Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication.

The domestication of crops, coupled with agroecosystem development, is associated with major environmental changes and provides an ideal model of phenotypic plasticity. Here, we examined 32 genotypes of three tetraploid wheat (Triticum turgidum L.) subspecies, wild emmer, emmer, and durum wheat, which are representative of the key stages in the domestication of tetraploid wheat. We developed a pipeline that integrates RNA-Seq data and population genomics to assess gene expression plasticity and identify selection signatures under diverse nitrogen availability conditions. Our analysis revealed differing gene expression responses to nitrogen availability across primary (wild emmer to emmer) and secondary (emmer to durum wheat) domestication. Notably, nitrogen triggered the expression of twice as many genes in durum wheat compared to that in emmer and wild emmer. Unique selection signatures were identified at each stage: primary domestication mainly influenced genes related to biotic interactions, whereas secondary domestication affected genes related to amino acid metabolism, in particular lysine. Selection signatures were found in differentially expressed genes (DEGs), notably those associated with nitrogen metabolism, such as the gene encoding glutamate dehydrogenase (GDH). Overall, our study highlights the pivotal role of nitrogen availability in the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions.

Molecular Mechanisms of Pseudomonas-Assisted Plant Nitrogen Uptake: Opportunities for Modern Agriculture.

Pseudomonas spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including Azotobacter vinelandii AvOP, Pseudomonas stutzeri A1501, Pseudomonas stutzeri DSM4166, Pseudomonas szotifigens 6HT33bT, and Pseudomonas sp. strain K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from Klebsiella pneumoniae, Pseudomonas stutzeri, and Azotobacter vinelandii. Today, this island is conserved in Pseudomonas spp. from different geographical locations, which, in turn, have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind Pseudomonas-driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N) and improving plant N content. We describe Pseudomonas-plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signaling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions and differs at sufficient and deficient N. The molecular controls behind different plant responses are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind Pseudomonas-driven nitrogen fixation and to point to possible agricultural solutions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

High light induces species specific changes in the membrane lipid composition of Chlorella.

Algae have evolved several mechanisms to adjust to changing environmental conditions. To separate from their surroundings, algal cell membranes form a hydrophobic barrier that is critical for life. Thus, it is important to maintain or adjust the physical and biochemical properties of cell membranes which are exposed to environmental factors. Especially glycerolipids of thylakoid membranes, the site of photosynthesis and photoprotection within chloroplasts, are affected by different light conditions. Since little is known about membrane lipid remodeling upon different light treatments, we examined light induced alterations in the glycerolipid composition of the two Chlorella species, C. vulgaris and C. sorokiniana, which differ strongly in their ability to cope with different light intensities. Lipidomic analysis and isotopic labeling experiments revealed differences in the composition of their galactolipid species, although both species likely utilize galactolipid precursors originated from the endoplasmic reticulum. However, in silico research of de novo sequenced genomes and ortholog mapping of proteins putatively involved in lipid metabolism showed largely conserved lipid biosynthesis pathways suggesting species specific lipid remodeling mechanisms, which possibly have an impact on the response to different light conditions.

Comparative Analysis Based on Transcriptomics and Metabolomics Data Reveal Differences between Emmer and Durum Wheat in Response to Nitrogen Starvation.

Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies: emmer and durum wheat. We found that durum wheat exhibits broader and stronger response in comparison to emmer as seen from the expression pattern of both genes and metabolites and gene enrichment analysis. They showed major differences in the responses to N starvation for transcription factor families, emmer showed differential reduction in the levels of primary metabolites while durum wheat exhibited increased levels of most of them to N starvation. The correlation-based networks, including the differentially expressed genes and metabolites, revealed tighter regulation of metabolism in durum wheat in comparison to emmer. We also found that glutamate and γ-aminobutyric acid (GABA) had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and glutamate signaling modulating shoot vs. root growth in the two different wheat subspecies.

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.

Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.

Impact of Modified Frozen Elephant Trunk Procedure on Downstream Aorta Remodeling in Acute Aortic Dissection: CT Scan Follow-Up.

OBJECTIVES: The aim was to evaluate the impact of a modified frozen elephant trunk procedure (mFET) on remodeling of the downstream aorta following acute aortic dissections. METHODS: Over a period of 8 years, 205 patients (mean age 62.6 ± 12.6 years) underwent a mFET (n = 69, 33.7%) or isolated ascending aorta replacement (n = 136, 66.3%) (iAoA). Aortic diameter was assessed at the aortic arch (AoA), at the mid of the thoracic aorta (mThA), at the thoracoabdominal transition (ThAbd) and at the celiac trunk level (AbdA). RESULTS: Mean follow-up was 3.3 ± 2.6 years. In-hospital mortality was 14% (n = 28), 7% in mFET and 17% in the iAoA group (p = 0.08). At the end of the follow-up, overall survival was 84% (95% CI 70-92%) and 75% (65-82%) and freedom from aorta-related reoperation was 100% and 95% (88-98%) for mFET and iAoA, respectively. At iAoA, the average difference in diameter change per year between mFET and iAoA was for total lumen 0 mm (- 0.95 to 0.94 mm, p = 0.99), and for true lumen, it was 1.23 mm (- 0.09 to 2.55 mm) per year, p = 0.067. False lumen demonstrated a decrease in diameter in mFET as compared to iAoA by - 1.43 mm (- 2.75 to - 0.11 mm), p = 0.034. In mFET, at the aortic arch level the total lumen diameter decreased from 30.7 ± 4.8 mm to 30.1 ± 2.5 mm (Δr + 2.90 ± 3.64 mm) and in iAoA it increased from 31.8 ± 4.9 to 34.6 ± 5.9 mm (Δr + 2.88 ± 4.18 mm). CONCLUSION: The mFET procedure provides satisfactory clinical outcome at short term and mid-term and has a positive impact on aorta remodeling, especially at the level of the aortic arch.

Echocardiographic and Clinical Follow-up After Aortic Valve Neocuspidization Using Autologous Pericardium.

INTRODUCTION: Mid-term data from a single centre showed the safety and durability of aortic valve neocuspidization using autologous pericardium (OZAKI procedure). Since validation data from other centres are missing, aim of this study was to analyze echocardiographic and clinical results of our first patients that were operated with the OZAKI technique. METHODS: Thirty-five patients (24 males, median (IQR) age 72.0 (59.0, 76.0) years) with aortic stenosis (AS; n = 10), aortic insufficiency (AR; n = 13) or a combination of both (AS/AR; n = 12), underwent aortic valve neocuspidization in our institution between September 2015 and May 2017. Echocardiographic follow-up was performed using a standardized examination protocol. RESULTS: Clinical follow-up was completed in 97% of the patients. Median (IQR) follow-up time was 645 (430, 813) days. Mortality rate was 9% (n = 1: aspiration pneumonia; n = 1: unknown; n = 1: anaphylactic shock), and the reoperation rate was 3% (n = 1: endocarditis). No pacemaker implantation was necessary after isolated OZAKI procedures. Echocardiographic follow-up was performed in 83% of the patients (n = 29; median (IQR) time 664 (497, 815) days). Median (IQR) mean and peak gradients were 6 (5,9) mmHg and 12 (8, 17) mmHg. Moderate aortic regurgitation was seen in 2 patients (7%). No severe aortic regurgitation or moderate or severe aortic stenosis occurred within the follow-up period. CONCLUSIONS: The OZAKI procedure is reliable and reoperation due to structural valve deterioration nil within a median 645 days follow-up period. The low rate of moderate aortic regurgitation will be surveilled very closely. Further studies are required to evaluate the significance of this procedure in aortic valve surgery. CLINICAL REGISTRATION NUMBER: ClinicalTrials.gov (ID NCT03677804).

Surgical repair of an esophageal perforation after radiofrequency catheter ablation for atrial fibrillation.

Recent reports have described the incidence of atrioesophageal fistulas (AEF), often resulting in death, from radiofrequency (RF) catheter ablation of atrial fibrillation (AF).1 Cases of esophageal perforation without concomitant AEF have not been described as extensively.1 The precise mechanisms leading to esophageal injury after catheter ablation without involvement of the left atrium are not fully understood. The surgical approach to treat esophageal perforation is strongly recommended.2 However, a unified surgical treatment approach has not yet been established. We describe a case of successful surgical repair of an esophageal perforation after ablation using surgical repair in combination with an omental wrap.

Quantitative 3D Analysis of Plant Roots Growing in Soil Using Magnetic Resonance Imaging.

Precise measurements of root system architecture traits are an important requirement for plant phenotyping. Most of the current methods for analyzing root growth require either artificial growing conditions (e.g. hydroponics), are severely restricted in the fraction of roots detectable (e.g. rhizotrons), or are destructive (e.g. soil coring). On the other hand, modalities such as magnetic resonance imaging (MRI) are noninvasive and allow high-quality three-dimensional imaging of roots in soil. Here, we present a plant root imaging and analysis pipeline using MRI together with an advanced image visualization and analysis software toolbox named NMRooting. Pots up to 117 mm in diameter and 800 mm in height can be measured with the 4.7 T MRI instrument used here. For 1.5 l pots (81 mm diameter, 300 mm high), a fully automated system was developed enabling measurement of up to 18 pots per day. The most important root traits that can be nondestructively monitored over time are root mass, length, diameter, tip number, and growth angles (in two-dimensional polar coordinates) and spatial distribution. Various validation measurements for these traits were performed, showing that roots down to a diameter range between 200 µm and 300 µm can be quantitatively measured. Root fresh weight correlates linearly with root mass determined by MRI. We demonstrate the capabilities of MRI and the dedicated imaging pipeline in experimental series performed on soil-grown maize (Zea mays) and barley (Hordeum vulgare) plants.

phenoVein-A Tool for Leaf Vein Segmentation and Analysis.

Precise measurements of leaf vein traits are an important aspect of plant phenotyping for ecological and genetic research. Here, we present a powerful and user-friendly image analysis tool named phenoVein. It is dedicated to automated segmenting and analyzing of leaf veins in images acquired with different imaging modalities (microscope, macrophotography, etc.), including options for comfortable manual correction. Advanced image filtering emphasizes veins from the background and compensates for local brightness inhomogeneities. The most important traits being calculated are total vein length, vein density, piecewise vein lengths and widths, areole area, and skeleton graph statistics, like the number of branching or ending points. For the determination of vein widths, a model-based vein edge estimation approach has been implemented. Validation was performed for the measurement of vein length, vein width, and vein density of Arabidopsis (Arabidopsis thaliana), proving the reliability of phenoVein. We demonstrate the power of phenoVein on a set of previously described vein structure mutants of Arabidopsis (hemivenata, ondulata3, and asymmetric leaves2-101) compared with wild-type accessions Columbia-0 and Landsberg erecta-0. phenoVein is freely available as open-source software.

Leaf wounding or simulated herbivory in young N. attenuata plants reduces carbon delivery to roots and root tips.

MAIN CONCLUSION: In Nicotiana attenuata seedlings, simulated herbivo ry by the specialist Manduca sexta decreases root growth and partitioning of recent photoassimilates to roots in contrast to increased partitioning reported for older plants. Root elongation rate in Nicotiana attenuata has been shown to decrease after leaf herbivory, despite reports of an increased proportion of recently mobilized photoassimilate being delivered towards the root system in many species after similar treatments. To study this apparent contradiction, we measured the distribution of recent photoassimilate within root tissues after wounding or simulated herbivory of N. attenuata leaves. We found no contradiction: herbivory reduced carbon delivery to root tips. However, the speed of phloem transport in both shoot and root, and the delivery of recently assimilated carbon to the entire root system, declined after wounding or simulated herbivory, in contrast with the often-reported increase in root partitioning. We conclude that the herbivory response in N. attenuata seedlings is to favor the shoot and not bunker carbon in the root system.

Simultaneous effects of leaf irradiance and soil moisture on growth and root system architecture of novel wheat genotypes: implications for phenotyping.

Plants in the field are exposed to varying light and moisture. Agronomic improvement requires knowledge of whole-plant phenotypes expressed in response to simultaneous variation in these essential resources. Most phenotypes, however, have been described from experiments where resources are varied singularly. To test the importance of varying shoot and root resources for phenotyping studies, sister pre-breeding lines of wheat were phenotyped in response to independent or simultaneous exposure to two light levels and soil moisture profiles. The distribution and architecture of the root systems depended strongly on the moisture of the deeper soil layer. For one genotype, roots, specifically lateral roots, were stimulated to grow into moist soil when the upper zone was well-watered and were inhibited by drier deep zones. In contrast, the other genotype showed much less plasticity and responsiveness to upper moist soil, but maintained deeper penetration of roots into the dry layer. The sum of shoot and root responses was greater when treated simultaneously to low light and low soil water, compared to each treatment alone, suggesting the value of whole plant phenotyping in response to multiple conditions for agronomic improvement. The results suggest that canopy management for increased irradiation of leaves would encourage root growth into deeper drier soil, and that genetic variation within closely related breeding lines may exist to favour surface root growth in response to irrigation or in-season rainfall.

Magnetic resonance imaging of sugar beet taproots in soil reveals growth reduction and morphological changes during foliar Cercospora beticola infestation.

Cercospora leaf spot (CLS) infection can cause severe yield loss in sugar beet. Introduction of Cercospora-resistant varieties in breeding programmes is important for plant protection to reduce both fungicide applications and the risk of the development of fungal resistance. However, in vivo monitoring of the sugar-containing taproots at early stages of foliar symptoms and the characterization of the temporal development of disease progression has proven difficult. Non-invasive magnetic resonance imaging (MRI) measurements were conducted to quantify taproot development of genotypes with high (HS) and low (LS) levels of susceptibility after foliar Cercospora inoculation. Fourteen days post-inoculation (dpi) the ratio of infected leaf area was still low (~7%) in both the HS and LS genotypes. However, during this period, the volumetric growth of the taproot had already started to decrease. Additionally, inoculated plants showed a reduction of the increase in width of inner cambial rings while the width of outer rings increased slightly compared with non-inoculated plants. This response partly compensated for the reduced development of inner rings that had a vascular connection with Cercospora-inoculated leaves. Hence, alterations in taproot anatomical features such as volume and cambial ring development can be non-invasively detected already at 14 dpi, providing information on the early impact of the infection on whole-plant performance. All these findings show that MRI is a suitable tool to identify promising candidate parent lines with improved resistance to Cercospora, for example with comparatively lower taproot growth reduction at early stages of canopy infection, for future introduction into breeing programmes.

Analyzing lateral root development: how to move forward.

Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Therefore, understanding the development and architecture of roots holds potential for the manipulation of root traits to improve the productivity and sustainability of agricultural systems and to better understand and manage natural ecosystems. While lateral root development is a traceable process along the primary root and different stages can be found along this longitudinal axis of time and development, root system architecture is complex and difficult to quantify. Here, we comment on assays to describe lateral root phenotypes and propose ways to move forward regarding the description of root system architecture, also considering crops and the environment.

Effects of light and circadian clock on growth and chlorophyll accumulation of Nannochloropsis gaditana.

Circadian clocks synchronize various physiological, metabolic and developmental processes of organisms with specific phases of recurring changes in their environment (e.g. day and night or seasons). Here, we investigated whether the circadian clock plays a role in regulation of growth and chlorophyll (Chl) accumulation in Nannochloropsis gaditana, an oleaginous marine microalga which is considered as a potential feedstock for biofuels and for which a draft genome sequence has been published. Optical density (OD) of N. gaditana culture was monitored at 680 and 735 nm under 12:12 h or 18:6 h light-dark (LD) cycles and after switching to continuous illumination in photobioreactors. In parallel, Chl fluorescence was measured to assess the quantum yield of photosystem II. Furthermore, to test if red- or blue-light photoreceptors are involved in clock entrainment in N. gaditana, some of the experiments were conducted by using only red or blue light. Growth and Chl accumulation were confined to light periods in the LD cycles, increasing more strongly in the first half than in the second half of the light periods. After switching to continuous light, rhythmic oscillations continued (especially for OD680 ) at least in the first 24 h, with a 50% decrease in the capacity to grow and accumulate Chl during the first subjective night. Pronounced free-running oscillations were induced by blue light, but not by red light. In contrast, the photosystem II quantum yield was determined by light conditions. The results indicate interactions between circadian and light regulation of growth and Chl accumulation in N. gaditana.

Seed coating with phages for sustainable plant biocontrol of plant pathogens and influence of the seed coat mucilage.

Pathogens resistant to classical control strategies pose a significant threat to crop yield, with seeds being a major transmission route. Bacteriophages, viruses targeting bacteria, offer an environmentally sustainable biocontrol solution. In this study, we isolated and characterized two novel phages, Athelas and Alfirin, which infect Pseudomonas syringae and Agrobacterium fabrum, respectively, and included the recently published Pfeifenkraut phage infecting Xanthomonas translucens. Using a simple immersion method, phages coated onto seeds successfully lysed bacteria post air-drying. The seed coat mucilage (SCM), a polysaccharide-polymer matrix exuded by seeds, plays a critical role in phage binding. Seeds with removed mucilage formed five to 10 times less lysis zones compared to those with mucilage. The podovirus Athelas showed the highest mucilage dependency. Phages from the Autographiviridae family also depended on mucilage for seed adhesion. Comparative analysis of Arabidopsis SCM mutants suggested the diffusible cellulose as a key component for phage binding. Long-term activity tests demonstrated high phage stability on seed surfaces and significantly increasing seedling survival rates in the presence of pathogens. Using non-virulent host strains enhanced phage presence on seeds but also has potential limitations. These findings highlight phage-based interventions as promising, sustainable strategies for combating pathogen resistance and improving crop yield.

Effects of altered α- and ß-branch carotenoid biosynthesis on photoprotection and whole-plant acclimation of Arabidopsis to photo-oxidative stress.

Functions of α- and ß-branch carotenoids in whole-plant acclimation to photo-oxidative stress were studied in Arabidopsis thaliana wild-type (wt) and carotenoid mutants, lutein deficient (lut2, lut5), non-photochemical quenching1 (npq1) and suppressor of zeaxanthin-less1 (szl1) npq1 double mutant. Photo-oxidative stress was applied by exposing plants to sunflecks. The sunflecks caused reduction of chlorophyll content in all plants, but more severely in those having high α- to ß-branch carotenoid composition (α/ß-ratio) (lut5, szl1npq1). While this did not alter carotenoid composition in wt or lut2, which accumulates only ß-branch carotenoids, increased xanthophyll levels were found in the mutants with high α/ß-ratios (lut5, szl1npq1) or without xanthophyll-cycle operation (npq1, szl1npq1). The PsbS protein content increased in all sunfleck plants but lut2. These changes were accompanied by no change (npq1, szl1npq1) or enhanced capacity (wt, lut5) of NPQ. Leaf mass per area increased in lut2, but decreased in wt and lut5 that showed increased NPQ. The sunflecks decelerated primary root growth in wt and npq1 having normal α/ß-ratios, but suppressed lateral root formation in lut5 and szl1npq1 having high α/ß-ratios. The results highlight the importance of proper regulation of the α- and ß-branch carotenoid pathways for whole-plant acclimation, not only leaf photoprotection, under photo-oxidative stress.

Root-root interactions: extending our perspective to be more inclusive of the range of theories in ecology and agriculture using in-vivo analyses.

BACKGROUND: There is a large body of literature on competitive interactions among plants, but many studies have only focused on above-ground interactions and little is known about root-root dynamics between interacting plants. The perspective on possible mechanisms that explain the outcome of root-root interactions has recently been extended to include non-resource-driven mechanisms (as well as resource-driven mechanisms) of root competition and positive interactions such as facilitation. These approaches have often suffered from being static, partly due to the lack of appropriate methodologies for in-situ non-destructive root characterization. SCOPE: Recent studies show that interactive effects of plant neighbourhood interactions follow non-linear and non-additive paths that are hard to explain. Common outcomes such as accumulation of roots mainly in the topsoil cannot be explained solely by competition theory but require a more inclusive theoretical, as well as an improved methodological framework. This will include the question of whether we can apply the same conceptual framework to crop versus natural species. CONCLUSIONS: The development of non-invasive methods to dynamically study root-root interactions in vivo will provide the necessary tools to study a more inclusive conceptual framework for root-root interactions. By following the dynamics of root-root interactions through time in a whole range of scenarios and systems, using a wide variety of non-invasive methods, (such as fluorescent protein which now allows us to separately identify the roots of several individuals within soil), we will be much better equipped to answer some of the key questions in root physiology, ecology and agronomy.

From genes to policy: mission-oriented governance of plant-breeding research and technologies.

Mission-oriented governance of research focuses on inspirational, yet attainable goals and targets the sustainable development goals through innovation pathways. We disentangle its implications for plant breeding research and thus impacting the sustainability transformation of agricultural systems, as it requires improved crop varieties and management practices. Speedy success in plant breeding is vital to lower the use of chemical fertilizers and pesticides, increase crop resilience to climate stresses and reduce postharvest losses. A key question is how this success may come about? So far plant breeding research has ignored wider social systems feedbacks, but governance also failed to deliver a set of systemic breeding goals providing directionality and organization to research policy of the same. To address these challenges, we propose a heuristic illustrating the core elements needed for governing plant breeding research: Genetics, Environment, Management and Social system (GxExMxS) are the core elements for defining directions for future breeding. We illustrate this based on historic cases in context of current developments in plant phenotyping technologies and derive implications for governing research infrastructures and breeding programs. As part of mission-oriented governance we deem long-term investments into human resources and experimental set-ups for agricultural systems necessary to ensure a symbiotic relationship for private and public breeding actors and recommend fostering collaboration between social and natural sciences for working towards transdisciplinary collaboration.