Meta-QTL Analysis in Rice and Cross-Genome Talk of the Genomic Regions Controlling Nitrogen Use Efficiency in Cereal Crops Revealing Phylogenetic Relationship

The phenomenal increase in the use of nitrogenous fertilizers coupled with poor nitrogen use efficiency is among the most important threats to the environment, economic, and social health. During the last 2 decades, a number of genomic regions associated with nitrogen use efficiency (NUE) and related traits have been reported by different research groups, but none of the stable and major effect QTL have been utilized in the marker-assisted introgression/pyramiding program. Compiling the data available in the literature could be very useful in identifying stable and major effect genomic regions associated with the root and NUE-related trait improving the rice grain yield. In the present study, we performed meta-QTL analysis on 1,330 QTL from 29 studies published in the past 2 decades. A total of 76 MQTL with a stable effect over different genetic backgrounds and environments were identified. The significant reduction in the confidence interval of the MQTL compared to the initial QTL resulted in the identification of annotated and putative candidate genes related to the traits considered in the present study. A hot spot region associated with correlated traits on chr 1, 4, and 8 and candidate genes associated with nitrate transporters, nitrogen content, and ammonium uptake on chromosomes 2, 4, 6, and 8 have been identified. The identified MQTL, putative candidate genes, and their orthologues were validated on our previous studies conducted on rice and wheat. The research-based interventions such as improving nitrogen use efficiency via identification of major genomic regions and candidate genes can be a plausible, simple, and low-cost solution to address the challenges of the crop improvement program.

Elementary vectors and autocatalytic sets for computational models of cellular growth

Traditional models of cellular growth involve an approximative biomass ''reaction'' which specifies biomass composition in terms of precursor metabolites (such as amino acids and nucleotides). On the one hand, biomass composition is often not known exactly and may vary drastically between extreme conditions; on the other hand, the predictions of computational models crucially depend on biomass. Even elementary flux modes (EFMs) depend on the biomass reaction. (To be specific: not just the numerical values of the EFMs, but also their supports and their number.) To better understand cellular phenotypes across conditions, we introduce and analyze new classes of elementary vectors for more comprehensive models of cellular growth, involving explicit synthesis reactions for all macromolecules. Growth modes (GMs) are given by stoichiometry, and elementary growth modes (EGMs) are GMs that cannot be decomposed without cancellations. Unlike EFMs, EGMs need not be support-minimal. Most importantly, every GM can be written as a sum of EGMs. In models with additional (capacity) constraints, growth vectors (GVs) and elementary growth vectors (EGVs) also depend on growth rate. In any case, EGMs/EGVs do not depend on the biomass composition. In fact, they cover all possible biomass compositions and can be seen as unbiased versions of elementary flux modes/vectors (EFMs/EFVs) used in traditional models. To relate the new concepts to other branches of theory, we define autocatalytic GMs and the corresponding autocatalytic sets of reactions. Further, we illustrate our results in a small model of a self-fabricating cell, involving glucose and ammonium uptake, amino acid and lipid synthesis, and the expression of all enzymes and the ribosome itself. In particular, we study the variation of biomass composition as a function of growth rate. In agreement with experimental data, low nitrogen uptake correlates with high carbon (lipid) storage.

RNA-Seq analysis and transcriptome assembly of Salicornia neei reveals a powerful system for ammonium detoxification

ABSTRACTBackgroundSalicornia neei is a halophyte plant that has been proposed for phytoremediation of saline wastewater generated by land-based aquaculture, which usually contains elevated concentrations of ammonium resulting from protein metabolism. To identify the molecular mechanisms related to ammonium response through of analysis results in silico and the Michaelis–Menten ammonium removal biokinetics and the transcriptome of S. neei in response to growth in saline water containing 3 mM ammonium.ResultsThe parameters for ammonium uptake by S. neei root cuttings were estimated: 1) maximum uptake rate Imax = 7.07 ± 0.27 mM N g−1 fresh weight h−1; and 2) half-saturation constant Km = 0.85 ± 0.12 mM N L−1. Further, a total of 45,327 genes were annotated, which represents 51.2% of the contig predicted from de novo assembly. A total of 9,140 genes were differentially expressed in response to ammonium in saline water, but only 7,396 could be annotated against functional databases. According to the GO enrichment and as well as KEGG pathway analyses showed these upregulated genes were involved in pr cellular anatomical entity, cellular process, and metabolic process, including biological KEGG pathways linked to biosynthesis amino acid biosynthesis, nitrogen metabolism and autophagy and other. In addiction, a set of 72 genes were directly involved in ammonium metabolism, including glutamine synthetase 1 (GLN1), glutamate synthase 1 (GLT1), and ferredoxin-dependent glutamate synthase chloroplastic (Fd-GOGAT).ConclusionOur results support the hypothesis that an ammonium detoxification system mediated by glutamine and glutamate synthase was activated in S. neei when exposed to ammonium and saline water. These results provide novel insight into understanding the molecular mechanisms of ammonium nutrition and aid for investigating the response of halophyte plants to saline wastewater from land-based aquaculture

Microalga-Mediated Tertiary Treatment of Municipal Wastewater: Removal of Nutrients and Pathogens

The microalgal strain Chlorella sorokiniana isolated from a waste stabilization pond was used for tertiary treatment of municipal wastewater. Three light:dark (L:D) regimes of 12:12, 16:8, and 24:0 were used for treating wastewater in microalga (A), microalga + sludge (A + S), and sludge (S) reactors. The removal of nutrients (N and P) was found to be the highest in the microalga-based reactor, with more than 80% removal of biochemical oxygen demand (BOD) and 1.2–5.6 log unit removal of pathogens. The addition of sludge improved chemical oxygen demand (COD) removal. Nitrifiers were found to be predominant in the A + S reactor. Algal biomass productivity was more than 280 mg/L/d in all the L:D regimes. The increase in light regime improved nutrient removal and biomass productivity in the algal reactor. Results of the kinetic study showed that (i) nitrifiers had more affinity for ammonium than microalga, and hence, most of the ammonia was oxidized to nitrate, (ii) microalga assimilated nitrate as the primary nitrogen source in the A + S reactor, and (iii) solubilization of particulate organic nitrogen originated from dead cells reduced the nitrogen removal efficiency. However, in the microalga-based reactor, the ammonium uptake was higher than nitrate uptake. Among pathogens, the removal of Salmonella and Shigella was better in the A + S reactor than in the other two reactors (microalga and sludge reactor). Additionally, the heterotrophic plate count was drastically reduced in the presence of microalga. No such drastic reduction was observed in the stand-alone sludge reactor. Kinetic modeling revealed that microalga–pathogen competition and pH-induced die-off were the two predominant factors for pathogen inactivation.

Systemic regulation of nitrogen acquisition and use in Oryza longistaminata ramets under nitrogen heterogeneity

Oryza longistaminata, a wild rice, vegetatively reproduces and forms a networked clonal colony consisting of ramets connected by rhizomes. Although water, nutrients, and other molecules can be transferred between ramets via the rhizomes, inter-ramet communication in response to spatially heterogeneous nitrogen availability is not well understood. We studied the response of ramet pairs to heterogeneous nitrogen availability by using a split hydroponic system that allowed each ramet root to be exposed to different conditions. Ammonium uptake was compensatively enhanced in the sufficient-side root when roots of the ramet pairs were exposed to ammonium-sufficient and deficient conditions. Comparative transcriptome analysis revealed that a gene regulatory network for effective ammonium assimilation and amino acid biosynthesis was activated in the sufficient-side roots. Allocation of absorbed nitrogen from the nitrogen-sufficient to the deficient ramets was rather limited. Nitrogen was preferentially used for newly growing axillary buds on the sufficient-side ramets. Biosynthesis of trans-zeatin, a cytokinin, was up-regulated in response to the nitrogen supply, but trans-zeatin appears not to target the compensatory regulation. Our results also implied that the O. longistaminata ortholog of OsCEP1 plays a role as a nitrogen-deficient signal in inter-ramet communication, providing compensatory up-regulation of nitrogen assimilatory genes. These results provide insights into the molecular basis for efficient growth strategies of asexually proliferating plants growing in areas where nitrogen distribution is spatially heterogeneous.

The Exudation of Surplus Products Links Plant Functional Traits and Plant-Microbial Stoichiometry

The rhizosphere is a hot spot of soil microbial activity and is largely fed by root exudation. The carbon (C) exudation flux, coupled with plant growth, is considered a strategy of plants to facilitate nutrient uptake. C exudation is accompanied by a release of nutrients. Nitrogen (N) and phosphorus (P) co-limit the productivity of the plant-microbial system. Therefore, the C:N:P stoichiometry of exudates should be linked to plant nutrient economies, plant functional traits (PFT) and soil nutrient availability. We aimed to identify the strongest links in C:N:P stoichiometry among all rhizosphere components. A total of eight grass species (from conservative to exploitative) were grown in pots under two different soil C:nutrient conditions for a month. As a result, a wide gradient of plant–microbial–soil interactions were created. A total of 43 variables of plants, exudates, microbial and soil C:N:P stoichiometry, and PFTs were evaluated. The variables were merged into four groups in a network analysis, allowing us to identify the strongest connections among the variables and the biological meaning of these groups. The plant–soil interactions were shaped by soil N availability. Faster-growing plants were associated with lower amounts of mineral N (and P) in the soil solution, inducing a stronger competition for N with microorganisms in the rhizosphere compared to slower-growing plants. The plants responded by enhancing their N use efficiency and root:shoot ratio, and they reduced N losses via exudation. Root growth was supported either by reallocated foliar reserves or by enhanced ammonium uptake, which connected the specific leaf area (SLA) to the mineral N availability in the soil. Rapid plant growth enhanced the exudation flux. The exudates were rich in C and P relative to N compounds and served to release surplus metabolic products. The exudate C:N:P stoichiometry and soil N availability combined to shape the microbial stoichiometry, and N and P mining. In conclusion, the exudate flux and its C:N:P stoichiometry reflected the plant growth rate and nutrient constraints with a high degree of reliability. Furthermore, it mediated the plant–microbial interactions in the rhizosphere.

Crocosphaera as a major consumer of fixed nitrogen despite its capability of nitrogen fixation

Crocosphaera watsonii (hereafter Crocosphaera) is a key nitrogen (N) fixer in the ocean, but its ability to consume combined N sources is still unclear. Using in situ microcosm incubations with an ecological model, we show that Crocosphaera has high competitive capability both under low and moderately high combined N concentrations. In field incubations, Crocosphaera accounted for the highest consumption of ammonium and nitrate, followed by pico-eukaryotes. The model analysis shows that cells have a high ammonium uptake rate (~7 mol N (mol N)-1 d-1 at the maximum), which allows them to compete against pico-eukaryotes and non-diazotrophic cyanobacteria when combined N is sufficiently available. Even when combined N is depleted, their capability of nitrogen fixation allows higher growth rates compared to potential competitors. These results suggest the high fitness of Crocosphaera in combined N limiting, oligotrophic oceans, and thus heightens its potential significance in its ecosystem and in biogeochemical cycling.

BZR1 Regulates Brassinosteroid-Mediated Activation of AMT1;2 in Rice

Although it is known that brassinosteroids (BRs) play pleiotropic roles in plant growth and development, their roles in plant nutrient uptake remain unknown. Here, we hypothesized that BRs directly regulate ammonium uptake by activating the expression of rice AMT1-type genes. Exogenous BR treatment upregulated both AMT1;1 and AMT1;2 expression, while this induction was impaired in the BR-receptor gene BRI1 mutant d61-1. We then focused on brassinazole-resistant 1 (BZR1), a central hub of the BR signaling pathway, demonstrating the important role of this signaling pathway in regulating AMT1 expression and rice roots NH4+ uptake. The results showed that BR-induced expression of AMT1;2 was suppressed in BZR1 RNAi plants but was increased in bzr1-D, a gain-of-function BZR1 mutant. Further EMSA and ChIP analyses showed that BZR1 bound directly to the BRRE motif located in the promoter region of AMT1;2. Moreover, cellular ammonium contents, 15NH4+ uptake, and the regulatory effect of methyl-ammonium on root growth are strongly dependent on the levels of BZR1. Overexpression lines of BRI1 and BZR1 and Genetic combination of them mutants showed that BZR1 activates AMT1;2 expression downstream of BRI1. In conclusion, the findings suggest that BRs regulation of NH4+ uptake in rice involves transcription regulation of ammonium transporters.