Nitrogen-use efficiency of indica varieties of rice is superior to that of japonica varieties. We apply 16S ribosomal RNA gene profiling to characterize root microbiota of 68 indica and 27 japonica varieties grown in the field. We find that indica and japonica recruit distinct root microbiota. Notably, indica-enriched bacterial taxa are more diverse, and contain more genera with nitrogen metabolism functions, than japonica-enriched taxa. Using genetic approaches, we provide evidence that NRT1.1B, a rice nitrate transporter and sensor, is associated with the recruitment of a large proportion of indica-enriched bacteria. Metagenomic sequencing reveals that the ammonification process is less abundant in the root microbiome of the nrt1.1b mutant. We isolated 1,079 pure bacterial isolates from indica and japonica roots and derived synthetic communities (SynComs). Inoculation of IR24, an indica variety, with an indica-enriched SynCom improved rice growth in organic nitrogen conditions compared with a japonica-enriched SynCom. The links between plant genotype and root microbiota membership established in this study will inform breeding strategies to improve nitrogen use in crops.

NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice

Contents Summary 35 I. Introduction 35 II. Nitrogen acquisition and assimilation 36 III. Root-to-shoot transport of nitrogen 38 IV. Nitrogen storage pools in vegetative tissues 39 V. Nitrogen transport from source leaf to sink 40 VI. Nitrogen import into sinks 42 VII. Relationship between source and sink nitrogen transport processes and metabolism 43 VIII. Regulation of nitrogen transport 43 IX. Strategies for crop improvement 44 X. Conclusions 46 Acknowledgements 47 References 47 SUMMARY: Nitrogen is an essential nutrient for plant growth. World-wide, large quantities of nitrogenous fertilizer are applied to ensure maximum crop productivity. However, nitrogen fertilizer application is expensive and negatively affects the environment, and subsequently human health. A strategy to address this problem is the development of crops that are efficient in acquiring and using nitrogen and that can achieve high seed yields with reduced nitrogen input. This review integrates the current knowledge regarding inorganic and organic nitrogen management at the whole-plant level, spanning from nitrogen uptake to remobilization and utilization in source and sink organs. Plant partitioning and transient storage of inorganic and organic nitrogen forms are evaluated, as is how they affect nitrogen availability, metabolism and mobilization. Essential functions of nitrogen transporters in source and sink organs and their importance in regulating nitrogen movement in support of metabolism, and vegetative and reproductive growth are assessed. Finally, we discuss recent advances in plant engineering, demonstrating that nitrogen transporters are effective targets to improve crop productivity and nitrogen use efficiency. While inorganic and organic nitrogen transporters were examined separately in these studies, they provide valuable clues about how to successfully combine approaches for future crop engineering.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.14876

Source and sink mechanisms of nitrogen transport and use

Precise Editing of a Target Base in the Rice Genome Using a Modified CRISPR/Cas9 System

Application of chemical fertilizers, especially nitrogen (N), to crops has increased dramatically in the last half century and therefore developing crop varieties with improved N use efficiency (NUE) is urgent for sustainable agriculture. N utilization procedures generally can be divided into uptake, transport, and assimilation. Transporters for nitrate or ammonium acquisition and enzymes for assimilation are among the essential components determining NUE, and many transcription factors also play a pivotal role in regulating N use-associated genes, thereby contributing to NUE. Although some efforts in improving NUE have been made in various plants, the regulatory mechanisms underlying NUE are still elusive, and NUE improvement in crop breeding is very limited. In this review, the crucial components involved in N utilization and the candidates with the potential for NUE improvement in dicot Arabidopsis and monocot rice are summarized. In addition, strategies based on new techniques which can be used for dissecting regulatory mechanisms of NUE and also the possible ways in which NUE can be improved in crops are discussed.

/pdf/nitrogen-use-efficiency-in-crops-lessons-from-arabidopsis-y12ia5qgn2.pdf

Nitrogen use efficiency in crops: lessons from Arabidopsis and rice.

Rice is a staple crop for half the world's population, which is expected to grow by 3 billion over the next 30 years. It is also a key model for studying the genomics of agroecosystems. This dual role places rice at the centre of an enormous challenge facing agriculture: how to leverage genomics to produce enough food to feed an expanding global population. Scientists worldwide are investigating the genetic variation among domesticated rice species and their wild relatives with the aim of identifying loci that can be exploited to breed a new generation of sustainable crops known as Green Super Rice.

The rice genome revolution: from an ancient grain to Green Super Rice

Asian cultivated rice (Oryza sativa L.) consists of two main subspecies, indica and japonica. Indica has higher nitrate-absorption activity than japonica, but the molecular mechanisms underlying that activity remain elusive. Here we show that variation in a nitrate-transporter gene, NRT1.1B (OsNPF6.5), may contribute to this divergence in nitrate use. Phylogenetic analysis revealed that NRT1.1B diverges between indica and japonica. NRT1.1B-indica variation was associated with enhanced nitrate uptake and root-to-shoot transport and upregulated expression of nitrate-responsive genes. The selection signature of NRT1.1B-indica suggests that nitrate-use divergence occurred during rice domestication. Notably, field tests with near-isogenic and transgenic lines confirmed that the japonica variety carrying the NRT1.1B-indica allele had significantly improved grain yield and nitrogen-use efficiency (NUE) compared to the variety without that allele. Our results show that variation in NRT1.1B largely explains nitrate-use divergence between indica and japonica and that NRT1.1B-indica can potentially improve the NUE of japonica.

Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies

In recent decades, water levels in many closed inland lakes over north-western China experienced severe declines, among which the Daihai Lake in Inner Mongolia, China was particularly significant. Remotely sensed investigations indicated that the Daihai Lake had shrunk approximately 64% in an area with the dramatic decline of water level approximately 9 m from the 1980 s to 2010 s, which has caused serious concern on the sustainable development of the surrounding region. Consequently, several previous studies have concentrated on the possible causes of lake shrinkage. However, predicting climate variability and anthropogenic activities’ relative contributions to lake water decline is challenging due to the lack of direct water consumption upstream and watershed-scale natural runoff observations. In this paper, a hydrological modeling approach was presented to quantitatively evaluate and separate the relative contributions of climate variations and intensifying anthropogenic activities. The simulation accuracy was evaluated through comparisons with observed data and cross-validation with previous studies. Based on a baseline period, the natural streamflow draining into the lake was reconstructed using the model. The results revealed that the water loss of the Daihai Lake was caused predominately by human activities rather than climate variability. Specifically, for wet conditions, the climate factors posed a negative effect on the water level decline of the lake and delayed the shrinking process of the lake area. The anthropogenic factors took a dominant role (roughly 58%) of lake shrinkage at the annual average scale for normal and dry conditions, while the climate factors accounted for approximately 42%. Hence, the rational policy for water resource management, ecological restoration, and dam and reservoir constructions/operations should be the essential precautions for sustainable development of the Daihai Lake and its surroundings. Additionally, the hydrological modeling approach adopted in this investigation serves as a useful example of the quantitative assessment of climate variations and human activities, especially for the ungauged catchments. 

Human-Induced Water Loss from Closed Inland Lakes: Hydrological Simulations in China’s Daihai Lake

Spatiotemporal green water dynamics and their responses to variations of climatic and underlying surface factors: A case study in the Sanjiang Plain, China

Complex terrain, the sparse distribution of rain gauges, and the poor resolution and quality of satellite data in remote areas severely restrict the development of watershed hydrological modeling, meteorology, and ecological research. In this study, based on the relationship between cloud optical and physical properties and precipitation, a daily geographically weighted regression (GWR) precipitation downscaling model was constructed for the Three Rivers Source region, China, for the period from 2010 to 2014. The GWR precipitation downscaling model combined three different satellite precipitation datasets (CMORPH, IMERG, and ERA5) which were downscaled from a coarse resolution (0.25° and 0.1°) to a fine resolution (1 km). At the same time, the preliminary downscaling results were calibrated and verified by employing the geographic difference analysis (GDA) and geographic ratio analysis (GRA) methods combined with rainfall data. Finally, the analytical hierarchy process (AHP) and the entropy weight method (EW) were adopted to fuse the three downscaled and calibrated satellite precipitation datasets into the merged satellite precipitation dataset (MSP), which provides a higher quality of data (CC = 0.790, RMSE = 2.189 mm/day, and BIAS = 0.142 mm). In summary, the downscaling calibration and precipitation fusion scheme proposed in this study is suitable for obtaining high-resolution daily precipitation data in the Three Rivers Source region with a complex climate and topography.

/pdf/downscaling-and-merging-of-daily-scale-satellite-dvlsku3x.pdf

Downscaling and Merging of Daily Scale Satellite Precipitation Data in the Three River Headwaters Region Fused with Cloud Attributes and Rain Gauge Data

Calibration and evaluation of Hargreaves-Samani equation for estimating reference evapotranspiration: A case study in the Amu Darya River Basin, Central Asia

Chi Xu

Papers

Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies

Human-Induced Water Loss from Closed Inland Lakes: Hydrological Simulations in China’s Daihai Lake

Spatiotemporal green water dynamics and their responses to variations of climatic and underlying surface factors: A case study in the Sanjiang Plain, China

Downscaling and Merging of Daily Scale Satellite Precipitation Data in the Three River Headwaters Region Fused with Cloud Attributes and Rain Gauge Data

Calibration and evaluation of Hargreaves-Samani equation for estimating reference evapotranspiration: A case study in the Amu Darya River Basin, Central Asia