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1. Anthropogenic nitrogen (N) deposition is exposing plants and their arbuscular mycorrhizal fungi (AMFs) to elevated N availability, often leading to shifts in communities of AMF. However, physiological trade-offs among AMF taxa in their response to N enrichment vs the ability to acquire other soil nutrients could have negative effects on plant and ecosystem productivity. It follows that information on the functional traits of AMF taxa can be used to generate predictions of their potential role in mediating ecosystem responses to N enrichment. 2. Arbuscular mycorrhizal fungi taxa that produce extensive networks of external hyphae should forage for N and phosphorus (P) more effectively, but these services incur greater carbon (C) costs to the plant. If N enrichment ameliorates plant nutrient limitation, then plants may reduce C available for AMF, which in turn could eliminate AMF taxa with large extensive external hyphae from the soil community. As a result, the remaining AMF taxa may confer less benefit to their host plants. 3. Using a synthesis of data from the literature, we found that the ability of a taxon to persist in the face of increasing soil N availability was particularly high in isolates from the genus Glomus, but especially low among the Gigasporaceae. Across AMF genera, our data support the prediction that AMF with a tolerance for high soil N may confer a lower P benefit to their host plant. Relationships between high N tolerance and production of external hyphae were mixed. 4. Synthesis. If the relationship between N tolerance and plant P benefit is widespread then shifts in arbuscular mycorrhizal fungi communities associated with N deposition could have negative consequences for the ability of plants to acquire P and possibly other nutrients via a mycorrhizal pathway. Based on this relationship, we predict that arbuscular mycorrhizal fungi responses could constrain net primary productivity in P-limited ecosystems exposed to N enrichment. This prediction could be tested in future empirical and modelling studies.

Partial nitrogen supply by biologically fixed nitrogen may well be an environment friendly and energy-saving improvement in production of cereals. Nitrogen fixing associations of various Hungarian rice cultivars were established with associative diazotrophic bacterium Azospirillum brasilense and endophytic diazotroph Herbaspirillum seropedicae. The cultivars expressed different susceptibility to accept the associations, as manifested in root and shoot growth. Established pattern of colonizing bacteria within the plantlets well correlated with the host plant responses. Growth promoting effect of A. brasilense was unambiguous while H. seropedicae elicited inconsequential plant reactions. Moreover, immobilized inoculum formula was developed in order to support protection and competitiveness of bacteria in the soil and provide agrotechnical advantages in the field.

Compared with ectomycorrhizal (ECM) forests, arbuscular mycorrhizal (AM) forests are hypothesized to have higher carbon (C) cycling rates and a more open nitrogen (N) cycle To test this hypothesis, we synthesized 645 observations, including 22 variables related to below-ground C and N dynamics from 100 sites, where AM and ECM forests co-occurred at the same site. Leaf litter quality was lower in ECM than in AM trees, leading to greater forest floor C stocks in ECM forests. By contrast, AM forests had significantly higher mineral soil C concentrations, and this result was strongly mediated by plant traits and climate. No significant differences were found between AM and ECM forests in C fluxes and labile C concentrations. Furthermore, inorganic N concentrations, net N mineralization and nitrification rates were all higher in AM than in ECM forests, indicating ‘mineral’ N economy in AM but ‘organic’ N economy in ECM trees. AM and ECM forests show systematic differences in mineral vs organic N cycling, and thus mycorrhizal type may be useful in predicting how different tree species respond to multiple environmental change factors. By contrast, mycorrhizal type alone cannot reliably predict below-ground C dynamics without considering plant traits and climate.

The intensive application of inorganic nitrogen underlies marked increases in crop production, but imposes detrimental effects on ecosystems 1 , 2 : it is therefore crucial for future sustainable agriculture to improve the nitrogen-use efficiency of crop plants. Here we report the genetic basis of nitrogen-use efficiency associated with adaptation to local soils in rice ( Oryza sativa L.). Using a panel of diverse rice germplasm collected from different ecogeographical regions, we performed a genome-wide association study on the tillering response to nitrogen—the trait that is most closely correlated with nitrogen-use efficiency in rice—and identified OsTCP19 as a modulator of this tillering response through its transcriptional response to nitrogen and its targeting to the tiller-promoting gene DWARF AND LOW-TILLERING ( DLT ) 3 , 4 . A 29-bp insertion and/or deletion in the OsTCP19 promoter confers a differential transcriptional response and variation in the tillering response to nitrogen among rice varieties. The allele of OsTCP19 associated with a high tillering response to nitrogen is prevalent in wild rice populations, but has largely been lost in modern cultivars: this loss correlates with increased local soil nitrogen content, which suggests that it might have contributed to geographical adaptation in rice. Introgression of the allele associated with a high tillering response into modern rice cultivars boosts grain yield and nitrogen-use efficiency under low or moderate levels of nitrogen, which demonstrates substantial potential for rice breeding and the amelioration of negative environment effects by reducing the application of nitrogen to crops. OsTCP19 is a modulator of the tillering response to nitrogen in rice, and introgression of an allele of OsTCP19 associated with a high tillering response into modern rice cultivars markedly improves their nitrogen-use efficiency.

Numerous compelling epidemiological studies have linked air pollution to Sudden Sensorineural Hearing Loss (SSNHL). However, the causal relationship behind this association has not yet been established. We employed a Two-Sample Mendelian Randomization (MR) approach to investigate the causal relationship between air pollution (nitrogen dioxide, nitrogen oxides, PM 2.5 , PM 10 , and PM 2.5–10 ) and SSNHL.Independent genetic variants associated with air pollution and SSNHL were selected as instrumental variables (IVs) at a genome-wide significance level. All summary data were obtained from GWAS databases. The primary method used for MR analysis was the Inverse Variance Weighted (IVW) method, supplemented by various MR analyses method, including weighted median, simple mode, weighted mode, and MR-Egger, to ensure robustness. Cochran’s Q test was employed for heterogeneity assessment. To identify potential pleiotropy, we utilized MR-Egger regression and the MR-PRESSO global test. Additionally, sensitivity analyses were performed using the leave-one-out approach. The MR analysis using the IVW method showed no substantial evidence supporting a direct causal relationship between air pollution and the risk of SSNHL (Nitrogen dioxide: P  = 0.488, Nitrogen oxides: P  = 0.572, PM 2.5 : P  = 0.480, PM 10 : P  = 0.225, and PM 2.5–10 : P  = 0.608). There was no evidence of heterogeneity or pleiotropy, and sensitivity analyses based on the leave-one-out approach indicated that individual single nucleotide polymorphisms (SNPs) did not affect the robustness of the results.This study found no substantial evidence to support a causal relationship between air pollution and the risk of SSNHL in the European population.

Background Nitrogen (N) is a macronutrient that is essential for optimal plant growth and seed yield. Allotetraploid rapeseed (A n A n C n C n , 2 n  = 4 x  = 38) has a higher requirement for N fertilizers whereas exhibiting a lower N use efficiency (NUE) than cereal crops. N limitation adaptation (NLA) is pivotal for enhancing crop NUE and reducing N fertilizer use in yield production. Therefore, revealing the genetic and molecular mechanisms underlying NLA is urgent for the genetic improvement of NUE in rapeseed and other crop species with complex genomes. Results In this study, we integrated physiologic, genomic and transcriptomic analyses to comprehensively characterize the adaptive strategies of oilseed rape to N limitation stresses. Under N limitations, we detected accumulated anthocyanin, reduced nitrate (NO 3 − ) and total N concentrations, and enhanced glutamine synthetase activity in the N-starved rapeseed plants. High-throughput transcriptomics revealed that the pathways associated with N metabolism and carbon fixation were highly over-represented. The expression of the genes that were involved in efficient N uptake, translocation, remobilization and assimilation was significantly altered. Genome-wide identification and molecular characterization of the microR827- NLA1 - NRT1.7 regulatory circuit indicated the crucial role of the ubiquitin-mediated post-translational pathway in the regulation of rapeseed NLA. Transcriptional analysis of the module genes revealed their significant functional divergence in response to N limitations between allotetraploid rapeseed and the model Arabidopsis. Association analysis in a rapeseed panel comprising 102 genotypes revealed that BnaC5.NLA1 expression was closely correlated with the rapeseed low-N tolerance. Conclusions We identified the physiologic and genome-wide transcriptional responses of oilseed rape to N limitation stresses, and characterized the global members of the BnamiR827- BnaNLA1s - BnaNRT1.7s regulatory circuit. The transcriptomics-assisted gene co-expression network analysis accelerates the rapid identification of central members within large gene families of plant species with complex genomes. These findings would enhance our comprehensive understanding of the physiologic responses, genomic adaptation and transcriptomic alterations of oilseed rape to N limitations and provide central gene resources for the genetic improvement of crop NLA and NUE.

Ecosystems often show differential sensitivity to chronic nitrogen (N) deposition; hence, a critical challenge is to improve our understanding of how and why site-specific factors mediate biogeochemical responses to N enrichment. We examined the extent to which N impacts on soil carbon (C) and N dynamics depend on microbial resource stoichiometry. We added N to forest plots dominated by ectomycorrhizal (ECM) trees, which have litter and soil pools rich in organic N and relatively wide C:N ratios, and adjacent forest plots dominated by arbuscular mycorrhizal (AM) trees, which have litter and soil pools rich in inorganic N and relatively narrow C:N ratios. While microbes in both plot types exhibited fairly strict biomass homeostasis, microbes in AM- and ECM-dominated plots differed in their physiological responses to N addition. Microbes in ECM plots responded to N enrichment by decreasing their investment in N-acquisition enzymes (relative to C-acquisition enzymes) and increasing N mineralization rates (relative to mineralization rates), suggesting that N addition alleviated microbial N demand. In contrast, heterotrophic microbial activities in AM plots were unaffected by N addition, most likely as a result of N-induced increases in net nitrification (60% increase relative to control plots) and nitrate mobilization (e.g., sixfold increases in mobilization relative to control plots). Combined, our findings suggest the stoichiometric differences between AM and ECM soils are the primary drivers of the observed responses. Plant and microbial communities characterized by wide C:N are more susceptible to N-induced changes in decomposition and soil dynamics, whereas communities characterized by narrow C:N are more susceptible to N-induced nitrate leaching losses. Hence, the biogeochemical consequences of N deposition in temperate forests may be driven by the stoichiometry of the dominant trees and their associated microbes.

Despite considerable efforts to identify cancer metabolic alterations that might unveil druggable vulnerabilities, systematic characterizations of metabolism as it relates to functional genomic features and associated dependencies remain uncommon. To further understand the metabolic diversity of cancer, we profiled 225 metabolites in 928 cell lines from more than 20 cancer types in the Cancer Cell Line Encyclopedia (CCLE) using liquid chromatography–mass spectrometry (LC-MS). This resource enables unbiased association analysis linking the cancer metabolome to genetic alterations, epigenetic features and gene dependencies. Additionally, by screening barcoded cell lines, we demonstrated that aberrant ASNS hypermethylation sensitizes subsets of gastric and hepatic cancers to asparaginase therapy. Finally, our analysis revealed distinct synthesis and secretion patterns of kynurenine, an immune-suppressive metabolite, in model cancer cell lines. Together, these findings and related methodology provide comprehensive resources that will help clarify the landscape of cancer metabolism.Systematic metabolite profiling across cancer cell lines uncovers patterns associated with genetic and epigenetic features and reveals dysregulated metabolic states that can be exploited for anticancer therapy

Key messageGWAS identified 347 QTLs associated with eight traits related to nitrogen use efficiency in a 389-count wheat panel. Four novel candidate transcription factor genes were verified using qRT-PCR.Nitrogen is an essential nutrient for plants that determines crop yield. Improving nitrogen use efficiency (NUE) should considerably increase wheat yield and reduce the use of nitrogen fertilisers. However, knowledge on the genetic basis of NUE during wheat maturity is limited. In this study, a diversity panel incorporating 389 wheat accessions was phenotyped for eight NUE-related agronomic traits across five different environments. A total of 347 quantitative trait loci (QTLs) for low nitrogen tolerance indices (ratio of agronomic characters under low and high nitrogen conditions) were identified through a genome-wide association study utilising 397,384 single nucleotide polymorphisms (SNPs) within the MLM (Q + K) model, including 11 stable QTLs. Furthermore, 69 candidate genes were predicted for low nitrogen tolerance indices of best linear unbiased predictions values of the eight studied agronomic traits, and four novel candidate transcription factors (TraesCS5A02G237500 for qFsnR5A.2, TraesCS5B02G384500 and TraesCS5B02G384600 for qSLR5B.1, and TraesCS3B02G068800 for qTKWR3B.1) showed differing expression patterns in contrasting low-nitrogen-tolerant wheat genotypes. Moreover, the number of favourable marker alleles calculated using NUE that were significantly related to SNP in accessions decreased over the decades, indicating a decline in the NUE of the 389 wheat varieties. These findings denote promising NUE markers that could be useful in breeding high-NUE wheat varieties, and the candidate genes could further detail the NUE-related regulation network in wheat.

Over-application of nitrogen fertilizer in fields has had a negative impact on both environment and human health. Domesticated rice varieties with high nitrogen use efficiency (NUE) reduce fertilizer for sustainable agriculture. Here, we perform genome-wide association analysis of a diverse rice population displaying extreme nitrogen-related phenotypes over three successive years in the field, and identify an elite haplotype of nitrate transporter OsNPF6.1 HapB that enhances nitrate uptake and confers high NUE by increasing yield under low nitrogen supply. OsNPF6.1 HapB differs in both the protein and promoter element with natural variations, which are differentially trans-activated by OsNAC42, a NUE-related transcription factor. The rare natural allele OsNPF6.1 HapB , derived from variation in wild rice and selected for enhancing both NUE and yield, has been lost in 90.3% of rice varieties due to the increased application of fertilizer. Our discovery highlights this NAC42-NPF6.1 signaling cascade as a strategy for high NUE and yield breeding in rice. Improving crop nitrogen use efficiency can facilitate sustainable production, however, the genetic mechanisms have not been fully revealed. Here, the authors discover the NAC42-NPF6.1 signaling cascade mainly derives from  indica and wild rice and demonstrate the potential of using the allele for cultivar improvement.