Although endophytic microorganisms play a critical role in plant growth and stress resilience, the genetic basis underlying host selection of beneficial microbiota-particularly within the xylem-remains poorly understood. Cucumber (Cucumis sativus), as a crop model with a well-developed system for studying vascular biology, offers a valuable system to investigate the host genetic determinants of xylem microbiome assembly. By conducting population-level microbiome profiling across 109 cucumber accessions, we identified a conserved xylem microbiota dominated by Proteobacteria. Within this community, 20 core amplicon sequence variants (ASVs) were consistently present in xylem sap. Genome-wide association mapping identified a host genetic locus, CsXPR1, which encodes a tetratricopeptide repeat protein that regulates the abundance of the dominant xylem-colonized Pseudomonas ASV_4. Colonization patterns of ASV_4 varied across host genotypes and were correlated with CsXPR1 expression levels, suggesting a precision genetic regulation of bacterial entry into vascular tissues. Pseudomonas fulva strain 220, with 97% 16S rRNA gene identity with ASV_4, could colonize in cucumber xylem by inoculation of either roots or leaves. Genome analysis and plate assays revealed the biosynthesis of indole-3-acetic acid (IAA), solubilization of phosphate, and a range of plant beneficial traits in strain 220. Inoculation with strain 220 significantly enhanced growth in cucumber, but only in CsXPR1 haplotype that exhibited high gene expression and higher recruitment capacity of the strain. These benefits included notable increases in plant height (38%), stem diameter (36%), leaf area (61%), fresh and dry weight (51% and 85%, respectively), and a 4.57-fold increase in 4-methyleneglutamine content within the xylem sap. Our findings reveal a complete "gene-to-function" pathway where the host gene CsXPR1 mediates a genotype-dependent growth promotion. It achieves this by regulating the xylem colonization of a beneficial bacterium, Pseudomonas fulva, which in turn enhances plant growth by enriching the xylem sap with the key metabolite 4-methyleneglutamine. Video Abstract.

Emergence of a novel transferable megaplasmid driving blaVIM-24 and tmexCD3-toprJ3 dissemination in clinical Pseudomonas fulva isolates.

Two new epimeric decalinoylspirotetramic acid derivatives, trichodecalins A and B (1 and 2), together with six known compounds (3-8), were isolated from the fungus Trichoderma sp. RSF-1, which is derived from the mangrove Acanthus ilicifolius. Their structures, including absolute configurations, were established using extensive spectroscopic methods (1D and 2D NMR, IR, HR-ESI-MS, ECD). Notably, compounds 1 and 2 were identified as new members of the decalinoylspirotetramic acid family. The cytotoxic and antibacterial activities of these compounds were evaluated. Compounds 1, 2 and four known compounds showed antibacterial activities against multiple pathogenic bacteria. Specifically, compound 2 exhibited strong inhibitory activity against Bacillus subtilis ATCC 19659 with a minimum inhibitory concentration (MIC) value of 6.25µg/mL, whereas compounds 1 and 2 showed moderate inhibitory activities against Escherichia coli ATCC 25922 and Pseudomonas fulva ZXM181.

This study aimed to identify bacterial isolates associated with mortality events in Salmo trutta rearing farms in Spain and to assess their antibiotic resistance profiles. The analysis covered five fish farms: two with a recent history of antibiotic use and three without any antibiotic application in the six months prior to sampling. Tissue samples were collected from moribund fish displaying clinical signs such as erratic swimming, ocular hemorrhages, fin hemorrhages, and skin lesions during disease outbreaks in 2022 and 2023. The samples were analyzed using real-time PCR, amplification and sequencing of the 16S rRNA gene and the ITS-1 intergenic spacer, and MALDI-TOF mass spectrometry. A total of 19 bacterial isolates were identified, with Gram-negative bacteria, particularly Aeromonas spp., being the most prevalent. Other identified taxa included Plesiomonas sp., Hafnia alvei, Pseudomonas fulva, and Kluyvera intermedia, as well as Gram-positive species such as Carnobacterium maltaromaticum, Lactococcus sp., and Enterococcus faecium. Notably, resistant strains were found in four of the five farms, even in those that had not administered antibiotics, suggesting that environmental contamination and anthropogenic factors may significantly contribute to the spread of resistance. Environmental stressors-such as sudden increases in water temperature and high turbidity caused by suspended organic matter-appeared to precede mortality peaks. The findings highlight the role of Aeromonas spp. as a key bacteria associated with mortality events in S. trutta and underscore the multifactorial nature of antibiotic resistance in aquaculture. No florfenicol-resistant isolates were detected in the farms where it is routinely used, indicating that florfenicol remains an effective antibiotic in aquaculture. However, the continuous and systematic monitoring of its use remains essential. The detection of bacteria not traditionally associated with fish pathology in samples from diseased animals suggests the need for further studies into their pathogenic potential. Overall, this descriptive study emphasizes the importance of preventive health strategies, prudent antibiotic use, and environmental monitoring to mitigate bacterial diseases and limit the spread of antimicrobial resistance in brown trout farming. These findings align with a One Health perspective, linking aquaculture practices, ecosystem integrity, and public health.

This study explored the biosynthetic mechanisms and structural diversity of pyoverdines (PVDs) produced by Pseudomonas fulva. Genomic analysis using antiSMASH identified the PVD biosynthetic gene cluster, although the C-terminal peptide sequence could not be predicted. Subsequent liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis revealed the full peptide structure, including modified residues, such as N-acetylhydroxyornithine and cyclohydroxyornithine, and confirmed the presence of several PVD isoforms with different chromophore side chains. Comparative LC-MS analysis across Pseudomonas species demonstrated that P. fulva produces unique PVD molecular mass patterns. The bioinformatic and structural modeling of non-ribosomal peptide synthetase PvdL open reading frame 3 revealed that the A2 and A3 adenylation domains are lysine selective. Although their sequences differ from known lysine-specific signatures, AlphaFold3-based structural prediction revealed conserved substrate-binding configurations, suggesting that similar substrate-binding features may have arisen independently. Notably, Thr297, a unique residue in the non-ribosomal code, likely plays a key role in lysine recognition. The high degree of sequence similarity between the A2 and A3 domains may reflect domain duplication and could be involved in the diversification of the PVD structure. Further functional and ecological studies are required to assess the physiological significance of P. fulva PVDs in microbial iron acquisition.

Adipic acid, a crucial monomer in polymer synthesis, plays a significant role in the production of food packaging materials. In the context of the "Dual Carbon" strategy, the advancement of biobased adipic acid is of critical importance. Here, we have developed an innovative photobacterial cascade reaction system for adipic acid synthesis, which represents a groundbreaking approach in production methodology. The pathway with l-lysine as the precursor is a potential pathway for adipic acid synthesis, but it is subject to low catalytic activity or unknown enzymes in some reactions. In this study, the biosynthesis pathway of l-2-aminoadipate, an intermediate metabolite of adipic acid synthesis with l-lysine as the precursor, was constructed in Corynebacterium glutamicum. It was determined that the coexpression of lysine 6-dehydrogenase from Geobillus sp. 12AMOR1 and aminoadipate semialdehyde dehydrogenase from Pseudomonas fulva 12-X was more beneficial to the synthesis of l-2-aminoadipate. Regulation of the expression of the above enzymes and overexpression of key genes in the precursor lysine synthesis pathway increased l-2-aminoadipate production to 1.02 g/L, which was 6.4 times higher than that of the parental strain. Subsequently, the synthesis of l-2-aminoadipate to adipic acid was realized by photocatalytic conversion instead of the conversion by unknown enzymes. A photocatalyst could complete the oxidation process of deamination by using electron-hole pairs. By optimizing the photocatalytic materials, the treated rape pollen (TRP) was determined as the better photocatalyst. TRP was added as a catalyst in the fermentation system of producing l-2-aminoadipate by C. glutamicum, and the light system was introduced to achieve the photocatalytic conversion of l-2-aminoadipate to adipic acid. 235 mg/L adipic acid could be produced after 48 h of fermentation. A method for producing adipic acid by microbial fermentation coupled with photocatalysis was successfully developed, which broadens the routes for the synthesis of adipic acid. In addition, the photomicrobial cascade reactions could replace the catalytic processes of unknown enzymes, providing new ideas for the synthesis of other important chemicals.

Bacterial-fungal interaction (BFI) has significant implications for the health of host plants. While the diffusible antibiotic metabolite-mediated competition in BFI has been extensively characterized, the impact of intercellular contact remains largely elusive. Here, we demonstrate that the intercellular contact is a prevalent mode of interaction between beneficial soil bacteria and pathogenic filamentous fungi. By generating antibiotics-deficient mutants in two common soil bacteria, Lysobacter enzymogenes and Pseudomonas fluorescens, we show that antibiotics-independent BFI effectively inhibits pathogenic fungi. Furthermore, transcriptional and genetic evidence revealed that this antibiotics-independent BFI relies on intercellular contact mediated by the type VI secretion system (T6SS), which may facilitate the translocation of bacterial toxic effectors into fungal cells. Finally, by using a "conidia enrichment" platform, we found that T6SS-mediated fungal inhibition resulting from intercellular contact naturally occurs within the soil microbiome, particularly represented by Pseudomonas fulva. Overall, these results demonstrate that bacteria from the soil microbiome can protect host plants from fungal infection through antibiotics-independent intercellular contacts, thus revealing a naturally occurring and ecologically important mode of BFI in agricultural contexts.

The structural diversity of marine natural products is considered a potential resource for the pharmaceutical industry. In our study of marine-derived compounds, one bacterium Bacillus licheniformis S-1 was discovered to have the ability to produce bioactive natural products. After a further chemistry investigation, one novel 4-aminopyridinium derivative, 4-(dimethylamino)-1-(2S-((4hydroxybenzoyl)oxy)propyl)pyridin-1-ium (1), along with 15 known cyclic dipeptides (2–16) were isolated from the bacterium B. licheniformis S-1 derived from a shallow sea sediment. The structures of compounds 1–16 were elucidated through comprehensive NMR spectroscopic and specific optical rotation (OR) data analyses. Compound 6 showed antibacterial activity against Pseudomonas fulva with an MIC value of 50 µg/mL. This is the first study to discover a pyridinium derivative and cyclic dipeptides from B. licheniformis.

Suppression of canary grass (Phalaris minor) with simultaneous use of rhizobacteria and sunflower allelopathy

Lepidopterans commonly feed on plant material, being the most significant insect herbivores in nature. Despite plant resistance to herbivory, such as producing toxic secondary metabolites, herbivores have developed mechanisms encoded in their genomes to tolerate or detoxify plant defensive compounds. Recent studies also highlight the role of gut microbiota in mediating detoxification in herbivores; however, convincing evidence supporting the significant contribution of gut symbionts is rare in Lepidoptera. Here, we show that the growth of various lepidopteran species was inhibited by a mulberry-derived secondary metabolite, 1-deoxynojirimycin (DNJ); as expected, the specialist silkworm Bombyx mori grew well, but interestingly, gut microbiota of early-instar silkworms was affected by the DNJ level, and several bacterial species responded positively to enriched DNJ. Among these, a bacterial strain isolated from the silkworm gut (Pseudomonas fulva ZJU1) can degrade and utilize DNJ as the sole energy source, and after inoculation into nonspecialists (e.g., beet armyworm Spodoptera exigua), P. fulva ZJU1 increased host resistance to DNJ and significantly promoted growth. We used genomic and transcriptomic analyses to identify genes potentially involved in DNJ degradation, and CRISPR-Cas9-mediated mutagenesis verified the function of ilvB, a key binding protein, in metabolizing DNJ. Furthermore, the ilvB deletion mutant, exhibiting normal bacterial growth, could no longer enhance nonspecialist performance, supporting a role in DNJ degradation in vivo. Therefore, our study demonstrated causality between the gut microbiome and detoxification of plant chemical defense in Lepidoptera, facilitating a mechanistic understanding of host-microbe relationships across this complex, abundant insect group.

Endocrine disruptors are potential environmental contaminants that can cause toxicity in aquatic ecosystems, so the Water Framework Directive has established limits for these compounds. During our research, 41 bacterial strains were isolated and identified from sewage effluent and tested for their degradation capacities for bisphenol A, 17β-estradiol, and nonylphenol. All the isolated bacteria belonged to the Gammaproteobacteria class of Pseudomonadota phylum (members of Citrobacter, Enterobacter, Escherichia, Klebsiella, Kluyvera, Leclercia, Raoultella, Shigella. Acinetobacter, Aeromonas, and Pseudomonas genera). During the experiments, only strains HF17, HF18 (Pseudomonas aeruginosa), and HF31 (Citrobacter freundii) were unable to grow on these compounds, all other bacterial strains could grow in the presence of the investigated endocrine disruptors. Based on the genomic analysis of the type strains, a set of genes involving aromatic compound degradation was detected, among the peripheral metabolic pathways, the quinate and benzoate degradation pathways proved to be widespread, among the central aromatic intermediates metabolism, the catechol branch of the beta-ketoadipate pathway was the most dominant. Pseudomonas fulva HF16 strain could utilize the investigated endocrine disruptors: bisphenol A by 34%, 17β-estradiol by 52%, and nonylphenol by 54%.

Comparing native and non-native seed-isolated strains for drought resilience in maize (Zea mays L.)

Canavalia rosea is an extremophilic legume that grows in hypersaline and nutrient-deficient ecosystems. The extremophilic nature of C. rosea may be attributed to its ability to establish symbiotic associations with nutrient mineralizing and plant growth promoting (PGP) bacteria housed in the nodules. This study examined legume-microbe symbiosis and plant nutrition of C. rosea growing in subtropical coastal zone in KwaZulu-Natal province, South Africa. Canavalia rosea adult plants of the same age from Westbrook, Scottburgh and Durban were collected for plant biomass and plant nutrition and root nodules were used for bacterial extraction and identification. Rhizosphere soils sampled from the three localities were used for bacterial extraction and identification, extracellular enzyme assays and soil characteristics (pH, nutrient concentrations, total cation, and exchange acidity). Westbrook, Scottburgh and Durban soils were nutrient-deficient with varying total cations, acid saturation and a pH range of 7.3–7.6. Soil nutrient mineralizing extracellular enzyme activities varied across study sites. The culturable bacterial strains isolated from the sampled soils belonged to the Pseudomonas, Pantoea and Flavobacterium genera. Canavalia rosea root nodules were nodulated by Pseudomonas guariconensis, Pseudomonas fulva, Pseudomonas fluorescens, Pseudomonas chlororaphis and Pseudomonas chlororaphis subsp. aurantiaca. Plants growing in Westbrook soils had a significantly higher total plant biomass compared to Scottburgh and Durban plants. Plant P concentration did not vary significantly between sites while plant N and C concentrations varied significantly. Plant-associated and soil bacteria with phosphorus (P) solubilising, nitrogen (N) cycling, and N fixing functions and associated enzymes seem to facilitate the mobilization of nutrients enabling C. rosea to thrive in hypersaline and low-nutrient environments.

The work investigated the species composition of the bacterial microbiome associated with stem crown galls on the grape variety Kishmish radiant (Cardinal x Kishmish pink). The result of the identification of bacterial isolates using MALDI-TOF mass spectrometry, molecular genetic analysis, and the cultural method on nutrient media made it possible to identify them in stem crown galls of grapes is presented. The following microorganisms were identified: Pseudomonas koreensis, Roaultella planticola, Enterobacter cloacae, Pseudomonas fulva, Xanthomonas bonasiae, Winslowiella toletana. Using a biological test on carrots, the pathogenicity of two species Xanthomonas bonasiae, Winslowiella toletana was determined by the ability to form galls, while no virulence genes were detected by PCR analysis using specific primer pairs of genes.

In the present work, we investigated the dynamics of the microbial communities in the wedge clam Donax trunculus (Linnaeus, 1758) from the Bulgarian coastal waters of the Black Sea. The samples were collected in the period of January 2020 until December 2022 from Arkutino, Ahtopol, Obzor and Tsarevo. The BIOLOG system was used for microbiological determination. In our investigation were isolated the following microorganisms: Enterococcus cancerogenus, Enterococcus hirae, Escherichia vulneris, Citrobacter farmeri, Acinetobacter gyllenbergii, Enterococcus hirae, Escherichia vulneris, Enterobacter cloacae, Escherichia hermannii, Pseudomonas mendocina, Pseudomonas fulva, Pseudomonas alcaligenes, Pseudomonas putida, Acinetobacter johnsonii, Acinetobacter gyllenbergii, Enterococcus hirae, Escherichia vulneris, Enterococcus gallinarum, Citrobacter sedakii, Pseudomonas putida, Streptococcus lugdunensis, Enterococcus casseliflavus, Vibrio cincinnatiensis, Vibrio alginolyticus, Vibrio parahaemolyticus, Enterococcus hirae, Streptococcus aureus, Staphylococcus lugdunensis and Enterococcus casseliflavus. During the winter period, we detected the presence of Pseudomonas sp. – P. alcaligenes, P. putida, and A. gyllenbergii. In the autumn months we isolated C. sedakii, C. farmeri, A. gyllenbergii, A. johnsonii, P. fulva and E. casseliflavus. In the spring, E. cancerogenus, E. hirae and Pseudomonas mendocina were found. During the summer, the highest biodiversity of microorganisms - E. hirae, E. vulneris, E. cloacae, E. gallinarum, P. putida, V. cincinnatiensis, V. alginolyticus, V. parahaemolyticus, S. aureus, E. hermannii and S. lugdunensis were registered. Although our three-year research showed that some species are permanent and others are transient, we tend to accept the conclusion that there is only a transient microbiota in mussels and it changes depending on environmental conditions or is a result of pollution of the Black Sea.

Lipopolysaccharides from a Shiraia fruiting body-associated bacterium elicit host fungal hypocrellin A biosynthesis through nitric oxide generation

Coffee Berry Borer (CBB) is a significant coffee pest worldwide. This includes Thailand. The arabica coffee plantations in Chiang Rai province, northern Thailand, have experienced significant economic losses as a consequence of this insect. The purpose of this study was to investigate changes in the gut bacterial community in response to caffeine concentrations in the growing environment, which may have implications for coffee pest insect control. A total of 38 species of gut microbiota were grown in non-caffeine conditions. On average, 14.5 ± 1.8 species were found in all 6 sampling sites. In caffeine conditions, the number of culturable gut bacteria was significantly decreased to 18 species with an average species abundance of 7.2 ± 3.1. The results revealed that Pseudomonas fulva and P. punonensis were caffeine-tolerant species that displayed significant growth at 20 mM caffeine concentration. The findings of this study will contribute to a better understanding of gut microbiota in CBBs and its potential application for coffee insect pest control, as well as valuable information on organic coffee from northern Thailand. HIGHLIGHTS Coffee Berry Borer, or CBB, (Hypothenemus hampei Ferrari; Coleoptera: Scolytidae), is the most serious coffee pest worldwide. This pest has evolved to be caffeine resistant, allowing it to survive and reproduce inside coffee fruits. Caffeine is an alkaloid found in coffee (genus Coffea), and comprises a chemical defense mechanism to protect against insect pests. It is critical for preventing pest outbreaks in Coffea and other commercial plants. Next generation sequencing of 16S rRNA was used to estimate the taxonomic abundance of CBB's gut microbiome, which has a symbiotic relationship with the insects. The gut bacterial community discovered in this study included at least 37 Proteobacteria species and 1 Bacteroidetes species. This study examined the effect of caffeine on the diversity of bacterial symbionts in the gut of CBBs. Gut bacterial diversity and abundance were significantly reduced in media containing 20 mM caffeine. GRAPHICAL ABSTRACT

A significant distinction between cigar production and tobacco lies in the necessary aging process, where intricate microbial growth, metabolic activities, enzymatic catalysis, and chemical reactions interact. Despite its crucial role in determining the final quality of cigars, our comprehension of the underlying chemical and biological mechanisms within this process remains insufficient. Biomass and alkaloids are the primary constituents that influence the flavor of cigars. Consequently, investigating the entire aging process could begin by exploring the involvement of microbes and enzymes in their biodegradation. In this study, handmade cigars were aged under different conditions. Metagenomic sequencing was employed to identify the microbes and enzymes responsible for the degradation of biomass and alkaloids derived from tobacco leaves. The results revealed that various environmental factors, including temperature, humidity, duration time, and turning frequency, yielded varying contents of total sugar and alkaloids in the cigars. Significant correlations were observed between microbial communities and starch, reducing sugars, total sugars, and alkaloids. Key species involved in the breakdown of biomass constituents, such as starch (Bacillus pumilus, Pseudomonas sp. 286, and Aspergillus cristatus), reducing sugars and total sugars (Aspergillus cristatus and Nitrolancea hollandica), were identified. Furthermore, Corynespora cassiicola and Pseudomonas fulva were found to potentially contribute to the degradation of alkaloid compounds, specifically nornicotine and neonicotinoid. Our work contributes to a deeper understanding of the microbial roles in the aging of cigars. Moreover, the selection of specific microbial strains or starter cultures can be employed to control and manipulate the aging process, thereby further refining the flavor development in cigar products.Graphical

Microbes influence plant growth and fitness. However, the structure and function of microbiomes associated with rare and endemic plants remain underexplored. To investigate the bacterial community structure of Ulleung-sanmaneul (U-SMN), an endemic plant in Korea, samples were collected from natural and cultivated habitats, and their 16S rDNA was sequenced. The root bacterial community structure differed from those of bulk soil and rhizosphere in both habitats. Endogenous bacteria in cultivated plants were less diverse than wild plants, but Luteibacter rhizovicinus, Pseudomonas fulva, and Sphingomonas pruni were shared. Co-inoculation of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486 promoted growth and induced salt stress resistance in Arabidopsis and chive. Changes in growth promotion and phenotypes of plants by co-inoculation were mediated by increased auxin production. Each strain colonized the roots without niche competition. The results indicated that host selectivity was influential than environmental factors in formulating endophytic bacterial composition, and domestication simplified the bacterial community diversity. Our results will contribute to the growth and maintenance of endemic U-SMN plants.

Cleansing and storage practices for reusable feeding tube stylets are varied and lack consensus guidelines. Almost 40% of critical care nurses do not cleanse reusable stylets. Our proof-of-concept study aimed to identify potential microbial contamination of stylets before and after cleansing with 70% isopropyl alcohol to establish practice standards. This prospective, exploratory pilot study sampled reusable feeding tube stylets using three different stylet sample sets. Set 1 included human participant stylets sampled for microbiome profile precleansing, and postcleansing and reinsertion into feeding tubes (n = 4). Sets 2 and 3 included stylets stored at the bedside. Set 2 included precleansed stylets for microbiome profiles (n = 5). Set 3 included precleansed and postcleansed stylets sampled for quantitative cultures (n = 5). Careful handling and storage protocols were used. Microbiome profiling used 16s ribosomal RNA gene amplicon sequencing. Bacterial species identified on stylets were primarily common microflora and opportunistic pathogens, including Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas fulva, Cutibacterium acnes, Prevotella melaninogenica, and Lactobacillus paracasei. Microbiological culturing of stylet samples (set 3) did not yield growth for 9/10 samples; Staphylococcus capitis was identified in one postcleansed sample. Mean bacterial species diversity (alpha diversity) decreased following alcohol cleansing (M = 2.54 pre, M = 1.5 post; P = 0.006). The abundance of several potentially opportunistic pathogens indicated plausible risk for gut contamination secondary to reinsertion of stylets into small-bore feeding tubes. Stylet cleansing with 70% isopropyl alcohol reduced bacterial burden on the stylets, although viability was unknown. Careful cleansing, handling, and storage protocols for reusable stylets are necessary to minimize contamination.