Interactions among rooting traits for deep water and nitrogen uptake in upland and lowland ecotypes of switchgrass (Panicum virgatum L.)

Tissue-specific chromatin accessibility and transcriptional regulation in maize cold stress response

Maize, a vital crop globally, faces significant yield losses due to its sensitivity to cold stress, especially in temperate regions. Understanding the molecular mechanisms governing maize response to cold stress is crucial for developing strategies to enhance cold tolerance. However, the precise chromatin-level regulatory mechanisms involved remain largely unknown. In this study, we employed DNase-seq and RNA-seq techniques to investigate chromatin accessibility and gene expression changes in maize root, stem, and leaf tissues subjected to cold treatment. We discovered widespread changes in chromatin accessibility and gene expression across these tissues, with strong tissue specificity. Cold stress-induced DNase I hypersensitive sites (coiDHSs) were associated with differentially expressed genes, suggesting a direct link between chromatin accessibility and gene regulation under cold stress. Motif enrichment analysis identified ERF transcription factors (TFs) as central regulators conserved across tissues, with ERF5 emerging as pivotal in the cold response regulatory network. Additionally, TF co-localization analysis highlighted six TF pairs (ERF115-SHN3, ERF9-LEP, ERF7-SHN3, LEP-SHN3, LOB-SHN3, and AS2-LOB) conserved across tissues but showing tissue-specific binding preferences. These findings indicate intricate regulatory networks in maize cold response. Overall, our study provides insights into the chromatin-level regulatory mechanisms underpinning maize adaptive response to cold stress, offering potential targets for enhancing cold tolerance in agricultural contexts.

Divide and conquer: using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods

Roots are important in agricultural and natural systems for determining plant productivity and soil carbon inputs. Sometimes, the amount of roots in a sample is too much to fit into a single scanned image, so the sample is divided among several scans, and there is no standard method to aggregate the data. Here, we describe and validate two methods for standardizing measurements across multiple scans: image concatenation and statistical aggregation. We developed a Python script that identifies which images belong to the same sample and returns a single, larger concatenated image. These concatenated images and the original images were processed with RhizoVision Explorer, a free and open-source software. An R script was developed, which identifies rows of data belonging to the same sample and applies correct statistical methods to return a single data row for each sample. These two methods were compared using example images from switchgrass, poplar, and various tree and ericaceous shrub species from a northern peatland and the Arctic. Most root measurements were nearly identical between the two methods except median diameter, which cannot be accurately computed by statistical aggregation. We believe the availability of these methods will be useful to the root biology community.

Paenibacillus lentimorbus alleviates nutrient deficiency-induced stress in Zea mays by modulating root system architecture, auxin signaling, and metabolic pathways

KEY MESSAGE

Paenibacillus lentimorbus reprograms auxin signaling and metabolic pathways for modulating root system architecture to mitigate nutrient deficiency in maize crops. The arable land across the world is having deficiency and disproportionate nutrients, limiting crop productivity. In this study, the potential of plant growth-promoting rhizobacteria (PGPR) viz., Pseudomonas putida, Paenibacillus lentimorbus, and their consortium was explored for growth promotion in maize (Zea mays) under nutrient-deficient conditions. PGPR inoculation improved the overall health of plants under nutrient-deficient conditions. The PGPR inoculation significantly improved the root system architecture and also induced changes in root cortical aerenchyma. Based on plant growth and physiological parameters inoculation with P. lentimorbus performed better as compared to P. putida, consortium, and uninoculated control. Furthermore, expression of auxin signaling (rum1, rul1, lrp1, rtcs, rtcl) and root hair development (rth)-related genes modulated the root development process to improve nutrient acquisition and tolerance to nutrient-deficient conditions in P. lentimorbus inoculated maize plants. Further, GC-MS analysis indicated the involvement of metabolites including carbohydrates and organic acids due to the interaction between maize roots and P. lentimorbus under nutrient-deficient conditions. These findings affirm that P. lentimorbus enhance overall plant growth by modulating the root system of maize to provide better tolerance to nutrient-deficient condition.

A temporal analysis and response to nitrate availability of 3D root system architecture in diverse pennycress (Thlaspi arvense L.) accessions

Introduction

Roots have a central role in plant resource capture and are the interface between the plant and the soil that affect multiple ecosystem processes. Field pennycress (Thlaspi arvense L.) is a diploid annual cover crop species that has potential utility for reducing soil erosion and nutrient losses; and has rich seeds (30-35% oil) amenable to biofuel production and as a protein animal feed. The objective of this research was to (1) precisely characterize root system architecture and development, (2) understand plastic responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity.

Methods

Using a root imaging and analysis pipeline, the 4D architecture of the pennycress root system was characterized under four nitrate regimes, ranging from zero to high nitrate concentrations. These measurements were taken at four time points (days 5, 9, 13, and 17 after sowing).

Results

Significant nitrate condition response and genotype interactions were identified for many root traits, with the greatest impact observed on lateral root traits. In trace nitrate conditions, a greater lateral root count, length, density, and a steeper lateral root angle was observed compared to high nitrate conditions. Additionally, genotype-by-nitrate condition interaction was observed for root width, width:depth ratio, mean lateral root length, and lateral root density.

Discussion

These findings illustrate root trait variance among pennycress accessions. These traits could serve as targets for breeding programs aimed at developing improved cover crops that are responsive to nitrate, leading to enhanced productivity, resilience, and ecosystem service.

Perennial grass root system specializes for multiple resource acquisitions with differential elongation and branching patterns

Roots optimize the acquisition of limited soil resources, but relationships between root forms and functions have often been assumed rather than demonstrated. Furthermore, how root systems co-specialize for multiple resource acquisitions is unclear. Theory suggests that trade-offs exist for the acquisition of different resource types, such as water and certain nutrients. Measurements used to describe the acquisition of different resources should then account for differential root responses within a single system. To demonstrate this, we grew Panicum virgatum in split-root systems that vertically partitioned high water availability from nutrient availability so that root systems must absorb the resources separately to fully meet plant demands. We evaluated root elongation, surface area, and branching, and we characterized traits using an order-based classification scheme. Plants allocated approximately 3/4th of primary root length towards water acquisition, whereas lateral branches were progressively allocated towards nutrients. However, root elongation rates, specific root length, and mass fraction were similar. Our results support the existence of differential root functioning within perennial grasses. Similar responses have been recorded in many plant functional types suggesting a fundamental relationship. Root responses to resource availability can be incorporated into root growth models via maximum root length and branching interval parameters.

Dynamics of Deep Water and N Uptake of Oilseed Rape (Brassica napus L.) Under Varied N and Water Supply

Enhanced nitrogen (N) and water uptake from deep soil layers may increase resource use efficiency while maintaining yield under stressed conditions. Winter oilseed rape (Brassica napus L.) can develop deep roots and access deep-stored resources such as N and water to sustain its growth and productivity. Less is known of the performance of deep roots under varying water and N availability. In this study, we aimed to evaluate the effects of reduced N and water supply on deep N and water uptake for oilseed rape. Oilseed rape plants grown in outdoor rhizotrons were supplied with 240 and 80 kg N ha-1, respectively, in 2019 whereas a well-watered and a water-deficit treatment were established in 2020. To track deep water and N uptake, a mixture of 2H2O and Ca(15NO3)2 was injected into the soil column at 0.5- and 1.7-m depths. δ2H in transpiration water and δ15N in leaves were measured after injection. δ15N values in biomass samples were also measured. Differences in N or water supply had less effect on root growth. The low N treatment reduced water uptake throughout the soil profile and altered water uptake distribution. The low N supply doubled the 15N uptake efficiency at both 0.5 and 1.7 m. Similarly, water deficit in the upper soil layers led to compensatory deep water uptake. Our findings highlight the increasing importance of deep roots for water uptake, which is essential for maintaining an adequate water supply in the late growing stage. Our results further indicate the benefit of reducing N supply for mitigating N leaching and altering water uptake from deep soil layers, yet at a potential cost of biomass reduction.