Search Results (414)

Soil-borne diseases pose a severe threat to global agricultural production and food security. Traditional chemical control methods face significant challenges, including environmental pressure, pathogen resistance, and food safety concerns. The rhizosphere microbial community, often termed the plant’s ‘second genome’, plays a pivotal role in maintaining plant health and defending against pathogen invasion. Recent advances in multi-omics technologies, synthetic microbial communities (SynComs) construction, and rhizosphere metabolomics have significantly advanced our understanding of the mechanisms by which rhizosphere microbiomes suppress soil-borne diseases. This review systematically summarizes the following: 1. key drivers of rhizosphere microbial community assembly, particularly plant “cry for help” signaling; 2. core beneficial microbial taxa and their disease-suppressive mechanisms; 3. the critical role of microbial interaction networks; 4. microbiome-based management strategies and their application progress; and 5. current challenges and future research directions. Compared with previous reviews that separately discussed rhizosphere microbiota, disease-suppressive soils, synthetic microbial communities (SynComs), or prebiotics, this review uniquely integrates multiple levels of regulation, from plant genetic determinants (‘M genes’) and root exudate-mediated ‘crying for help’ to microbiome engineering (SynComs and prebiotics) and cross-kingdom interactions (bacteria–fungi–protists–phages). A central conceptual axis of ‘M genes → microbiome engineering → breeding’ is proposed, bridging plant genetics, microbial ecology, and crop improvement for durable disease suppression. Ultimately, this work aims to provide a theoretical foundation for developing efficient and sustainable green control technologies against soil-borne diseases. Full article

Background: Konjac (Amorphophallus spp.) is an economically important crop valued for the glucomannan content in its corms. Currently, the konjac industry faces germplasm degeneration due to long-term asexual propagation. Developing tissue culture and genetic transformation techniques is essential for its genetic improvement. The WUSCHEL-related homeobox (WOX) transcription factors are critical regulators of somatic embryogenesis and stem cell maintenance in plants. Methods: In this study, we performed genome-wide identification and characterization of WOX genes in the A. konjac reference genome. Furthermore, comparative transcriptomic analyses and functional verification were conducted in A. bulbifer. Results: A total of 12 AkWOX genes were identified in A. konjac, and their structural features were documented. Comparative transcriptomic analysis of A. bulbifer revealed that AbWOX genes were differentially expressed between embryogenic calli (EC) and non-embryogenic calli (nEC). Notably, AbWOX2 was significantly upregulated in EC. Overexpression of AbWOX2 significantly promoted callus proliferation and shoot regeneration in A. bulbifer. Furthermore, AbWOX2-overexpressing lines exhibited a 5.3-fold increase in genetic transformation efficiency (from 5.12% to 27.31%) compared to the control. Conclusions: We characterized the diverse expression patterns of the WOX gene family in Amorphophallus. Crucially, we identified specific individual members—most notably the markedly upregulated AbWOX2—that function as pivotal drivers of somatic embryogenesis and serve as promising candidates for enhancing regeneration and genetic engineering efficiency in Amorphophallus species. Full article

Genetically modified (GM) plants have been commercially grown for 30 years, and their acceptance depends on a thorough risk assessment. Environmental Risk Assessment (ERA) evaluates potential impacts of releasing GM plants into the environment, whether through cultivation or import for food, feed, and processing. A key component is assessing potential gene flow to crop wild relatives or non-GM crops. For gene flow to significantly affect the environment, transferred genes must provide a selective advantage. Since most GM plants are engineered for herbicide tolerance, insect resistance, or stacked traits, evaluating such advantages is relatively straightforward. New genomic techniques (NGTs) can generate plants with a wider range of traits, including tolerance to biotic and abiotic stress. Although still considered GM in the EU, their genomic changes can complicate detection, identification, and ERA, especially when such traits may offer advantages under stress conditions. This scoping review focuses on gene flow in two crops: oilseed rape (canola) (Brassica napus L.) and potato (Solanum tuberosum L.). In canola, transgene movement can increase weediness, fitness, herbicide resistance, or genetic diversity in feral or related populations. Gene flow in potato is less studied, with concerns centered on contamination risks in the Andean diversity center. Limited data exist for NGT plants, though many are expected to resemble conventionally bred varieties, suggesting comparable environmental impacts. Full article

Chronic crop diseases caused by uncultured, obligate, or host-dependent pathogens challenge traditional pathogen-centric paradigms that often interpret symptoms as direct outcomes of pathogen toxins, effectors, or tissue colonization. Here, we advance a host-centric immune framework that reframes disease as an emergent consequence of dysregulated host immune network activity, including prolonged activation, signaling miscoordination, and systemic physiological disruption. Using citrus huanglongbing (HLB) as a primary exemplar and canola clubroot as a parallel system, we synthesize evidence that persistent immune stimulation can drive self-damaging outputs, including sustained reactive oxygen species accumulation, chronic vascular and transport dysfunction, hormone imbalance, and growth–defense trade-offs. While many observations derive from transcriptomic, physiological, and genetic studies conducted under controlled experimental conditions, the available evidence collectively suggests that persistent immune activation may contribute substantially to disease-associated decline in these systems. We argue that pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) operate as an integrated immune network whose feedback structure can become destabilized under chronic infection, generating immune states that are simultaneously harmful and often ineffective at pathogen clearance. We further discuss how panomic profiling, spatially resolved analyses, and network inference can diagnose host immune states at tissue and cell-type resolution, and how genome editing enables causal tests and rational immune tuning strategies that optimize defense amplitude, timing, and localization rather than indiscriminately amplifying resistance. By centering the host immune system as both a source of protection and pathology, this framework provides a conceptual and practical roadmap for understanding and engineering resilience in HLB, clubroot, and other chronic crop diseases in which pathogen biology remains experimentally opaque. Full article

Fructokinase (FRK) initiates fructose phosphorylation, channeling carbon into central metabolic pathways, yet its functional diversity and regulatory networks in C₄ cereals remain poorly understood. Here, we performed a comprehensive pan-genome analysis of the FRK gene family in foxtail millet (Setaria italica), identifying 697 SiFRKs across 110 accessions and revealing extensive presence–absence variation shaped by evolution and domestication. Among nine characterized members in the reference genome, SiFRK4 exhibited broad and high expression, a diurnal rhythm, and substantial natural variation. Biochemical assays confirmed its fructokinase activity in vitro. We discovered a novel physical interaction between SiFRK4 and the key photoreceptor Phytochrome C (SiPhyC), which co-localized in the cytoplasm. Functional analysis of SiPhyC mutants demonstrated that loss of SiPhyC disrupted carbohydrate homeostasis, elevating fructose while depleting sucrose and starch. Our findings reveal a physical and genetic link between the light-signaling component SiPhyC and the metabolic enzyme SiFRK4, suggesting their interaction influences carbon partitioning. This study provides foundational insights into the sugar metabolism network of a resilient C₄ model crop and identifies potential targets for metabolic engineering and breeding. Full article

Drought and salt stresses severely impair plant growth and development worldwide. DEHYDRATION-RESPONSIVE ELEMENT BINDING proteins (DREBs), as a subfamily of the AP2/ERF transcription factor superfamily, play critical regulatory roles in plant biological processes including growth and development, as well as the adaptive response to various abiotic stresses. Based on the transcriptome data analysis of Medicago truncatula under saline-alkali stress previously conducted in our laboratory, a gene responsive to saline-alkali stress, Medtr3g110205, was identified, and its homologous gene in Arabidopsis thaliana, AtERF41 (AT5G11590), was obtained via BLAST (version BLAST+ 2.17.0.). The mutant erf41 was used to explore its biological functions in response to drought and salt stresses. The results showed that under salt and drought stress conditions, the seed germination rate, and growth status of the erf41 mutant were all better than those of the wild type. Further determination of physiological and biochemical indicators revealed that the leaf contents of superoxide dismutase (SOD) and proline (Pro) in the leaves of the mutant plants were significantly higher than those in the wild type, while the malondialdehyde (MDA) content was significantly decreased. In conclusion, the AtERF41 gene negatively regulates salt and drought tolerance in Arabidopsis thaliana, providing a potential target for the genetic improvement of crop stress tolerance. This study not only deepens our understanding of the role of DREB transcription factors in plant stress response but also provides a theoretical basis for improving crop stress tolerance using genetic engineering technology in the future. Full article

This paper explores the intertwined relationship between food systems and climate change, emphasizing their role in achieving the global target of limiting warming to 1.5 °C above pre-industrial levels. Food systems contribute significantly to greenhouse gas emissions; approximately 30% of global CO₂ emanates from agricultural practices, livestock production, and export-oriented supply chains. Conversely, climate change disrupts food production via rising temperatures, sea-level rise, and water scarcity, particularly in vulnerable regions such as Namibia and other parts of the Southern Hemisphere. In contrast, the European Arctic faces unique opportunities and challenges. This paper highlights mitigation and adaptation strategies, including smart agriculture technologies and genetic crop engineering. Behavioural shifts toward plant-based diets and strengthening local food systems are identified as critical for reducing emissions and enhancing resilience. Furthermore, the value of Indigenous knowledge and traditional food systems, which promote biodiversity, minimize fossil fuel use, and offer climate-resilient crops, is highlighted. Institutional capacity and governance frameworks are pivotal for implementing these solutions. The authors advocate for co-production of knowledge between the Northern and Southern Hemispheres, ensuring equitable adaptation rather than one-way technology transfer. Ultimately, integrated strategies combining technological innovation, policy reform, and cultural resilience are essential to break the cycle between food systems and climate change, fostering global cooperation toward the 1.5 °C goal. Full article

Chilli pepper agroecosystems (Capsicum annuum L.) are increasingly threatened by cadmium (Cd) contamination, with emerging climatic stressors such as drought further exacerbating risks to food safety and crop productivity. This review synthesizes current evidence on microbiome-mediated Cd phytostabilisation in chilli pepper, with a particular focus on the roles of capsaicinoids and cultivar-specific genetic regulation in shaping rhizosphere microbial communities. Existing studies demonstrate that capsaicinoid-rich cultivars selectively recruit specialized rhizosphere microbes, enhancing root-level Cd sequestration and achieving Cd retention efficiencies of approximately 40–55%, thereby substantially restricting Cd translocation to edible fruit tissues. Multi-strain plant growth-promoting rhizobacteria (PGPR) consortia, especially when combined with structured organic amendments, have been reported to reduce fruit Cd and nickel (Ni) accumulation by more than 87% in contaminated soils. These responses are regulated by pungency-associated genetic loci, including Pun1 (pungency locus 1) and Pun4 (pungency locus 4) genes, which influence secondary metabolism and microbial assembly under metal stress conditions. The review highlights key knowledge gaps regarding the long-term stability of engineered rhizobiomes, the in situ dynamics of the Capsicum volatilome as a microbial recruitment signal, and the interactive effects of Cd contamination and drought in field environments. Overall, this synthesis provides a mechanistic framework for deploying high-pungency cultivars and microbiome-based strategies to improve Cd phytostabilisation, with important implications for sustainable chilli production in drought-prone, metal-contaminated agroecosystems. Full article

Plant-parasitic nematodes (PPNs) cause big crop losses globally. Safe/reliable methods for their durable management strategies can harness various beneficial relationships among the plant immune system and related microbiomes. Molecular mechanisms basic to these relations reveal wide arrays of significant roles for plant-healthy growth. This review focuses on such relations of microbiomes to prime and immunize plants against PPNs. It also highlights molecular issues facing PPN-resistant varieties with possible solutions such as genetic breeding/engineering, grafting, PPN-antagonistic root exudates, and novel resistant cultivars. These issues call for optimal uses of various widespread groups of microbiomes. Related plant signaling hormones and transcription factors that regulate gene expression and modulate nematode-responsive genes to ease positive/negative adaptation are presented. Exploring PPN-resistance genes, their activation mechanisms, and signaling networks offers a holistic grasp of plant defense related to biotic/abiotic factors. Such factors relevant to systemic acquired resistance (SAR) via plant–microbe interactions to manage PPNs are stressed. The microbiomes can be added as inoculants and/or steering the indigenous rhizosphere ones. Consequently, SAR is mediated by the accumulation of salicylic acid and the subsequent expression of pathogenesis-related genes. To activate SAR, adequate priming and induction of plant defense against PPNs would rely on closely linked factors. They mainly include the engaged microbiome species/strains, plant genotypes, existing fauna/flora, compatibility with other involved biologicals, and methods/rates of the inoculants. To operationalize improved plant resistance and the microbiome’s usage, novel actionable insights for research and field applications are necessary. Synthesis of adequate screening techniques in plant breeding would better use multiple parameters (molecular and classical ones)-based ratings for PPN-host suitability designation. Sound statistical analyses and interpretation approaches can better identify genotypes with high-level, stable resistance to PPNs than the commonly used ones. Linking molecular mechanisms to consistent field relevance can be progressed via dissemination of many advanced techniques. The CRISPR/Cas9 system has been effective in knocking out both the OsHPP04 gene in rice to confer resistance against Meloidogyne graminicola and the GhiMLO3 gene in cotton to minimize the Rotylenchulus reniformis reproduction. Its genetic modifications in crops synthesized “transgene-free” PPN-resistant plants without decreased growth/yield. Characterizing microbiome species/strains needed to prime and immunize plants requires better molecular tools for fine-scale taxonomic resolution than the common ones used. The former can distinguish closely related ones that exhibit divergent phenotypes for key attributes like stability and production of enzymes and secondary metabolites. As PPN-control strategies via tritrophic interactions are more sensitive to the relevant settings than chemical nematicides, it is suggested herein to test these settings on a case-by-case basis to avoid erratic/contradictory results. Moreover, expanding the use of automated systems to expedite detection/count processes of PPN and related microbes with objectivity/accuracy is discussed. When PPNs and their related microbial distribution patterns were modeled, more aspects of their field distributions were discovered in order to optimize their integrated management. Hence, the feasibility of site-specific microbiome application in PPN–hotspot infections can be evaluated. The main technical challenges and controversies in the field are also addressed herein. Their conceptual revision based on harnessing novel techniques/tools is direly needed for future clear trends. This review also engages raising growers’ awareness to leverage such strategies for enhancing plant resistance and advancing the microbiome role. Microbiomes enjoy wide spectrum efficacy, low fitness cost, and inheritance to next generations in durable agriculture. Full article

Drought and salinity are among the most severe abiotic stresses limiting global agricultural productivity, and their frequency and intensity are expected to increase under ongoing climate change. Concurrently, the growing human population necessitates the development of crop varieties that combine high yield with enhanced stress tolerance. Jasmonates, including jasmonic acid (JA) and its derivatives, play pivotal roles in plant responses to abiotic stresses and are widely regarded as stress hormones. The bioactive conjugate jasmonoyl-isoleucine (JA-Ile) acts as a ligand for the coronatine insensitive 1 (COI1) receptor. Jasmonates regulate essential physiological processes, including leaf senescence, secondary metabolism, and nutrient homeostasis, which collectively contribute to plant adaptation to drought and salinity stress. In this review, we summarize recent advances in understanding the role of jasmonate signaling in plant responses to drought and salinity, with particular emphasis on the initiation and progression of leaf senescence and chlorophyll degradation pathways. By integrating genetic, biochemical, and physiological evidence, we discuss how targeted modulation of jasmonate levels and signaling components may be exploited to breed or engineer crops with improved tolerance to water-deficit and saline conditions. Full article

Field-evolved resistance of Helicoverpa zea to crops expressing Cry insecticidal proteins from Bacillus thuringiensis (Bt) is widespread across the United States. To comparatively evaluate physiological factors associated with Bt susceptibility, we analyzed two laboratory strains (Benzon and SIMRU) and one field colony obtained from a commercial corn field near Pickens, Arkansas. Biochemical assays of larval midgut extracts showed that Pickens exhibited significantly altered activities of chymotrypsin-like proteases, aminopeptidase N (APN), and alkaline phosphatase (ALP) compared with the SIMRU or Benzon colonies, with differences varying by larval instar. In contrast, trypsin-like protease activities did not differ significantly among the three colonies. Gene expression analyses of ten serine protease genes and seven candidate Cry receptor genes (including cadherin, ATP-binding cassette family C2, ALP, and four APN genes) revealed significant transcriptional differences in the Pickens relative to the lab colonies. Collectively, these results suggest that chymotrypsin-like proteases may play an important role in the activation of Cry toxins in H. zea. Altered chymotrypsin and APN activities, together with differential gene expressions in the Pickens population, likely contribute to reduced Bt susceptibility. The biochemical and molecular differences provide insight into potential physiological factors underlying reduced Bt susceptibility and may inform future Bt resistance monitoring and management strategies. Full article

Genetically modified (GM) forage crops engineered to accumulate elevated levels of lipids offer potential benefits for ruminant nutrition and greenhouse gas mitigation. However, robust and reproducible workflows for producing, harvesting, and preserving GM forage biomass under containment remain a critical bottleneck, particularly where regulatory constraints preclude field-scale evaluation. Here, we describe a controlled-environment workflow for the repeated cultivation, harvesting, and ensiling of GM high-metabolizable-energy (HME) perennial ryegrass and corresponding null controls. Plants were grown under greenhouse containment, subjected to multiple regrowth cycles, and harvested biomass was wilted and ensiled using small-scale laboratory silos. Silage fermentation characteristics, total lipid content, and fatty acid (FA) composition were assessed following short- and long-term storage. Over 16 months, approximately 130 kg dry matter (DM) of each genotype was produced across multiple harvests and ensiling batches. Seasonal variation strongly influenced herbage composition, with water-soluble carbohydrate concentrations 4–5-fold higher in spring–summer than autumn–winter. Following ensiling, HME silage consistently retained elevated FA content compared with null controls (4.85% vs. 2.75% DM) and higher gross energy (18.1 vs. 17.5 MJ kg⁻¹ DM). FA profiling indicated that major FA classes in HME were preserved across storage durations. After 342 days of storage, HME silage maintained 76% higher FA content, 4% greater DM digestibility, and 0.3–0.8 MJ kg⁻¹ DM higher metabolizable energy. Both genotypes exhibited good fermentation quality, with pH consistently below 4.1 and adequate lactic acid production. This study does not evaluate animal performance or methane mitigation outcomes but establishes a practical and reproducible methodology for generating characterized GM silage material under containment suitable for subsequent in vivo studies, addressing a key translational gap between GM forage development and animal-based evaluation. Full article

This review explores the innovative approaches in the development of next-generation biopesticides, focusing on molecular and microbial strategies for effective control of fungal plant pathogens. As agricultural practices increasingly seek sustainable solutions to combat plant diseases, biopesticides have emerged as a promising alternative to chemical pesticides, offering reduced environmental impact and enhanced safety for non-target organisms. The review begins by outlining the critical role of fungal pathogens in global agriculture, emphasizing the need for novel control methods that can mitigate their detrimental effects on crop yields. Key molecular strategies discussed include the use of genetic engineering to enhance the efficacy of biopesticides, the application of RNA interference (RNAi) techniques to target specific fungal genes, and the development of bioactive compounds derived from natural sources. Additionally, this review highlights the potential of microbial agents, such as beneficial bacteria and fungi, in establishing biocontrol mechanisms that promote plant health and resilience. Through a comprehensive review of recent studies and advancements in the field, this manuscript illustrates how integrating molecular and microbial strategies can lead to the development of effective biopesticides tailored to combat specific fungal threats. The implications of these strategies for sustainable agriculture are discussed, alongside the challenges and future directions for research and implementation. Ultimately, this review aims to provide a thorough understanding of the transformative potential of next-generation biopesticides in the fight against fungal plant pathogens, contributing to the broader goal of sustainable food production. Full article

Sugarcane (Saccharum spp.) is a globally important crop for sugar and bioenergy production. However, genetic improvement through conventional breeding is constrained by long breeding cycles, low genetic gain, and considerable operational complexity arising from its highly allopolyploid and aneuploid genome. With the increasing global demand for sustainable food and renewable energy, sugarcane breeding programs must accelerate the development of high-yielding, stress-tolerant cultivars through the integration of advanced biotechnological tools with traditional breeding approaches. Recent advances in genetic engineering, genomic selection (GS), and high-throughput omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and phenomics, have substantially enhanced the efficiency of trait improvement related to growth, development, yield, and stress resilience. The integration of multi-omics data enables the dissection of regulatory networks linking genotype to phenotype, improves predictive accuracy, and provides deeper insights into the molecular mechanisms underlying complex traits. These integrative approaches support more informed selection decisions and accelerate genetic gain in sugarcane breeding programs. This review synthesizes recent technological developments and their practical applications in sugarcane improvement. It highlights the strategic implementation of transgenic and genome-editing technologies, genomic selection, and multi-omics integration to enhance yield potential and resistance to biotic and abiotic stresses, thereby contributing to sustainable sugarcane production and global food and bioenergy security. Full article

Two genetically engineered Bacillus subtilis strains, BMV9 and BsB6, were evaluated in terms of culture medium (effect of nutrients on surfactin yield) and potential biotechnological applications of surfactin in agriculture and the petrochemical industry. BMV9 (spo0A3; abrB*; ΔmanPA; sfp+) is, to date, the highest surfactin producer reported scientifically, and BsB6 is a sfp+ laboratory derivative strain that has also demonstrated considerable production potential. To assess their performance, fermentation experiments were conducted in shake flasks using two different culture media, a mineral salt medium and a complex medium, each supplemented with 2% (w/v) glucose. Lipopeptides (surfactin and fengycin) were extracted and quantified at multiple time points (up to 48 h) via high-performance thin-layer chromatography (HPTLC). Optical density, residual glucose, and pH were monitored throughout the cultivation. In parallel, microbial growth in both media were also validated in small-scale cultivation approaches. Antifungal activity of culture supernatants and lipopeptide extracts was tested against two Diaporthe species, key phytopathogens in soybean crops. Given the agricultural relevance of these pathogens, the biocontrol potential of lipopeptides represents a sustainable alternative to conventional chemical fungicides. Additionally, oil displacement tests were performed to evaluate the efficacy of surfactin in enhanced oil recovery (EOR), bioremediation, and related petrochemical processes. High-resolution LC-MS/MS analysis enabled structural characterization and relative quantification of the lipopeptides. Overall, these investigations provide a comprehensive comparison of strain production performance and the associated impact of cultivation media, aiming to define the optimal conditions for economically viable surfactin production and to explore its broader biotechnological applications in agriculture and the petrochemical industry. Full article