Physiological, molecular, and environmental insights into plant nitrogen uptake, and metabolism under abiotic stresses

Nitrogen (N) as an inorganic macronutrient is inevitable for plant growth, development, and biomass production. Many external factors and stresses, such as acidity, alkalinity, salinity, temperature, oxygen, and rainfall, affect N uptake and metabolism in plants. The uptake of ammonium (NH4 +) and nitrate (NO3 -) in plants mainly depends on soil properties. Under the sufficient availability of NO3 - (>1 mM), low-affinity transport system is activated by gene network NRT1, and under low NO3 - availability (<1 mM), high-affinity transport system starts functioning encoded by NRT2 family of genes. Further, under limited N supply due to edaphic and climatic factors, higher expression of the AtNRT2.4 and AtNRT2.5T genes of the NRT2 family occur and are considered as N remobilizing genes. The NH4 + ion is the final form of N assimilated by cells mediated through the key enzymes glutamine synthetase and glutamate synthase. The WRKY1 is a major transcription factor of the N regulation network in plants. However, the transcriptome and metabolite profiles show variations in N assimilation metabolites, including glycine, glutamine, and aspartate, under abiotic stresses. The overexpression of NO3 - transporters (OsNRT2.3a and OsNRT1.1b) can significantly improve the biomass and yield of various crops. Altering the expression levels of genes could be a valuable tool to improve N metabolism under the challenging conditions of soil and environment, such as unfavorable temperature, drought, salinity, heavy metals, and nutrient stress.

Pyisotopomer: A Python package for obtaining intramolecular isotope ratio differences from mass spectrometric analysis of nitrous oxide isotopocules

RATIONALE

Obtaining nitrous oxide isotopocule measurements with isotope ratio mass spectrometry (IRMS) involves analyzing the ion current ratios of the nitrous oxide parent ion (N₂ O⁺ ) as well as those of the NO⁺ fragment ion. The data analysis requires correcting for "scrambling" in the ion source, whereby the NO⁺ fragment ion obtains the outer N atom from the N₂ O molecule. While descriptions exist for this correction, and interlaboratory intercalibration efforts have been made, there has yet to be published a package of code for implementing isotopomer calibrations.

METHODS

We developed a user-friendly Python package (pyisotopomer) to determine two coefficients (γ and κ) that describe scrambling in the IRMS ion source, and then used this calibration to obtain intramolecular isotope deltas in N₂ O samples.

RESULTS

With two appropriate reference materials, γ and κ can be determined robustly and accurately for a given IRMS system. An additional third reference material is needed to define the zero-point of the delta scale. We show that IRMS scrambling behavior can vary with time, necessitating regular calibrations. Finally, we present an intercalibration between two IRMS laboratories, using pyisotopomer to calculate γ and κ, and to obtain intramolecular N₂ O isotope deltas in lake water unknowns.

CONCLUSIONS

Given these considerations, we discuss how to use pyisotopomer to obtain high-quality N₂ O isotopocule data from IRMS systems, including the use of appropriate reference materials and frequency of calibration.

Isotopically characterised N2 O reference materials for use as community standards

RATIONALE

Information on the isotopic composition of nitrous oxide (N2 O) at natural abundance supports the identification of its source and sink processes. In recent years, a number of mass spectrometric and laser spectroscopic techniques have been developed and are increasingly used by the research community. Advances in this active research area, however, critically depend on the availability of suitable N2 O isotope Reference Materials (RMs).

METHODS

Within the project Metrology for Stable Isotope Reference Standards (SIRS), seven pure N2 O isotope RMs have been developed and their 15 N/14 N, 18 O/16 O, 17 O/16 O ratios and 15 N site preference (SP) have been analysed by specialised laboratories against isotope reference materials. A particular focus was on the 15 N site-specific isotopic composition, as this measurand is both highly diagnostic for source appointment and challenging to analyse and link to existing scales.

RESULTS

The established N2 O isotope RMs offer a wide spread in delta (δ) values: δ15 N: 0 to +104‰, δ18 O: +39 to +155‰, and δ15 NSP : -4 to +20‰. Conversion and uncertainty propagation of δ15 N and δ18 O to the Air-N2 and VSMOW scales, respectively, provides robust estimates for δ15 N(N2 O) and δ18 O(N2 O), with overall uncertainties of about 0.05‰ and 0.15‰, respectively. For δ15 NSP , an offset of >1.5‰ compared with earlier calibration approaches was detected, which should be revisited in the future.

CONCLUSIONS

A set of seven N2 O isotope RMs anchored to the international isotope-ratio scales was developed that will promote the implementation of the recommended two-point calibration approach. Particularly, the availability of δ17 O data for N2 O RMs is expected to improve data quality/correction algorithms with respect to δ15 NSP and δ15 N analysis by mass spectrometry. We anticipate that the N2 O isotope RMs will enhance compatibility between laboratories and accelerate research progress in this emerging field.

Nitrous oxide nitrification and denitrification 15N enrichment factors from Amazon forest soils

The isotopic signatures of 15N and 18O in N2O emitted from tropical soils vary both spatially and temporally, leading to large uncertainty in the overall tropical source signature and thereby limiting the utility of isotopes in constraining the global N2O budget. Determining the reasons for spatial and temporal variations in isotope signatures requires that we know the isotope enrichment factors for nitrification and denitrification, the two processes that produce N2O in soils. We have devised a method for measuring these enrichment factors using soil incubation experiments and report results from this method for three rain forest soils collected in the Brazilian Amazon: soil with differing sand and clay content from the Tapajos National Forest (TNF) near Santarém, Pará, and Nova Vida Farm, Rondônia. The 15N enrichment factors for nitrification and denitrification differ with soil texture and site: -111 per thousand +/- 12 per thousand and -31 per thousand +/- 11 per thousand for a clay-rich Oxisol (TNF), -102 per thousand +/- 5 per thousand and -45 per thousand +/- 5 per thousand for a sandier Ultisol (TNF), and -10.4 per thousand +/- 3.5 per thousand (enrichment factor for denitrification) for another Ultisol (Nova Vida) soil, respectively. We also show that the isotopomer site preference (delta15Nalpha - delta15Nbeta, where alpha indicates the central nitrogen atom and beta the terminal nitrogen atom in N2O) may allow differentiation between processes of production and consumption of N2O and can potentially be used to determine the contributions of nitrification and denitrification. The site preferences for nitrification and denitrification from the TNF-Ultisol incubated soils are: 4.2 per thousand +/- 8.4 per thousand and 31.6 per thousand +/- 8.1 per thousand, respectively. Thus, nitrifying and denitrifying bacteria populations under the conditions of our study exhibit significantly different 15N site preference fingerprints. Our data set strongly suggests that N2O isotopomers can be used in concert with traditional N2O stable isotope measurements as constraints to differentiate microbial N2O processes in soil and will contribute to interpretations of the isotopic site preference N2O values found in the free troposphere.

Gas chromatography/isotope-ratio mass spectrometry method for high-precision position-dependent 15N and 18O measurements of atmospheric nitrous oxide

We describe an automated gas chromatography/isotope-ratio mass spectrometry (GC/IRMS) method for the determination of the (18)O and position-resolved (15)N content of nitrous oxide at natural isotope abundance. The position information is obtained from successive measurement of the isotopic composition of the N(2)O(+) ion at m/z 44, 45, 46 and the NO(+) fragment ion at m/z 30, 31. The fragment ion analysis is complicated by a non-linearity in the mass spectrometer that has to be taken into account. Evaluation of the absolute peak areas allows for a simultaneous determination of the N(2)O mixing ratio for atmospheric samples. Samples with mixing ratios ranging from a few nmol/mol up to the percent level can be analyzed using different sample inlet systems. The high concentration inlet system provides an easy and quick method to carry out various diagnostic tests, in particular to perform realistic linearity tests. A gas chromatographic set-up with a split column and a backflush possibility improves analytical precision and excludes interferences by substances with long retention times from preceding runs. We also describe a new open split interface that uses only a single transfer capillary to the mass spectrometer for sample and reference gas.