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Background Lysobacter species are Gram-negative bacteria widely distributed in soil, plant and freshwater habitats. Lysobacter owes its name to the lytic effects on other microorganisms. To better understand their ecology and interactions with other (micro)organisms, five Lysobacter strains representing the four species L. enzymogenes, L. capsici , L. gummosus and L. antibioticus were subjected to genomics and metabolomics analyses. Results Comparative genomics revealed a diverse genome content among the Lysobacter species with a core genome of 2,891 and a pangenome of 10,028 coding sequences. Genes encoding type I, II, III, IV, V secretion systems and type IV pili were highly conserved in all five genomes, whereas type VI secretion systems were only found in L. enzymogenes and L. gummosus . Genes encoding components of the flagellar apparatus were absent in the two sequenced L. antibioticus strains . The genomes contained a large number of genes encoding extracellular enzymes including chitinases, glucanases and peptidases. Various nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) gene clusters encoding putative bioactive metabolites were identified but only few of these clusters were shared between the different species. Metabolic profiling by imaging mass spectrometry complemented, in part, the in silico genome analyses and allowed visualisation of the spatial distribution patterns of several secondary metabolites produced by or induced in Lysobacter species during interactions with the soil-borne fungus Rhizoctonia solani . Conclusions Our work shows that mining the genomes of Lysobacter species in combination with metabolic profiling provides novel insights into the genomic and metabolic potential of this widely distributed but understudied and versatile bacterial genus.

Hz25 is a novel strain that was isolated from the rhizosphere of the relict endemic plant Peschkova (Fabaceae), which grows on carbonate soils in the Baikal region of Russia. This work presents the complete genome sequence of Hz25 (5.98 Mb, 66.94% GC), which was obtained using a hybrid assembly method combining Oxford Nanopore and Illumina sequencing. Phylogenetic analysis based on 47 genomes and an average nucleotide identity (ANI) value of 96% confirmed its affiliation with . A comparative pan-genome analysis with three closely related strains (13-6, 76, and ATCC 29479) identified 554 strain-specific genes. This significant genomic plasticity likely reflects adaptation to the sharply continental climate, high insolation, and low free iron content of the native soil. The genome encodes a comprehensive micropredator arsenal, including: seven chitinase genes (GH18 and GH19 families); bacteriolytic enzymes (Blp, L1, L4, Ami); a complete type III secretion system (T3SS) with predicted effectors; type IV pili (including the PilZ-PilB regulatory complex); and siderophore biosynthesis genes (lysochelin). The genome contains genes of an arsenic resistance system, but lacks the ACR3 efflux pump, suggesting that these genes may have alternative functions. Genes involved in calcium homeostasis (Excalibur domain, Na /Ca antiporter) were also identified. These features make Hz25 a promising candidate for biocontrol applications in cold climates and metal-contaminated environments.

Rhizosphere microbes benefit plant growth and health. How plant-microbe interactions regulate fruit quality remains poorly understood. Here, we elucidate the multi-level modulation of vitamin accumulation in tomato by flavonoid-mediated crosstalk between host plants and rhizosphere microbes. SlMYB12- overexpressing plants with up-regulated flavonoid biosynthesis accumulate higher levels of vitamins C and B 6 in fruits compared to wild-type plants grown in natural soil. Flavonoid-mediated improvement of fruit quality depends on the presence of soil microbiomes and relates to rhizosphere enrichment of key taxa (e.g. Lysobacter ). Multi-omics analyses reveal that flavonoids attract Lysobacter soli by stimulating its twitching motility and spermidine biosynthesis, which in turn boosts vitamin accumulation in fruits across tomato cultivars and soil types. RpoN acts as a dual regulator in L. soli that is responsive to flavonoids, controlling bacterial motility and spermidine production. Our study provides insight into flavonoid-mediated rhizosphere signalling and underscores plant-microbiome orchestration for improved tomato fruit quality. How fruit quality is regulated by plant microbiome remains poorly understood. Here, the authors reveal that flavonoids secreted by tomato roots can recruit specific soil microbes to the rhizosphere and stimulate spermidine biosynthesis, which can induce vitamin accumulation in tomato fruits.

Effector proteins secreted by bacteria that infect mammalian and plant cells often subdue eukaryotic host cell defenses by simultaneously affecting multiple targets. However, instances when a bacterial effector injected in the competing bacteria sabotage more than a single target have not been reported. Here, we demonstrate that the effector protein, LtaE, translocated by the type IV secretion system from the soil bacterium Lysobacter enzymogenes into the competing bacterium, Pseudomonas protegens, affects several targets, thus disabling the antibacterial defenses of the competitor. One LtaE target is the transcription factor, LuxR1, that regulates biosynthesis of the antimicrobial compound, orfamide A. Another target is the sigma factor, PvdS, required for biosynthesis of another antimicrobial compound, pyoverdine. Deletion of the genes involved in orfamide A and pyoverdine biosynthesis disabled the antibacterial activity of P. protegens, whereas expression of LtaE in P. protegens resulted in the near-complete loss of the antibacterial activity against L. enzymogenes. Mechanistically, LtaE inhibits the assembly of the RNA polymerase complexes with each of these proteins. The ability of LtaE to bind to LuxR1 and PvdS homologs from several Pseudomonas species suggests that it can sabotage defenses of various competitors present in the soil or on plant matter. Our study thus reveals that the multi-target effectors have evolved to subdue cell defenses not only in eukaryotic hosts but also in bacterial competitors.

One of the most pressing issues in modern biomedicine is the search for new antimicrobial agents – antibiotics, peptides, bacteriolytic enzymes. This study, using transcriptomic and proteomic approaches, identified a new extracellular bacteriolytic enzyme of Lysobacter capsici XL1 – the amidase Ami. The enzyme was isolated and characterized. Ami was found to hydrolyze the amide bond between the carbohydrate and peptide fragments in bacterial peptidoglycans of chemotypes A1γ, A3α, and A4α. Ami lysed live target cells of opportunistic bacteria Micrococcus luteus Ac-2230 T , Bacillus cereus 217, Staphylococcus aureus 209P, Enterococcus faecium FS86, phytopathogenic bacteria Bacillus megaterium MS941, Curtobacterium flaccumfaciens pv. flaccumfaciens , and pathogenic bacteria of various strains of B. anthracis , including plasmid strains 71/12 and ΔAmes, as well as strains of B. cereus with hemolytic, lecithinase, and phosphatase activities. Thus, the bacteriolytic amidase Ami is a promising candidate for the development of next-generation antimicrobial drugs.

Mechanisms of bacterial predation are crucial for revealing microbial adaptation strategies and interaction behaviors in the environment, yet they remain poorly understood. Previously, predators were reported to localize prey via specific cues. However, the process and mechanisms by which these cues, including signaling molecules, mediate predator localization remain unclear. Herein, we investigate the dynamic interaction between the predatory bacteria Lysobacter enzymogenes and its prey bacteria. By integrating genetic manipulation, transcriptomic analysis, biochemical assays, and live-cell tracking microscopy at the single-cell level, we present a novel predation strategy mediated by peptidoglycan hydrolase LssL, named peptidoglycan hydrolase-driven Prey Localization and Utilization System (phPLUS). In phPLUS, predators secrete LssL to initiate the Step I of the localization process. LssL then hydrolyzes prey and releases small molecules of glycine, which serve as signaling cues to guide the predator’s directional movement and promote the Step II of localization. In turn, prey signals upregulate the expression of LssL, which synergize with type VI secretion system to ultimately mediate prey killing through a novel regulatory pathway. This study reveals a new two-step localization strategy in bacterial predation, highlighting a previously unrecognized predation process and signal regulation mechanism, and expanding our understanding of predator–prey interactions and microbial ecological dynamics.

Secreted bacteriolytic proteases L1 and L5 of the Gram-negative bacterium Lysobacter capsici XL hydrolyze peptide bridges in bacterial peptidoglycans. Such specificity of action determines the prospects of these enzymes for medicine with the view of creating new antimicrobial drugs to combat antibiotic-resistant strains of pathogens. This research concerns the development of successful expression systems for producing active enzymes L1 and L5 in sufficient amounts for comprehensive studies. Based on L. capsici XL strains with deletions in the alpA (enzyme L1) and alpB (enzyme L5) genes and the constructed expression vectors pBBR1-MCS5 PT5–alpA and pBBR1-MCS5 PT5–alpB, we obtained expression strains L. capsici PT5–alpA and L. capsici PT5–alpB, respectively. The yields of enzymes L1 and L5 in the developed strains increased by 4 and 137 times, respectively, as compared to the wild-type strain. The cultivation of the expression strains was successfully scaled up under non-selective conditions in a 10-L bioreactor. After fermentation, the yields of enzymes L1 and L5 were 35.48 mg/L and 57.11 mg/L, respectively. The developed homologous expression systems of bacteriolytic proteases L1 and L5 have biotechnological value as compared to those obtained by us earlier based on heterologous expression systems, which have lower yields and labor-intensive purification schemes.

Lysobacter is known as a bacterial genus with biotechnological potential, producing an array of enzymes, antimicrobial metabolites, and bioactive antioxidant compounds, including aryl polyene (APE) pigments that have been described as protecting substances against photooxidative damage and lipid peroxidation. In this study, the pigment extracted from keratinolytic Lysobacter sp. A03 isolated from Antarctic environment was characterized. The results of KOH test, UV–vis spectroscopy, CIELAB color system, 1 H-NMR, and FTIR-ATR spectroscopy suggest the pigment is a yellow xanthomonadin-like pigment. The in vitro antioxidant activity of the pigment was confirmed by the scavenging of ABTS and DPPH radicals. In silico analysis of the genome through antiSMASH software was also performed and the secondary metabolite gene clusters for APE and resorcinol synthesis were identified, suggesting that proteins responsible for the pigment biosynthesis are encoded in Lysobacter A03 genome.

A novel proteobacterial strain designated SYSU H10001T was isolated from a soil sample collected from plateau meadow in Hongyuan county, Sichuan province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU H10001T was most closely related to Lysobacter soli KCTC 22011T (98.6%, sequence similarity) and Lysobacter panacisoli JCM 19212T (98.2%). The prediction result of secondary metabolites based on genome shown that the strain SYSU H10001T contained 3 clusters of bacteriocins, 1 cluster of non-ribosomal peptide synthetase, 1 cluster of type 1 polyketide synthase and 1 cluster of arylpolyene. In addition, the major isoprenoid quinone was Q-8 and the major fatty acids were identified as iso-C15:0, iso-C17:0 and Summed feature 9. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and three unidentified phospholipids. The genomic DNA G + C content of strain SYSU H10001T was 66.5% (genome). On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU H10001T represents a novel species of the genus Lysobacter, for which the name Lysobacter prati sp. nov. is proposed. The type strain is SYSU H10001T (= KCTC 72062T = CGMCC 1.16662T).

Heat-stable antifungal factor (HSAF) is a newly identified and broad-spectrum antifungal antibiotic from Lysobacter enzymogenes , a ubiquitous environmental proteobacterium. Yet, the regulatory mechanism for HSAF biosynthesis in L . enzymogenes remains poorly understood. Here, we report the identification of a TetR-family protein Le1552 (LetR) from L. enzymogenes strain OH11 that is involved in transcriptional repression of HSAF production. Bacterial one-hybrid and gel mobility shift assays show that LetR directly binds to PHSAF (the promoter region of the HSAF biosynthesis operon). A DNA truncation assay further reveals a core region in PHSAF that is responsible for LetR binding. In-frame deletion of letR in wild-type OH11 is found to significantly increase HSAF levels and key biosynthetic gene transcription, while overexpression of letR in the wild-type background remarkably reduces HSAF levels as well as related gene expression instead. Together, we have identified not only a new regulator for the HSAF biosynthesis but also constructed a higher HSAF-producing deletion strain (Δ letR ) of L. enzymogenes , which shall be of great value in promoting HSAF production for pharmaceutical and biological control purposes.