen removal from rural rivers.

Comprehensive Proteomic Analysis of Brucella melitensis ATCC23457 Strain Reveals Metabolic Adaptations in Response to Nutrient Stress.

In the present study, a comprehensive proteomic analysis of Brucella melitensis (B. melitensis) strain ATCC23457 was carried out to investigate proteome alterations in response to in vitro-induced nutrient stress. Our analysis resulted in the identification of 2440 proteins, including 365 hypothetical proteins and 850 potentially secretory proteins representing ~77.8% of the B. melitensis proteome. Utilizing a proteogenomics approach, we provide translational evidence for eight novel putative protein-coding genes and confirmed the coding potential of 31 putatively annotated pseudogenes, thus refining the existing genome annotation. Further, using a label-free quantitative proteomic approach, new insights into the cellular processes governed by nutrient stress, including enrichment of amino acid metabolism (E), transcription (K), energy production and conversion (C), and biogenesis (J) processes were obtained. Pathway analysis revealed the enrichment of survival and homeostasis maintenance pathways, including type IV secretion system, nitrogen metabolism, and urease pathways in response to nutrient limitation. To conclude, our analysis demonstrates the utility of in-depth proteomic analysis in enabling improved annotation of the B. melitensis genome. Further, our results indicate that B. melitensis undergoes metabolic adaptations during nutrient stress similar to other Brucella. sp, and adapts itself for long-term persistence and survival.

Phylogenomic analysis of Citrobacter sp. strain AAK_AS5 and its metabolic capabilities to support nitrogen removal behavior.

Despite the ubiquity of the genus Citrobacter in clinical, industrial, and environmental scenarios, a large number of Citrobacter strains have not been explored at the genome-scale level. In this study, accurate taxonomic assignment of strain AAK_AS5 isolated from activated sludge was achieved by in-silico genomic comparison using Overall Genome-based Relatedness Indices (ANI(OAT): 97.55%, ANIb:97.28%, and ANIm: 97.83%) that indicated its closest identity to the related strain Citrobacter portucalensis A60T . Results were consistent with a digital DNA-DNA hybridization value of 80% with C. portucalensis A60T which was greater than the species boundary value >70% for delineating closely related bacterial species. Gene mining through Kyoto Encyclopedia of Genes and Genomes (KEGG), and annotation using rapid annotation subsystem technology (RAST) revealed the notable gene contents for nitrogen metabolism and other pathways associated with nitrate/nitrite ammonification (28 genes), ammonia assimilation (22 genes), and denitrification pathways (14 genes). Furthermore, the strain AAK_AS5 also exhibited a high soluble chemical oxygen demand (sCOD), NH4 + -N, and NO3 - -N removal efficiency of 91.4%, 90%, and 93.6%, respectively thus validating its genetic capability for utilizing both (NH4 )2 SO4 and KNO3 as the nitrogen source. The study provided deeper insights into the phylogenomics and the genetic potential of Citrobacter, sp. strain AAK AS5 associated with nitrogen metabolism thus signifying the potential application of the isolate for treating nitrogen-rich wastewaters.

Regulation of salt tolerance in the roots of Zea mays by L-histidine through transcriptome analysis.

Soil salinization is an important worldwide environmental problem and the main reason to reduce agricultural productivity. Recent findings suggested that histidine is a crucial residue that influences the ROS reduction and improves the plants' tolerance to salt stress. Herein, we conducted experiments to understand the underlying regulatory effects of histidine on maize root system under salt stress (100 mM NaCl solution system). Several antioxidant enzymes were determined. The related expressed genes (DEGs) with its pathways were observed by Transcriptome technologies. The results of the present study confirmed that histidine can ameliorate the adverse effects of salt stress on maize root growth. When the maize roots exposed to 100 mM NaCl were treated with histidine, the accumulation of superoxide anion radicals, hydrogen peroxide, and malondialdehyde, and the content of nitrate nitrogen and ammonium nitrogen were significantly reduced; while the activities of superoxide dismutase, peroxidase, catalase, nitrate reductase, glutamine synthetase, and glutamate synthase were significantly increased. Transcriptome analysis revealed that a total of 454 (65 up-regulated and 389 down-regulated) and 348 (293 up-regulated and 55 down-regulated) DEGs were observed when the roots under salt stress were treated with histidine for 12 h and 24 h, respectively. The pathways analysis of those DEGs showed that a small number of down-regulated genes were enriched in phytohormone signaling and phenylpropanoid biosynthesis at 12 h after histidine treatment, and the DEGs involved in the phytohormone signaling, glycolysis, and nitrogen metabolism were significantly enriched at 24 h after treatment. These results of gene expression and enzyme activities suggested that histidine can improve the salt tolerance of maize roots by enriching some DEGs involved in plant hormone signal transduction, glycolysis, and nitrogen metabolism pathways.