Search Results (171)

Ionotropic receptors (IRs) are a divergent subfamily of ionotropic glutamate receptors (iGluRs) that detect olfactory and environmental cues, influencing behaviors such as foraging and adaptation. To explore the evolution of IRs in relation to feeding ecology, we identified IRs and iGluRs from the genomes of four gastropods with distinct diets: Pomacea canaliculata (9 IRs/18 iGluRs), Bellamya purificata (10/22), Cipangopaludina chinensis (11/23), and Babylonia areolata (22/41). IRs were markedly expanded in B. areolata, suggesting lineage-specific diversification. Phylogenetic analysis grouped IRs and iGluRs into three clades, with IRs clustered with GluD, supporting early functional divergence following gene duplication. In all species, IR25b showed tandem duplication and played a central role in protein–protein interaction (PPI) networks. Most IRs were acidic, whereas IR-A and IR-C subgroups were basic, suggesting functional specialization among subfamilies. Structural analysis showed that IRs share conserved domains and motifs across species. Most IRs experienced purifying selection, while P. canaliculata showed relaxed constraints, suggesting weaker functional limitation. Collinearity analysis identified conserved genes, such as BarIR-A.6 and BarIR-D.1, across species. qPCR confirmed tissue-specific expression of IRs in multiple organs. Together, these results reveal the molecular features and evolutionary patterns of IRs in gastropods, highlighting their potential roles in olfaction and dietary adaptation. Full article

Tuber melanosporum, the black truffle, is a fungus of high economic and ecological value, but its underground detection remains a challenge due to the lack of reliable, non-invasive methods. This study presents the development and proof of concept of a portable optoelectronic nose that integrates nine optical sensors and one electrochemical sensor for the in vitro identification of T. melanosporum. The optical sensors use colorimetric and fluorogenic molecular indicators supported on UVM-7, alumina, and silica. Tests were performed with truffles at different depths and in the presence of soil and compost to evaluate the device’s multi-source response. Partial least squares discriminant analysis (PLS-DA) models showed robust discrimination between soil, compost, and truffles, with an accuracy of 0.91 under most conditions. Detection at 30 cm showed an accuracy of 0.94, confirming the system’s ability to differentiate between sample types. Performance improved in simplified scenarios based on the presence or absence of truffles. Furthermore, the artificial neural network models achieved optimal results in binary classification. Taken together, the results support the system’s potential as an accurate, non-invasive tool with possible application to the agronomic management of truffle orchards. Full article

Natural products represent one of the most diverse and functionally sophisticated groups of bioactive molecules found across plants, fungi, bacteria, and marine organisms. Recent advances in genomics, metabolomics, and chemical ecology have fundamentally redefined how these compounds are generated, regulated, and functionally deployed in nature. Increasing evidence reveals that chemical diversity arises not solely from taxonomic lineage but from ecological pressures, evolutionary innovation, and multi-organism interactions that shape biosynthetic pathways over time. Hybrid metabolic architectures, context-dependent activation of biosynthetic gene clusters, and cross-kingdom metabolic integration collectively portray a biosynthetic landscape far more dynamic and interconnected than previously understood. At the same time, mechanistic studies demonstrate that natural products rarely act through single-target interactions. Instead, they influence redox dynamics, membrane architecture, chromatin accessibility, and intracellular signaling in distributed and synergistic ways that reflect both ecological function and evolutionary design. This review synthesizes emerging insights into the evolutionary drivers, ecological determinants, and mechanistic foundations of natural product diversity, highlighting the central role of silent biosynthetic gene clusters, meta-organismal chemistry, and network-level modes of action. By integrating these perspectives, we outline a conceptual and methodological framework capable of unlocking the vast biosynthetic potential that remains dormant within natural systems. Collectively, these advances reposition natural product research as a deeply integrative discipline at the intersection of molecular biology, ecology, evolution, and chemical innovation. Full article

The growth process of poplar faces severe environmental challenges. Notably, poplar canker, caused by Botryosphaeria dothidea, has significantly impaired poplar productivity and ecological functions. However, research on the molecular mechanisms underlying poplar resistance to this disease remains incomplete. This study systematically elucidated the molecular mechanisms of Populus davidiana × P. alba var. pyramidalis (Pdpap) in response to B. dothidea stress by integrating phenotypic, physiological, biochemical, and transcriptomic analyses. The results demonstrated that 5 d post-inoculation with B. dothidea, the stem wound sites darkened and developed lesions. Following pathogen infection, H₂O₂ content and SOD and POD activity initially increased then decreased, while MDA content overall showed a declining trend with prolonged infection time. KEGG enrichment analysis revealed that DEGs were significantly enriched in the MAPK signaling pathway, plant hormone signal transduction, and phenylpropanoid biosynthesis pathways. Gene modules significantly associated with physiological indices were screened using WGCNA. Within these modules, hub genes in the regulatory network were further identified, leading to the selection of P2C76. The genome-wide identification of PtrPP2Cs classified 124 members into 13 subgroups. Collectively, this study dissects the gene expression regulation and molecular defense mechanisms of poplar under B. dothidea infection, providing novel molecular insights for its molecular breeding. Full article

Oil pollution poses a persistent threat to soil ecosystems globally, and bioremediation using bacterial consortia has emerged as a cost-effective remediation strategy. However, the role of weak petroleum-degrading bacteria in enhancing the efficiency of specialized petroleum-degrading bacteria remains unclear. This study explores the synergy and remediation potential of a two-bacterial consortium: the petroleum-degrading bacterium Rhodococcus sp. OS62-1 and the weak petroleum-degrading bacterium Pseudomonas sp. P35. A 25-day microcosm experiment was conducted with petroleum-contaminated soil, and four treatments were set: (1) uninoculated control, (2) inoculation with Rhodococcus sp. OS62-1 alone, (3) inoculation with Pseudomonas sp. P35 alone, and (4) inoculation with the consortium. Soil samples were collected periodically to analyze petroleum degradation efficiency, soil enzyme activities (dehydrogenase, catalase, polyphenol oxidase, and lipase), and microbial community composition (16S rRNA gene sequencing). Inoculating the soils with this consortium produced a higher petroleum degradation rate, microbial activity, and soil enzyme activity than inoculation with strain OS62-1 or P35 alone. Inoculation with strain P35 also contributed to the maintenance of strain OS62-1 during bioremediation. The study of microbial community structure found that the relative abundance of phylum Acidobacteriota (57.6 ± 5.3% to 75.6 ± 8.1%) and the Nocardioides genus (36.4 ± 4.5% to 53.0 ± 9.2%) increased dramatically during the bioremediation process. Pearson’s correlation analysis revealed that inoculation with strain OS62-1 and/or strain P35 increases the soil enzyme activity, boosts native oil-degrading bacteria, and accelerates the degradation of petroleum contaminants. Molecular ecological networks analysis revealed that inoculation with strain OS62-1 and/or strain P35 increased the complexity and robustness of the microbial network. These findings confirm that weak petroleum-degrading bacteria can synergistically enhance the bioremediation efficiency of specialized petroleum-degrading bacteria, providing a practical strategy for optimizing the design of bacterial consortia in the bioremediation of oil-polluted soils. Full article

Dark fermentative hydrogen production is constrained by challenges including low hydrogen yield and operational instability. Magnetic nanoparticles (MNPs) have emerged as promising additives for enhancing biohydrogen production due to their unique physicochemical characteristics, such as high specific surface area, excellent electrical conductivity, and inherent magnetic recyclability. This review systematically compares the enhancement mechanisms of MNPs in two distinct microbial systems: pure cultures and mixed cultures. In pure cultures, MNPs function primarily at the cellular and molecular levels through the following: (1) serving as sustained-release sources of essential metallic cofactors like Fe and Ni to promote hydrogenase synthesis and activation; (2) acting as efficient electron carriers that facilitate intracellular and extracellular electron transfer; and (3) redirecting central carbon metabolism toward high-hydrogen-yield acetate-type fermentation. In mixed cultures, which are more representative of practical applications, MNPs operate at the ecological level through the following: (1) modifying microenvironmental niches to exert selective pressure that enriches hydrogen-producing bacteria, such as Clostridium; (2) forming conductive networks that promote direct interspecies electron transfer and strengthen syntrophic metabolism; and (3) enhancing system robustness via toxin adsorption and pH buffering. Despite promising phenomenological improvements, critical knowledge gaps remain, including unclear structure–activity relationships of MNPs, insufficient quantification of electron transfer pathways, unknown genetic regulatory mechanisms, and overlooked magnetobiological effects. Future research should integrate electrochemical monitoring, multi-omics analyses, and advanced characterization techniques to deepen the mechanistic understanding of nanomaterial–microbe interactions. This review aims to provide theoretical insights and practical strategies for developing efficient and sustainable MNP–microorganism hybrid systems for scalable biohydrogen production. Full article

Background: Gastrodiae Rhizoma, the dried tuber of Gastrodia elata Bl. (Orchidaceae), is a traditional Chinese medicinal (TCM) and edible plant. Its quality formation is closely associated with rhizosphere microorganisms; however, the specific underlying mechanisms remain unclear. Methods: Tubers and rhizosphere soils were collected from seven major production regions of G. elata. Soil physicochemical properties were analyzed, and integrative analyses combining soil microbiome and untargeted metabolome profiling were conducted. The anti-inflammatory activity of G. elata extracts was evaluated using a RAW264.7 macrophage model. Multivariate statistical approaches, including OPLS-DA and correlation network analysis, were used to decipher relationships among environmental factors, microbial communities, metabolic profiles, and bioactivities. Results: A total of 39,250 bacterial ASVs and 10,544 fungal ASVs were identified. The bacterial community, dominated by Proteobacteria and Acidobacteria, was strongly influenced by soil chemical factors, including pH and total nitrogen. The fungal community, primarily composed of Ascomycota and Basidiomycota, exhibited marked sensitivity to altitudinal gradients. Correlation analysis revealed that key secondary metabolites, including flavonoids and phenolic acids, along with their anti-inflammatory activities, were significantly associated with rhizosphere microorganisms such as Edaphobaculum, Hypocrea, and Pseudomonas. Conclusions: Our findings outline the pathways connecting environmental factors, the microbiome, and functional metabolites in G. elata, highlighting the importance of environmental–microbial interactions in determining metabolic outcomes. This work provides new insights into the ecological and molecular mechanisms behind the quality formation of this medicinal plant. Full article

The endangered Rhinogobio ventralis, endemic to the upper Yangtze River, is dependent on captive breeding for its conservation. However, this highly stress-sensitive species is exceptionally susceptible to Ichthyophthirius multifiliis, leading to severe pathology and high mortality in culture. Elevated salinity holds potential for managing key aquaculture pathogens, including Ichthyophthirius multifiliis and Saprolegnia spp. However, its potential unintended ecological consequences remain insufficiently understood. This study evaluated the systemic impacts of 5‰ salinity on the culture environment of the endangered species Rhinogobio ventralis, using integrated 16S/18S rRNA gene sequencing and water quality analysis. The results demonstrated that while salinity treatment effectively reduced the environmental molecular signal of harmful eukaryotes such as Ichthyophthirius and Saprolegnia, it also induced significant ecological shifts: (1) aquatic prokaryotic diversity increased, yet the self-purification capacity of the water was compromised, indicated by elevated dissolved oxygen, nitrate nitrogen, and total nitrogen; (2) in the fish intestinal microbiome, a decline in potentially beneficial taxa (e.g., Exiguobacterium) co-occurred with an enrichment of genera containing potentially pathogenic species (e.g., Staphylococcus and Pseudomonas), collectively suggesting a state of dysbiosis; (3) co-occurrence network analysis revealed that the aquatic microbial community developed greater complexity, while the intestinal network became structurally simplified and more antagonistic. These findings reveal that elevating salinity in freshwater aquaculture systems compromises both host microbiome health and aquatic ecosystem functioning. As such, future aquaculture management should integrate supportive measures like probiotic supplementation to maintain overall system stability. Full article

(1) This study explored Lacticaseibacillus rhamnosus MS27, a newly isolated strain, as a potential probiotic candidate for alleviating the onset and severity of ulcerative colitis (UC). (2) L. rhamnosus MS27 was isolated and subjected to biochemical identification, antibiotic sensitivity testing, and antibacterial activity assessment. Dextran sulfate sodium (DSS) colitis model mice were used to evaluate its alleviating effects. In this study, 16S rRNA microbiome and eukaryotes reference transcriptome analyses were conducted to investigate its impact on intestinal microbial ecology and potential molecular mechanisms. (3) L. rhamnosus MS27 exhibits high acid tolerance at pH 3.23 and maintains a high viable bacterial count for 24 h. It can utilize sucrose, lactose, maltose, inulin, esculin, salicin, and mannitol but not raffinose, and it is sensitive to carbenicillin, erythromycin, tetracycline, chloramphenicol, clindamycin, and penicillin. It effectively increases the abundance of beneficial microbes, particularly Akkermansia, Muribaculaceae, and Limosilactobacillus reuteri (p < 0.05), while significantly reducing microorganisms linked to human pathogens causing diarrhea and gastroenteritis (p < 0.05). Transcriptomic analysis demonstrated that the expression levels of Igkv16-104 and C1qtnf3 were significantly downregulated in the presence of L. rhamnosus MS27 treatment compared to DSS treatment alone (p < 0.05). Further analysis revealed significant differences in genes related to immune functions, antigen presentation, and immune cell markers, indicating potential protein–protein interaction networks, particularly among genes of the major histocompatibility complex (MHC). (4) L. rhamnosus MS27, as a novel strain, demonstrates a significant capacity to alleviate inflammatory phenotypes. L. rhamnosus MS27 exhibits distinctive metabolic characteristics in lactic acid utilization, acetic acid and oleic acid production. Furthermore, it contributes to systemic homeostasis regulation by modulating Turicibacter to link intestinal microbiota composition with host immune function. Full article

Urban green spaces are essential components of city ecosystems, providing environmental and social benefits while simultaneously serving as potential entry points for invasive plant pathogens. In recent years, increasing attention has been directed toward the role of urban environments as reservoirs and transmission corridors for oomycetes, a group of highly destructive microorganisms affecting trees and shrubs. This study aimed to investigate the diversity and potential introduction pathways of oomycetes in three Warsaw parks representing distinct ecological settings: a historical city park, a large landscape park with aquatic features, and a newly constructed linear park. Samples of soil, and surface water were collected and analysed using standard isolation and molecular identification methods. Four species were identified: Phytophthora cactorum, P. cambivora, Phytopythium vexans, and Ph. montanum—the latter two representing first records for urban parks in Poland. The results indicate that nursery plant material, surface water systems, and wildlife activity, particularly birds, are likely contributors to the introduction and spread of these pathogens in city landscapes. The findings underscore the growing phytosanitary risk associated with urban greenery, where the interplay of anthropogenic disturbance, high plant turnover, and complex hydrological networks facilitates pathogen establishment. This research highlights the urgent need to integrate urban biosecurity strategies with routine molecular monitoring, nursery inspections, and wildlife surveillance to limit further dissemination of invasive oomycetes and enhance the resilience of urban tree populations. Full article

Salinity is a long-standing global environmental stressor of terrestrial agroecosystems, with important implications for viticulture sustainability, especially in arid and semi-arid environments. Salt-induced physiological and biochemical disruptions to grapevines undermine yield and long-term vineyard sustainability. This review aims to integrate physiological, molecular, and omics-based insights to elucidate how grapevine rootstocks confer salinity tolerance and to identify future breeding directions for sustainable viticulture. This review critically assesses the ecological and molecular processes underlying salt stress adaptation in grapevine (Vitis spp.) rootstocks, with an emphasis on their contribution to modulating scion performance under saline conditions. Core adaptive mechanisms include morphological plasticity, ion compartmentalization, hormonal regulation, antioxidant defense, and activation of responsive genes to stress. Particular emphasis is given to recent integrative biotechnological developments—including transcriptomics, proteomics, metabolomics, and genomics—that reveal the intricate signaling and regulatory networks enabling rootstock-mediated tolerance. By integrating advances across eco-physiological, agronomic, and molecular realms, this review identifies rootstock selection as a promising strategy for bolstering resilience in grapevine production systems confronted by salinization, a phenomenon increasingly exacerbated by anthropogenic land use and climate change. The research highlights the value of stress ecology and adaptive root system strategies for alleviating the environmental consequences of soil salinity for perennial crop systems. Full article

Apple represents one of the most economically significant fruit crops worldwide, and the performance of its scion is largely determined by the physiological and genetic characteristics of the rootstock. Despite their superior ecological adaptability and growth-controlling attributes, many dwarfing apple rootstocks exhibit inherently poor rooting competence, which poses a critical limitation to their large-scale clonal propagation and commercial utilization. Adventitious root (AR) formation is a pivotal yet highly intricate developmental process that governs the success of asexual propagation. It is orchestrated by a complex network of hormonal signaling, transcriptional regulation, metabolic reprogramming, and environmental cues. Over the past decade, remarkable advances have elucidated the physiological, biochemical, and molecular frameworks underpinning AR formation in apple rootstocks. This review provides an integrative synthesis of current progress in vegetative propagation techniques—including cutting, layering, and tissue culture—and systematically dissects the endogenous and exogenous factors influencing AR development. Particular emphasis is placed on the regulatory interplay among phytohormones, carbohydrate and nitrogen metabolism, phenolic compounds, transcription factors (such as WUSCHEL-RELATED HOMEOBOX (WOX), LATERAL ORGAN BOUNDARIES DOMAIN (LBD), and RESPONSE FACTOR (ARF families), and epigenetic modulators that collectively coordinate root induction and emergence. Furthermore, emerging insights into multi-omics integration and genotype-specific molecular regulation are discussed as strategic pathways toward enhancing propagation efficiency. Collectively, this review establishes a comprehensive theoretical framework for optimizing the asexual propagation of apple rootstocks and provides critical molecular guidance for breeding novel, easy-to-root genotypes that can drive the sustainable intensification of global apple production. Full article

Leguminous plants are critical global crops for food security, animal feed, and ecological sustainability due to their ability to establish nitrogen-fixing symbioses with rhizobia and their high nutritional value. Autophagy, a highly conserved eukaryotic catabolic process, mediates the degradation and recycling of cytoplasmic components through the fusion of autophagosome with vacuole/lysosome and plays essential roles in plant growth, stress adaptation, and cellular homeostasis. This review systematically summarizes current knowledge of autophagy in both Arabidopsis and leguminous plants. We first outline the conserved molecular machinery of autophagy, focusing on core autophagy-related (ATG) genes in Arabidopsis and key legume species such as Glycine max, Arachis hypogaea, Pisum sativum, Cicer arietinum, and Medicago truncatula. Furthermore, the review dissects the intricate molecular regulatory networks controlling autophagy, with an emphasis on the roles of phytohormones, transcription factors, and epigenetic modifications. We then highlight the multifaceted physiological functions of autophagy in these plants. Additionally, a preliminary analysis of the ATG8 gene family in peanut indicates that its members may be involved in seed development, biological nitrogen fixation, and drought resistance. Finally, it highlights key unresolved challenges in legume autophagy research and proposes future research directions. This review aims to provide a comprehensive theoretical framework for understanding the unique regulatory mechanisms of autophagy in legumes and to provide insights for molecular breeding aimed at developing stress-resilient, high-yielding, and high-quality legume cultivars. Full article

Endocrine-disrupting chemicals (EDCs) are widespread contaminants that interfere with hormonal signaling and compromise reproductive success in aquatic organisms. Vitellogenin (VTG) is one of the most widely established biomarkers of estrogenic exposure, especially in males and juveniles. However, evidence from multi-omics studies indicates that VTG induction occurs within broader transcriptional and regulatory networks, involving genes such as cyp19a1 (aromatase), cyp1a (cytochrome P4501A), and other stress-responsive genes, underscoring the complexity of endocrine disruption. This review focuses on nuclear receptor isoforms, including estrogen receptor alpha (ERα), estrogen receptor beta (ERβ), and androgen receptor (AR) variants. We examine the diversification of vtg gene repertoires across teleost genomes and epigenetic mechanisms, such as DNA methylation and microRNAs, that modulate sex-dependent sensitivity. In addition, we discuss integrative approaches that combine VTG with transcriptomic, epigenetic, and histological endpoints. Within the Adverse Outcome Pathway (AOP) and weight-of-evidence (WoE) frameworks, these strategies provide mechanistic links between receptor activation and reproductive impairment. Finally, we outline future directions, focusing on the development of sex-specific biomarker panels, the integration of omics-based data with machine learning, and advances in ecogenomics. Embedding molecular responses into ecological and regulatory contexts will help bridge mechanistic insights with environmental relevance and support sustainability goals such as SDG 14 (Life Below Water). Full article

Leptospirosis is a globally distributed zoonosis of major public health and veterinary relevance, caused by pathogenic species of the genus Leptospira. Brazil is a hotspot for transmission due to its ecological diversity and complex host–environment interfaces. This study explored the genetic diversity and structure of circulating pathogenic Leptospira spp. in Brazil through a single-locus sequence typing (SLST) analysis based on the secY gene. A total of 531 sequences were retrieved from GenBank and subjected to phylogenetic and haplotype diversity analyses. Maximum likelihood reconstruction revealed strongly supported clades for seven species, with L. interrogans being the most prevalent and broadly distributed across hosts and regions. This species showed evidence of clonal expansion, with a dominant haplotype (n = 242) shared by humans, domestic animals, and wildlife. In contrast, L. santarosai and L. noguchii exhibited high haplotypic diversity and reticulated network structures, reflecting greater evolutionary variability. The species L. kirschneri and L. borgpetersenii displayed reduced haplotypic variation, the latter mainly associated with cattle, consistent with its host-adapted profile. Host- and biome-based haplotype networks revealed both the broad ecological adaptability of certain lineages and the exclusive presence of haplotypes restricted to specific environments, such as those found in marine mammals from the Atlantic Ocean. Genetic distance analyses confirmed the strong taxonomic resolution of the gene secY, which effectively distinguished closely related species while capturing intraspecific diversity. These findings provide a comprehensive molecular overview of pathogenic Leptospira in Brazil, highlighting ecological connectivity across hosts and biomes, as well as the contrasting evolutionary dynamics among species. Beyond describing genetic patterns, our analyses emphasize evolutionary processes, host–environment connectivity, and the implications for One Health. This integrative framework strengthens the basis for surveillance and control strategies in other endemic regions in the world. Full article