Search Results (209)

Fusarium oxysporum-associated disease symptoms in rice (Oryza sativa L.) seedlings represent an experimentally tractable model for evaluating microbiome-mediated disease suppression under controlled conditions. Biological control of Fusarium-associated disease development in rice provides a promising ecological alternative to chemical fungicides. However, the mechanisms underlying the spatial reconfiguration of the host plant multicompartment microbiome in response to complex inoculants remain insufficiently understood. In this study, we investigated the ability of the monoculture Bacillus amyloliquefaciens Bn1 (B. amyloliquefaciens Bn) and phototrophic–heterotrophic consortia composed of Nostoc sp. J-1 and B. amyloliquefaciens Bn1 to suppress Fusarium oxysporum infection, with parallel profiling of bacterial and fungal communities in rhizosphere soil, the root endosphere, and the phyllosphere using 16S rRNA and ITS amplicon sequencing. Phenotypic screening showed that microbial inoculant application significantly reduced the disease index by up to 55% while maintaining plant dry weight. The protective phenotype was not primarily associated with shifts in alpha diversity, but rather with compartment-specific reorganization of microbial communities. These findings suggest that biological control efficacy was associated less with the overall taxonomic scale of microbiome disturbance than with the formation of a functionally balanced, compartment-specific holobiont architecture but by the formation of a functionally balanced, compartment-specific holobiont architecture, providing a conceptual basis for the targeted design of next-generation phototrophic–heterotrophic biopreparations. Full article

Chinese Cordyceps (Ophiocordyceps sinensis) and Xinjiang Cordyceps (Paraisaria gracilis) are related entomopathogenic fungi that occupy different elevations and habitats. Whether their holobiont architectures have diverged accordingly is unknown. In this hypothesis-generating study based on samples from single locations (Altai Mountains for Xinjiang Cordyceps and Nagqu, Tibet for Chinese Cordyceps), we compared the two species using amplicon sequencing, untargeted metabolomics, and comparative genomics. Chinese Cordyceps from the sampled site comprises a specialized parasitic fungus and host-adapted bacteria for nutrient acquisition. Xinjiang Cordyceps from the Altai site contains diverse saprotrophic fungi and a rhizosphere-like bacterial consortium enriched in oxidative defense and biofilm genes, a finding that may explain why its sclerotia remain intact for 3–5 years in this population. Metabolomic profiles distinguish the two species at these sites. Xinjiang Cordyceps shows upregulation of tyrosine and porphyrin pathways, and its bacterial community shows functional enrichment in the same pathways, suggesting cross-kingdom coordination. P. gracilis has lost many gene families, and the retained species-specific genes are linked to cell adhesion and acyltransferase activity. Xinjiang Cordyceps is not a simple substitute for Chinese Cordyceps but appears to represent a different ecological strategy shaped by genome streamlining and host–microbe coadaptation. Our findings generate testable hypotheses for future large-scale, multi-population investigations. Full article

Aquaponics is a production system that results from the interaction between aquaculture and hydroponics. Whereas the mechanistic view of aquaculture and hydroponics has been explained using a simplistic nitrogen (N) cycle pathway, a new perspective on aquaponics could be obtained through the lens of a meta-holobiont. In this perspective, the symbiotic interplay across levels involving fish, plants, and microbes will be crucial for understanding and engineering aquaponics. With the advent of omics technology, it has become easier to explain the molecular basis of nutrient cycling and system stability. Although most available data are descriptive at present, they provide a foundation for understanding microbial interactions within the system. In this paper, we examine the genomic signatures of the N cycle, focusing on the roles of comammox bacteria and nifH-mediated N fixation. Moreover, the functionality of siderophore-producing microbes in enhancing nutrient bioavailability will be analyzed. Additionally, we explore the molecular mechanisms involved in the synthesis of secondary metabolites and Induced Systemic Resistance. Lastly, we discuss the path to aquaponics 4.0 and bio-digital twin modeling in aquaponics. Full article

Increasing evidence suggests pancreatic cancer develops within a host–microbe ecosystem in which microbial communities across anatomical niches interact with tumour biology, immune regulation, metabolism, and therapeutic response. This review examines pancreatic cancer through the lens of humans as holobionts, integrating evidence from the oral, gut, biliary, and intratumoural microbiomes. Epidemiological and sequencing studies demonstrate consistent microbial alterations across these niches in pancreatic cancer, including oral dysbiosis associated with periodontal pathogens, gut microbial shifts toward pro-inflammatory taxa, disease-specific biliary microbial signatures, and the presence of distinct intratumoural microbial communities. Mechanistic studies indicate that intestinal barrier disruption, microbial translocation, immune and metabolite signalling can influence tumour immune architecture, macrophage polarisation, T-cell infiltration, oncogenic signalling pathways, and chemotherapeutic metabolism, particularly inactivation by tumour-associated bacteria. Microbiome-driven shifts in immunometabolism can reprogramme immune-cell metabolic pathways, impairing effective T-cell activation, promoting tumour-supportive macrophage phenotypes. Emerging therapeutic strategies aim to modulate the microbiome–tumour axis, including dietary interventions, probiotics and immunonutrition, faecal microbiota transplantation, engineered microbial therapies, and microbiome-informed antibiotic strategies. While pre-clinical findings are compelling and early-phase clinical studies suggest feasibility, most evidence remains associative and heterogeneous across cohorts and methodologies. Understanding pancreatic cancer as a multi-site ecological system may help explain inter-patient variability in disease progression and treatment response. This could usher in a new era for therapeutic manipulation where future progress will depend on longitudinal, multi-omic, and interventional studies to determine whether microbiome-targeted strategies can produce clinically meaningful improvements in pancreatic cancer outcomes. Full article

Ticks harbor complex microbial communities composed of symbionts, commensals, and tick-borne pathogens (TBPs). Together, these microorganisms form the tick holobiont. Within this system, the tick’s physiological architecture structures microbial communities by distributing microorganisms across distinct tissues. This compartmentalization creates spatially distinct ecological niches, which in turn shape how microbial communities assemble and interact. In this review, we integrate ecological theory with current knowledge of tick microbiome research to examine how pathogen–pathogen and pathogen–microbiome interactions emerge within these tissue-structured microbial communities. We first outline how baseline ecological filters, including tick species, developmental stage, tissue identity, vertical transmission, and environmental context, shape the microbiome configuration through community assembly processes. We then examined how TBPs, as high-impact colonizers, can further modify microbial networks by altering host-mediated selective pressures, influencing interaction topology, and reshaping community stability. Based on these observations, we propose a dual selective pressure framework in which (i) baseline ecological structuring processes and (ii) pathogen-associated selective pressures interact to determine the microbial network configuration and functional outcomes within the tick holobiont. These interacting forces may drive shifts in diversity, modularity, keystone taxa emergence, and network resilience, ultimately influencing vector competence. This review frames the microbial communities within the tick holobiont as spatially structured ecological systems shaped by multilevel selective pressures. This conceptual foundation provides a coherent framework for understanding microbial interactions in arthropod vectors and highlights avenues for mechanistic research and microbiome-based strategies to mitigate tick-borne diseases. Full article

The gut microbiota, acting as a critical extrinsic endocrine organ, is profoundly involved in the pathological evolution and therapeutic response of hormone-dependent malignancies. This review elucidates the core mechanisms governing the microbiota, endocrine, and immune triple-axis. Multi-omic and biochemical evidence demonstrates that microbial metabolic networks, comprising the estrobolome, androbolome, and progestobolome/corticobolome, rely on enzymatic systems such as β-glucuronidases (GUS) and steroid-17,20-desmolases to execute hormone deconjugation and structural modification, thereby modulating systemic steroid exposure. Concurrently, microbe-derived metabolites, such as secondary bile acids and purine derivatives, act as inter-kingdom messengers. These metabolites remodel the tumor immune microenvironment by antagonizing hormone receptors and activating specific signaling axes, such as the Inosine-A2AR pathway. By modulating localized immune cells like effector T cells and myeloid cells, they play a pivotal role in tumor immune evasion. Furthermore, pharmacomicrobiomics reveals a bidirectional regulation between anti-tumor agents and the gut microbiota, where endocrine and immunotherapeutic drugs can induce microbial dysbiosis, while specific gut taxa contribute to primary or acquired resistance by enzymatically inactivating drugs (e.g., reductive inactivation of Enzalutamide) or providing hormonal precursors through bypass pathways. Facing translational challenges, such as real-world microbiome complexity and the colonization resistance of indigenous flora, we propose treating the human body as a unified host–microbe holobiont system. Future research should leverage gnotobiotic models and genetic causal inference to establish functional causality. These efforts will facilitate the development of precision tools, including ubiquitin–proteasome system (UPS) modulators, microbial enzyme inhibitors, and engineered live biotherapeutics. Collectively, these systems biology strategies offer a robust framework for overcoming therapeutic resistance in hormone-dependent malignancies. Full article

Coral reefs are biodiversity hotspots increasingly threatened by climate-induced bleaching, yet profiling the coral holobiont—the host and its associated microbiota—remains technically challenging due to high host-DNA contamination (often >95%) and the lack of comprehensive reference databases. Here, we present holo-2bRAD, a type IIB restriction site-associated DNA sequencing approach. This method, strategically integrated with a meticulously curated hologenome database (comprising 404,946 microbial genomes and 56 coral-derived metagenome-assembled genomes), effectively overcomes overwhelming host contamination (~99%). We demonstrate its exceptional species specificity (99.92%) in profiling Galaxea fascicularis (Linnaeus, 1767; Order Scleractinia, Family Euphylliidae) holobionts across bleaching severities, thereby validating its technical feasibility. Leveraging this high-resolution tool, our hologenome analysis revealed significant restructuring of coral-associated microbiota during bleaching, where microbial shifts (e.g., depletion of beneficial Thermoanaerobacterium thermosaccharolyticum and enrichment of stress-responsive bacteria) correlated more strongly with bleaching phenotypes than host genetic variation. By providing cost-effective, multi-domain hologenome profiling at unprecedented resolution, holo-2bRAD offers a practical tool for investigating holobiont dynamics and developing microbiome-informed coral conservation strategies. Full article

The plant holobiont comprises the host plant and its associated microbial communities functioning together as a single ecological and evolutionary unit that influences plant health, productivity, and environmental adaptability. Endophytes, formerly classified primarily as plant growth-promoting agents, are currently gaining traction as integral components of plant-associated microbiomes such as the rhizobiome and phytobiome. They can alter host-mediated root exudation patterns, microbial community structure, and nutrient dynamics within the rhizosphere. Endophytes play an important role in modulating host signaling pathways, thus influencing plant growth. Various mechanisms by which endophytes contribute to improved plant performance include soil microbiome dynamics, carbon sequestration, and strengthening the host’s ability to tolerate abiotic stressors. Multi-omics, single-cell, and systems-level approaches integrated with CRISPR, metabolic engineering, and AI, together with systems biology, guided by in vitro and field studies, support predictive modeling and provide evidence for the evolution of system-driven strategies for developing effective bioinoculants. This review highlights the potential of endophytes to serve as a scalable and sustainable component of climate-resilient and regenerative agricultural systems, while acknowledging ecological variability and field-level constraints. Full article

Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches—marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays—and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge–cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship. Full article

Background: Medicinal plants function as complex holobionts, with their therapeutic potential significantly shaped by the associated microbiome, particularly endophytic fungi. These symbionts engage in a sophisticated “chemical signaling” with their hosts, acting as biotic elicitors that modulate plant secondary metabolism while simultaneously responding to host cues to activate their own cryptic biosynthetic gene clusters (BGCs). This review aims to critically summarize the multi-layered mechanisms driving this metabolic crosstalk and evaluate strategies to harness this symbiotic intelligence for natural product discovery. Methods: A systematic literature survey spanning the last decade was conducted across major databases. The search specifically targeted studies investigating endophytic fungi in medicinal plants, focusing on experimental designs for BGC activation, applications of spatial metabolomics (matrix-assisted laser desorption/ionization mass spectrometry imaging, MALDI-MSI), and the structural elucidation of novel bioactive natural products through co-culture or in planta models. Results: Our analysis reveals that host-derived chemical cues, such as specific root exudates and oxylipins, act as primary triggers to awaken silent fungal BGCs. We collated numerous recently discovered bioactive metabolites—including novel polyketides, highly rearranged terpenoids, and unique alkaloids—demonstrating their potent antimicrobial and cytotoxic properties. Furthermore, a critical evaluation of spatial metabolomics studies demonstrates that metabolic exchange is highly localized at the plant–fungus interface, providing contextual insights that traditional bulk tissue extraction fails to capture. Conclusions: This review bridges the gap between ecological understanding and synthetic biology applications. We conclude that translating the mechanisms of this “chemical signaling” into biotechnological strategies offers a sustainable pathway for the bioproduction of high-value pharmaceuticals, thereby reducing reliance on the wild harvesting of medicinal plants. Full article

Droughts are considered one of the major abiotic limitations constraining global plant productivity. Recent findings suggest that water-deficit responses in plants are largely mediated by associated microbial communities, instead of being purely genetically based in plants. Of these beneficial microbes, pink-pigmented, facultative, methylotrophic bacteria in the genus Methylobacterium have been recognized for their immense potential as plant-growth-promoting agents. These microbes have the ability to generate phytohormones, especially cytokinins and auxins, as well as manipulate host metabolic pathways. This review aims to compile available knowledge on hormonal and metabolic interactions in the plant holobiont mediated by Methylobacterium species, especially in relation to drought stress. Firstly, the review discusses the microbial production of phytohormones, specifically cytokinins (such as trans-zeatin) and auxins (like indole-3-acetic acid, or IAA), and their effects on plant roots and shoots. Next, the review aims to discuss metabolic priming approaches induced by Methylobacterium in plants exposed to drought, which include priming for osmolyte biosynthesis (proline, glycine betaine, trehalose, etc.) and activating antioxidant defenses. Furthermore, the review aims to explain how these interactions and responses collectively contribute to developing plant drought stress resilience via improved plant–water relations, postponing senescence, maintaining photosystem efficiency and elucidating mechanisms using omics approaches. Full article

Submerged aquatic macrophytes and their microbiomes can help mitigate eutrophication, yet how microbial communities and functions differ across specific plant-associated and surrounding niches remains unclear. Here, we profiled bacterial community composition (16S rRNA gene sequencing) and quantified nitrogen and phosphorus cycling genes (narG, nirK, nirS, nosZ, phoD by qPCR) across eight distinct compartments associated with the submerged macrophyte Hydrilla verticillata in a eutrophic freshwater wetland. The niches spanned open water, bulk sediment, rhizosphere, and plant phyllosphere (leaf/stem surfaces) and endosphere (leaf/stem/root interiors). Alpha diversity differed significantly among niches: sediments (non-rhizosphere and rhizosphere) exhibited the highest Operational Taxonomic Unit (OTU) richness and diversity, whereas leaf-associated niches (phyllosphere and endosphere) had the lowest. Beta diversity showed clear separation by niche, indicating strong habitat filtering. Community composition also varied markedly: the water column was dominated by Bacteroidota (~51% of sequences), plant-associated communities were enriched in Pseudomonadota (43–90%), and sediment niches were dominated by Firmicutes (23~48%). Functional gene abundances showed pronounced niche partitioning. Nitrate/nitrite reduction genes (narG, nirK, nirS) were most enriched on leaf phyllosphere, with narG abundance equally high in the water, whereas the N₂O reductase gene nosZ peaked in sediment niches. The alkaline phosphatase gene phoD had its highest copy numbers in leaf biofilms, with significantly lower levels in internal plant tissues. Overall, neutral processes explained ~61% of community variation, but deterministic assembly was evident in the well-connected water and leaf surface niches. These findings reveal strong niche differentiation in plant-associated microbiomes and suggest that compartmentalized microbial functional capacity within the H. verticillata holobiont enhances nitrogen removal and phosphorus cycling in eutrophic waters. Full article

Symbiotic dinoflagellates from the family Symbiodiniaceae play a central role in coral reef ecosystems by forming mutualistic relationships with reef invertebrates, particularly stony corals. These relationships underpin reef productivity in nutrient-poor waters but are vulnerable to disruption from marine heatwaves and climate change. While laboratory culturing of symbionts has enabled controlled studies of thermal stress, prolonged culturing may lead to physiological changes that do not reflect in hospite conditions. Here, we examined the thermal stress responses of two axenic cultures of Symbiodinium A1, freshly isolated and long-term cultured (2.5 years), originally from the jellyfish Cassiopea andromeda in the Red Sea. Both cultures were exposed to a daily temperature increase of 1 °C, up to 37 °C. Freshly isolated symbionts consistently showed higher photochemical efficiency (0.515 ± 0.007) and growth rates (1.68 ± 0.60 µ day⁻¹) compared to long-term cultured cells (0.401 ± 0.007; −2.25 ± 0.38 µ day⁻¹), which collapsed at 37 °C. Heat stress also led to decreases in O₂ and increases in pCO₂ across treatments. Long-term cultured symbionts exhibited greater lipid body accumulation, suggesting a shift to anaerobic metabolism. These findings demonstrate that extended batch culturing alters symbiont physiology and stress responses, highlighting the need to consider culture history in experimental designs to avoid bias in interpreting holobiont resilience. Full article

Understanding the intimate interactions between plants and their microbiota at the cellular level is essential for unlocking the full potential of plant holobionts in agricultural systems. Traditional bulk and microbial community-level sequencing approaches reveal broad community patterns but fail to resolve how distinct plant cell types interact with or regulate microbial colonization, as well as the diverse antagonistic and synergistic interactions and responses existing between various microbial populations. Recent advances in single-cell and spatial multi-omics have transformed our understanding of plant cell identities as well as gene regulatory programs and their dynamic regulation in response to environmental stresses and plant development. In this review, we highlight the single-cell discoveries that uncover the plant cell-type-specific microbial perception, immune activation, and symbiotic differentiation, particularly in roots, nodules, and leaves. We further discuss how integrating transcriptomic, epigenomic, and spatial data can reconstruct multilayered interaction networks that connect plant cell-type-specific regulatory states with microbial spatial niches and inter-kingdom signaling (e.g., ligand–receptor and metabolite exchange), providing a foundation for developing new strategies to engineer crop–microbiome interactions to support sustainable agriculture. We conclude by outlining key methodological challenges and future research priorities that point toward building a fully integrated cellular interactome of the plant holobiont. Full article

Soil acidification is among the primary abiotic stress factors that constrain plant growth. The adoption of acid-tolerant plant varieties and the inoculation of plant growth-promoting rhizobacteria have the distinct advantages of simultaneously increasing soil fertility and ensuring crop growth in acidic soil. However, how acid-tolerant plant varieties interact with the associated rhizosphere microbiota still needs to be explored. In this study, acid-tolerant peanut varieties were screened and planted in natural and sterile environments. The results revealed significant differences in growth performance among the varieties in acidic soil and between natural and sterile environments, revealing that the rhizosphere microbiota is dependent on acid tolerance. Through high-throughput sequencing analysis, the key taxa Sinomonas and Aspergillus were identified, and subsequent greenhouse verification experiments demonstrated their function in promoting peanut plant growth in acidic soil. In total, our findings suggest that the holobiont of tolerant plants and the rhizosphere microbiota is important for stress resistance. This perspective opens up new avenues for improving crop cultivation in soils with different stresses, in which both plant and associated microbial properties are considered. Full article