Microbiological Research

Colletotrichum graminicola causes significant losses of the staple crop maize worldwide. The fungus produces two distinct asexual spore types, oval and falcate conidia, which show unique processes in development and plant interaction. Based on genome resequencing of our laboratory strain (CgM2/ M1.001), we investigated the gene expression profiles of oval and falcate conidia during development and early leaf infection using RNA-seq. Our results reveal specific gene expression profiles between the two spore types, indicating fundamental differences in their developmental programs that reflect different modes of infection. We identified expression patterns discriminating both conidia types from mycelium and spore type-specific ones for genes encoding transcription factors, conserved fungal developmental genes, transporters, genes of secondary metabolite clusters, and pathogenicity-related functions, including effectors and carbohydrate-active enzymes (CAZymes). Our study shows that despite the identical genomic basis, oval and falcate conidia show unique transcriptomes across vegetative development and early plant interaction. Taking together, these results provide new insights into the molecular mechanisms determining the biology of C. graminicola and its interaction with the plant host.

Plant growth-promoting bacterial endophytes represent a sustainable strategy for enhancing agricultural productivity while reducing reliance on synthetic fertilizers and pesticides. This study focused on the genomic and functional characterization of two endophytic bacterial strains, R11F and R19M, isolated from bean and maize roots, respectively. Comparative analyses based on 16S rRNA gene sequences, average nucleotide identity (ANI), and genome-to-genome distance calculations (GGDC) classified both isolates as Pseudomonas palleroniana. Comparative genomic analyses revealed highly conserved genomes containing genes associated with plant colonization, phosphate solubilization, stress adaptation, heavy metal resistance, and hydrocarbon degradation. Genome mining further identified 17 and 18 biosynthetic gene clusters (BGCs) in R11F and R19M, respectively, including non-ribosomal peptide synthetases (NRPS), pyoverdine, NRP-metallophores, RiPP-like compounds, arylpolyenes, {beta}-lactones, terpenes, NAGGN, and hydrogen cyanide. Strain-specific BGCs associated with syringomycin and viscosin biosynthesis were identified in R11F, whereas R19M harbored clusters related to asplenin and kolossin biosynthesis. In vitro assays confirmed indole production, phosphate solubilization, and siderophore production, as well as the ability of both strains to grow in nitrogen-free medium. Both strains significantly inhibited the growth of Fusarium oxysporum, Phytophthora cinnamomi, and Colletotrichum gloeosporioides. Furthermore, plant inoculation assays demonstrated host-dependent growth promotion, with R11F showing the most consistent improvements in plant growth parameters in tomato, wheat, and lentil. Overall, the integration of comparative genomics and experimental validation demonstrates that P. palleroniana R11F and R19M possess complementary traits associated with plant growth promotion, pathogen suppression, saline stress adaptation, and bioremediation.

The Pseudomonas syringae species complex includes major crop pathogens that use a type III secretion system (T3SS) to inject effectors into plant cells, suppressing immunity and promoting disease. The cherry canker pathogen Pseudomonas amygdali pv. morsprunorum (Pam) carries the effector gene hopAR1 on a prophage, PamPP1, which belongs to a novel Caudoviricetes family widespread across the P. syringae complex and likely acquired before pathovar divergence. Deletion of PamPP1 shows that this prophage enhances Pam virulence independently of hopAR1, instead it alters the T3SS operon expression both in vitro and in planta. These prophage-driven transcriptional changes likely reshape how Pam interacts with plant immunity, highlighting how bacteriophages rewire bacterial transcriptomes and contribute to the evolution and emergence of plant diseases.

Spores are the primary means of fungal reproduction, contributing to genetic diversity, colonization, and adaptation. Although spore formation is a pivotal part of the fungal life cycle, its genetic underpinnings remain poorly known. In this study, we characterize transcriptomic changes from late meiosis to early basidiospore formation in the mushroom-forming fungus Coprinopsis cinerea, decipher several cellular processes, and identify novel genes involved in this process. We identify distinct trajectories of gene expression, each of which display different functional signals, corresponding to meiotic and morphogenetic processes and transitions between these. Our analyses identify diverse arrays of fungal cell wall modifying carbohydrate-active enzymes, ferritins, a putative catechol-melanin synthesis pathway, as well as components of the mitotic/meiotic apparatus. We present twelve highly conserved genes with roles specific to sexual sporulation in both budding yeast and C. cinerea, indicating deep conservation of the gene networks driving sexual spore formation. Reverse genetics identified three conserved but functionally poorly characterized genes conferring sporeless and spore-poor phenotypes that result from postmeiotic developmental arrests stemming from spore inflation and nuclear migration problems. Overall, this study provides novel insight into basidiomycete spore formation and highlights the cornucopia of novel functions encoded by functionally dark genes.

Fusarium head blight (FHB) is driven by co-occurring Fusarium species. Yet the molecular bases of their competitive interactions, particularly at the strain level, remain largely unknown. We performed an integrated multi-omic investigation of four Fusarium isolates cultivated in monoculture, self-confrontation (SC) and inter-specific confrontation (C) assays: two Fusarium graminearum strains FgrI349 and FgrPH-1, and two Fusarium avenaceum strains FaveI494 and FaLH03. Light microscopy and quantitative colorimetry revealed marked phenotypic heterogeneity. the F. graminearum strains formed expansive, red-pigmented colonies with rapid radial growth, whereas the F. avenaceum isolates grew more slowly and displayed distinct colony morphologies and pigmentation patterns. Untargeted LC-HRMS detected 1,008 metabolites in monocultures and 938 metabolites in confrontation zones. Species-level chemical signatures were confirmed, and strain-specific metabolite sets were identified, with FaLH03 producing more than 60 % of the metabolites being made exclusively by a single strain, highlighting its exceptionally unique metabolic profile. RNA-seq uncovered extensive transcriptional reprogramming during competition. In self-confrontations, strain-specific differences persisted but no major morphological or metabolic shifts were observed. Inter-specific confrontations elicited partner-dependent responses: FgrI349 up-regulated 1,492 genes against FaveI494 (including secondary-metabolite biosynthesis, oxidoreductase activity and transport) but only 407 genes against FaLH03, while down-regulating secondary-metabolite genes in the conspecific confrontation. Conversely, the F. avenaceum isolates showed opposite trends; FaLH03 strongly repressed ribosome-biogenesis and cell-wall genes while inducing oxidative-metabolism pathways, whereas FaveI494 displayed a modest transcriptional response dominated by down-regulation of cell-division and chromosome-segregation genes. Gene-ontology enrichment highlighted an opponent-specific reversal of the secondary-metabolite biosynthetic process category in F. graminearum: down-regulated in intra-specific confrontation but up-regulated in both inter-specific encounters. Collectively, our results demonstrate that competitive outcomes are shaped more by strain identity than by species identity, with each strain deploying a distinct molecular arsenal, ranging from metabolite-mediated antagonism to targeted transcriptional shutdown, when confronted with a specific opponent. These findings refine our understanding of Fusarium community dynamics and provide a framework for developing strain-targeted biocontrol strategies against FHB.

Plant growth-promoting bacteria are gaining significant attention as promising biofertilizers. However, the inconsistency between in vitro plant growth-promoting traits and actual field performance remains a challenge, driven partly by a limited understanding of in situ colonization. This study characterized the colonization patterns of Citrobacter sedlakii CESi7, a novel plant growth-promoting bacterium, isolated from oil palm waste compost, during Brassica rapa cultivation. The in situ behavior of CESi7 was observed in both sterilized medium and non-sterilized soil using fluorescence in situ hybridization with a strain-targeting probe. The results revealed that CESi7 can establish both epiphytic and endophytic populations that transiently colonize roots. In a sterilized medium, CESi7 was widely distributed throughout the root tissues. Conversely, in non-sterilized soil, the bacterium formed dense aggregates specifically at the root tips. This study provides direct microscopic evidence of the colonization strategy of CESi7, offering crucial insights for its development as an effective biofertilizer.

Symbiotic interactions between plants and nitrogen-fixing microorganisms are essential for sustainable agriculture, yet the molecular mechanisms underlying plant-cyanobacterium symbiosis remain poorly understood. In particular, the nature of the signalling mechanisms mediating partner recognition in associations involving Nostoc species is largely unknown. Recent proteomic analyses have identified proteins homologous to rhizobial Nod factors biosynthetic enzymes in Nostoc punctiforme, suggesting the existence of a Nod-like signalling system. However, the functional role of these components has not been experimentally validated. Here, we investigate the contribution of nod-like biosynthetic and regulatory genes to symbiosis by analysing mutants of N. punctiforme affected in genes with homology to nodB and nodD. Phenotypic characterization revealed that disruption of nodB-like genes does not impair free-living growth but affects early stages of plant association and colonization. Specifically, the nodB1 mutant is impaired in plant association and shows a mild defect in colonization, whereas the nodB3 mutant exhibits a severe defect in colonization. In contrast, nodD-like mutants exhibited altered symbiotic phenotypes, with specific regulators differentially affecting interaction and colonization efficiency in rice (Oryza sativa). In particular, mutation of nodD2 and nodD3 reduced plant association and severely compromised colonization in Oryza sativa, with a more pronounced phenotype in nodD3 mutant. Altogether, our results provide genetic evidence supporting the involvement of Nod-like components in cyanobacterial symbiosis and suggest the existence of a regulatory and biosynthetic module contributing to plant colonization. These findings shed new light on the evolution and diversity of symbiotic signalling mechanisms across plant-microbe interactions.

The presence of Enterococcus lactis in semi-arid "resource islands" the remarkable ecological plasticity of a species often associated with host-related environments. Characterizing the genomic mechanisms that facilitate its persistence in extreme edaphic niches is crucial for exploring its biotechnological potential in arid agriculture. This study characterized the genomic architecture, abiotic stress tolerance, and plant growth-promoting (PGP) capabilities of six E. lactis strains isolated from the rhizosphere of Pithecellobium dulce and Haematoxylum brasiletto in La Guajira, Colombia. We compared the pangenomes of the isolates with clinical and environmental reference strains. Genomic predictions were validated through in vitro assays for thermal, saline, and pH stress, PGP traits, and biosafety (hemolysis, biofilm formation). Analysis revealed a pangenome with a conserved 2,113-gene core and a highly plastic 3,134-gene accessory genome. The core genome encodes robust machinery for osmotic stress (e.g., opuA-C operons) and DNA repair (uvrC), while the accessory genome is heavily shaped by Horizontal Gene Transfer, containing abundant Mobile Genetic Elements (6.3%-16.4%). Phenotypically, strains exhibited high resilience to heat (50{degrees}C), salinity (5% NaCl), and alkalinity (pH 12). Adaptation in these isolates favors metabolic parsimony: rather than complex phytohormone synthesis, the strains prioritize inorganic phosphate solubilization (conserved pst system) and harbor a complete 2,3-butanediol cluster for volatile-mediated plant interaction. Notably, strain IS_B39 produced siderophores and carried a specific RiPP-like biosynthetic cluster, indicating niche-specific functional diversification. Genomic and phenotypic screening confirmed a safe profile, lacking key virulence factors. These findings define a robust, low-risk genomic toolkit, supporting the potential of E. lactis as a tailored bioinoculant for sustainable agriculture in extreme, water-limited environments. ImportanceEnterococcus species are traditionally studied as clinical pathogens or dairy-associated bacteria, leaving their ecological role in natural, non-host environments largely overlooked. This study challenges conventional paradigms by exploring Enterococcus lactis strains naturally persisting in the extreme, water-limited soils of semi-arid "resource islands" in La Guajira, Colombia. Through functional genomics and laboratory validation, we demonstrated how these bacteria utilize a specialized genetic toolkit to withstand extreme heat and alkalinity, while actively promoting plant resilience. Rather than relying on complex hormone production, they optimize vital nutrient uptake like phosphorus. These findings significantly advance environmental microbiology by uncovering the hidden survival strategies of lactic acid bacteria in arid lands, showcasing their immense potential as sustainable bioinoculants to support global dryland agriculture under climate change stress.

Endosymbiosis is widespread throughout the tree of life. Understanding how the transition of a bacterial endosymbiont from facultative to host-dependent obligate life occurs is an important question for defining the origin of endosymbiosis. A novel gram-positive bacillus, Brevibacillus sp. TJ4 was isolated from the nitrogen-fixing yeast Rhodotorula mucilaginosa JGTA-S1, which houses several endobacteria within its cells. TJ4 can survive independently of yeast but exhibits genomic and metabolic features characteristic of an evolving endosymbiont, slowly assuming a host-dependent, obligate lifestyle. The TJ4 genome contains several incomplete pathways for carbohydrate, amino acid, vitamin, and cofactor metabolism, which is reflected in its increased reliance on host-derived nutrients and auxotrophy compared with that of other Brevibacillus spp. Comparative genomics revealed widespread genome rearrangements, loss of synteny, and multiple cross-genus and inter-kingdom horizontal gene transfer (HGT) events in TJ4 compared to other Brevibacillus spp. These HGTs include the acquisition of genes from bacteriophages and co-resident endobacteria of JGTA-S1. One such horizontally acquired gene, Type II 3-dehydroquinate dehydratase (AroQ), appears to have originated from the Rhodotorula host itself. This acquisition functionally restores the shikimate pathway in strain TJ4, as evidenced by the phylogenetic placement of AroQ from TJ4 within the clade of fungal AroQ homologs. Potential exploitation of the host JGTA-S1 appears to be a probable mode of endosymbiosis of TJ4, an evolving endosymbiont that we named Brevibacillus rhodotorulae sp. nov.

From Brazilian limestone caves, we isolated 29 bacteria utilizing phenol (23 bacteria), toluene (all bacteria), and/or benzene (all bacteria) as sole carbon sources. One isolate showed phosphate solubilization, while lipase/esterase activity occurred in two isolates; no amylase activity was detected, but 16 isolates ([~]55%) exhibited protease activity. Among them, Nocardioides sp. SF1 was selected for whole-genome sequencing due to its aromatic compound tolerance and protease activity. Additionally, catechol cleavage assays yielded unexpected purple pigmentation, suggesting non-canonical aromatic metabolism. Its high-quality draft genome (4.25 Mbp, 16 contigs, N50 of 887 kb) lacks canonical phenol hydroxylase but encodes alternative oxidation systems, phenylacetyl-CoA pathway, besides, desferrioxamine siderophore, biosurfactants, and phosphate solubilization, key adaptations for oligotrophic caves and biotechnologically interesting activities. Whole-genome comparisons (TYGS/GGDC, OrthoANI and k-mer) suggest potential new species. Lacks acquired antimicrobial resistance genes (ResFinder) and pathogenicity potential (PathogenFinder). Nocardioides sp. SF1 emerges as a non-pathogenic candidate for aromatic bioremediation and plant growth promotion in contaminated, nutrient-poor environments, highlighting cave actinobacterias unexplored biotechnological potential.

Bacillus velezensis is a widely used plant growth-promoting rhizobacterium whose effectiveness under natural conditions is strongly influenced by interactions with surrounding microorganisms. While bacterial secondary metabolites are known to shape these interactions, little is known about their long-term evolutionary consequences. Here, we show that repeated exposure of B. velezensis GA1 to secondary metabolites produced by the competing rhizobacterium Pseudomonas sessilinigenes CMR12a drives the emergence of an adapted subpopulation with enhanced ecological fitness. Multi-omics analyses revealed extensive metabolomic and transcriptional changes associated with altered growth dynamics, sporulation, motility, and biofilm formation. Importantly, the evolved variant exhibited improved tomato root colonization and reduced the abundance of the competing Pseudomonas strain in planta. Together, our results demonstrate that prolonged exposure to diffusible bacterial metabolites can drive rapid adaptive diversification in rhizosphere-associated bacteria and highlight the importance of long-term interbacterial interactions in shaping the outcome of plant microbiome assembly and biocontrol performance.

This study evaluates the novel bacteriophage UCB24 as an eco-friendly biocontrol agent against Erwinia amylovora, the bacterial pathogen responsible for fire blight. Following purification, UCB24 was characterized for its optimal multiplicity of infection (MOI), infection kinetics, and environmental stability across diverse pH and temperature ranges. Microtitration assays and scanning electron microscopy (SEM) confirmed distinct morphology of the phage and its potent capacity to disrupt E. amylovora biofilms. Whole-genome sequencing and phylogenetic profiling identified UCB24 as a genetically distinct relative of four known phages. Furthermore, protein-protein interaction analyses revealed a strong binding affinity between the phage lysin and the hosts N-acetylmuramic-acid 6-phosphate etherase, uncovering the precise molecular mechanism driving targeted host destruction. In vivo plant trials demonstrated exceptional protective efficacy in Apple cv. Gala (88.61%) and Quince cv. Esme (81.37%), significantly outperforming traditional copper treatments under severe baseline pathogen pressure. Consequently, UCB24 represents a highly effective and sustainable biopesticide for managing fire blight in susceptible orchard ecosystems.

The Type VI secretion system (T6SS) is a bacterial nanoweapon that injects toxic effectors into prokaryotic and eukaryotic cells. It is widely found among gram-negative bacteria and provides a significant fitness advantage in interbacterial competition. Pseudomonas putida KT2440 possesses three T6SS clusters (K1-, K2- and K3-T6SS) that combat phytopathogens. This makes this strain a potent biocontrol agent that protects plants from pathogens and can be further enhanced by a better understanding of its T6SS regulation. Although the core components of T6SS are conserved, the elements controlling its regulation differ among bacterial species. T6SS activity is regulated by various factors acting at different levels, from transcription to post-translational modification, to ensure precise control of its activity. Here, we demonstrate the critical importance that the three Rsm proteins, RsmIEA, have in controlling the K1-T6SS structural components and related orphan elements at the post-transcriptional level in Pseudomonas putida. We identified multiple Rsm-binding sites responsible for directly repressing the translation of T6SS proteins (Hcp1 and Hcp5) and their associated effectors (Tke2 and Tke7). Derepression of K1-T6SS mRNA in the rsmIEA mutant led to enhanced translation and expression of the K1-T6SS components and effectors, and critically increased the number of cells in the population with assembled T6SS. This results in a greater capacity to secrete toxins and kill prey cells via the T6SS-dependent mechanism. Finally, we demonstrate the K1-T6SS ability to kill environmental pathogens, including Salmonella enterica and Erwinia amylovora.

Rhizosphere microbial communities contribute to the growth and health of their host but may be altered by the incidence of soil-borne pathogens. In avocado, the oomycete Phytophthora cinnamomi, causal agent of Phytophthora root rot (PRR), has been shown to alter rhizosphere bacterial communities, although its effect on fungal communities has seldom been explored. Our objective was thus to determine whether P. cinnamomi induced shifts in diversity, composition and co-occurrence networks of fungal communities in the rhizosphere of avocado trees, and to identify potential antagonists of P. cinnamomi that could be further considered for disease management. Fungal communities associated with the rhizosphere of asymptomatic and PRR-symptomatic avocado trees were studied through ITS metabarcoding. Although -diversity metrics were not significantly different between asymptomatic and PRR-symptomatic trees, differences in {beta}-diversity of rhizosphere fungal communities were detected. Moreover, PRR led to the enrichment of saprotrophic taxa and opportunistic pathogens such as Fusarium, Cladosporium or Plectosphaerella in the avocado rhizosphere, which were possibly attracted by the release of resources from necrosed roots. Co-occurrence network analysis revealed that fungal networks in the rhizosphere of PRR-symptomatic trees were more complex and connected than those from asymptomatic trees, suggesting a response of fungal communities to the disturbance caused by the pathogen. Some connector taxa from the PRR-symptomatic networks (Gibellulopsis, Cladorrhinum or Mycenella) were also identified as members of the P. cinnamomi pathobiome. Their negative correlations with the pathogen indicate they may act as potential antagonists, which calls for further isolation efforts to confirm their biocontrol activity of PRR.

Seed transmission is a critical pathway for the dispersal of phytopathogenic bacteria. This transmission can occur through three main routes: floral, internal, and external. Yet the relative contribution of individual transmission routes remains poorly characterized. Using a pathosystem based on Xanthomonas citri pv. fuscans (Xcf) and common bean (Phaseolus vulgaris cv. Flavert), we quantified the efficiency of each route. Under our experimental conditions, the vascular route was the most efficient with 25% of contaminated seeds and population sizes averaging 107 CFU per contaminated seed. Deploying this experimental framework to ten seed-borne bacterial strains isolated from bean revealed that almost none transmitted to seeds through any route, or at best at low efficiency. However, most of the strains were capable of surviving and disseminating within the vascular system. A major bottleneck for seed transmission was identified for pod vascular organs colonization and the similar behavior of an Xcf mutant, deficient in the T3SS, suggested that plant immunity could be involved at this step. Co-inoculation of a consortium composed of the seed-borne strains with Xcf reduced the number of seeds contaminated by Xcf at the highest inoculum concentration, although other consortia members were never recovered from seeds. This suggests that the strains are recognized by the plant and trigger defense responses. These findings also raise questions about the mechanisms used by seed-associated bacteria to colonize seeds in situ.

Bacterial extracellular vesicles (bEVs) are emerging as key players in interkingdom communication, yet their role in delivering functional proteins to host cells during symbiosis remains unexplored. This study shows that Sinorhizobium fredii HH103 packages a PIN-like auxin transporter, AuxT, into bEVs that traffic within the peribacteroid space of soybean nodules. AuxT is chromosomally encoded and constitutively expressed, genetically uncoupled from the flavonoid-inducible auxin biosynthesis machinery located on the symbiotic plasmid. Structural prediction reveals that AuxT adopts an eight-transmembrane-helix architecture with striking homology to plant PIN auxin exporters, despite negligible sequence identity. Molecular docking demonstrates that AuxT binds indole-3-acetic acid within a central cavity, with dimerization inducing ligand-specific conformational changes consistent with transport activity. The auxT mutant exhibits significant symbiotic defects including reduced shoot biomass, nodule number, and nodule mass that are fully restored by complementation. Critically, AuxT-enriched bEVs contain elevated auxin levels, and nodules colonized by the complemented strain accumulate more auxin specifically within the bEVs peribacteroid space, while bacteroids themselves show no auxin retention. We postulate that bEV-associated AuxT mediates localized auxin export into the symbiosome, modulating the host hormonal environment to optimize symbiotic development. This work reveals a previously unrecognized mechanism of interdomain hormonal modulation, where a bacterium uses a structurally convergent transporter and vesicular delivery to actively shape host physiology and to improve the symbiotic performance.

Caldimonas thermodepolymerans is a thermophilic polyhydroxyalkanoate (PHA)-producing bacterium with strong potential for sustainable bioplastic production. Besides serving as intracellular carbon and energy storage compounds, PHAs are increasingly associated with bacterial stress resistance and cellular robustness. This study aimed to investigate the physiological and transcriptomic response of C. thermodepolymerans to osmotic stress induced by elevated NaCl concentrations. Growth analysis demonstrated tolerance up to a supplementation of 2% NaCl, while moderate salt concentrations enhanced PHA accumulation, reaching 65% cell dry weight at 1.5% NaCl supplementation. To better understand the bacterial response to osmotic stress, RNA sequencing was performed under sublethal salt stress conditions. Differential expression analysis revealed major changes in genes related to osmoprotection, trehalose metabolism and type VI secretion systems, whereas motility and chemotaxis genes were strongly repressed. Phenotypic assays confirmed increased biofilm formation and reduced swarming motility under salt-induced osmotic stress. Although canonical PHA biosynthesis genes were not significantly differentially expressed, increased polymer accumulation suggests other underlying mechanisms linked to osmoadaptation. Together, these findings demonstrate that osmotic stress induces metabolic, physiological and regulatory responses in C. thermodepolymerans, highlighting the importance of PHA in stress adaptation besides its industrial applicability.

Biological control strategies are increasingly being explored as sustainable alternatives for managing rice blast disease caused by Magnaporthe oryzae. In this study, we characterized three Bacillus pumilus isolates (DC01, DC09, and DC13) and evaluated their antifungal and plant-beneficial properties against M. oryzae. Whole genome sequencing revealed multiple biosynthetic gene clusters associated with the production of antimicrobial metabolites. All three isolates inhibited fungal growth in dual-culture assays, whereas heat-stable diffusible antifungal activity was primarily associated with the cell-free supernatants of DC09 and DC13. Exposure to bacterial supernatants disrupted fungal development, inducing abnormal hyphal morphology characterized by bulbous swelling, altered polarity, and increased branching in M. oryzae. Volatile organic compound assays further revealed that the DC isolates suppress fungal growth in the absence of physical contact. The isolates additionally inhibited the growth of other phytopathogenic fungi and selected human bacterial pathogens. All strains exhibited plant growth-promoting traits, including indole-3-acetic acid production and osmotic stress tolerance, whereas DC09 also displayed phosphate-solubilizing activity. Importantly, root inoculation with the DC isolates significantly reduced rice blast disease severity and induced expression of defense-associated genes involved in jasmonic acid/ethylene signaling and immune priming. Collectively, these findings identify the DC isolates, particularly DC09 and DC13, as promising multi-mechanistic biological control agents for sustainable rice blast management.

Bacterial cell wall (CW), primarily composed of the biopolymer peptidoglycan, serve as essential protective barriers against external stresses and the internal turgor pressure. The peptidoglycan (PG) biosynthetic pathway encompasses sequential enzymatic reactions in the cytoplasm and in the membrane that involve critical enzymes susceptible to antibiotic targeting. Virtually each step of the pathway is the target of a known antibiotic. Antibiotic-induced inhibition of PG assembly typically weakens the sacculus, often leading to cell lysis. However, the cascade of events that follow inhibition of a specific enzyme of the pathway, and how these culminate in cell death remain largely unknown. Here, we investigated the effects on growing Bacillus subtilis cells of two categories of CW antibiotics: inhibitors of the synthesis of soluble PG precursors in the cytoplasm (fosfomycin and D-cycloserine) and inhibitors of the polymerisation and crosslinking reactions at the outer leaflet of the membrane, which incorporate newly externalised precursors into the existing network (vancomycin and penicillin). In B. subtilis, the latter reactions are catalysed along the sidewalls by the Rod complex, thought to primarily build the sacculus, and by class A penicillin-binding proteins (aPBPs), thought to add to repair it. Our findings reveal that the two antibiotic groups lead to growth arrest, sacculus thinning, and eventual cell lysis. However, while the impact of vancomycin and penicillin G is rapid, lacking morphological deformation, fosfomycin and D-cycloserine induce cell widening and bulging before lysis. During shortage of PG precursors, dysregulated PG hydrolytic activity contributes to elevated cell lysis but is not responsible of bulging. Instead, dispersed PG synthesis by aPBPs persists while the activity of the Rod system is rapidly arrested, resulting in cell rounding. We propose that this facilitates the redirection of the limited PG precursors to sites of CW repair, thereby preserving cell integrity and allowing for prolonged growth during antibiotic challenge.

Candida auris (currently Candidozyma auris) is an emerging fungal pathogen responsible for dramatic global increase in invasive candidiasis with high mortality. Most concerning, C. auris has a high propensity to colonize patients and persist and develop multidrug resistance to main classes of antifungals. In this study, we investigated the genetic and phenotypic diversity and resistance mechanisms of C. auris clinical isolates recovered from hospitalized infected patients. A total of 53 isolates from 38 unique patients were recovered from various clinical sources and evaluated for susceptibility to routine antifungal drugs. Whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analysis were performed to generate a phylogenetic network to infer population structure and identify mutations associated with drug resistance development. Isolates were also phenotypically evaluated for ability to form biofilms and aggregate, and cell wall adhesins gene expression studies were performed to provide mechanistic insights into C. auris phenotypic plasticity. Except for one clade III isolate, all isolates belonged to clade I and all were resistant to fluconazole with incidence of resistance to amphotericin B, echinocandins or both. Non-synonymous SNPs were found in genes associated with antifungal resistance including ERG11, TAC1B, CDR1 and FKS1. Phenotypically, isolates varied in their ability to form biofilm and aggregate which correlated with expression of the Scf1 and Als4112 cell wall adhesins genes highlighting C. auris phenotypic plasticity in circulating clinical strains. These findings underscore the growing clinical threat posed by C. auris and reinforce the need for optimized surveillance and treatment strategies for controlling its spread.