Search Results (877)

Inflammatory bowel disease (IBD) is a chronic inflammatory condition resulting from complex interactions between the immune system, genetic predisposition, and the gut microbiota. In this context, Escherichia coli (E. coli) plays a dual role in the human gut, ranging from harmless commensal strains to pathobionts capable of promoting intestinal inflammation. A growing body of evidence suggests that specific E. coli pathotypes, such as adherent-invasive E. coli (AIEC) and diffusely adherent E. coli (DAEC), contribute to the development and progression of IBD. This narrative review critically examines the microbiological, immunological, and clinical evidence supporting the role of E. coli in IBD, with particular emphasis on mechanisms of mucosal colonization, host–microbe interactions, and persistence within the inflamed intestinal environment. Furthermore, the lack of a standardized operational definition and the limited reproducibility of the AIEC phenotype are addressed, as well as uncertainty about the role played by E. coli as a primary initiator of the disease or as an opportunistic amplifier of intestinal inflammation, and the varying strength of evidence supporting associations with Crohn’s disease versus ulcerative colitis. Diagnostic implications, antimicrobial resistance, and therapeutic aspects are addressed as downstream and context-dependent consequences of E. coli–host interactions, with relevance for disease management and therapeutic response in patients with established IBD. By integrating data from experimental models, clinical studies, and translational research, the review identifies areas of consensus, ongoing controversy, and major knowledge gaps in IBD pathophysiology and clinical practice. Full article

Bark beetle–fungus associations are essential for nutrition, detoxification, and host colonisation, but their composition and function vary across developmental stages and environmental contexts. Hence, we characterised the fungal communities associated with two pine-feeding bark beetles, Ips sexdentatus (ISX) and Ips. acuminatus (IAC), across developmental stages and compared wild-collected and laboratory-bred populations using ITS2 amplicon sequencing. Both beetle species maintained a stable core mycobiome dominated by Kuraishia, Ogataea, Ophiostoma, Graphilbum, and Cyberlindnera. These taxa have been earlier reported to be associated with nutrient provisioning, detoxification of host secondary metabolites, and chemical signalling. Adult beetles showed species-specific community differences, whereas wild-collected beetles, particularly IAC, harboured higher fungal diversity than laboratory populations, indicating a strong environmental effect. Beetles shared more fungal taxa with control wood than with gallery wood, suggesting possible fungal acquisition during feeding and concurrent restructuring of the wood mycobiome during infestation. Monoterpene bioassays with selected yeast symbionts showed differential growth responses to α-pinene, 3-carene, and terpinolene, and their mixture, with the mixture producing stronger inhibition than individual compounds. These yeast symbionts further displayed selective antagonistic activity in vitro against selected filamentous fungi, including entomopathogenic taxa, along with detectable lytic and digestive enzyme activities. Together, our findings highlight a link between community structure, predicted functions, and observed interaction phenotypes, providing a strong basis for future mechanistic studies of beetle–fungus–conifer interactions. Full article

Marine endophytic fungi inhabit the internal tissues of seaweed, seagrass, and mangroves without causing harm. These fungi are known to produce extracellular enzymes, including proteases and cellulases, which play crucial roles in various biological processes and have potential applications in diverse industrial sectors. This study aimed to screen the enzymatic potential of marine endophytic fungi, identify selected isolates, and characterize their enzyme activities. A total of 20 fungal isolates were obtained, comprising 16 isolates from seaweed, three from seagrass, and one from mangrove leaves, collected from the coastal areas of the Seribu Islands (Jakarta), Sukabumi (West Java), Nusa Dua (Bali), and the Buton Islands (Southeast Sulawesi). Screening results showed that 50% of the isolates exhibited proteolytic activity on skim milk agar, while 40% demonstrated cellulolytic activity on carboxymethylcellulose (CMC) agar. Two isolates with the highest clear zone indices for protease and cellulase activity were identified as Penicillium citrinum and Fomitopsis sp., with distinct morphological characteristics including velvety colonies and filamentous hyphal structures. The specific activities of the protease and cellulase were 5475.42 ± 2724.25 U/mg protein and 620.77 ± 607.71 U/mg protein, respectively, indicating high catalytic potential. Full article

Benthic foraminifera, single-cell marine organisms found worldwide, represent an important component of seabed ecosystems. Due to their sensitivity to environmental pollution, they are often used as bioindicators, providing an efficient tool in toxicity studies. Among the pollutants affecting marine coastal and estuarine environments, persistent flame retardants, such as polybrominated diphenyl ethers (PBDEs), are frequently found. Low-level exposure to BDE-47, a PBDE congener, is known to affect organismal development. In this framework, this study aims to assess the effects of BDE-47 exposure on benthic foraminifera from coastal marine environments. Foraminifera specimens belonging to the symbiont-bearing Peneroplidae family were sampled and exposed to two different BDE-47 concentrations for up to 48 h. Vitality indicators such as changes in pseudopodial activity, movement, reproduction, loss of symbiont algae, and occasional mortality events were monitored during the experiment. Exposure to BDE-47 induced alterations in pseudopodial activity, movement, reproduction, and symbiont retention, with the progressive loss of vitality and limited mortality at increasing exposure levels, highlighting the sensitivity of this species to BDE-47. These findings suggest the harmful repercussions of PBDE pollution on marine coastal ecosystems, affecting benthic organisms and potentially contributing to biomagnification processes within the food web, with possible implications for human health. Full article

Wolbachia is an obligate endosymbiotic alphaproteobacterium that is widely distributed among insects. It also infects the European orthopteran Chorthippus parallelus parallelus (Cpp). In this subspecies, Wolbachia induces a reproductive barrier through uni- and bidirectional cytoplasmic incompatibilities. Recently, we found that it also modifies the expression of genes related to essential physiological pathways in Cpp. Here, we have analysed the influence of Wolbachia infection on the epigenetic profiles in Cpp gonads of infected and uninfected males and females, since they constitute Wolbachia’s main target. We characterised de novo nine genes related to epigenetic mechanisms and their transcriptional activity, together with global DNA methylation levels. The results indicate that Wolbachia influences the epigenetic mechanisms in Cpp mainly in females, inducing the expression of genes related to histone deacetylation and reducing the global DNA methylation percentage. This study provides the first evidence of Wolbachia’s ability to alter epigenetic processes in Cpp, increasing our understanding of this symbiotic relationship, with potential implications for the induced reproductive isolation within and between subspecies of C. parallelus. It also offers new insights into the molecular basis of host–symbiont biology in a group for which this information is rather scarce. Full article

Understanding the factors that determine the success of lichen translocations is critical for effective conservation of lichen biodiversity. Both physiological acclimation and the genetic structure of source populations can influence conservation outcomes. This study examined seasonal variation in physiological parameters (specific thallus mass—STM, chlorophyll a fluorescence—F_V/F_M, and chlorophyll content) of Lobaria pulmonaria (L.) Hoffm. across one year, selecting three source populations along a latitudinal gradient in Mediterranean forests in Italy. Genetic structure of their mycobiont and photobiont were also characterized. STM differed significantly among populations and seasons, with consistent increases from March to September. In contrast, F_V/F_M remained relatively stable, while chlorophyll content showed the highest values in December. Genetic analyses revealed clear differentiation among populations for both symbionts. These results suggest that L. pulmonaria can acclimate physiologically to seasonal environmental changes and highlight the importance of considering local genetic structure when selecting source populations for translocation. Integrating physiological and genetic information provides a robust framework for improving conservation strategies for this species. Full article

Thismia species are non-photosynthetic plants entirely dependent on fungal partners for carbon and nutrients. While their arbuscular mycorrhizal associations are well-documented, bacterial symbiont roles remain unexplored. Using 16S rRNA gene amplicon sequencing, we investigated endophytic bacterial communities in T. gardneriana, T. javanica, and T. mirabilis from geographically distinct locations in Thailand. Despite geographic separation, Thismia spp. consistently harbored bacterial compositions taxonomically and functionally distinct from surrounding soil microbiomes. Root endospheres were significantly enriched in Pseudomonadota and Bacteroidota, particularly Puia, while showing reduced compositional dynamics of Acidobacteriota and Planctomycetota. Bacterial communities in Thismia roots were markedly distinct from surrounding soil, while root endosphere communities from geographically distinct habitats clustered together regardless of spatial separation. Mantel and partial Mantel tests confirmed that host species identity, not geographical location, was the primary predictor of root bacterial community structure. Functional prediction analyses suggested root-associated communities were enriched for nitrogen cycling pathways, particularly nitrogen fixation and nitrate reduction. The selective enrichment of Bacteroidota, known for nitrogen fixation and phosphate mobilization, suggests these bacteria provide critical nutritional support in nutrient-poor forest floor environments. Isolated root strains belonged exclusively to Bacillota, including Neobacillus with plant growth-promoting traits. Our findings highlight the importance of tripartite plant–fungal–bacterial interactions in Thismia nutritional ecology. Full article

Plant defences are assumed to evolve in response to the negative effects of virus infection on plant fitness (virulence), and to drive plant–virus coevolution. However, viruses are not always antagonistic symbionts of plants, and the expression of defence traits is environment-dependent. Thus, understanding plant–virus interactions requires analysing the expression of defence traits in the host’s native habitat. Here we analyse the effect of cucumber mosaic virus (CMV) infection, and the expression of resistance and tolerance in the native habitat of a wild Arabidopsis thaliana population. Plants from ten genotypes from that population, which have been shown to differ in resistance and tolerance to CMV in a greenhouse, were inoculated with an Arabidopsis isolate of CMV and transplanted to their habitat. Resistance was rated based on virus accumulation in leaves, and tolerance was rated based on the effect of infection on plant fecundity relative to virus accumulation. Consistent with the greenhouse assays, virulence depended on the host genotype, and polymorphisms for resistance and tolerance were expressed in the field, supporting the validity of the conclusions from the greenhouse assays. Our results also support theoretical predictions on the relationships between pathogen multiplication and virulence and between resistance and tolerance. Full article

Endosymbiotic bacteria in insects are known to influence plant–insect interactions by altering host plant physiology. This study reveals that the endosymbiont Wolbachia significantly impairs photosynthesis in cotton plants. Comparative transcriptomic analysis of cotton leaves infested by Wolbachia-infected spider mites (Tt-I) and uninfected spider mites (Tt-UI) identified 1912 differentially expressed genes (DEGs). Photosynthesis was the most adversely affected biological process, with 17 genes downregulated in the photosynthesis pathway (e.g., key genes psbW and PETF), as supported by GO and KEGG enrichment analyses. Gene co-expression network analysis further highlighted core genes involved in photosynthesis disruption and carbon fixation. Physiological assessments showed that Wolbachia infection led to significantly reduced chlorophyll content and elevated reactive oxygen species (ROS) levels, inducing oxidative stress. These findings demonstrate that Wolbachia disrupts cotton photosynthesis through transcriptional repression and ROS-mediated oxidative stress, providing novel insights into plant–insect-symbiont interactions and a theoretical basis for managing mite pests in cotton. Full article

Honey bees rely on a specialized gut microbiota for nutrition, detoxification, and immune function, yet the effects of emerging insecticides on this symbiotic system remain poorly understood. We compared the acute toxicity and short-term gut microbiota responses of Apis mellifera ligustica workers exposed to two insecticides with contrasting toxicity classes: the highly toxic emamectin benzoate-lufenuron (EB-LFR) and the low-toxicity ecdysone agonist RH-5849. EB-LFR was associated with observed reductions in core gut symbionts (Gilliamella, Snodgrassella, Lactobacillus), a transient increase in Bifidobacterium, and the detection of opportunistic taxa such as Serratia marcescens and Enterobacter hormaechei. In contrast, RH-5849 was associated with broad reductions in beneficial bacteria without detectable pathogen emergence, suggesting a more moderate alteration of microbiota composition. Because microbiota analyses were based on single pooled samples per treatment, these results represent exploratory, qualitative insights into early microbial responses. Together with acute toxicity data, the findings suggest that insecticides with contrasting toxicity classes may differentially affect gut microbiota composition in honey bees and highlight the value of incorporating gut microbiota endpoints into pesticide risk-assessment frameworks to better anticipate sublethal effects on pollinator health. 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

Mediterranean-type ecosystems (METs) occur on five continents and represent some of the most climatically constrained yet biologically rich regions on Earth. In these environments, legumes and their nitrogen-fixing rhizobial symbionts—including widely distributed genera such as Rhizobium, Bradyrhizobium, and Ensifer—play a pivotal role in sustaining plant productivity, nutrient cycling, and ecosystem resilience. This review synthesizes current knowledge on the environmental regulation of legume–Rhizobium symbiosis specifically within Mediterranean-type ecosystems, focusing on how nitrogen (N) and phosphorus (P) availability, light conditions, and carbon allocation trade-offs shape symbiotic performance across the five Mediterranean-type regions of the world (California, central Chile, the Cape Region of South Africa, southwestern Australia, and the Mediterranean Basin). By integrating physiological, ecological, and biogeochemical perspectives, we highlight how the shared features of these regions—strong seasonal drought, chronic nutrient limitation (particularly P in southwestern Australia and the Cape Region), recurrent fires, and exceptionally high plant diversity—constrain and, at the same time, favor the ecological success of symbiotic legumes. Throughout the review, we use case studies from key legume genera such as Lupinus in Chile and southwestern Australia, Virgilia and other Cape legumes in South Africa, Acacia in Australian kwongan and woodlands, and Medicago and Cytisus in the Mediterranean Basin and California to illustrate how general principles of legume–Rhizobium ecology manifest under Mediterranean-type climatic and edaphic constraints. Beyond summarizing established mechanisms, we critically examine the limitations of current metagenomic approaches, which often provide descriptive inventories of soil microbial communities without linking microbial composition to functional outcomes. We argue that advancing the field requires integrated, hypothesis-driven research that combines multi-omic tools with plant eco-physiology, soil nutrient dynamics, and temporal replication. Finally, we outline key priorities for future research, including the integration of functional ‘omics’, the study of microbiome interactions beyond rhizobia, the development of predictive models for Mediterranean-type ecosystems under climate change, and the application of symbiotic principles to restoration and agroecological management. By bridging molecular, physiological, and ecosystem perspectives, this review provides a conceptual framework for understanding and enhancing legume–Rhizobium symbiosis across five continents in a rapidly changing world. Full article

The cell membrane serves as the first line of defense against adverse environmental factors and is first to adapt to changing conditions. Cell membranes in both coral and its symbionts, which use different membrane adaptation strategies, have to acclimatize to various abiotic stressors. As our molecular-genetics analysis showed, colonies of Junceella fragilis were associated with dinoflagellates Cladocopium thermophilum, Gerakladium endoclionum and Breviolum minutum. We analyzed the phospholipid (PL) molecular species of the wild and cultivated Junceella fragilis and their dinoflagellates (phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylinositol (PI), ceramideaminoethylphosphonate (CAEP)), as well as thylakoid membrane lipids of dinoflagellates (glycolipids and betaine lipids). When comparing wild and cultivated J. fragilis colonies, there were no significant differences in thylakoid lipids, but there were differences in host membrane phospholipids, namely in PC, PE and PS. Thus, the profile of PL molecular species of the membrane is very sensitive to environmental factors, which probably explains the observed differences in the profiles of molecular PL species in this study. Full article

The genomic basis underlying the remarkable ecological flexibility of endophytic fungi (EF), particularly their potential to transition between symbiotic, saprophytic, and pathogenic lifestyles, remains poorly understood. Through comparative genomics of 75 Ascomycota and a validation set of 36 Fusarium genomes, we uncovered a distinct pattern of genome evolution in EF, contrasting with the well-known “gene loss” model in obligate symbionts. Our analysis reveals that EF genomes are significantly expanded, primarily driven by the accumulation of DNA transposable elements (TEs). Crucially, this TE-mediated genomic plasticity is coupled with the retention and significant expansion of gene families for both saprotrophy and potential pathogenesis. We propose a novel “dual-trophic potential” model: TE-driven genomic expansion and plasticity provide the genetic raw material for EF to maintain a versatile repertoire of ecological tools, facilitating adaptive shifts across the endophytic–saprophytic–pathogenic continuum. This study reframes our understanding of fungal endophytism from a static symbiotic state to a dynamic, genetically enabled ecological strategy. Full article

The mycoheterotrophic plant Monotropa uniflora relies on fungal symbionts for carbon and nutrient acquisition. However, its interactions with other microbial groups, beyond ectomycorrhizal fungi, remain unexplored. Here, we characterized bacterial and fungal communities associated with M. uniflora across two compartments: ectomycorrhizospheric soil linked to the mycorrhizal network and the surface-sterilized lower stem endosphere. Microbial community composition was assessed using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. Fungal richness was consistently higher in ectomycorrhizospheric soil than in the stem endosphere, whereas bacterial alpha diversity showed no consistent differences between compartments. Multivariate analyses suggested compartment-associated patterns in both bacterial and fungal community composition. Ectomycorrhizospheric soil was dominated by saprotrophic fungal taxa and bacterial groups with predicted metabolic potential, including taxa associated with iron, sulfur and nitrogen cycling. In contrast, the lower stem endosphere was enriched in bacterial taxa commonly associated with anaerobic and nitrogen-related metabolisms. Functional predictions further suggested an increase of carbon fixation-related pathways in rhizosphere-associated bacterial communities. Together, these results indicate that M. uniflora is associated with distinct and structured microbial assemblages across soil and internal plant compartments, highlighting the predicted functional potential of bacterial communities in nutrient- and carbon-related processes in mycoheterotrophic plant–soil systems alongside fungal partners. Full article