As a ubiquitous bacterial second messenger, cyclic di-GMP (c-di-GMP) governs diverse physiological processes by directly binding to transcriptional regulators or other effector proteins. Enhancer-binding proteins (EBPs) are a distinct class of transcriptional regulators that, together with σ54-RNA polymerase, promote downstream gene expression through ATP hydrolysis. To date, no EBP other than FleQ has been reported to interact with c-di-GMP in Pseudomonas aeruginosa. By systematically screening P. aeruginosa EBPs for c-di-GMP binding, we identified SfnR1 as a novel receptor. SfnR1 is known to promote msuEDC and sfnG expression, enabling bacteria to utilize nonpreferred sulfur sources (including DMSO and DMSO2) under sulfur limitation. However, whether SfnR1 is regulated by c-di-GMP and how this regulation affects its transcriptional activity remain unknown. Here, we demonstrate that c-di-GMP binding to SfnR1 prevents SfnR1 from binding to the msuEDC and sfnG promoters, thereby downregulating their expression. This impairs P. aeruginosa assimilation of nonpreferred sulfur sources and ultimately restricts its growth under sulfur-limiting conditions. In contrast, modulation of c-di-GMP levels in P. aeruginosa has no effect on growth under normal conditions. Collectively, our findings establish that c-di-GMP binding to SfnR1 selectively restricts P. aeruginosa growth under sulfur limitation, uncovering a novel mechanism whereby this second messenger modulates bacterial adaptation to nutrient stress.

Chronic diarrhea (CD) severely affects patients' quality of life and is linked to ulcerative colitis, inflammatory bowel disease, and colorectal cancer. Gut microbiota dysbiosis plays a crucial role in intestinal health, with Lactobacillus reuteri emerging as a key regulator. However, its role in chronic diarrhea remains unclear. In this study, we observed macaques with spontaneous diarrhea and investigated microbial and metabolic changes. We also developed a chronic diarrhea mouse model using dextran sulfate sodium. CD group of both models revealed a significant reduction of L. reuteri. L. reuteri transplantation alleviates intestinal injury in CD by secreting D-lactate and modulates macrophage polarization. L. reuteri-derived D-lactate binds to IARS2 in intestinal epithelial macrophages, reducing mitochondrial IARS2 activation and suppressing cGAS-STING pathway activation. This preserves mitochondrial function while decreasing M1 macrophage polarization. Our research revealed the significance of microbiota dysbiosis in CD with both non-human primate and murine model, and highlighted the critical role of L. reuteri, which is conducted with D-lactate-mediated modulation of macrophage function and offered new insights into probiotic therapy for CD.

Methane oxidation represents a vital biological sink for mitigating methane emissions and climate warming. However, the responses of methane oxidation to antibiotic exposure, together with the associated ecological consequences, remain insufficiently understood. This review synthesizes current evidence on the environmental consequences of antibiotic-induced perturbations to methane oxidation and the mechanisms underlying these effects across multiple scales and environmental compartments, including soils, freshwater sediments, estuarine wetlands, aquaculture sediments, and biofilms in constructed wetlands. Particular attention is given to aerobic methane oxidation and denitrifying anaerobic methane oxidation, with antibiotic effects evaluated at the molecular, physiological, microbial-community, and ecosystem levels. At the cellular level, antibiotics may interfere with particulate methane monooxygenase activity and induce reactive oxygen species-mediated oxidative stress, whereas dose- and exposure-duration-dependent effects may produce low-dose stimulation, high-dose inhibition, or other non-monotonic response patterns. At broader ecological scales, these direct effects are further modulated by antibiotic-induced changes in redox conditions, nitrogen and sulfur cycling, microbial community composition, microbial interaction networks, and antibiotic resistance gene enrichment; collectively, these changes reshape methane oxidation capacity. Available evidence therefore indicates strong environmental-compartment dependence, process specificity, and dose-time dependence in the response of methane oxidation to antibiotic exposure. By altering the balance between methane production and consumption, these perturbations may ultimately modify net methane fluxes and thereby generate additional feedbacks to climate warming. This review provides a mechanistic framework for understanding antibiotic-induced perturbations of methane oxidation, identifies priorities for future research, and supports the integration of methane-cycle responses into ecological risk assessment and environmental management across diverse environmental compartments.

HelD protein, also named HelR (encoded by MSMEG_2174 in Mycobacterium smegmatis), interacts with mycobacterial RNA polymerase (RNAP) and affects rifampicin resistance in Mycobacterium abscessus. Here, we provide data on rifampicin resistance and helD presence in the genomes of other clinically relevant nontuberculous mycobacteria. We show that helD is primarily found in rapidly growing mycobacteria, such as M. smegmatis, where we detected HelD at a subset of promoters that can also associate with CarD and RbpA. Transcriptome analysis of a helD deletion strain revealed that HelD has a dual role in gene regulation: it enhances transcription during exponential growth but reduces it in stationary phase. We show that transcription downregulation in stationary phase is accompanied by decreased amounts of the transcription initiation factors RbpA and CarD. In addition, we characterized HelD-containing RNAP complexes using native cryo-EM. Based on these data, we propose that HelD acts as a general transcription factor that releases stalled RNAP complexes and dissociates RNAP from promoters. HelD demonstrates how a single protein can perform fundamentally different tasks, mediating both antibiotic resistance and efficient transcription, and thereby shaping bacterial adaptability.

Cadmium (Cd) contamination poses a serious threat to rice production and food safety because of its high mobility in soil and its accumulation in edible rice tissues. Although beneficial microorganisms and plant signaling regulators have individually shown potential for alleviating Cd stress, whether their combined application can reduce Cd accumulation by restructuring rhizosphere microbial functions remains poorly understood. This study investigated the effects of two Cd-tolerant, plant growth-promoting Streptomyces strains, alone or in combination with jasmonic acid (JA), on Cd stress, Cd accumulation, and rhizosphere microbial communities and functions in rice. The results indicated that Streptomyces co-inoculation improved rice growth, photosynthetic performance, antioxidant defense, and osmotic regulation. It also reduced soil Cd bioavailability and altered Cd partitioning within rice plants. JA alone exerted relatively limited effects on the rhizosphere microbiome but strengthened Streptomyces-mediated physiological and microbial responses when applied in combination. Metagenomic analysis showed that the treatments altered microbial community composition and enriched COG functions associated with inorganic ion transport, signal transduction, and cell envelope biogenesis. KEGG analysis further revealed changes in pathways associated with environmental sensing and Cd detoxification, particularly the two-component system and glutathione metabolism. BacMet analysis identified 37 Cd-related resistance genes. Streptomyces co-inoculation broadly enriched resistance modules involved in metal sensing, transport, efflux, and detoxification, whereas the combined treatment selectively enriched core resistance genes, including czcA, czcP, zntA, and nccB. These changes were consistent with the reduced bioavailable Cd in rhizosphere soil and lower Cd accumulation in rice. Rather than increasing the number of responsive genes, the addition of JA to Streptomyces co-inoculation was associated with a more focused Cd resistance gene response, particularly involving metal transport and efflux. Overall, the reduction in Cd accumulation was associated with coordinated changes in rhizosphere microbial communities, metabolic pathways, and Cd resistance genes. These findings highlight the potential of combining Streptomyces co-inoculation with JA as a microbiome based strategy for rice cultivation in Cd contaminated soils.

Paraquat (PQ; methyl viologen, MV) is a redox-cycling herbicide that causes oxidative injury through the continuous generation of reactive oxygen species (ROS). However, the genetic and extracellular mechanisms underlying cyanobacterial protection against MV-induced oxidative stress remain incompletely understood. Here, we investigated selected stress-responsive genes within the rfb-associated gene cluster spanning slr0978 to slr1611 in Synechocystis sp. PCC 6803. This cluster contains genes predicted to participate in sugar-nucleotide metabolism, polysaccharide assembly and modification, and ABC transporter-associated export, suggesting a potential role in maintaining cell-surface polysaccharide homeostasis. Deletion of slr0978, co-deletion of slr0978 and slr0980, or deletion of slr0983 markedly increased MV sensitivity, with the M0983 mutant showing the strongest phenotype. M0983 exhibited severe growth inhibition, reduced extracellular polysaccharide (EPS) accumulation, elevated ROS accumulation, and impaired photosynthetic efficiency. M0978 and M0978/0980 also displayed stress-sensitive phenotypes, consistent with partially overlapping contributions of these genes to MV stress tolerance. Targeted qPCR revealed local and gene-specific expression changes following gene deletion. Chlorophyll fluorescence kinetics, untargeted LC-MS-based metabolomic profiling, and protein-association analyses collectively indicated that Slr0983 may contribute to polysaccharide-associated homeostasis, redox buffering, and oxidative stress acclimation. Equal-volume supplementation of M0983 cultures with WT-derived EPS preparations partially restored growth under MV stress, supporting an extracellular protective contribution of EPS. Together, these findings indicate that selected genes within the rfb-associated gene cluster contribute to EPS-associated oxidative stress tolerance in Synechocystis, with slr0983 representing a functionally important component of this cluster.

Plant-associated bacteria offer a sustainable alternative to chemical inputs in agriculture, yet the field performance of microbial inoculants remains inconsistent. A central but frequently overlooked cause is that bioprospecting pipelines still select strains on the basis of plant-growth-promoting activities, while the bacterial genetic traits that determine whether a strain can reach, colonise and persist in a given root compartment are rarely assessed. Previous reviews have largely catalogued growth-promoting functions or described root microbiome assembly from the plant's perspective, here we take the bacterium's. We trace the journey of a bacterium from bulk soil to its final niche and, at each stage, identify the genes and pathways (genetic determinants) that encode key bacterial traits involved, such as chemotaxis and motility, nutrient acquisition and metabolic independence, competitive and defensive arsenals, attachment and biofilm formation, evasion of plant immunity, and endophytic entry and persistence. Throughout, we use evidence from comparative genomics and metagenomics, (meta)transcriptomics, targeted mutagenesis and genome-wide screens such as Tn-seq, obtained in systems ranging from binary interactions to synthetic communities and natural soils. For each stage we examine the current state of knowledge, identify critical gaps, and propose avenues to deepen our mechanistic understanding of the bacterial traits involved in plant colonisation. We argue that this mechanistic understanding is the missing foundation for developing inoculants with more consistent and robust performance across diverse agroecosystems.

As part of the Cell Envelope Stress (CES) response orchestrated by the two-component system CesSR in lactococci, the FtsH protease is expected to play a role in counteracting stress, as observed in other bacteria. However, neither its specific role nor its substrates have been identified in this genus. The primary objective of this study was therefore to elucidate the FtsH function in the context of CES. A Lactococcus cremoris NZ9000 ΔftsH exhibited an extended lag phase, increased salt and heat sensitivity and lysozyme resistance. However, only the salt and heat sensitive phenotype could be restored by complementation of the ftsH deletion. Whole-genome sequencing revealed putative compensatory mutations in ΔftsH, including genes encoding a transcriptional regulator and components of ABC transporters. Although awaiting experimental validation, these mutations may nevertheless underscore the broader physiological significance of FtsH in L. cremoris. Furthermore, a comparative proteomic analysis of L. cremoris NZ9000 ΔftsH under CES conditions identified putative FtsH substrates. In vivo degradation experiments demonstrated an extended half-life of the RNA-binding protein Tex and the Phage-Shock Protein YthA in a growth-phase dependent manner, thereby proposing these proteins as putative FtsH substrates in L. cremoris. While the specific function of Tex remains to be elucidated, the regulated degradation of YthA suggests that proteolysis may represent an additional regulatory layer within the lactococcal CES response.

Chronic pancreatitis (CP) is a progressive fibroinflammatory disorder with limited disease-modifying options. Human CP studies report gut microbial and intestinal-barrier alterations, predominantly in cross-sectional cohorts. This review integrates CP-specific clinical and experimental observations with mechanistic evidence from cell, rodent, and non-CP human studies. Barrier disruption can increase lipopolysaccharide exposure and engage Toll-like receptor 4-associated inflammatory and fibrogenic signaling, whereas microbial and host-derived metabolites regulate enteroendocrine L-cell secretion through defined receptor-mediated and metabolic pathways. Human glucagon-like peptide-1 (GLP-1) studies in CP show heterogeneous responses, while CP trials have not yet connected microbiota-driven GLP-1 changes to disease progression. Evidence for direct pancreatic GLP-1 receptor (GLP-1R) signaling is strongest in β cells; reported immune, stellate-cell, and exocrine effects derive largely from preclinical or pharmacological studies and should not be equated with physiological endogenous GLP-1 exposure. CP-specific animal studies reported attenuated fibrosis or improved barrier and immune endpoints after microbiota-directed interventions, whereas limited human synbiotic trials reported improvements in selected gastrointestinal or perioperative outcomes but did not assess endogenous GLP-1, microbiome engraftment, pancreatic fibrosis, or disease progression. Together, these findings support a biologically coherent and testable microbiota-metabolite-endogenous GLP-1 framework for CP, with causal direction and clinical relevance requiring longitudinal validation. Translation requires microbiome-stratified CP trials incorporating functional microbiome and metabolite profiling; basal and meal-stimulated measurements of active and total GLP-1, together with peptide YY; prespecified clinical outcomes; mediation and treatment-by-biomarker analyses; and long-term safety assessment.

Soilborne fungal pathogens must locate host roots, stably attach to their surface and assemble a persistent mycelial network before invading the plant, yet how host perception is coupled to these cellular outputs remains poorly understood. Here, we characterize HAM-7, a GPI-anchored cell wall protein of Fusarium oxysporum and orthologue of the Neurospora crassa cell wall integrity sensor, and show that it is required for two mechanistically distinct processes essential for root colonization. Targeted deletion of ham-7 strongly impaired stable mycelial retention on tomato roots while leaving germling adhesion to abiotic surfaces and biofilm formation unaffected, indicating a defect in fusion-dependent cohesion rather than in surface adhesion. This defect is coupled with a complete loss of vegetative hyphal fusion (23% WT vs. 0% ham-7Δ), preventing the formation of interconnected mycelial networks that promote stable retention of fungal biomass on the root surface. In parallel, ham-7Δ mutants are severely defective in chemotropism toward plant peroxidases but retain intact responses to synthetic α-pheromone, revealing a specific requirement for HAM-7 upstream of the redox-dependent branch of host cue perception. Consistent with this, ham-7Δ mutants constitutively downregulate nox genes under basal conditions and fail to upregulate noxB and noxR upon exposure to tomato root exudates. Accordingly, exogenous H2O2 fully rescues the chemotropism defect but leaves the fusion deficiency intact, demonstrating that HAM-7 acts upstream of two separable downstream pathways. Combined, these defects significantly attenuate virulence on tomato plants, identifying HAM-7 as an upstream actor of Nox-dependent signalling.

Cryoconite granule formation underpins the physical structure and biogeochemical functioning of glacier cryoconite holes. Central to this process is the extracellular polymeric substance (EPS) matrix, produced by microorganisms, which binds microbial cells and mineral particles into stable aggregates while retaining organic matter and nutrients. However, the physiological traits governing the EPS matrix construction and degradation remain poorly understood. Here, we investigated microbial capacities for biofilm formation, EPS-related substrate utilization, and extracellular hydrolysis in Antarctic cryoconite communities over a 40-day melt season. After five weeks of incubation, 49 of 56 (88%) cryoconite debris samples formed detectable biofilms, with biofilm-forming capacity peaking in samples collected after 30 days and significantly exceeding that at the beginning and after 10 days of the melt season (p < 0.05). Across the melt season, the proportion of C-, N-, P- and S-containing substrates utilized increased from 33% to 90% of the 260 compounds tested, with significantly greater utilization of organic nitrogenous compounds than other substrate groups (p < 0.05). Biofilm-forming capacity correlated positively with utilization of EPS-backbone precursors, EPS-associated glycosides, and compounds associated with EPS modification (Spearman's ρ = 0.6, p < 0.05). Forty bacterial genera were recovered, dominated by Cryobacterium, Polaromonas, Arthrobacter, and Chryseobacterium, with representative isolates exhibiting biofilm-forming phenotypes and diverse extracellular enzyme activities. Together, these findings demonstrate complementary microbial capacities for biofilm formation and EPS matrix-associated organic matter transformation that may influence carbon and nutrient cycling in Antarctic cryoconite ecosystems.

Fusarium spp. include major soilborne pathogens that cause vascular wilt diseases in diverse crops. Fusaric acid (FA) is a non-host-specific toxin produced by some Fusarium species and contributes to virulence in several, but not all, host-pathogen systems. Traditionally, FA has been regarded as a broad-spectrum phytotoxin. However, emerging evidence indicates that FA acts beyond direct cellular damage, promoting pathogen colonization through the systematic reprogramming of host physiological processes. Herein, we proposed a pathogenic model with three interacting layers: (i) perturbation of plasma membrane function and ion homeostasis, including effects on H+-ATPase activity and ion transport; (ii) amplification through reactive oxygen species (ROS), lipid peroxidation and mitochondrial and chloroplast dysfunction; and (iii) modulation of hormone-redox signalling and programmed cell death (PCD). The strength and sequence of these responses depend on FA concentration, exposure time, host genotype and pathosystem. FA biosynthesis is controlled primarily by the FUB gene cluster and by broader transcriptional, nutritional and stress-responsive networks, but the relationship between FA production and virulence is context dependent. This review integrates current evidence on FA biosynthesis, stage-associated functions during infection, and cellular toxicity. Building upon these mechanistic insights, we discuss emerging mitigation strategies, including microbial degradation, targeted inhibition of FA biosynthesis, enhancement of host resistance, and metal ion antagonism. Collectively, this work establishes a conceptual framework for understanding Fusarium pathogenesis and provides a foundation for developing sustainable strategies for disease management.

Bacteriophages have gained renewed attention as antibacterial agents because they inhibit bacteria through mechanisms distinct from those of antibiotics. However, the practical use of natural phages remains limited by their narrow host range and reduced activity in complex environments. Although phages are abundant in nature, the isolation and screening of phages with properties suited to specific applications can be time-consuming and labor-intensive. Phage engineering offers a means to overcome these limitations by modifying natural phage properties and introducing defined functions. Advances in genetic technologies have enabled the construction of engineered phages with tailored biological activities. Their host specificity and capacity to deliver genetic material also provide a basis for diverse biomedical applications. This review discusses major phage engineering strategies and their applications in bacterial control and detection. These applications include host-range modification, enhancement of antibacterial activity, suppression of bacterial virulence, programmable delivery of genetic payloads, phage-based nanotechnology, and bacterial detection. By integrating engineering strategies with functional applications, this review examines the development of engineered phages from genetic design and functional validation to clinical translation.

This study investigates a non-ureolytic approach to fungal-based Microbially Induced Calcium Carbonate Precipitation (MICP) using organic calcium sources. As prior research has mainly focused on bacterial-based MICP, this study systematically evaluates the ability of filamentous fungi to induce non-ureolytic calcium carbonate formation. Five fungal strains, i.e., Trichoderma reesei, Neurospora crassa, Penicillium chrysogenum, Fusarium oxysporum, and Pleurotus ostreatus, were assessed using calcium acetate and calcium lactate as organic calcium sources. All strains, except P. ostreatus, facilitated calcium precipitation under at least one of the tested conditions. Notably, P. chrysogenum achieved apparent precipitation efficiencies around 90%, while F. oxysporum exceeded 96% under selected acetate and lactate conditions and exhibited more consistent growth across the tested conditions. Structural characterisation confirmed that calcium carbonate deposited on and around fungal biomass, with calcite and vaterite crystals identified as the main polymorphs. These findings show that filamentous fungi can mediate non-ureolytic calcium carbonate precipitation from organic calcium sources, with clear differences in growth, pH response, calcium removal, and mineral formation among fungal species. The study provides a microbiological basis for understanding fungal-driven carbonate biomineralisation and supports further investigation of filamentous fungi under non-ureolytic MICP conditions.

While many root-associated bacteria promote plant growth or induce resistance, Bacillus marisflavi interaction enhanced wheat crown rot (WCR) caused by Fusarium pseudograminearum. Unlike typical beneficial Bacillus species, B. marisflavi did not directly affect wheat growth but significantly increased pathogen colonization of roots and stem bases, exacerbating WCR incidence. This occurred via activation of F. pseudograminearum genes linked to growth and pathogenicity. The B. marisflavi metabolite D-mannitol promoted proliferation of F. pseudograminearum and related Fusarium spp., elevated mycotoxin (deoxynivalenol, DON) production, and potentially shielded pathogens against plant reactive oxygen species (ROS) defenses. This contrasts with the typical biocontrol role of Bacillus. Our findings reveal that previously overlooked soil bacteria can facilitate fungal disease within the same niche, even without direct plant effects. This highlights that neglecting specific microbes or their metabolites may contribute to the limited field efficacy of antagonistic biocontrol agents targeting pathogens.