Search Results (1,948)

Constructed wetlands (CWs) are sustainable and cost-effective systems that utilise plant–microbe interactions and natural processes for wastewater treatment. Microbial communities play a pivotal role in pollutant removal by crucial processes like nitrogen transformations, phosphorus cycling, organic matter degradation and the breakdown of emerging contaminants. Dominant phyla, such as Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes, collectively orchestrate these biogeochemical functions. Advances in molecular tools, including high-throughput sequencing and metagenomics, have revealed the diversity and functional potential of wetland microbiomes, while environmental factors, i.e., temperature, pH and hydraulic retention time, strongly influence their performance. Phosphorus removal efficiency is often lower than nitrogen, and large land requirements and long start-up times restrict broader application. Microplastic accumulation, the spread of antibiotic resistance genes and greenhouse gas emissions (methane, nitrous oxide) present additional challenges. The possible persistence of pathogenic microbes further complicates system safety. Future research should integrate engineered substrates, biochar amendments, optimised plant–microbe interactions and hybrid CW designs to enhance treatment performance and resilience in the era of climate change. By acknowledging the potential and constraints, CWs can be further developed as next-generation, nature-based solutions for sustainable water management in the years to come. Full article

Background and Objectives: Avian influenza poses a continuous public health threat, particularly to individuals with occupational exposure to poultry such as farm workers, live animal market employees, and processing plant staff. This study aimed to investigate the systemic metabolic effects of such exposure and to identify potential biomarkers for early detection and health risk assessment. Materials and Methods: An untargeted liquid chromatography–mass spectrometry (LC-MS)-based metabolomics approach was applied to analyze serum samples from occupationally exposed individuals and healthy controls. Multivariate statistical analysis, pathway enrichment, and topology analysis were performed to identify significantly altered metabolites and metabolic pathways. The least absolute shrinkage and selection operator (LASSO) algorithm was employed to select key metabolites. Results: Multivariate statistical analysis revealed a clear separation between the exposure group and control, suggesting distinct metabolic profiles between the two populations. Pathway analysis indicated significant alterations in alanine, aspartate, and glutamate metabolism, as well as tryptophan metabolism, which are closely linked to immune regulation, energy metabolism, and host–pathogen interactions. LASSO feature selection and subsequent manual verification identified 17 key metabolites with strong discriminative power. Furthermore, lipidomic profiling revealed a pronounced increase in lysophosphatidylcholine (LPC) levels and a concurrent decrease in phosphatidylcholine (PC) species in exposed individuals. Conclusions: This study reveals metabolic disruptions associated with occupational avian influenza exposure and identifies potential serum biomarkers related to immune and lipid metabolism. These findings provide novel insights into host responses to avian influenza exposure and may support early detection and health risk assessment in high-risk occupational populations. Full article

Chitinases have been demonstrated to enhance plant resistance to fungi in various pathosystems. Although there is evidence of the effectiveness of these proteins in coffee–fungus interactions, no genome-wide identification or characterization of coffee chitinases has been performed. In this study, we employed phylogenetic analysis, domain architecture, gene structure analysis, and subcellular localization to identify and characterize putative genes and proteins in the genomes of Coffea arabica and its progenitors, Coffea canephora and Coffea eugenioides. A total of 113, 47, and 69 putative chitinase proteins were identified in C. arabica, C. canephora, and C. eugenioides, respectively. These chitinases were classified according to their catalytic domains, GH18 and GH19, and into Classes I, II, III, IV, and V, as determined through phylogenetic analysis based on the Arabidopsis thaliana classification. Furthermore, based on orthologous analysis, we identified ten, six, and seven putative chitinases associated with fungal defense responses in C. arabica, C. canephora, and C. eugenioides, respectively. These findings are valuable for future studies focusing on coffee chitinases, particularly on genetic programs involved in plant pathogen resistance. Full article

Biological control with beneficial bacteria offers a sustainable alternative to synthetic agrochemicals for managing plant pathogens and enhancing plant health. However, bacterial biocontrol agents (BCAs) remain underexploited due to regulatory hurdles (such as complex registration timelines and extensive dossier requirements) and limited strain characterization. Recent advances in omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have strengthened the bioprospecting pipeline by uncovering key microbial traits involved in biocontrol. Genomics enables the identification of biosynthetic gene clusters, antimicrobial pathways, and accurate taxonomy, while comparative genomics reveals genes relevant to plant–microbe interactions. Metagenomics uncovers unculturable microbes and their functional roles, especially in the rhizosphere and extreme environments. Transcriptomics (e.g., RNA-Seq) sheds light on gene regulation during plant-pathogen-bacteria interactions, revealing stress-related and biocontrol pathways. Metabolomics, using tools like Liquid Chromatography–Mass Spectrometry (LC-MS) and Nuclear Magnetic Resonance spectroscopy (NMR), identifies bioactive compounds such as lipopeptides, Volatile Organic Compounds (VOCs), and polyketides. Co-culture experiments and synthetic microbial communities (SynComs) have shown enhanced biocontrol through metabolic synergy. This review highlights how integrating omics tools accelerates the discovery and functional validation of new BCAs. Such strategies support the development of effective microbial products, promoting sustainable agriculture by improving crop resilience, reducing chemical inputs, and enhancing soil health. Looking ahead, the successful application of omics-driven bioprospection of BCAs will require addressing challenges of large-scale production, regulatory harmonization, and their integration into real-world agricultural systems to ensure reliable, sustainable solutions. Full article

To elucidate the molecular mechanisms underlying salt tolerance in rice (Oryza sativa L.), this study investigated differential transcriptional responses during the tillering stage. Salt-tolerant (N14) and salt-sensitive (N6) varieties were subjected to 0.3% and 0.6% NaCl treatments for 72 h, and their transcriptomes were analyzed via RNA-Seq. The results revealed distinct response strategies: 372 differentially expressed genes (DEGs) were identified in N14 and 393 in N6, with only 17 genes responding similarly. Gene Ontology (GO) analysis showed the tolerant N14 activated protein phosphorylation and lipid transport, primarily in the membrane and extracellular regions (e.g., ATP binding), whereas the sensitive N6 activated photosynthesis and protein folding, localized to chloroplasts and peroxisomes. KEGG analysis highlighted the activation of “Plant-pathogen interaction” in N14 versus “Metabolic pathways” in N6. Differential transcription factor activation was also observed, with N14 mobilizing 52 TFs (mainly WRKY and MYB) and N6 mobilizing 36 TFs (mainly MYB and b-ZIP). This study demonstrates that N14 and N6 utilize significantly different molecular pathways to cope with salinity, providing a crucial theoretical foundation for identifying novel salt tolerance genes and developing molecular breeding strategies. Full article

In the long-term evolutionary process, species maintain a natural balance within certain limits through communication. As plants grow and function as producers, root enrichment fosters a dynamic rhizosphere microbiome, which serves not only as a disintegrator within the ecological niche but also as a medium for interaction between the host and the soil environment. The life cycle of fungi within the microbiome alternates between single-cell resting spores and multicellular trophic mycelia. This cycle not only establishes a stable rhizosphere environment but also plays a crucial role in regulating both intra- and interspecific information transmission, significantly impacting the environment and plant health. The rhizosphere microbiome, particularly the fungi it contains, can be harnessed to repair environmental damage and either promote the growth of the plant host or inhibit pathogens. However, the mechanisms underlying these actions remain inadequately understood, hindering the advancement of artificial regulation. Additionally, the variability of influencing factors, along with unstable genes and traits, poses challenges to industrial development. In conclusion, this paper focuses on the fungal components of the rhizosphere microbiome, introduces the mechanisms of communication and current applications, and further analyzes existing bottlenecks and potential solutions. The aim is to provide theoretical support for achieving green, sustainable agriculture through biological means. Full article

The Stockholm Paradigm, a multilevel framework for studying coevolutionary interactions, it is a promising method for obtaining a globally relevant understanding of the emergence of present and past host–parasite and insect–plant interactions. This research aimed to expand the application of the Paradigm to virus–host interactions, considering that viruses are being subjected to the same evolutionary forces as any other living organism. By applying different data science techniques, we described and discussed capacity and opportunity traits for Influenza A H1N1 strains, and how they might influence the pathogen’s host repertoire evolution, and thus ranked different strains according to their emergence risk in the human population. We hope to contribute to the application of different methods for understanding disease emergence, and consequently to the development of new public health strategies for preventing (re)emerging diseases. Full article

Plant seedlings are sensitive to cultivation environment factors and highly susceptible to pathogenic infections under adverse conditions such as inappropriate light environment. In this study, five kinds of LED lighting sources with different red (R) and blue (B) light combinations were set up: R10B0, R7B3, R5B5, R2B8 and R0B10 (with R:B ratios of 10:0, 7:3, 5:5, 2:8 and 0:10, respectively) to explore their effects on tomato seedlings’ growth, AsA-GSH cycle, endogenous hormones, and resistance to Phytophthora infestans, providing a basis for factory seedling light-quality selection. The results showed that with the increase in the proportion of blue light in the composite light, the growth indicators, photosynthetic characteristic parameters and enzyme activities of tomato seedlings generally increased. The contents of AsA, reduced glutathione, and oxidized glutathione all reached the maximum under high-proportion blue-light treatments (R2B8 and R0B10). The high-blue-light groups (R2B8 and R0B10) had the highest AsA and glutathione contents. The red–blue combinations reduced inhibitory ABA and increased growth-promoting hormones (e.g., melatonin), while monochromatic light increased ABA to inhibit growth. After inoculation with P. infestans, the apoplastic glucose content was the highest under the red–blue-combined treatments (R5B5 and R2B8), while the total glucose content in leaves was the highest under the combined light R2B8 treatment. In conclusion, high-proportion blue-light treatment can greatly promote the photosynthetic process of tomato, enhance the AsA-GSH cycle, and achieve the best effect in improving the resistance of tomatoes to P. infestans. Given these, the optimal light environment setting was R:B = 2:8. Full article

Conventional plant disease management primarily depends on chemical pesticides. However, with the rising concerns related to human health, environmental sustainability, and the emergence of resistant pathogens, biocontrol agents (BCAs) have gained more attention as eco-friendly alternatives. Among the potential biocontrol agents, yeasts stand out due to their safety, adaptability, and diverse antagonistic mechanisms, ranging from competition and enzyme secretion to volatile compound production and immunity induction. Despite their potential, yeast-based BCAs face limitations in field efficacy, regulation, and an incomplete understanding of their molecular interactions. Most current studies focus on simple, pairwise interactions, overlooking the complexity of agroecosystems, where plants, pathogens, and BCAs interact within broader microbial communities. This review addresses the importance of understanding tripartite interactions among plants, pathogens, and yeasts, supported by integrated transcriptomic and comparative genomic approaches, as well as meticulous observations of phenotypic expressions to uncover strain-specific defense mechanisms and mode of action. By referring to well-studied models like Blumeria graminis f.sp. hordei–Hordeum vulgare–Pseudozyma flocculosa and Trichoderma tripartite systems, we highlight the underexplored potential of yeasts to modulate plant immunity and influence pathogen behavior through complex molecular crosstalk. Bridging these knowledge gaps through integrating proteomic, metabolomic, and transcriptomic analyses, we can better harness yeasts in sustainable and targeted biocontrol strategies. Full article

Antibiotic resistance remains one of the most formidable challenges to modern medicine, threatening to outpace therapeutic innovation and undermine decades of clinical progress. While resistance was once viewed narrowly as a clinical phenomenon, it is now understood as the outcome of complex ecological and molecular interactions that span soil, water, agriculture, animals, and humans. Environmental reservoirs act as silent incubators of resistance genes, with horizontal gene transfer and stress-induced mutagenesis fueling their evolution and dissemination. At the molecular level, advances in genomics, structural biology, and systems microbiology have revealed intricate networks involving plasmid-mediated resistance, efflux pump regulation, integron dynamics, and CRISPR-Cas interactions, providing new insights into the adaptability of pathogens. Simultaneously, the environmental dimensions of resistance, from wastewater treatment plants and aquaculture to airborne dissemination, highlight the urgency of adopting a One Health framework. Yet, alongside this growing threat, novel therapeutic avenues are emerging. Innovative β-lactamase inhibitors, bacteriophage-based therapies, engineered lysins, antimicrobial peptides, and CRISPR-driven antimicrobials are redefining what constitutes an “antibiotic” in the twenty-first century. Furthermore, artificial intelligence and machine learning now accelerate drug discovery and resistance prediction, raising the possibility of precision-guided antimicrobial stewardship. This review synthesizes molecular insights, environmental drivers, and therapeutic innovations to present a comprehensive landscape of antibiotic resistance. By bridging ecological microbiology, molecular biology, and translational medicine, it outlines a roadmap for surveillance, prevention, and drug development while emphasizing the need for integrative policies to safeguard global health. Full article

14-3-3 proteins are highly conserved regulatory molecules in plants. In grapevine (Vitis vinifera L.), 14-3-3 proteins are studied under abiotic stress. However, the role of 14-3-3 proteins in the interaction between grapevine and downy mildew is yet to be studied. In this study, we identified a highly conserved 14-3-3 protein in grapevine and performed a phylogenetic analysis, revealing a close relationship between one of its homologs, 14-3-3ω proteins from Arabidopsis thaliana and Nicotiana benthamiana. We designated this homolog as Vv14-3-3ω. Subcellular localization studies showed that Vv14-3-3ω resides in the plasma membrane and cytoplasm. Expression analysis revealed a strong induction of Vv14-3-3ω at early time points following Plasmopara viticola infection, correlating with enhanced pathogen sporulation in grapevine. Furthermore, transient overexpression of Vv14-3-3ω in N. benthamiana increased susceptibility to the Phytophthora capsici pathogen and suppressed Flg22-induced pattern-triggered immunity (PTI) responses. Overexpression of Vv14-3-3ω in Nb14-3-3-silenced N. benthamiana plants resulted in increased susceptibility to P. capsici, suggesting functional conservation of this isoform. These findings indicate that Vv14-3-3ω functions as a susceptibility factor, facilitating pathogen infection and disease progression in grapevine, and highlight its potential role for improving resistance against downy mildew. Full article

Understanding the soil fungal community in vineyards sheds light on the interactions between plants and their associated microorganisms. For example, identifying arbuscular mycorrhizal fungi (AMF), which are beneficial to grapevine growth, is a good indicator of soil health. In contrast, other fungi, such as the pathogen group, can be detrimental to vine growth. The present study aimed to characterize the soil fungal community and the fungal diversity present at six Mediterranean vineyards located in Burgos (Spain), delving into fungal functional guilds and focusing on AMF and pathogenic fungal groups. The fungal structure was investigated using DNA metabarcoding in three soil samples taken from each vineyard, and differences in the abundance of functional guilds were assessed. Similar soil fungal community structures were observed among soil sample repetitions within vineyards. In contrast, adjacent vineyards presented differences in their microbial composition. Saprophytes followed by pathogens were the dominant fungal functional guilds across all vineyards. However, no differences in the relative abundance of the different fungal functional groups were observed among sites. The vineyard with the highest relative abundance of AMF (0.5%) also had the lowest pathogen relative abundance from all the sites (29.76%). Also, sites presenting a high relative abundance of pathogens in soil (>35%) had a low relative abundance of AMF (<0.05%). Our results suggest that the fungal community is affected by the intrinsic properties of the soil and the characteristics of each vineyard’s microsite over the effect of the geographical proximity. In addition, to improve our understanding of the soil microbial ecology, we highlight the necessity of prospecting soil fungal analyses into functional groups, interpreting diversity results within taxonomic groups alongside the total abundance of target groups/species. Full article

Plants have evolved a complex, multilayered immune system that integrates molecular recognition, signaling pathways, epigenetic regulation, and small RNA-mediated control. Recent studies have shown that DNA-level regulatory mechanisms, such as RNA-directed DNA methylation (RdDM), histone modifications, and chromatin remodeling, are critical for modulating immune gene expression, allowing for rapid and accurate pathogen-defense responses. The epigenetic landscape not only maintains immunological homeostasis but also promotes stress-responsive transcription via stable chromatin modifications. These changes contribute to immunological priming, a process in which earlier exposure to pathogens or abiotic stress causes a heightened state of preparedness for future encounters. Small RNAs, including siRNAs, miRNAs, and phasiRNAs, are essential for gene silencing before and after transcription, fine-tuning immune responses, and inhibiting negative regulators. These RNA molecules interact closely with chromatin features, influencing histone acetylation/methylation (e.g., H3K4me3, H3K27me3) and guiding DNA methylation patterns. Epigenetically encoded immune memory can be stable across multiple generations, resulting in the transgenerational inheritance of stress resilience. Such memory effects have been observed in rice, tomato, maize, and Arabidopsis. This review summarizes new findings on short RNA biology, chromatin-level immunological control, and epigenetic memory in plant defense. Emerging technologies, such as ATAC-seq (Assay for Transposase-Accessible Chromatin using Sequencing), ChIP-seq (Chromatin Immunoprecipitation followed by Sequencing), bisulfite sequencing, and CRISPR/dCas9-based epigenome editing, are helping researchers comprehend these pathways. These developments hold an opportunity for establishing epigenetic breeding strategies that target the production of non-GMO, stress-resistant crops for sustainable agriculture. Full article

Microplastic (MPL) and nanoplastic (NPL) contamination in soils is widespread, impacting soil invertebrates, microbial communities, and soil–plant systems. Here, we compiled the information from 100 research articles from 2018 onwards to enhance and synthesize the status quo of MPLs’ and NPLs’ impacts on such groups. The effects of these pollutants depend on multiple factors, including polymer composition, size, shape, concentration, and aging processes. Research on soil invertebrates has focused on earthworms and some studies on nematodes and collembolans, but studies are still limited to other groups, such as mites, millipedes, and insect larvae. Beyond soil invertebrates, plastics are also altering microbial communities at the soil–plastic interface, fostering the development of specialized microbial assemblages and shifting microbial functions in ways that remain poorly understood. Research has largely centered on bacterial interactions with MPLs, leaving understudied fungi, protists, and other soil microorganisms. Furthermore, MPLs and NPLs also interact with terrestrial plants, and their harmful effects, such as adsorption, uptake, translocation, and pathogen vectors, raise public awareness. Given the complexity of these interactions, well-replicated experiments and community- and ecosystem-level studies employing objective-driven technologies can provide insights into how MPLs and NPLs influence microbial and faunal diversity, functional traits, and soil ecosystem stability. Full article

HaWRKY33 is induced by salicylic acid and participates in the disease resistance signaling pathway of sunflower rust disease; however, the transcriptional regulatory mechanism of this protein against Sclerotinia sclerotiorum in sunflowers remains unclear. Given this, we conducted a survey of 426 sunflower accessions at the natural disease nursery in Gannan County and identified a single dominant physiological race, MCG1, using simple sequence repeat methods. Additionally, we performed indoor inoculation tests using this dominant race and obtained disease-resistant varieties, W227 and BC2202-03, as well as susceptible varieties, N241 and Z155. Further, we inoculated the above resistant and susceptible combination materials with MCG1 and conducted transcriptomic analysis and RT-qPCR validation. Through KEGG analysis, we found that HaWRKY33 is involved in the plant–pathogen interaction pathway, suggesting that HaWRKY33 may regulate sunflower defense responses against Sclerotinia sclerotiorum through the plant–pathogen interaction pathway. Finally, yeast two-hybrid screening and AI prediction using AlphaFold 3 revealed strong interactions between ARG-189 and GLU-344 amino acids in the HaWRKY33-AOA251SVV7 proteins, indicating that the HaWRKY33-AOA251SVV7 pattern regulates the sunflower defense response against Sclerotinia sclerotiorum in a transcriptional complex form. In summary, these results provide new insights into the disease resistance mechanisms of sunflowers against Sclerotinia sclerotiorum and promote the development of molecular breeding for sunflower resistance to Sclerotinia sclerotiorum. Full article