Enhancing climate change resilience in agricultural crops

The promise of resurrection plants in enhancing crop tolerance to water scarcity

Climate change affects the agricultural sector by modifying precipitation patterns, increasing extreme weather events, and geographically shifting agriculturally viable areas. These climate alterations substantially impact plant resilience to abiotic stress and, consequently, agricultural productivity. A better understanding of plant adaptations to tolerate extreme environmental conditions could pave the way for future advances in agricultural sustainability. One such adaptation is vegetative desiccation tolerance (VDT), which enables some species, known as 'resurrection plants', to undergo almost complete drying without losing viability. The current review discusses how incorporating different molecular and biochemical mechanisms underlying VDT into crops might expand the time during which crops can continue growing under limiting water conditions and perhaps broaden the range of survivable negative water potentials that a crop can endure under drought stress. Such possibilities could alleviate the detrimental consequences of low water availability to crops. Understanding how plants survive extreme dehydration has the potential to enlighten new strategies to improve the climate resiliency of crops, thereby positively impacting worldwide food security and sustainability.This article is part of the theme issue 'Crops under stress: can we mitigate the impacts of climate change on agriculture and launch the 'Resilience Revolution'?'.

Advancing Climate-Resilient Sorghum: the Synergistic Role of Plant Biotechnology and Microbial Interactions

Climate-related problems such as drought stress, extreme temperature, erratic rainfall patterns, soil degradation, heatwaves, flooding, water logging, pests and diseases afflict the production and sustainability of sorghum. These challenges may be addressed by adopting climate-resilient practices and using advanced agronomic techniques. These challenges are being addressed through innovative applications of plant biotechnology and microbiology, which offer targeted solutions to enhance sorghum's resilience. For instance, biotechnological tools like CRISPR/Cas9 enable precise genetic modifications to improve drought and heat tolerance, while microbial inoculants, such as plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF), enhance nutrient uptake and stress tolerance through symbiotic interactions. However, biotechnological tools lead to the development of sorghum varieties with heat, drought and salinity tolerance, while marker-assisted selection significantly accelerates breeding for stress-resilient traits. When genetic engineering is introduced, genes encoding heat shock proteins, Osmo protectants and antioxidant pathways are introduced to increase plant resistance to abiotic stress. These compounds stabilise cellular structures, protect enzymes, and maintain osmotic balance, enhancing the plant's ability to survive and function in adverse environmental conditions. At the same time, it is reported that microbiology offers beneficial microbes, nitrogen-fixing bacteria, phosphate-solubilizing microorganisms, and arbuscular mycorrhizal fungi that help enhance nutrient availability, soil health and water uptake. Combinations of endophytes and microbial inoculants enhance plant immunity to pests and diseases while increasing tolerance to stress. Biocontrol agents such as Bacillus and Trichoderma contain suppression of pathogens and need less dependence on the use of chemical pesticides. On top of that, genetic modification increases the nutritional quality of sorghum biofortified. This is where biotechnology and microbiology work together to deliver sustainable farming systems reducing environmental impacts, boosting yields and securing food supply under environmental stresses. This review aims to examine the synergistic integration of plant biotechnology and microbial interactions as a strategy to enhance sorghum's resilience to climate-induced stresses, including drought, elevated temperatures, and nutrient-deficient soils. It highlights recent advancements in biotechnological tools such as gene editing, marker-assisted selection, and tissue culture, alongside the emerging role of plant-beneficial microbes in promoting stress tolerance and improving soil health. By synthesizing current knowledge across these disciplines, this review seeks to outline a framework for future research that harnesses the intersection of biotechnology and microbial ecology to support the sustainable improvement of sorghum resilience.

Hormonal and transcriptomic regulation of drought adaptation in barley roots and leaves

Drought poses a significant threat to global crop productivity and food security. In this study, we aimed to elucidate the impact of drought on transcriptional regulation and alternative splicing in barley (Hordeum vulgare), and to determine whether these transcriptomic alterations correlate with changes in hormonal profiles. We hypothesized that drought stress induces extensive reprogramming of gene expression, including alternative splicing events, and that these molecular responses are accompanied by tissue-specific shifts in hormone levels, ultimately underpinning adaptive responses in both leaves and roots. To test this, we performed RNA-seq and comprehensive hormone profiling on leaves and roots sampled at 25 days after planting under both optimal and drought conditions. Our analysis identified over 6,655 differentially expressed genes, with a substantial subset exhibiting differential alternative splicing. In leaves, drought primarily downregulated photosynthesis-related genes while upregulating pathways involved in water stress and abscisic acid (ABA) signaling. In contrast, roots displayed broader metabolic adjustments and significant isoform switching. Hormone analysis revealed marked ABA accumulation, particularly in roots, alongside organ-specific modulation of jasmonates and auxins. A limited assessment of the rhizosphere microbial community revealed low transcript abundance, underscoring the primacy of intrinsic plant responses. Collectively, these findings provide valuable insights into the multilayered adaptive strategies of barley under drought stress.

Proteome Reprogramming and Acquired Stress Tolerance in Potato Cells Exposed to Acute or Stepwise Water Deficit

Water deficit negatively impacts crop productivity and quality. Plants face these challenges by adjusting biological processes and molecular functions according to the intensity and duration of the stress. The cultivated potato (Solanum tuberosum) is considered sensitive to water deficit, thus breeding efforts are needed to enhance its resilience. To capture novel functional information and gene regulatory networks, we carried out mass spectrometry-based proteomics in potato cell suspensions exposed to abrupt or stepwise osmotic stresses. Both forms of stress triggered significant alterations in protein expression, though with divergent response mechanisms. Stress response pathways orchestrated by key proteins enrolled in primary and secondary metabolism, antioxidant processes, transcriptional and translational machinery and chromatin organization were found in adapted cells. Target metabolites and reactive oxygen species levels were quantified to associate functional outcomes with the proteome study. Remarkably, we also showed that adapted cells tolerate an array of diverse conditions, including anoxia, salt and heat stress. Finally, the expression patterns of genes encoding selected differentially expressed proteins were investigated in potato plants subjected to either drought or salt stress. Collectively, our findings reveal the complex cellular strategies of osmotic stress adaptation, identifying new fundamental genes that could enhance potato resilience.

The next Green Revolution: integrating crop architectype and physiotype

In the middle of the last century, the Green Revolution dramatically increased crop yields and transformed global agriculture. As current food production is increasingly challenged by the demands of the growing population, climate change, and environmental degradation, a new Green Revolution is urgently needed. This Review highlights recent progress in defining the morphological ideotypes of four major crops, and proposes essential physiological traits critical for crop improvement and environmental adaptation. We introduce two concepts: the 'architectype' representing optimized morphological features, and the 'physiotype' encompassing improved physiological traits. By integrating these concepts through advanced genomic technologies and precision management practices, the next Green Revolution could potentially enhance crop yields and resource use efficiency by over 20-30%, thereby ensuring sustainable food production.

A Near-Infrared Fluorescent Nanosensor for Direct and Real-Time Measurement of Indole-3-Acetic Acid in Plants

Auxin, particularly indole-3-acetic acid (IAA), is a phytohormone critical for plant growth, development, and response to environmental stresses like shade avoidance syndrome and thermomorphogenesis. Despite its importance, there is no existing method that allows for convenient and direct detection of IAA in various plant species. Here, we introduce a near-infrared fluorescent nanosensor that directly measures IAA in planta using corona phase molecular recognition with high selectivity, specificity, and spatiotemporal resolution. The IAA sensor can be conveniently functionalized to living plants and localized in various tissues, including leaf, cotyledon, and root tip, with the capability to visualize intrinsic IAA distribution. The IAA nanosensor was further tested in Arabidopsis thaliana leaf with tunable levels of endogenous IAA, in which the sensor measured dynamic and spatiotemporal changes of IAA. We also showed that the IAA sensor can be used for qualitative and quantitative mapping of IAA induction and spatial movement in various plant species undergoing environmental or stress response, such as shade avoidance syndrome, high temperature stress, and gravitropism. This highlights the potential application of IAA sensor for monitoring plant health in agriculture.

Plant-aphid interactions: recent trends in plant resistance to aphids

Aphids are highly destructive agricultural pests characterized by complex life cycles and phenotypic variability, facilitating their adaptation to diverse climates and host plants. Their feeding behavior leads to plant deformation, wilting, stunted growth, disease transmission, and significant yield losses. Given the economic risks aphids pose, regular updates on their seasonal behaviors, adaptive mechanisms, and destructive activities are critical for improving management strategies to mitigate crop losses. This review comprehensively synthesizes recent studies on aphids as plant pests, the extrinsic factors influencing their life cycles, and the intricate interactions between aphids and their hosts. It also highlights recent advancements in biological control measures, including natural enemies, antibiosis, and antixenosis. Additionally, we explore plant defense mechanisms against aphids, focusing on the roles of cell wall components such as lignin, pectin and callose deposition and the genetic regulations underlying these defenses. Aphids, however, can evolve specialized strategies to overcome general plant defenses, prompting the development of targeted mechanisms in plants, such as the use of resistance (R) genes against specific aphid species. Additionally, plant pattern recognition receptors (PRRs) recognize compounds in aphid saliva, which triggers enhanced phloem sealing and more focused immune responses. This work enhances understanding of aphid-plant interaction and plant resistance and identifies key research gaps for future studies.

Transcriptional Profiling to Assess the Effects of Biological Stimulant Atlanticell Micomix on Tomato Seedlings Under Salt Stress

Recent environmental changes in the Mediterranean region, attributable to anthropogenic climate change, present a substantial challenge to the adaptive evaluation of crops and the development of novel improvement strategies. In this study, we established a hydroponic tomato cultivation protocol under in vitro conditions to analyze the transcriptomic profile of seedlings exposed to salinity stress. The study also examined the impact of Atlanticell Micomix, a biological stimulant derived from a mixture of mycorrhizal microorganisms and rhizobacteria, on plant growth and development under standard conditions and in response to moderate salinity. Our transcriptomic analysis indicated a differential effect of biostimulant inoculation compared to the effect induced by salinity stress, involving genes such as GOX3 or DIR1, which are associated with the plant's defense response to adverse conditions. In addition, the presence of a cross-regulatory module between jasmonic acid and auxin, involving potential orthologs of IAA29 and JAZ, was proposed. The application of the biostimulant demonstrated a potential priming effect on the tomato seedlings, which might be useful in reversing the transcriptomic effects caused by salt stress. A comprehensive analysis of the pathways differentially affected by the treatments facilitates further investigation into the mechanisms underlying these effects.

Navigating plant stress response: from nucleus to peroxisomes

The early stages of abscisic acid (ABA) signaling are well understood, but less is known about how plants maintain prolonged stress responses without the adverse effects of continuous ABA exposure. A recent study (Lu et al.) highlights the pivotal role of N-glycosylation in regulating Sucrose nonfermenting-1 Related Kinase 2 (SnRK2) kinase function during prolonged ABA signaling.

Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato

Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, and flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Désirée) under heat, drought, and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising proteomics, targeted transcriptomics, metabolomics, and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analyzed at the end of the stress period. We performed integrative multi-omics data analysis using a bioinformatic pipeline that we established based on machine learning and knowledge networks. Waterlogging produced the most immediate and dramatic effects on potato plants, interestingly activating ABA responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids, and diverse stress-induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies toward climate-adapted potato varieties.

Agricultural landscape genomics to increase crop resilience

Populations are continually adapting to their environment. Knowledge of which populations and individuals harbor unique and agriculturally useful variations has the potential to accelerate crop adaptation to the increasingly challenging environments predicted for the coming century. Landscape genomics, which identifies associations between environmental and genomic variation, provides a means for obtaining this knowledge. However, despite extensive efforts to assemble and characterize ex situ collections of crops and their wild relatives, gaps remain in the genomic and environmental datasets needed to robustly implement this approach. This article outlines the history of landscape genomics, which, to date, has mainly been used in conservation and evolutionary studies, provides an overview of crops and wild relative collections that have the necessary data for implementation and identifies areas where new data generation is needed. We find that 60% of the crops covered by the International Treaty on Plant Genetic Resources for Food and Agriculture lack the data necessary to conduct this kind of analysis, necessitating identification of crops in need of more collections, sequencing, or phenotyping. By highlighting these aspects, we aim to help develop agricultural landscape genomics as a sub-discipline that brings together evolutionary genetics, landscape ecology, and plant breeding, ultimately enhancing the development of resilient and adaptable crops for future environmental challenges.

Wheat2035: Integrating pan-omics and advanced biotechnology for future wheat design

Wheat (Triticum aestivum) production is vital for global food security, providing energy and protein to millions of people worldwide. Recent advancements in wheat research have led to significant increases in production, fueled by technological and scientific innovation. Here, we summarize the major advancements in wheat research, particularly the integration of biotechnologies and a deeper understanding of wheat biology. The shift from multi-omics to pan-omics approaches in wheat research has greatly enhanced our understanding of the complex genome, genomic variations, and regulatory networks to decode complex traits. We also outline key scientific questions, potential research directions, and technological strategies for improving wheat over the next decade. Since global wheat production is expected to increase by 60% in 2050, continued innovation and collaboration are crucial. Integrating biotechnologies and a deeper understanding of wheat biology will be essential for addressing future challenges in wheat production, ensuring sustainable practices and improved productivity.

Maize transcriptome profiling reveals low temperatures affect photosynthesis during the emergence stage

Introduction

Earlier sowing is a promising strategy of ensuring sufficiently high maize yields in the face of negative environmental factors caused by climate change. However, it leads to the low temperature exposure of maize plants during emergence, warranting a better understanding of their response and acclimation to suboptimal temperatures.

Materials and Methods

To achieve this goal, whole transcriptome sequencing was performed on two maize inbred lines - tolerant/susceptible to low temperatures, at the 5-day-old seedling stage. Sampling was performed after 6h and 24h of treatment (10/8°C). The data was filtered, mapped, and the identified mRNAs, lncRNAs, and circRNAs were quantified. Expression patterns of the RNAs, as well as the interactions between them, were analyzed to reveal the ones important for low-temperature response.

Results and Discussion

Genes involved in different steps of photosynthesis were downregulated in both genotypes: psa, psb, lhc, and cab genes important for photosystem I and II functioning, as well as rca, prk, rbcx1 genes necessary for the Calvin cycle. The difference in low-temperature tolerance between genotypes appeared to arise from their ability to mitigate damage caused by photoinhibition: ctpa2, grx, elip, UF3GT genes showed higher expression in the tolerant genotype. Certain identified lncRNAs also targeted these genes, creating an interaction network induced by the treatment (XLOC_016169-rca; XLOC_002167-XLOC_006091-elip2). These findings shed light on the potential mechanisms of low-temperature acclimation during emergence and lay the groundwork for subsequent analyses across diverse maize genotypes and developmental stages. As such, it offers valuable guidance for future research directions in the molecular breeding of low-temperature tolerant maize.

Past and future of cytoplasmic male sterility and heterosis breeding in crop plants

Plant breeding needs to embrace genetic innovations to ensure stability in crop yields under fluctuating climatic conditions. Development of commercial hybrid varieties has proven to be a sustainable and economical alternative to deliver superior yield, quality and resistance with uniformity in a number of food crops. Cytoplasmic male sterility (CMS), a maternally inherited inability to produce functional pollen, facilitates a three-line system for efficient hybrid seed production strategies in crops. The CMS system has illustrated its potential as a robust pollination control mechanism to support the billion-dollar seed industry. In plants, CMS arises due to a genomic conflict between mitochondrial open reading frames (orfs) and nuclear-encoding restoration-of-fertility (Rf) genes, leading to floral abnormalities and pollen sterility. Research on pollen sterility and fertility restoration provides deeper insights into cytoplasmic-nuclear interplay in plants and elucidates key molecular targets for hybrid breeding in crops. More recently, programmable gene editing (e.g., TALEN, CRISPR-Cas) has emerged as a promising tool to functionally validate CMS and Rf genes and obviate the need for pollen donors or Rf-genes for hybrid breeding. Modern genomic prediction models have allowed establishment of high-performing heterotic groups and patterns for sustaining long-term gain in hybrid breeding. This article reviews latest discoveries elucidating the molecular mechanisms behind CMS and fertility restoration in plants. We then present our perspective on how evolving genetic technologies are contributing to advance fundamental knowledge of the CMS-Rf genetic system for producing crop hybrids with high heterosis.

Disruption of cell wall and membrane integrity as antioomycete and antifungal mode of action by fusaric and 9,10-dehydrofusaric acids from endophytic fungus Fusarium lactis strain SME13-2

AIMS

This study aimed to assess the mode of action of fusaric and 9,10-dehydrofusaric acids on cell respiration by measuring the hyphal oxygen consumption rate, and the effects on cell membrane integrity by determining the electrical conductivity of the mycelium.

METHODS AND RESULTS

Bioactivity-directed fractionation of the active culture medium and mycelium organic extracts from the Fusarium lactis strain SME13-2 isolated from Sapium macrocarpum led to the isolation of two known alkylpicolinic acid derivatives: fusaric acid and 9,10-dehydrofusaric acid, along with the known polyketide bikaverin. Fusaric acid and 9,10-dehydrofusaric acid exhibited antioomycete and antifungal activities, significantly inhibiting the radial growth of Phytophthora capsici, Pythium aphanidermatum, Alternaria alternata, and F. oxysporum. Additionally, they induced changes in colony morphology and negative effects on the ultrastructure of their hyphae. To date, the antimicrobial mode of action of fusaric acid and other alkylpicolinic acid derivatives is not thoroughly understood. Therefore, we investigated their effect on cellular respiration by measuring the oxygen consumption rate of the hyphae and their impact on cell membrane integrity by determining the electrical conductivity of the mycelium. Fusaric and 9,10-dehydrofusaric acids inhibited the respiration of the mycelium and altered the permeability of the cell membrane in the tested phytopathogenic microorganisms in a concentration and exposure time-dependent manner, exerting a greater effect on oomycetes. The disruption of cell membrane integrity resulted in the leakage of cytoplasmic electrolytes into the extracellular medium, which, coupled with respiratory inhibition, could lead to cell death.

CONCLUSIONS

Fusaric and 9,10-dehydrofusaric acids show potential for the development of new fungicides and anti-oomycetes agents.

Enhancing the Resilience of Agroecosystems Through Improved Rhizosphere Processes: A Strategic Review

As farming practices evolve and climate conditions shift, achieving sustainable food production for a growing global population requires innovative strategies to optimize environmentally friendly practices and minimize ecological impacts. Agroecosystems, which integrate agricultural practices with the surrounding environment, play a vital role in maintaining ecological balance and ensuring food security. Rhizosphere management has emerged as a pivotal approach to enhancing crop yields, reducing reliance on synthetic fertilizers, and supporting sustainable agriculture. The rhizosphere, a dynamic zone surrounding plant roots, hosts intense microbial activity fueled by root exudates. These exudates, along with practices such as green manure application and intercropping, significantly influence the soil's microbial community structure. Beneficial plant-associated microbes, including Trichoderma spp., Penicillium spp., Aspergillus spp., and Bacillus spp., play a crucial role in improving nutrient cycling and promoting plant health, yet their interactions within the rhizosphere remain inadequately understood. This review explores how integrating beneficial microbes, green manures, and intercropping enhances rhizosphere processes to rebuild microbial communities, sequester carbon, and reduce greenhouse gas emissions. These practices not only contribute to maintaining soil health but also foster positive plant-microbe-rhizosphere interactions that benefit entire ecosystems. By implementing such strategies alongside sound policy measures, sustainable cropping systems can be developed to address predicted climate challenges. Strengthening agroecosystem resilience through improved rhizosphere processes is essential for ensuring food security and environmental sustainability in the future. In conclusion, using these rhizosphere-driven processes, we could develop more sustainable and resilient agricultural systems that ensure food security and environmental preservation amidst changing climate situations.

Proline and ROS: A Unified Mechanism in Plant Development and Stress Response?

The proteinogenic amino acid proline plays crucial roles in both plant development and stress responses, far exceeding its role in protein synthesis. However, the molecular mechanisms and the relative importance of these additional functions of proline remain under study. It is well documented that both stress responses and developmental processes are associated with proline accumulation. Under stress conditions, proline is believed to confer stress tolerance, while under physiological conditions, it assists in developmental processes, particularly during the reproductive phase. Due to proline's properties as a compatible osmolyte and potential reactive oxygen species (ROS) scavenger, most of its beneficial effects have historically been attributed to the physicochemical consequences of its accumulation in plants. However, emerging evidence points to proline metabolism as the primary driver of these beneficial effects. Recent reports have shown that proline metabolism, in addition to supporting reproductive development, can modulate root meristem size by controlling ROS accumulation and distribution in the root meristem. The dynamic interplay between proline and ROS highlights a sophisticated regulatory network essential for plant resilience and survival. This fine-tuning mechanism, enabled by the pro-oxidant and antioxidant properties of compartmentalized proline metabolism, can modulate redox balance and ROS homeostasis, potentially explaining many of the multiple roles attributed to proline. This review uniquely integrates recent findings on the dual role of proline in both ROS scavenging and signaling, provides an updated overview of the most recent research published to date, and proposes a unified mechanism that could account for many of the multiple roles assigned to proline in plant development and stress defense. By focusing on the interplay between proline and ROS, we aim to provide a comprehensive understanding of this proposed mechanism and highlight the potential applications in improving crop resilience to environmental stress. Additionally, we address current gaps in understanding and suggest future research directions to further elucidate the complex roles of proline in plant biology.

Unlocking diversity from wild relatives of perennial fruit crops in the pan-genomics era

Crop wild relatives of perennial fruit crops have a wealth of untapped genetic diversity that can be utilized for cultivar development. However, barriers such as linkage drag, long juvenility, and high heterozygosity have hindered their utilization. Advancements in genome sequencing technologies and assembly methods, combined with the integration of chromosome conformation capture have made it possible to construct high-quality reference genomes. These genome assemblies can be combined into pan-genomes, capturing inter- and intraspecific variations across coding and non-coding regions. Pan-genomes of perennial fruit crops are being developed to identify the genetic basis of traits. This will help overcome breeding challenges, enabling faster and more targeted development of new cultivars with novel traits through breeding and biotechnology.

Drought-tolerant wheat for enhancing global food security

Wheat is among the most produced grain crops of the world and alone provides a fifth of the world's calories and protein. Wheat has played a key role in food security since the crop served as a Neolithic founder crop for the establishment of world agriculture. Projections showing a decline in global wheat yields in changing climates imply that food security targets could be jeopardized. Increased frequency and intensity of drought occurrence is evident in major wheat-producing regions worldwide, and notably, the wheat-producing area under drought is projected to swell globally by 60% by the end of the 21st century. Wheat yields are significantly reduced due to changes in plant morphological, physiological, biochemical, and molecular activities in response to drought stress. Advances in wheat genetics, multi-omics technologies and plant phenotyping have enhanced the understanding of crop responses to drought conditions. Research has elucidated key genomic regions, candidate genes, signalling molecules and associated networks that orchestrate tolerance mechanisms under drought stress. Robust and low-cost selection tools are now available in wheat for screening genetic variations for drought tolerance traits. New breeding techniques and selection tools open a unique opportunity to tailor future wheat crop with optimal trait combinations that help withstand extreme drought. Adoption of the new wheat varieties will increase crop diversity in rain-fed agriculture and ensure sustainable improvements in crop yields to safeguard the world's food security in drier environments.

Microbiomes of urban trees: unveiling contributions to atmospheric pollution mitigation

Urban trees are crucial in delivering essential ecosystem services, including air pollution mitigation. This service is influenced by plant associated microbiomes, which can degrade hydrocarbons, support tree health, and influence ecological processes. Yet, our understanding of tree microbiomes remains limited, thus affecting our ability to assess and quantify the ecosystem services provided by trees as complex systems. The main hypothesis of this work was that tree microbiomes concur to hydrocarbon biodegradation, and was tested through three case studies, which collectively investigated two tree micro-habitats (phyllosphere and tree cavity organic soil-TCOS) under various conditions representing diverse ecological scenarios, by applying different culture-based and molecular techniques and at different scales. The integration of all results provided a more comprehensive understanding of the role of microbiomes in urban trees. Firstly, bacterial strains isolated from the phyllosphere of Quercus ilex were characterized, indicating the presence of Plant-Growth Promoting bacteria and strains able to catabolize PAHs, particularly naphthalene and phenanthrene. Secondly, naphthalene biodegradation on artificially spiked Hedera helix leaves was quantified in greenhouse experiments on inoculated and untreated plants. The persistence of the inoculated strain and community structure of epiphytic bacteria were assessed by Illumina sequencing of V5-V6 hypervariable regions of 16S rRNA gene. Results showed that naphthalene degradation was initially faster on inoculated plants but later the degradation rates became similar, probably because bacterial populations with hydrocarbon-degrading abilities gradually developed also on non-inoculated plants. Finally, we explored bacterial and fungal biodiversity hosted by TCOS samples, collected from six large trees located in an urban park and belonging to different species. Microbial communities were characterized by Illumina sequencing of V5-V6 hypervariable regions of bacterial gene 16S rRNA and of fungal ITS1. Results indicated TCOS as a distinct substrate, whose microbiome is determined both by the host tree and by canopy environmental conditions and has a pronounced aerobic hydrocarbon degradation potential. Overall, a better assessment of biodiversity associated with trees and the subsequent provision of ecosystem services constitute a first step toward developing future new microbe-driven sustainable solutions, especially in terms of support for urban green planning and management policy.

A molecular perspective on the role of FERONIA in root growth, nutrient uptake, stress sensing and microbiome assembly

BACKGROUND

Roots perform multifaceted functions in plants such as movement of nutrients and water, sensing stressors, shaping microbiome, and providing structural support. How roots perceive and respond above traits at the molecular level remains largely unknown. Despite the enormous advancements in crop improvement, the majority of recent efforts have concentrated on above-ground traits leaving significant knowledge gaps in root biology. Also, studying root system architecture (RSA) is more difficult due to its intricacy and the difficulties of observing them during plant life cycle which has made it difficult to identify desired root traits for the crop improvement. However, with the aid of high-throughput phenotyping and genotyping tools many developmental and stress-mediated regulation of RSA has emerged in both model and crop plants leading to new insights in root biology. Our current understanding of upstream signaling events (cell wall, apoplast) in roots and how they are interconnected with downstream signaling cascades has largely been constrained by the fact that most research in plant systems concentrate on cytosolic signal transduction pathways while ignoring the early perception by cells' exterior parts. In this regard, we discussed the role of FERONIA (FER) a cell wall receptor-like kinase (RLK) which acts as a sensor and a bridge between apoplast and cytosolic signaling pathways in root biology.

AIM OF THE REVIEW

The goal of this review is to provide valuable insights into present understanding and future research perspectives on how FER regulates distinct root responses related to growth and stress adaptation.

KEY SCIENTIFIC CONCEPTS OF REVIEW

In plants, FER is a unique RLK because it can act as a multitasking sensor and regulates diverse growth, and adaptive traits. In this review, we mainly highlighted its role in root biology like how it modulates distinct root responses such as root development, sensing abiotic stressors, mechanical stimuli, nutrient transport, and shaping microbiome. Further, we provided an update on how FER controls root traits by involving Rapid Alkalinization Factor (RALF) peptides, calcium, reactive oxygen species (ROS) and hormonal signaling pathways.. We also highlight number of outstanding questions in FER mediated root responses that warrants future investigation. To sum up, this review provides a comprehsive information on the role of FER in root biology which can be utilized for the development of future climate resilient and high yielding crops based on the modified root system.

Leveraging multi-omics tools to comprehend responses and tolerance mechanisms of heavy metals in crop plants

Extreme anthropogenic activities and current farming techniques exacerbate the effects of water and soil impurity by hazardous heavy metals (HMs), severely reducing agricultural output and threatening food safety. In the upcoming years, plants that undergo exposure to HM might cause a considerable decline in the development as well as production. Hence, plants have developed sophisticated defensive systems to evade or withstand the harmful consequences of HM. These mechanisms comprise the uptake as well as storage of HMs in organelles, their immobilization via chemical formation by organic chelates, and their removal using many ion channels, transporters, signaling networks, and TFs, amid other approaches. Among various cutting-edge methodologies, omics, most notably genomics, transcriptomics, proteomics, metabolomics, miRNAomics, phenomics, and epigenomics have become game-changing approaches, revealing information about the genes, proteins, critical metabolites as well as microRNAs that govern HM responses and resistance systems. With the help of integrated omics approaches, we will be able to fully understand the molecular processes behind plant defense, enabling the development of more effective crop protection techniques in the face of climate change. Therefore, this review comprehensively presented omics advancements that will allow resilient and sustainable crop plants to flourish in areas contaminated with HMs.

Omics-Driven Strategies for Developing Saline-Smart Lentils: A Comprehensive Review

A number of consequences of climate change, notably salinity, put global food security at risk by impacting the development and production of lentils. Salinity-induced stress alters lentil genetics, resulting in severe developmental issues and eventual phenotypic damage. Lentils have evolved sophisticated signaling networks to combat salinity stress. Lentil genomics and transcriptomics have discovered key genes and pathways that play an important role in mitigating salinity stress. The development of saline-smart cultivars can be further revolutionized by implementing proteomics, metabolomics, miRNAomics, epigenomics, phenomics, ionomics, machine learning, and speed breeding approaches. All these cutting-edge approaches represent a viable path toward creating saline-tolerant lentil cultivars that can withstand climate change and meet the growing demand for high-quality food worldwide. The review emphasizes the gaps that must be filled for future food security in a changing climate while also highlighting the significant discoveries and insights made possible by omics and other state-of-the-art biotechnological techniques.

Drought-Induced Alterations in Carbon and Water Dynamics of Chinese Fir Plantations at the Trunk Wood Stage

Over the past three decades, China has implemented extensive reforestation programs, primarily utilizing Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) in southern China, to mitigate greenhouse gas emissions and counter extreme climate events. However, the effects of drought on the carbon sequestration capacity of these forests, particularly during the trunk wood stage, remain unclear. This study, conducted in Huitong, Hunan, China, from 2008 to 2013, employed the eddy covariance method to measure carbon dioxide (CO2) and water fluxes in Chinese fir forests, covering a severe drought year in 2011. The purpose was to elucidate the dynamics of carbon and water fluxes during a drought year and across multi-normal year averages. The results showed that changes in soil water content (-8.00%), precipitation (-18.45%), and relative humidity (-5.10%), decreases in air temperature (-0.09 °C) and soil temperature (-0.79 °C), and increases in vapor pressure deficit (19.18%) and net radiation (8.39%) were found in the drought year compared to the normal years. These changes in environmental factors led to considerable decreases in net ecosystem exchange (-40.00%), ecosystem respiration (-13.09%), and gross ecosystem productivity (-18.52%), evapotranspiration (-12.50%), and water use efficiency (-5.83%) in the studied forests in the drought year. In this study, the occurrence of seasonal drought due to uneven precipitation distribution led to a decrease in gross ecosystem productivity (GEP) and evapotranspiration (ET). However, the impact of drought on GEP was greater than its effect on ET, resulting in a reduced water use efficiency (WUE). This study emphasized the crucial role of water availability in determining forest productivity and suggested the need for adjusting vegetation management strategies under severe drought conditions. Our results contributed to improving management practices for Chinese fir plantations in response to changing climate conditions.

Effects of long-term continuous cultivation on the structure and function of soil bacterial and fungal communities of Fritillaria Cirrhosa on the Qinghai-Tibetan Plateau

Fritillaria cirrhosa, an endangered medicinal plant in the Qinghai-Tibet Plateau, is facing resource scarcity. Artificial cultivation has been employed to address this issue, but problems related to continuous cultivation hinder successful transplantation. Imbalanced microbial communities are considered a potential cause, yet the overall changes in the microbial community under continuous cropping systems remain poorly understood. Here, we investigated the effects of varying durations of continuous cropping on the bacterial and fungal communities, as well as enzymatic activities, in the rhizospheric soil of F. cirrhosa. Our findings revealed that continuous cropping of F. cirrhosa resulted in soil acidification, nutrient imbalances, and increased enzyme activity. Specifically, after 10 years of continuous cropping, there was a notable shift in the abundance and diversity (e.g., Chao1 index) of soil bacteria and fungi. Moreover, microbial composition analyses revealed a significant accumulation of harmful microorganisms associated with soil-borne diseases (e.g., Luteimonas, Parastagonospora, Pseudogymnoascus) in successively cropped soils, in contrast to the significant reduction of beneficial microorganisms (e.g., Sphingomonas, Lysobacter, Cladosporium) that promote plant growth and development and protect against diseases such as Fusarium sp.These changes led to decreased connectivity and stability within the soil microbial community. Structural equation modeling and redundancy analysis revealed that alkaline hydrolytic nitrogen and available phosphorus directly influenced soil pH, which was identified as the primary driver of soil microbial community changes and subsequently contributed to soil health deterioration. Overall, our results highlight that soil acidification and imbalanced rhizosphere microbial communities are the primary challenges associated with continuous cropping of F. cirrhosa. These findings establish a theoretical foundation for standardized cultivation practices of F. cirrhosa and the bioremediation of continuously cultivated soils.

Spectral-genomic chain-model approach enhances the wheat yield component prediction under the Mediterranean climate

In light of the changing climate that jeopardizes future food security, genomic selection is emerging as a valuable tool for breeders to enhance genetic gains and introduce high-yielding varieties. However, predicting grain yield is challenging due to the genetic and physiological complexities involved and the effect of genetic-by-environment interactions on prediction accuracy. We utilized a chained model approach to address these challenges, breaking down the complex prediction task into simpler steps. A diversity panel with a narrow phenological range was phenotyped across three Mediterranean environments for various morpho-physiological and yield-related traits. The results indicated that a multi-environment model outperformed a single-environment model in prediction accuracy for most traits. However, prediction accuracy for grain yield was not improved. Thus, in an attempt to ameliorate the grain yield prediction accuracy, we integrated a spectral estimation of spike number, being a major wheat yield component, with genomic data. A machine learning approach was used for spike number estimation from canopy hyperspectral reflectance captured by an unmanned aerial vehicle. The spectral-based estimated spike number was utilized as a secondary trait in a multi-trait genomic selection, significantly improving grain yield prediction accuracy. Moreover, the ability to predict the spike number based on data from previous seasons implies that it could be applied to new trials at various scales, even in small plot sizes. Overall, we demonstrate here that incorporating a novel spectral-genomic chain-model workflow, which utilizes spectral-based phenotypes as a secondary trait, improves the predictive accuracy of wheat grain yield.

Enhancing intercropping sustainability: Manipulating soybean rhizosphere microbiome through cropping patterns

Understanding the responses of soybean rhizosphere and functional microbiomes in intercropping scenarios holds promise for optimizing nitrogen utilization in legume-based intercropping systems. This study investigated three cropping layouts under film mulching: sole soybean (S), soybean-maize intercropping in one row (IS), and soybean-maize intercropping in two rows (IIS), each subjected to two nitrogen levels: 110 kg N ha-1 (N110) and 180 kg N ha-1 (N180). Our findings reveal that cropping patterns alter bacterial and nifh communities, with approximately 5 % of soybean rhizosphere bacterial amplicon sequence variants (ASVs) and 42 % of rhizosphere nifh ASVs exhibiting altered abundances (termed sensitive ASVs). Root traits and soil properties shape these communities, with root traits exerting greater influence. Sensitive ASVs drive microbial co-occurrence networks and deterministic processes, predicting 85 % of yield variance and 78 % of partial factor productivity of nitrogen, respectively. These alterations impact bacterial and nifh diversity, complexity, stability, and deterministic processes in legume-based intercropping systems, enhancing performance in terms of yield, nitrogen utilization efficiency, land equivalent ratio, root nodule count, and nodule dry weight under IIS patterns with N110 compared to other treatments. Our findings underscore the importance of field management practices in shaping rhizosphere-sensitive ASVs, thereby altering microbial functions and ultimately impacting the productivity of legume-based intercropping systems. This mechanistic understanding of soybean rhizosphere microbial responses to intercropping patterns offers insights for sustainable intercropping enhancements through microbial manipulation.

Chickpea production restored through upscaling crowdsourcing winner varieties and planting date adjustments in the Ada'a district, East Shoa zone, Ethiopia

Chickpea is an important cash crop for Ada'a farmers as it does for farmers in Ethiopia and elsewhere in the world. Its production, however, has been dwindling due to biotic and abiotic stresses. According to participant farmers from Ada'a district, the production of chickpea in some Kebeles of Ada'a such as Gubasaye has been abandoned because of root rot and foliar diseases such as fusarium wilt. This paper presents the evaluation of upscaled varieties' performance assessed by metric data as well as through beneficiary farmers' self-assessment data. Recognizant to the problem, five varieties of chickpea tested in the Goro district of the Southwest Shoa zone, were introduced as part of the upscaling of crowdsourcing winner crop varieties in Ethiopia. Crowdsourcing is an approach of outsourcing variety evaluation, selection, and dissemination to volunteer crowds of farmers. The introduction of the winner varieties and adjustment of the planting time was found effective in the Ada'a district. Higher grain yield was obtained from the upscaled winner varieties in the range of 2.4-2.53 t/ha, with slight variations over varieties. Habru variety showed slightly higher performance than the others. Survey participant farmers have reported an increase in GY due to growing the winner varieties compared with varieties they used to grow before and gained higher annual income due to higher productivity, market demand of the upscaled varieties, and premium market price with 6-25 Ethiopian birr (ETB) per kilogram of sold grain of these varieties. High productivity is attributed to the genetic potential of the varieties, their response to farm management, and better adaptation to the local growing conditions. Participant farmers perceived that their livelihood has been improving because of the adoption of the upscaled varieties' productivity and market demand. The annual income of participant farmers is estimated to be 2500 to 181,000 ETB for growing the winner varieties. The results indicate that upscaling pre-tested chickpea varieties and delaying their planting time to early September are effective mechanisms for reducing yield loss to fusarium wilt and root rot diseases. It can be inferred that using the crowdsourcing approach for variety evaluation and selection for upscaling is a robust approach to improve the adoption and dissemination of improved agricultural technologies.

Gene-Based Developments in Improving Quality of Tomato: Focus on Firmness, Shelf Life, and Pre- and Post-Harvest Stress Adaptations

Tomato (Solanum lycopersicum) is a widely consumed vegetable crop with significant economic and nutritional importance. This review paper discusses the recent advancements in gene-based approaches to enhance the quality of tomatoes, particularly focusing on firmness, shelf life, and adaptations to pre- and post-harvest stresses. Utilizing genetic engineering techniques, such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated proteins 9 (CRISPR/Cas9) and Transcription Activator-like Effector Nucleases (TALENs), researchers have made remarkable progress in developing tomatoes with improved traits that address key challenges faced during cultivation, storage, and transportation. We further highlighted the potential of genetic modifications in enhancing tomato firmness, thereby reducing post-harvest losses and improving consumer satisfaction. Furthermore, strategies to extend tomato shelf life through genetic interventions are discussed, emphasizing the importance of maintaining quality and freshness for sustainable food supply chains. Furthermore, the review delves into the ways in which gene-based adaptations can bolster tomatoes against environmental stresses, pests, and diseases, thereby enhancing crop resilience and ensuring stable yields. Emphasizing these crucial facets, this review highlights the essential contribution of genetic advancements in transforming tomato production, elevating quality standards, and promoting the sustainability of tomato cultivation practices.

The Role of Plant Ubiquitin-like Modifiers in the Formation of Salt Stress Tolerance

The climate-driven challenges facing Earth necessitate a comprehensive understanding of the mechanisms facilitating plant resilience to environmental stressors. This review delves into the crucial role of ubiquitin-like modifiers, particularly focusing on ATG8-mediated autophagy, in bolstering plant tolerance to salt stress. Synthesising recent research, we unveil the multifaceted contributions of ATG8 to plant adaptation mechanisms amidst salt stress conditions, including stomatal regulation, photosynthetic efficiency, osmotic adjustment, and antioxidant defence. Furthermore, we elucidate the interconnectedness of autophagy with key phytohormone signalling pathways, advocating for further exploration into their molecular mechanisms. Our findings underscore the significance of understanding molecular mechanisms underlying ubiquitin-based protein degradation systems and autophagy in salt stress tolerance, offering valuable insights for designing innovative strategies to improve crop productivity and ensure global food security amidst increasing soil salinisation. By harnessing the potential of autophagy and other molecular mechanisms, we can foster sustainable agricultural practices and develop stress-tolerant crops resilient to salt stress.

Abiotic Stress Tolerance Boosted by Genetic Diversity in Plants

Plant breeding [...].

Plant Biotechnology-An Indispensable Tool for Crop Improvement

Traditional plant breeding has helped to increase food production dramatically over the past five decades, and many countries have managed to produce enough food for the growing population, particularly in the developing world [...].

Designing future peanut: the power of genomics-assisted breeding

KEY MESSAGE

Integrating GAB methods with high-throughput phenotyping, genome editing, and speed breeding hold great potential in designing future smart peanut cultivars to meet market and food supply demands. Cultivated peanut (Arachis hypogaea L.), a legume crop greatly valued for its nourishing food, cooking oil, and fodder, is extensively grown worldwide. Despite decades of classical breeding efforts, the actual on-farm yield of peanut remains below its potential productivity due to the complicated interplay of genotype, environment, and management factors, as well as their intricate interactions. Integrating modern genomics tools into crop breeding is necessary to fast-track breeding efficiency and rapid progress. When combined with speed breeding methods, this integration can substantially accelerate the breeding process, leading to faster access of improved varieties to farmers. Availability of high-quality reference genomes for wild diploid progenitors and cultivated peanuts has accelerated the process of gene/quantitative locus discovery, developing markers and genotyping assays as well as a few molecular breeding products with improved resistance and oil quality. The use of new breeding tools, e.g., genomic selection, haplotype-based breeding, speed breeding, high-throughput phenotyping, and genome editing, is probable to boost genetic gains in peanut. Moreover, renewed attention to efficient selection and exploitation of targeted genetic resources is also needed to design high-quality and high-yielding peanut cultivars with main adaptation attributes. In this context, the combination of genomics-assisted breeding (GAB), genome editing, and speed breeding hold great potential in designing future improved peanut cultivars to meet market and food supply demands.

Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity

The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.