Bacillus subtilis biofilm formation and social interactions

Surfactin accelerates Bacillus subtilis pellicle biofilm development

Surfactin is a biosurfactant produced by many B. subtilis strains with a wide variety of functions from lowering surface tension to allowing motility of bacterial swarms, acting as a signaling molecule, and even exhibiting antimicrobial activities. However, the impact of surfactin during biofilm formation has been debated with variable findings between studies depending on the experimental conditions. B. subtilis is known to form biofilms at the solid-air, the solid-medium, and the liquid-air interfaces, the latter of which is known as a pellicle biofilm. Pellicle formation is a complex process requiring coordinated movement to the liquid-air interface and subsequent cooperative production of biofilm matrix components to allow robust pellicle biofilm formation. This makes pellicle formation a promising model system for assaying factors in biofilm formation and regulation. Here, we assayed the influence of surfactin and additional metabolites on the timing of pellicle biofilm formation. Using time-lapse imaging, we assayed pellicle formation timing in 12 B. subtilis isolates and found that one, MB9_B4, was significantly delayed in pellicle formation by approximately 10 h. MB9_B4 was previously noted to lack robust surfactin production. Indeed, deletion of surfactin synthesis in the other isolates delayed pellicle formation. Further, pellicle delay was rescued by addition of exogeneous surfactin. Testing reporters of biofilm-related gene expression revealed that induction of pellicle formation was caused by a combination of increased gene expression of one of the biofilm components and promotion of growth.

Electrogenic dynamics of biofilm formation: Correlation between genetic expression and electrochemical activity in Bacillus subtilis

Biofilms are structured microbial communities, known for their electron transfer properties, which are essential for metabolic processes and microbial survival. Here, we investigated the electrogenic properties of Bacillus subtilis, a bacterial producer of electron-donating biofilms. Interdigitated gold electrodes were utilized to continuously measure the electrochemical activity of biofilm-forming B. subtilis cells and genetic mutants unable to create them (biofilm-deficient). The formation of extracellular polymeric substances (EPS) and filamentous appendages was monitored via scanning electron microscopy (SEM). Chronoamperometry was used to assess electrochemical activity, which showed fluctuations in electrical current at specific time points in biofilm-forming cells. Cyclic voltammetry (CV) revealed significant differences between the voltammograms of biofilm-forming and biofilm-deficient cells, hypothesized to be a result of the reduction of secreted flavodoxin. Electrochemical impedance spectroscopy (EIS) was also performed at various intervals and analyzed using an equivalent circuit. We identified the presence of a charge transfer resistance (Rct) exclusively in biofilm which correlated to the time of increased electrochemical activity measured using chronoamperometry. Finally, through confocal microscopy, we found that the expression of a gene involved in biofilm matrix formation, tasA, was correlated with the time when charge transfer was measured. These results indicate that electrochemical activity is primarily present in biofilm-forming cells rather than in biofilm-deficient mutants. By combining electrochemical and microscopic methods, we developed a methodology to continuously monitor the stages of biofilm formation and showed that electrochemical activities within biofilms vary over time and there is a temporal relationship between these processes and the expression of genes responsible for biofilm development.

Nanomedicines as disruptors or inhibitors of biofilms: Opportunities in addressing antimicrobial resistance

The problem of antimicrobial resistance (AMR) has caused global concern due to its great threat to human health. Evidences are emerging for a critical role of biofilms, one of the natural protective mechanisms developed by bacteria during growth, in resisting commonly used clinical antibiotics. Advances in nanomedicines with tunable physicochemical properties and unique anti-biofilm mechanisms provide opportunities for solving AMR risks more effectively. In this review, we summarize the five "A" stages (adhesion, amplification, alienation, aging and allocation) of biofilm formation and mechanisms through which they protect the internal bacteria. Aimed at the characteristics of biofilms, we emphasize the design "THAT" principles (targeting, hacking, adhering and transport) of nanomedicines in their interactions with biofilms and internal bacteria. Furthermore, recent progresses in multimodal antibacterial nanomedicines, including biofilms disruption and bactericidal activity, and the types of currently available antibiofilm nanomedicines contained organic and inorganic nanomedicines are outlined and highlighted their potential applications in the development of preclinical research. Last but not least, we offer a perspective for the effectiveness of nanomedicines designed to address AMR and challenges associated with their clinical translation.

Protein Homeostasis Impairment Alters Phenotypic Heterogeneity of Biofilm Communities

Biofilms are highly organized, cooperating communities of microorganisms encased in a self-produced extracellular matrix, providing resilience against external stress such as antimicrobial agents and host defenses. A hallmark of biofilms is their phenotypic heterogeneity, which enhances the overall growth and survival of the community. In this study, we demonstrate that removing the dnaK and tig genes encoding the core molecular chaperones DnaK (Hsp70 homolog) and Trigger factor disrupted protein homeostasis in Bacillus subtilis and resulted in the formation of an extremely mucoid biofilm with aberrant architecture, compromised structural integrity, and altered phenotypic heterogeneity. These changes include a large reduction in the motile subpopulation and an overrepresentation of matrix producers and endospores. Overproduction of poly-γ-glutamic acid contributed crucially to the mucoid phenotype and aberrant biofilm architecture. Homeostasis impairment, triggered by elevated temperatures, in wild-type cells led to mucoid and aberrant biofilm phenotypes similar to those observed in strains lacking both dnaK and tig. Our findings show that disruption of protein homeostasis, whether due to the absence of molecular chaperones or because of environmental factors, severely changes biofilm features.

Sugar transporters: mediators of carbon flow between plants and microbes

Pathogens and symbiotic microorganisms significantly influence plant growth and crop productivity. Enhancing crop disease resistance and maximizing the beneficial role of symbiotic microorganisms in agriculture constitute critical areas of scientific investigation. A fundamental aspect of plant-microorganisms interactions revolves around nutritional dynamics, characterized by either "food shortage" or "food supply" scenarios. Notably, pathogenic and symbiotic microorganisms predominantly utilize photosynthetic sugars as their primary carbon source during host colonization. This phenomenon has generated substantial interest in the regulatory mechanisms governing sugar transport and redistribution at the plant-microorganism interface. Sugar transporters, which primarily mediate the allocation of sugars to various sink organs, have emerged as crucial players in plant-pathogen interactions and the establishment of beneficial symbiotic associations. This review systematically categorized plant sugar transporters and highlighted their functional significance in mediating plant interactions with pathogenic and beneficial microorganisms. Furthermore, we synthesized recent advancements in understanding the molecular regulatory mechanisms of these transporters and identified key scientific questions warranting further investigation. Elucidating the roles of sugar transporters offers novel strategies for enhancing crop health and productivity, thereby contributing to agricultural sustainability and global food security.

Efficient production, structural characterization and bioactivity of an extracellular polysaccharide from Grifola frondosa endophytic Burkholderia sp

Endophytic bacteria Burkholderia sp. (GFB) was firstly identified and isolated from Grifola frondosa. An exopolysaccharide (GFB-MP) of GFB strain was obtained following fermentation optimization, resulting in a maximum yield of 11.36 g/L in 5 L fed-batch fermentation. GFB-MP (MW 432.05 kDa) comprised mainly galactose, glucose, and mannose with a ratio of 39.52:14.22:46.26, indicating a mannose-enriched polysaccharide. Methylation and NMR analysis revealed that GFB-MP consisted of the main chain that was repeat units →4)-α-D-Glcp-(1 → bonded →6)-β-D-Galp-1 → repeat units and three O-6-linked branched chains. Antibacterial activity suggested that GFB-MP can effectively inhibit food pathogen bacteria Listeria and Escherichia coli with inhibition ratios of 73.4 % and 81.6 %, respectively. In addition, GFB-MP exhibited remarkable growth-promoting activity on probiotics with >50 % increments of cell growth. This study demonstrates that GFB-MP has the potential for health-beneficial food. Knowledge of endophyte polysaccharides in G. frondosa is important to understand their physiological activities and symbiotic interactions.

Bacillus subtilis Utilizes Decarboxylated S-Adenosylmethionine for the Biosynthesis of Tandem Aminopropylated Microcin C, a Potent Inhibitor of Bacterial Aspartyl-tRNA Synthetase

The biosynthetic pathways of natural products involve unusual biochemical reactions catalyzed by unique enzymes. Aminopropylation, although apparently simple, is an extremely rare modification outside polyamine biosynthesis. The canonical pathway used in the biosynthesis of peptide-adenylate antibiotic microcin C of E. coli (Eco-McC) entails alkylation by the S-adenosyl-methionine-derived 3-amino-3-carboxypropyl group of the adenylate moiety and subsequent decarboxylation to yield the bioactive aminopropylated compound. Here, we report the structure and biosynthesis of a new member of the microcin C family of antibiotics, Bsu-McC, produced by Bacillus subtilis MG27, which employs an alternative aminopropylation pathway. Like Eco-McC, Bsu-McC consists of a peptide moiety that facilitates prodrug import into susceptible bacteria and a warhead, a nonhydrolyzable modified isoasparaginyl-adenylate, which, when released into the cytoplasm, binds aspartyl-tRNA synthetase (AspRS) inhibiting translation. In contrast to the Eco-McC, whose warhead carries a single aminopropyl group attached to the phosphate moiety of isoasparaginyl-adenylate, the warhead of Bsu-McC is decorated with a tandem of two aminopropyl groups. Our in silico docking of the Bsu-McC warhead to the AspRS-tRNA complex suggests that two aminopropyl groups form extended interactions with the enzyme and tRNA, stabilizing the enzyme-inhibitor complex. We show that tandem aminopropylation results in a 32-fold increase in the biological activity of peptidyl-adenylate. We also show that B. subtilis adopted an alternative pathway for aminopropylation in which two homologous 3-aminopropyltransferases utilize decarboxylated S-adenosylmethionine as a substrate. Additionally, Bsu-McC biosynthesis alters the social behavior of the B. subtilis producer strain, resulting in a sharp decrease in their ability to form biofilms.

Large scale identification of pellicle and cell-free liquid phase associated proteins in Bacillus amyloliquefaciens L-17

Bacillus amyloliquefaciens is a soil-associated and plant growth-promoting bacterium. It is the focus of numerous studies due to its ability to sporulate, form biofilms, produce antimicrobial peptides and commercial enzymes. The ability of B. amyloliquefaciensl-17 to form floating biofilm at the air-liquid interface "pellicle" was previously demonstrated. This pellicle exhibits a highly structured architecture which is provided by loosely and tightly matrix bound polysaccharides and proteins. In this study, a first large scale proteomic investigation of both the pellicle and the cell-free liquid phase of l-17 strain was performed. An approach based on physical and chemical extraction of the pellicular matrix combined with protein analysis by mass spectrometry identified 87 weakly matrix-bound proteins and 62 tightly bound proteins. A total of 131 pellicle-associated proteins were identified, including (i) the conserved proteins TasA and TapA, involved in biofilm formation and cohesion (ii) BslA, important for biofilm hydrophobicity (iii) several enzymes that make nutrients available and protect the biofilm from competitors (iv) flagellin and (v) proteins involved in the sporulation process. Proteomic characterization of the cell-free liquid phase underlying the analyzed pellicle allowed the identification of 423 proteins including 118 proteins yet identified in the matrix of the pellicle. The proteins identified specifically in the liquid phase include enzymes involved in the biosynthesis process of non-ribosomal peptides and a variety of commercial enzymes such as proteases, lipases, aminotransferases, peroxidases and phytases. This provides valuable clues to promote the industrial and agricultural application of the cell-free liquid phase of B. amyloliquefaciensl-17.

Microbial diversity and interactions: Synergistic effects and potential applications of Pseudomonas and Bacillus consortia

Microbial diversity and interactions in the rhizosphere play a crucial role in plant health and ecosystem functioning. Among the myriads of rhizosphere microbes, Pseudomonas and Bacillus are prominent players known for their multifaceted functionalities and beneficial effects on plant growth. The molecular mechanism of interspecies interactions between natural isolates of Bacillus and Pseudomonas in medium conditions is well understood, but the interaction between the two in vivo remains unclear. This paper focuses on the possible synergies between Pseudomonas and Bacillus associated in practical applications (such as recruiting beneficial microbes, cross-feeding and niche complementarity), and looks forward to the application prospects of the consortium in agriculture, human health and bioremediation. Through in-depth understanding of the interactions between Pseudomonas and Bacillus as well as their application prospects in various fields, this study is expected to provide a new theoretical basis and practical guidance for promoting the research and application of rhizosphere microbes.

Bacillus Subtilis as an Excellent Microbial Treatment Agent for Environmental Pollution: A Review

The use of microorganisms in environmental biotreatment is gaining attention, particularly Bacillus subtilis (B. subtilis), recognized for its effectiveness in wastewater treatment and soil remediation. Its success stems from its diverse biological activities and adaptability, which improve environmental quality and ecological balance. This paper reviews the remediation capabilities and mechanisms of B. subtilis, focusing on its applications in water purification and soil pollution management. B. subtilis facilitates pollutant degradation and adsorption through enzyme production, organic acids, unique cell wall properties, and interactions with other microorganisms. The article addresses current challenges and future directions, emphasizing the need for enhanced cultivation, screening, and genetic engineering of functional strains. Understanding the interactions of these strains with other microorganisms and studying their ecological and toxicological impacts are essential for optimizing microbial remediation, providing both theoretical and practical foundations for bioremediation efforts.

High-Efficiency CRISPR-Cas9 Genome Editing Unveils Biofilm Insights and Enhances Antimicrobial Activity in Bacillus velezensis FZB42

Bacillus velezensis FZB42 is a prominent plant growth-promoting rhizobacterium and biocontrol agent known for producing a wide array of antimicrobial compounds. The capability to genetically manipulate this strain would facilitate understanding its metabolism and enhancing its sustainable agriculture applications. In this study, we report the first successful implementation of high-efficiency CRISPR-Cas9 genome editing in B. velezensis FZB42, enabling targeted genetic modifications to gain insights into its plant growth-promotion and biocontrol properties. Deletion of the slrR gene, a key regulator of biofilm formation, resulted in significant alterations in biofilm structure and development, as demonstrated by scanning electron microscopy and quantitative biofilm assays. These findings provide valuable insights into the mechanisms of biofilm formation, which are critical for root colonization and plant growth promotion. Additionally, we overexpressed the bac gene cluster responsible for bacilysin biosynthesis by replacing its native promoter with the strong constitutive promoter P43 and integrating an additional copy of the bacG gene. This genetic manipulation led to a 2.7-fold increase in bacB gene expression and significantly enhanced antibacterial activity against Escherichia coli and Lactobacillus diolivorans. The successful implementation of the CRISPR-Cas9 system for genome editing in FZB42 provides a valuable tool for genetic engineering, with the potential to improve its biocontrol efficacy and broaden its applications in agriculture and other biotechnology areas. Our principles and procedures are broadly applicable to other agriculturally significant microorganisms.

Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges

SUMMARYThe development of multicellularity represents a key evolutionary transition that is crucial for the emergence of complex life forms. Although multicellularity has traditionally been studied in eukaryotes, it originates in prokaryotes. Coordinated aggregation of individual cells within the confines of a colony results in emerging, higher-level functions that benefit the population as a whole. During colony differentiation, an almost infinite number of ecological and physiological population-forming forces are at work, creating complex, intricate colony structures with divergent functions. Understanding the assembly and dynamics of such populations requires resolving individual cells or cell groups within such macroscopic structures. Addressing how each cell contributes to the collective action requires pushing the resolution boundaries of key technologies that will be presented in this review. In particular, single-cell techniques provide powerful tools for studying bacterial multicellularity with unprecedented spatial and temporal resolution. These advancements include novel microscopic techniques, mass spectrometry imaging, flow cytometry, spatial transcriptomics, single-bacteria RNA sequencing, and the integration of spatiotemporal transcriptomics with microscopy, alongside advanced microfluidic cultivation systems. This review encourages exploring the synergistic potential of the new technologies in the study of bacterial multicellularity, with a particular focus on individuals in differentiated bacterial biofilms (colonies). It highlights how resolving population structures at the single-cell level and understanding their respective functions can elucidate the overarching functions of bacterial multicellular populations.

Multiwalled Carbon Nanotubes Promoted Biofilm Formation and Rhizosphere Colonization of Bacillus subtilis Tpb55

Plant growth-promoting bacteria (PGPB) achieve effective colonization by forming a biofilm on the root surface. However, the promoting effects and mechanisms of nanomaterials on PGPB biofilm formation and rhizosphere colonization are rarely studied. This study investigated the effects and the potential mechanism of multiwalled carbon nanotubes (MWCNTs) on biofilm formation and rhizosphere colonization of PGPB Bacillus subtilis. 10 and 100 mg/L MWCNTs increased biofilm biomass, extracellular polymeric substance components, live/dead cell ratio, and spores in biofilms. MWCNTs induced B. subtilis Tpb55 upregulated gene expressions of malL, sacX, tasA-tapA, and epsA-O correlated with carbohydrate metabolism and biofilm formation. MWCNTs first stimulated Tpb55 flagellar motility and then increased biofilm formation, thus promoting colonization in the tobacco rhizosphere. Greenhouse experiments showed that the combination of MWCNTs and Tpb55 reduced the occurrence of tobacco black shank. Therefore, MWCNTs have broad application potential in enhancing the effectiveness of PGPB in agricultural disease control and yield enhancement.

A novel regulation on the developmental checkpoint protein Sda that controls sporulation and biofilm formation in Bacillus subtilis

Biofilm formation by Bacillus subtilis is triggered by an unusually simple environmental sensing mechanism. Certain serine codons, the four TCN codons (N for A, T, C, or G), in the gene for the biofilm repressor SinR caused lowered SinR translation and subsequent biofilm induction during transition from exponential to stationary growth. Global ribosome profiling showed that ribosomes pause when translating the four UCN (U for T on the mRNA) serine codons on mRNA, but not the two AGC/AGU serine codons. We proposed a serine codon hierarchy (AGC/AGT vs TCN) in that genes enriched in the TCN serine codons may experience reduced translation efficiency when serine is limited. In this study, we designed an algorithm to score all protein-coding genes in B. subtilis NCIB3610 based on the serine codon hierarchy. We generated a short list of 50 genes that could be subject to regulation by this novel mechanism. We further investigated one such gene from the list, sda, which encodes a developmental checkpoint protein regulating both sporulation and biofilm formation. We showed that synonymously switching the TCN serine codons to AGC in sda led to delayed biofilm formation and sporulation. This engineered strain also outgrew strains with other synonymously substituted sda alleles (TCN) in competition assays for biofilm formation and sporulation. Finally, we showed that the AGC serine codon substitutions in sda elevated the Sda protein levels. This serine codon hierarchy-based novel signaling mechanism could be exploited by bacteria in adapting to stationary phase and regulating important biological processes.

IMPORTANCE

Genome-wide ribosome profiling in Bacillus subtilis shows that under serine limitation, ribosomes pause on the four TCN (N for A, C, G, and T), but not AGC/AGT serine codons, during translation at a global scale. This serine codon hierarchy (AGC/T vs TCN) differentially influences the translation efficiency of genes enriched in certain serine codons. In this study, we designed an algorithm to score all 4,000+ genes in the B. subtilis genome and generated a list of 50 genes that could be subject to this novel serine codon hierarchy-mediated regulation. We further investigated one such gene, sda, encoding a developmental checkpoint protein. We show that sda and cell developments controlled by Sda are also regulated by this novel mechanism.

Cryo-EM analysis of the Bacillus thuringiensis extrasporal matrix identifies F-ENA as a widespread family of endospore appendages across Firmicutes

For over 100 years, Bacillus thuringiensis (Bt) has been used as an agricultural biopesticide to control pests caused by insect species in the orders of Lepidoptera, Diptera and Coleoptera. Under nutrient starvation, Bt cells differentiate into spores and associated toxin crystals that can adopt biofilm-like aggregates. We reveal that such Bt spore/toxin biofilms are embedded in a fibrous extrasporal matrix (ESM), and using cryoID, we resolved the structure and molecular identity of an uncharacterized type of pili, referred to here as Fibrillar ENdospore Appendages or 'F-ENA'. F-ENA are monomolecular protein polymers tethered to the exosporium of Bt and are decorated with a flexible tip fibrillum. Phylogenetic analysis reveals that F-ENA is widespread not only in the class Bacilli, but also in the class Clostridia, and the cryoEM structures of F-ENA filaments from Bacillus, Anaerovorax and Paenibaccilus reveal subunits with a generic head-neck domain structure, where the b-barrel neck of variable length latch onto a preceding head domain through short N-terminal hook peptides. In Bacillus, two collagen-like proteins (CLP) respectively tether F-ENA to the exosporium (F-Anchor), or constitute the tip fibrillum at the distal terminus of F-ENA (F-BclA). Sedimentation assays point towards F-ENA involvement in spore-spore clustering, likely mediated via F-BclA contacts and F-ENA bundling through the antiparallel interlocking of the head-neck units.

Mitigating the vertical migration and leaching risks of antibiotic resistance genes through insect fertilizer application

The leaching and vertical migration risks of antibiotic resistance genes (ARGs) from fertilized soil to groundwater poses a significant threat to ecological and public safety. Insect fertilizer, particularly black soldier fly organic fertilizer (BOF), renowned for its minimal antibiotic resistance, emerge as a promising alternative for sustainable agricultural fertilization. This study employs soil-column leaching experiments to evaluate the impact of BOF on the leaching behavior of ARGs. Our results reveal that BOF significantly reduces the leaching risks of ARGs by 22.1 %-49.3 % compared to control organic fertilizer (COF). Moreover, BOF promotes the leaching of beneficial Bacillus and, according to random forest analysis, is the most important factor in predicting ARG profiles (3.02 % increase in the MSE). Further network analysis and mantel tests suggest that enhanced nitrogen metabolism in BOF leachates could foster Bacillus biofilm formation, thereby countering antibiotic-resistant bacteria (ARB) and mitigating antibiotic resistance. In addition, linear regression analysis revealed that Bacillus biofilm-associated genes pgaD (biofilm PGA synthesis protein), slrR (biofilm formation regulator), and kpsC (capsular polysaccharide export protein) were identified as pivotal in the elimination of ARGs, which can serve as effective indicators for assessing antibiotic resistance in groundwater. Collectively, this study demonstrates that BOF as an environmentally friendly fertilizer could markedly reduce the vertical migration risks of ARGs and proposes Bacillus biofilm formation related genes as reliable indicators for monitoring antibiotic resistance in groundwater.

Dynamic and intricate regulation by the Csr sRNAs in the Arctic Pseudoalteromonas fuliginea

The Csr (Carbon Storage Regulator) system is pivotal in controlling various cellular functions in most bacteria, primarily through the CsrA protein and its antagonistic sRNAs. However, riboregulatory networks are less explored in non-model organisms, particularly those in extreme environments. In this study, we discovered two new sRNAs of the Csr system, Pf2 and Pf3, in the Arctic bacterium Pseudoalteromonas fuliginea BSW20308, along with the previously known Pf1. By studying the impact of these Pf sRNAs on CsrA targetomes and physiological processes, we found a significant influence on various cellular functions and a collective effect on the interaction dynamics between CsrA and RNAs. Furthermore, we identified additional sRNAs that can interact with CsrA and mRNAs. Overall, our results emphasize the growing influence of the Csr system on cellular physiology through intricate sRNA regulation of CsrA, revealing riboregulatory network complexity and significance in non-model organisms.

Arginine kinase McsB and ClpC complex impairs the transition to biofilm formation in Bacillus subtilis

Robust biofilm formation on host niches facilitates beneficial Bacillus to promote plant growth and inhibit plant pathogens. Arginine kinase McsB is involved in bacterial development and stress reaction by phosphorylating proteins for degradation through a ClpC/ClpP protease. Conversely, cognate arginine phosphatase YwlE counteracts the process. Regulatory pathways of biofilm formation have been studied in Bacillus subtilis, of which Spo0A∼P is a master transcriptional regulator, which is transcriptionally activated by itself in biofilm formation. Previous studies have shown that Spo0A∼P transcript regulation controls biofilm formation, where MecA binds ClpC to inhibit Spo0A∼P-dependent transcription without triggering degradation. It remains unclear whether McsB and ClpC regulate biofilm formation together and share a similar non-proteolytic mechanism like MecA/ClpC complex. In this study, we characterized McsB and ClpC as negative regulators of biofilm formation and matrix gene eps expression. Our genetic and morphological evidence further indicates that McsB and ClpC inhibit eps expression by decreasing the spo0A and sinI expression, leading to the release of SinR, a known repressor of eps transcription. Given that the spo0A and sinI expression is transcriptionally activated by Spo0A∼P in biofilm formation, we next demonstrate that McsB interacts with Spo0A directly by bacterial two-hybrid system and Glutathione transferase pull-down experiments. Additionally, we present that McsB forms a complex with ClpC to dampen biofilm formation in vivo. Finally, we show that YwlE acts as a positive regulator of biofilm formation, counteracting the function of McsB. These findings suggest that McsB, ClpC, and YwlE play vital roles in the transition to biofilm formation in Bacillus subtilis, providing new insights into the regulatory mechanisms underlying biofilm development and sharing a similar non-proteolytic mechanism in biofilm formation as MecA/ClpC complex.

Bacillus subtilis inoculated in organic compost could improve the root architecture and physiology of soybean under water deficit

Bacillus subtilis is known to promote root growth and improve plant physiology, while organic compost enhances soil water retention. This study explored the combined effect of inoculating B. subtilis in organic compost on soybean growth under water deficit. The treatments included chemical fertilization, non-inoculated organic compost, and organic compost inoculated with B. subtilis which were assessed under well-watered and water-deficit conditions. The organic compost inoculated with B. subtilis increased root biomass, length, volume, and the number of root tips under well-watered conditions, although it reduced root diameter. Under water deficit, the organic compost inoculated with B. subtilis increased root tip number (∼150%), biomass (∼95%) and number (∼85%) of nodules. Water deficit negatively affected soybean physiology, reduced photosynthesis, transpiration, and stomatal conductance, while increased internal CO₂ concentration. However, the organic compost inoculated with B. subtilis mitigated these effects, enhancing photosynthesis (∼20%) and water use efficiency (∼25%). Under water deficit, this treatment also increased shoot biomass by 15% and the drought tolerance index by 51% compared to the control. The combination of B. subtilis and organic compost improved root architecture, nodulation, and drought tolerance. These results suggest that B. subtilis inoculated in the organic compost is a promising strategy for enhancing soybean productivity and resilience under water stress, offering a novel approach to mitigating drought effects in agriculture.

The extracytoplasmic sigma factor σX supports biofilm formation and increases biocontrol efficacy in Bacillus velezensis 118

Plant growth promoting rhizobacteria (PGPR) offer an environmentally friendly and sustainable approach to combat pathogens and enhance crop production. The biocontrol activity of PGPR depends on their ability to colonize plant roots and synthesize antimicrobial compounds that inhibit pathogens. However, the regulatory mechanisms underlying these processes remain unclear. In this study, we isolated and characterized Bacillus velezensis 118, a soil isolate that exhibits potent biocontrol activity against Fusarium wilt of banana. Deletion of sigX, encoding an extracytoplasmic function (ECF) sigma factor previously implicated in controlling biofilm architecture in B. subtilis, reduced biocontrol efficacy. The B. velezensis 118 sigX mutant displayed reduced biofilm formation but had only a minor defect in swarming motility and a negligible impact on lipopeptide production. These findings highlight the importance of regulatory processes important for root colonization in the effectiveness of Bacillus spp. as biocontrol agents against phytopathogens.

Cryo-EM analysis of the Bacillus thuringiensis extrasporal matrix identifies F-ENA as a widespread family of endospore appendages across the Firmicutes phylum

For over 100 years, Bacillus thuringiensis (Bt) has been used as an agricultural biopesticide to control pests caused by insect species in the orders of Lepidoptera, Diptera and Coleoptera. Under nutrient starvation, Bt cells differentiate into spores and associated toxin crystals that can adopt biofilm-like aggregates. We reveal that such Bt spore/toxin biofilms are embedded in a fibrous extrasporal matrix (ESM), and using cryoID, we resolved the structure and molecular identity of an uncharacterized type of pili, referred to here as Fibrillar ENdospore Appendages or 'F-ENA'. F-ENA are monomolecular protein polymers tethered to the exosporium of Bt and are decorated with a flexible tip fibrillum. Phylogenetic analysis reveals that F-ENA is widespread not only in the class Bacilli, but also in the class Clostridia, and the cryoEM structures of F-ENA filaments from Bacillus, Anaerovorax and Paenibaccilus reveal subunits with a generic head-neck domain structure, where the β-barrel neck of variable length latch onto a preceding head domain through short N-terminal hook peptides. In Bacillus, two collagen-like proteins (CLP) respectively tether F-ENA to the exosporium (F-Anchor), or constitute the tip fibrillum at the distal terminus of F-ENA (F-BclA). Sedimentation assays point towards F-ENA involvement in spore-spore clustering, likely mediated via F-BclA contacts and F-ENA bundling through the antiparallel interlocking of the head-neck units.

Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion

Bacterial biofilms are complex cell communities within a self-produced extracellular matrix, crucial in various fields but challenging to analyze in 3D. We developed a "biofilm-in-capillary" growth method compatible with full-rotation soft X-ray tomography, enabling high-resolution 3D imaging of bacterial cells and their matrix during biofilm formation. This approach offers 50 nm isotropic spatial resolution, rapid imaging, and quantitative native analysis of biofilm structure. Using Bacillus subtilis biofilms, we detected coherent alignment and chaining of wild-type cells towards the oxygen-rich capillary tip. In contrast, the ΔtasA genetic knock-out showed a loss of cellular orientation and changes in the extracellular matrix. Adding TasA protein to the ΔtasA strain restored matrix density and led to cell assembly compaction, but without the chaining observed in wild-type biofilms. This scalable and transferable approach opens new avenues for examining biofilm structure and function across various species, including mixed biofilms, and response to genetic and environmental factors.

Design and regulation of engineered bacteria for environmental release

Emerging products of biotechnology involve the release of living genetically modified microbes (GMMs) into the environment. However, regulatory challenges limit their use. So far, GMMs have mainly been tested in agriculture and environmental cleanup, with few approved for commercial purposes. Current government regulations do not sufficiently address modern genetic engineering and limit the potential of new applications, including living therapeutics, engineered living materials, self-healing infrastructure, anticorrosion coatings and consumer products. Here, based on 47 global studies on soil-released GMMs and laboratory microcosm experiments, we discuss the environmental behaviour of released bacteria and offer engineering strategies to help improve performance, control persistence and reduce risk. Furthermore, advanced technologies that improve GMM function and control, but lead to increases in regulatory scrutiny, are reviewed. Finally, we propose a new regulatory framework informed by recent data to maximize the benefits of GMMs and address risks.

Persistent glucose consumption under antibiotic treatment protects bacterial community

Antibiotics typically induce major physiological changes in bacteria. However, their effect on nutrient consumption remains unclear. Here we found that Escherichia coli communities can sustain normal levels of glucose consumption under a broad range of antibiotics. The community-living resulted in a low membrane potential in the bacteria, allowing slow antibiotic accumulation on treatment and better adaptation. Through multi-omics analysis, we identified a prevalent adaptive response characterized by the upregulation of lipid synthesis, which substantially contributes to sustained glucose consumption. The consumption was maintained by the periphery region of the community, thereby restricting glucose penetration into the community interior. The resulting spatial heterogeneity in glucose availability protected the interior from antibiotic accumulation in a membrane potential-dependent manner, ensuring rapid recovery of the community postantibiotic treatment. Our findings unveiled a community-level antibiotic response through spatial regulation of metabolism and suggested new strategies for antibiotic therapies.

Whole-genome sequencing of three extremophile Bacillus sp. strains isolated from the Atacama Desert

The Atacama Desert is home to bacteria that use biofilms as a means of protecting themselves against the harsh environment. To inform research regarding this survival mechanism, we cultured and sequenced the genomes of three Bacillus sp. isolates from Atacama Desert soil.

Active Microrobots for Dual Removal of Biofilms via Chemical and Physical Mechanisms

Bacterial biofilms are complex multicellular communities that adhere firmly to solid surfaces. They are widely recognized as major threats to human health, contributing to issues such as persistent infections on medical implants and severe contamination in drinking water systems. As a potential treatment for biofilms, this work proposes two strategies: (i) light-driven ZnFe2O4 (ZFO)/Pt microrobots for photodegradation of biofilms and (ii) magnetically driven ZFO microrobots for mechanical removal of biofilms from surfaces. Magnetically driven ZFO microrobots were realized by synthesizing ZFO microspheres through a low-cost and large-scale hydrothermal synthesis, followed by a calcination process. Then, a Pt layer was deposited on the surface of the ZFO microspheres to break their symmetry, resulting in self-propelled light-driven Janus ZFO/Pt microrobots. Light-driven ZFO/Pt microrobots exhibited active locomotion under UV light irradiation and controllable motion in terms of "stop and go" features. Magnetically driven ZFO microrobots were capable of maneuvering precisely when subjected to an external rotating magnetic field. These microrobots could eliminate Gram-negative Escherichia coli (E. coli) biofilms through photogenerated reactive oxygen species (ROS)-related antibacterial properties in combination with their light-powered active locomotion, accelerating the mass transfer to remove biofilms more effectively in water. Moreover, the actuation of magnetically driven ZFO microrobots allowed for the physical disruption of biofilms, which represents a reliable alternative to photocatalysis for the removal of strongly anchored biofilms in confined spaces. With their versatile characteristics, the envisioned microrobots highlight a significant potential for biofilm removal with high efficacy in both open and confined spaces, such as the pipelines of industrial plants.

Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits

BACKGROUND

The widespread selective pressure of antibiotics in the environment has led to the propagation of antibiotic resistance genes (ARGs). However, the mechanisms by which microbes balance population growth with the enrichment of ARGs remain poorly understood. To address this, we employed microcosm cultivation at different antibiotic (i.e., Oxytetracycline, OTC) stresses across the concentrations from the environmental to the clinical. Paired with shot-gun metagenomics analysis and quantification of bacterial growth, trait-based assessment of soil microbiota was applied to reveal the association between key ARG subtypes, representative bacterial taxa, and functional-gene features that drive the growth of ARGs.

RESULTS

Our results illuminate that resistome variation is closely associated with bacterial growth. A non-monotonic change in ARG abundance and richness was observed over a concentration gradient from none to 10 mg/l. Soil microbiota exposed to intermediate OTC concentrations (i.e., 0.1 and 0.5 mg/l) showed greater increases in the total abundance of ARGs. Community compositionally, the growth of representative taxa, i.e., Pseudomonadaceae was considered to boost the increase of ARGs. It has chromosomally carried kinds of multidrug resistance genes such as mexAB-oprM and mexCD-oprJ could mediate the intrinsic resistance to OTC. Streptomycetaceae has shown a better adaptive ability than other microbes at the clinical OTC concentrations. However, it contributed less to the ARGs growth as it represents a stress-tolerant lifestyle that grows slowly and carries fewer ARGs. In terms of community genetic features, the community aggregated traits analysis further indicates the enhancement in traits of resource acquisition and growth yield is driving the increase of ARGs abundance. Moreover, optimizations in energy production and conversion, alongside a streamlining of bypass metabolic pathways, further boost the growth of ARGs in sub-inhibitory antibiotic conditions.

CONCLUSION

The results of this study suggest that microbes with competitive lifestyles are selected under the stress of environmental sub-inhibitory concentrations of antibiotics and nutrient scarcity. They possess greater substrate utilization capacity and carry more ARGs, due to this they were faster growing and leading to a greater increase in the abundance of ARGs. This study has expanded the application of trait-based assessments in understanding the ecology of ARGs propagation. And the finding illustrated changes in soil resistome are accompanied by the lifestyle switching of the microbiome, which theoretically supports the ARGs control approach based on the principle of species competitive exclusion. Video Abstract.

Surfactin facilitates establishment of Bacillus subtilis in synthetic communities

Soil bacteria are prolific producers of a myriad of biologically active secondary metabolites. These natural products play key roles in modern society, finding use as anti-cancer agents, as food additives, and as alternatives to chemical pesticides. As for their original role in interbacterial communication, secondary metabolites have been extensively studied under in vitro conditions, revealing many roles including antagonism, effects on motility, niche colonization, signaling, and cellular differentiation. Despite the growing body of knowledge on their mode of action, biosynthesis, and regulation, we still do not fully understand the role of secondary metabolites on the ecology of the producers and resident communities in situ. Here, we specifically examine the influence of Bacillus subtilis-produced cyclic lipopeptides during the assembly of a bacterial synthetic community, and simultaneously, explore the impact of cyclic lipopeptides on B. subtilis establishment success in a synthetic community propagated in an artificial soil microcosm. We found that surfactin production facilitates B. subtilis establishment success within multiple synthetic communities. Although neither a wild type nor a cyclic lipopeptide non-producer mutant had a major impact on the synthetic community composition over time, both the B. subtilis and the synthetic community metabolomes were altered during co-cultivation. Overall, our work demonstrates the importance of surfactin production in microbial communities, suggesting a broad spectrum of action of this natural product.

Bacillus lipopeptides as key players in rhizosphere chemical ecology

Microbial natural products are widely explored for their therapeutic potential. Understanding the underlying evolutionary and adaptive forces driving their production remains a fundamental question in biology. Amphiphilic cyclic lipopeptides (CLPs), a prominent category of bacterial specialized metabolites, show strong antimicrobial activity, particularly against phytopathogens. It is thus assumed that these compounds are deployed by soil- or rhizosphere-dwelling bacteria as microbial weapons in competitive natural environments. Here, we challenge this reductionist perspective and present evidence that Bacillus CLPs are prominent chemical mediators of ecological interactions. They help Bacillus to communicate, compete, defend against predators, or cooperate and establish mutualistic relationships with other (micro)organisms. Additional parallel examples are highlighted in other genera, such as Pseudomonas. This broader perspective underscores the need for further investigation into the role of CLPs in shaping the adaptive strategies of key rhizobacterial species.

A Comparison of Antibiotics' Resistance Patterns of E. coli and B. subtilis in their Biofilms and Planktonic Forms

BACKGROUND

A biofilm refers to a community of microbial cells that adhere to surfaces that are surrounded by an extracellular polymeric substance. Bacteria employ various defence mechanisms, including biofilm formation, to enhance their survival and resistance against antibiotics.

OBJECTIVE

The current study aims to investigate the resistance patterns of Escherichia coli (E. coli) and Bacillus subtilis (B. subtilis) in both biofilms and their planktonic forms.

METHODS

E. coli and B. subtilis were used to compare resistance patterns in biofilms versus planktonic forms of bacteria. An antibiotic disc diffusion test was performed to check the resistance pattern of biofilm and planktonic bacteria against different antibiotics such as penicillin G, streptomycin, and ampicillin. Biofilm formation and its validation were done by using quantitative (microtiter plate assay) and qualitative analysis (Congo red agar media).

RESULTS

A study of surface-association curves of E. coli and B. subtilis revealed that surface adhesion in biofilms was continuously constant as compared to their planktonic forms, thereby confirming the increased survival of bacteria in biofilms. Also, biofilms have shown high resistance towards the penicillin G, ampicillin and streptomycin as compared to their planktonic form.

CONCLUSION

It is safely inferred that E. coli and B. subtilis, in their biofilms, become increasingly resistant to penicillin G, ampicillin and streptomycin.

Flagellar rotation facilitates the transfer of a bacterial conjugative plasmid

Conjugation-mediated DNA delivery is the primary mode for antibiotic resistance spread in bacteria; yet, molecular mechanisms regulating the conjugation process remain largely unexplored. While conjugative plasmids typically require bacterial attachment to solid surfaces for facilitation of donor-to-recipient proximity, the pLS20 conjugative plasmid, prevalent among Gram-positive Bacillus spp., uniquely requires fluid environments to enhance its transfer. Here, we show that pLS20, carried by Bacillus subtilis, induces multicellular clustering, which can accommodate various species, hence offering a stable platform for DNA delivery in a liquid milieu. We further discovered that induction of pLS20 promoters, governing crucial conjugative genes, is dependent on the presence of donor cell flagella, the major bacterial motility organelle. Moreover, the pLS20 regulatory circuit is controlled by a mechanosensing signal transduction pathway responsive to flagella rotation, thus activating conjugation gene expression exclusively during the host motile phase. This flagella-conjugation coupling strategy may allow the dissemination of the plasmid to remote destinations, allowing infiltration into new niches.

An Agent-Based Model of Metabolic Signaling Oscillations in Bacillus subtilis Biofilms

Microbes of nearly every species can form biofilms, communities of cells bound together by a self-produced matrix. It is not understood how variation at the cellular level impacts putatively beneficial, colony-level behaviors, such as cell-to-cell signaling. Here we investigate this problem with an agent-based computational model of metabolically driven electrochemical signaling in Bacillus subtilis biofilms. In this process, glutamate-starved interior cells release potassium, triggering a depolarizing wave that spreads to exterior cells and limits their glutamate uptake. More nutrients diffuse to the interior, temporarily reducing glutamate stress and leading to oscillations. In our model, each cell has a membrane potential coupled to metabolism. As a simulated biofilm grows, collective membrane potential oscillations arise spontaneously as cells deplete nutrients and trigger potassium release, reproducing experimental observations. We further validate our model by comparing spatial signaling patterns and cellular signaling rates with those observed experimentally. By oscillating external glutamate and potassium, we find that biofilms synchronize to external potassium more strongly than to glutamate, providing a potential mechanism for previously observed biofilm synchronization. By tracking cellular glutamate concentrations, we find that oscillations evenly distribute nutrients in space: non-oscillating biofilms have an external layer of well-fed cells surrounding a starved core, whereas oscillating biofilms exhibit a relatively uniform distribution of glutamate. Our work shows the potential of agent-based models to connect cellular properties to collective phenomena and facilitates studies of how inheritance of cellular traits can affect the evolution of group behaviors.

In vitro biofilm formation only partially predicts beneficial Pseudomonas fluorescens protection against rhizosphere pathogens

Plant roots form associations with both beneficial and pathogenic soil microorganisms. While members of the rhizosphere microbiome can protect against pathogens, the mechanisms are poorly understood. We hypothesized that the ability to form a robust biofilm on the root surface is necessary for the exclusion of pathogens; however, it is not known if the same biofilm formation components required in vitro are necessary in vivo. Pseudomonas fluorescens WCS365 is a beneficial strain that is phylogenetically closely related to an opportunistic pathogen P. fluorescens N2C3 and confers robust protection against P. fluorescens N2C3 in the rhizosphere. We used this plant-mutualist-pathogen model to screen collections of P. fluorescens WCS365 increased attachment mutants (iam) and surface attachment defective (sad) transposon insertion mutants that form increased or decreased levels of biofilm on an abiotic surface, respectively. We found that while the P. fluorescens WCS365 mutants had altered biofilm formation in vitro, only a subset of these mutants, including those involved in large adhesion protein (Lap) biosynthesis, flagellin biosynthesis and O-antigen biosynthesis, lost protection against P. fluorescens N2C3. We found that the inability of P. fluorescens WCS365 mutants to grow in planta, and the inability to suppress pathogen growth, both partially contributed to loss of plant protection. We did not find a correlation between the extent of biofilm formed in vitro and pathogen protection in planta indicating that biofilm formation on abiotic surfaces may not fully predict pathogen exclusion in planta. Collectively, our work provides insights into mechanisms of biofilm formation and host colonization that shape the outcomes of host-microbe-pathogen interactions.

Kaempferol restores the susceptibility of ESBLs Escherichia coli to Ceftiofur

Introduction

The development of extended-spectrum-beta-lactamase (ESBLs) Escherichia coli (E. coli) has become a global threat to public health. An alternative strategy to alleviate this is identifying potential natural compounds to restore antibiotic activity against ESBLs E. coli. This study aimed to find a possible compound to restore ESBLs E. coli sensitivity to ceftiofur.

Methods

The synergistic effect of kaempferol and ceftiofur against ESBLs E. coli was investigated by checkerboard assays, time-kill, growth curves, and scanning electronic microscope. The impact of kaempferol with ceftiofur on the biofilm of ESBLs E. coli was evaluated by crystal violet staining and laser scanning confocal microscopy and this study also assessed the effect of kaempferol on the initial adhesion and aggregation of E. coli (SY20) by examining motility, adhesion, and surface characteristics. The RT-qPCR was used to determine the effect of kaempferol on the expression of genes related to the LuxS/AI-2 quorum sensing system in ESBLs E. coli, and the effect of kaempferol on AI-2 signaling molecules was determined by molecular docking and bioassay. The impact of kaempferol on the activity of blaCTX-M-27 protein was determined by RT-qPCR, molecular docking, and nitrofen experiments, the results were further verified by transcriptome analysis. The mouse infection model was established, and the inhibitory mechanism of kaempferol with ceftiofur on bacteria in vivo was further verified by HE staining and immunohistochemistry.

Results and discussion

Kaempferol with ceftiofur exerts synergistic antibacterial and bactericidal effects on ESBLs E. coli by influencing β-lactamase activity, biofilm formation, and LuxS/AI-2 QS system. In vivo, kaempferol protected the small intestinal villi from the damage of ESBLs E. coli. Furthermore, kaempferol fully restores the activity of ceftiofur in animal infection models by relieving the TLR4/NF-κb pathway. In conclusion, the sensitivity of ESBLs E. coli to ceftiofur in vitro and in vivo could be enhanced by kaempferol, which showed that kaempferol may be a kind of antibiotic adjuvant.

Harnessing biosynthesized selenium nanoparticles for recruitment of beneficial soil microbes to plant roots

Root exudates can benefit plant growth and health by reshaping the rhizosphere microbiome. Whether nanoparticles biosynthesized by rhizosphere microbes play a similar role in plant microbiome manipulation remains enigmatic. Herein, we collect elemental selenium nanoparticles (SeNPs) from selenobacteria associated with maize roots. In vitro and soil assays show that the SeNPs enhanced plant performance by recruiting plant growth-promoting bacteria (e.g., Bacillus) in a dose-dependent manner. Multiomic profilings unravel a cross-kingdom-signaling cascade that mediates efficient biosynthesis of SeNPs by selenobacteria. Specifically, maize roots perceive histamine signaling from Bacillus spp., which stimulates the plant to produce p-coumarate via root exudation. The rpoS gene in selenobacteria (e.g., Pseudomonas sp. ZY71) responds to p-coumarate signaling and positively regulates the biosynthesis of SeNPs. This study demonstrates a novel mechanism for recruiting host-beneficial soil microbes by microbially synthesized nanoparticles and unlocks promising possibilities for plant microbiome manipulation.

Bridging the Gap: Biofilm-mediated establishment of Bacillus velezensis on Trichoderma guizhouense mycelia

Bacterial-fungal interactions (BFIs) are important in ecosystem dynamics, especially within the soil rhizosphere. The bacterium Bacillus velezensis SQR9 and the fungus Trichoderma guizhouense NJAU 4742 have gathered considerable attention due to their roles in promoting plant growth and protecting their host against pathogens. In this study, we utilized these two model microorganisms to investigate BFIs. We firstly demonstrate that while co-inoculation of B. velezensis and T. guizhouense could promote tomato growth, these two microorganisms display mutual antagonism on agar solidified medium. To resolve this contradiction, we developed an inoculation method, that allows B. velezensis colonization of T. guizhouense hyphae and performed a transcriptome analysis. During colonization of the fungal hyphae, B. velezensis SQR9 upregulates expression of biofilm related genes (e.g. eps, tasA, and bslA) that is distinct from free-living cells. This result suggested an intricate association between extracellular matrix expression and hyphae colonization. In accordance, deletion epsD, tasA, or both epsD and tasA genes of B. velezensis diminished colonization of the T. guizhouense hyphae. The insights from our study demonstrate that soil BFIs are more complex than we understood, potentially involving both competition and cooperation. These intricate biofilm-mediated BFI dynamics might contribute to the remarkable diversity observed within soil microbiota, providing a fresh perspective for further exploration of BFIs in the plant rhizosphere.

Soy protein hydrolysates induce menaquinone-7 biosynthesis by enhancing the biofilm formation of Bacillus subtilis natto

Menaquinone-7 (MK-7) is a form of vitamin K2 with health-beneficial effects. A novel fermentation strategy based on combining soy protein hydrolysates (SPHs) with biofilm-based fermentation was investigated to enhance menaquinone-7 (MK-7) biosynthesis by Bacillus subtilis natto. Results showed the SPHs increased MK-7 yield by 199.4% in two-stage aeration fermentation as compared to the SP-based medium in submerged fermentation, which was related to the formation of robust biofilm with wrinkles and the enhancement of cell viability. Moreover, there was a significant correlation between key genes related to MK-7 and biofilm synthesis, and the quorum sensing (QS) related genes, Spo0A and SinR, were downregulated by 0.64-fold and 0.39-fold respectively, which promoted biofilm matrix synthesis. Meanwhile, SPHs also enhanced the MK-7 precursor, isoprene side chain, supply, and MK-7 assembly efficiency. Improved fermentation performances of bacterial cells during fermentation were attributed to abundant oligopeptides (Mw < 1 kDa) and moderate amino acids, particularly Arg, Asp, and Phe in SPHs. All these results revealed that SPHs were a potential and superior nitrogen source for MK-7 production by Bacillus subtilis natto.

Emerging antibiotic and heavy metal resistance in spore-forming bacteria from pig manure, manure slurry and fertilized soil

Spore-forming bacteria (SFB), like Bacillus, are the gram-positive bacteria with broad-spectrum activity that is one of the commonly used strains of probiotics. However, these bacteria also have significant resistance. In this study, we systematically investigated pig manure, manure slurry and soil by 16S rRNA high-throughput sequencing and traditional culture techniques. We found the SFB was widespread in manure, manure slurry and soil, Firmicutes was one of the main dominant phyla in pig manure, manure slurry and soil, the relative abundance of Bacillus were 0.98%, 0.01%, and 2.57%, respectively, and metals such as copper have complex relationships with bacteria. We isolated 504 SFB from 369 samples, with the highest number identified as Bacillus subtilis. SFB strains showed varying degrees of antibiotic resistance; the greatest against erythromycin, followed by imipenem. The MICs of SFB varied greatly against different heavy metals; with high (est) resistance against Zn2+, followed by Cu2+. Second-generation whole genome sequencing (WGS) revealed that nine Bacillus strains carried different subtypes of vancomycin resistance genes, among which vanRM had the highest frequency. The strain W129 included the vanRA-vanRM-vanSA-vanZF cluster. The nine Bacillus strains also contained antibiotic genes such as aminoglycoside (ant(9)-Ia), β-lactam (bcII), and macrolide (msrE). Twenty-six Bacillus isolates carried copper resistance clusters, including csoR-copZ, copA-copZ-csoR, and copZ-copA. WGS showed that strain W166 carried 11 vancomycin resistance genes and 11 copper resistance genes. There were 4 vancomycin resistance genes and 14 copper resistance genes on the W129 chromosome. Strain W129 also harbors the plasmid pLKYM01 that contains an intact transposon consisting of insertion sequence and vancomycin resistance genes vanYF and vanRA. This study explores the potential risks of using pig manure and fertilized soil to inform safe and effective use of probiotics in agriculture. It highlights scientific evidence for concern over the safe utilization and control of animal waste products.

Growth promotion on maize and whole-genome sequence analysis of Bacillus velezensis D103

Root-associated microorganisms, particularly plant growth-promoting rhizobacteria (PGPR) from the Bacillus genus, play a crucial role in enhancing crop yield and health. In this study, a Bacillus strain was isolated from the rhizosphere soil of maize and identified as Bacillus velezensis D103. The primary objective of this research was to evaluate the potential of D103 as a PGPR. Laboratory tests demonstrated that D103 is capable of nitrogen fixation, inorganic phosphorus solubilization, potassium solubilization, and the synthesis of indole-3-acetic acid, ammonia, siderophores, amylase, protease, cellulase, β-1,3-glucanase, and 1-aminocyclopropane-1-carboxylate deaminase. Additionally, D103 exhibited swimming and swarming motility, biofilm formation, and an antagonistic activity against pathogenic fungi. Genome mining identified genes associated with growth promotion and biocontrol activities. In a hydroponics experiment, maize plants treated with a D103 suspension at a cell density of 103 CFU·mL-1 resulted in the most pronounced showed significant growth stimulation, with shoot length and total root length increasing by 43% and 148%, respectively. These results support the potential of D103 as an effective PGPR for promoting maize crop growth.

IMPORTANCE

In this study, we assessed the capacity of D103 to promote plant growth and examined the effects of hydroponic experiments inoculated with this strain on the growth of maize seedlings. We sequenced and analyzed the complete genome of D103, identifying several genes and gene clusters associated with plant growth promotion and resistance to pathogenic fungi, thus revealing the plant growth-promoting mechanisms of this strain. The isolation and characterization of new strains with beneficial traits are essential for expanding microbial resources available for biofertilizer production. Collectively, these findings highlight the promising potential of Bacillus velezensis D103 as a biofertilizer for agricultural applications.

Mechanisms of rhizosphere plant-microbe interactions: molecular insights into microbial colonization

The rhizosphere, as the "frontline" of plant life, connects plant roots, rhizosphere microorganisms, and surrounding soil, plays a crucial role in plant growth and health, particularly in sustainable agriculture. Despite the well-established contribution of plant-microbe interactions to plant health, the specific molecular mechanisms remain insufficiently understood. This review aims to summarize the physiological adjustments and signal modulation that both plants and microorganisms undergo within this unique ecological niche to ensure successful colonization. By analyzing key processes such as chemotaxis, root attachment, immune evasion, and biofilm formation, we uncover how plants precisely modulate root exudates to either recruit or repel specific microorganisms, thereby shaping their colonization patterns. These findings provide new insights into the complexity of plant-microbe interactions and suggest potential directions for future research in sustainable agriculture.

The biology and chemistry of a mutualism between a soil bacterium and a mycorrhizal fungus

Arbuscular mycorrhizal (AM) fungi (e.g., Rhizophagus species) recruit specific bacterial species in their hyphosphere. However, the chemical interplay and the mutual benefit of this intricate partnership have not been investigated yet, especially as it involves bacteria known as strong producers of antifungal compounds such as Bacillus velezensis. Here, we show that the soil-dwelling B. velezensis migrates along the hyphal network of the AM fungus R. irregularis, forming biofilms and inducing cytoplasmic flow in the AM fungus that contributes to host plant root colonization by the bacterium. During hyphosphere colonization, R. irregularis modulates the biosynthesis of specialized metabolites in B. velezensis to ensure stable coexistence and as a mechanism to ward off mycoparasitic fungi and bacteria. These mutual benefits are extended into a tripartite context via the provision of enhanced protection to the host plant through the induction of systemic resistance.

Autoinducer-2 relieves soil stress-induced dormancy of Bacillus velezensis by modulating sporulation signaling

The collective behavior of bacteria is regulated by quorum sensing (QS). Autoinducer-2 (AI-2) is a common QS signal that regulates the behavior of both Gram-positive and Gram-negative bacteria. Despite the plethora of processes described to be influenced by AI-2 in diverse Gram-negative bacteria, the AI-2-regulated processes in Bacilli are relatively unexplored. Here, we describe a novel function for AI-2 in Bacillus velezensis SQR9 related to the sporulation. AI-2 inhibited the initiation of sporulation through the phosphatase RapC and the DNA binding regulator ComA. Using biochemistry experiments, we demonstrated that AI-2 interacts with RapC to stimulate its binding to ComA, which leads to an inactive ComA and subsequently a sporulation inhibition. The AI-2 molecule could be shared across species for inhibiting Bacillus sporulation and it also plays the same role in different soil conditions. Our study revealed a novel function and regulatory mechanism of AI-2 in inhibiting sporulation in Bacilli.

A phosphate starvation induced small RNA promotes Bacillus biofilm formation

Currently, almost all known regulators involved in bacterial phosphorus metabolism are proteins. In this study, we identified a conserved new small regulatory RNA (sRNA), named PhoS, encoded in the 3' untranslated region (UTR) of the phoPR genes in Bacillus velezensis and B. subtilis. Expression of phoS is strongly induced upon phosphorus scarcity and stimulated by the transcription factor PhoP. Conversely, PhoS positively regulates PhoP translation by binding to the ribosome binding site (RBS) of phoP mRNA. PhoS can promote Bacillus biofilm formation through, at least in part, enhancing the expression of the matrix-related genes, such as the eps genes and the tapA-sipW-tasA operon. The positive regulation of phoP expression by PhoS contributes to the promoting effect of PhoS on biofilm formation. sRNAs regulating biofilm formation have rarely been reported in gram-positive Bacillus species. Here we highlight the significance of sRNAs involved in two important biological processes: phosphate metabolism and biofilm formation.

Flagellar point mutation causes social aggregation in laboratory-adapted Bacillus subtilis under conditions that promote swimming

Motility allows microbes to explore and maximize success in their environment; however, many laboratory bacterial strains have a reduced or altered capacity for motility. Swimming motility in Bacillus subtilis depends on peritrichous flagella and is carried out individually as cells move by biased random walks toward attractants. Previously, we adapted Bacillus subtilis strain 3610 to the laboratory for 300 generations in lysogeny broth (LB) batch culture and isolated lab-adapted strains. Strain SH2 is motility-defective and in broth culture forms large, frequently spherical aggregates of cells. A single point mutation in the flagellin gene hag that causes amino acid 259 to switch from A to T is necessary and sufficient to cause these social cell aggregates, and aggregation occurs between flagellated cells bearing this point mutation regardless of the strain background. Cells associate when bearing this mutation, but flagellar rotation is needed to pull associating cells into spherical aggregates. Using electron microscopy, we are able to show that the SH2 flagellar filament has limited polymorphism when compared to other flagellar structures. This limited polymorphism hinders the flagellum's ability to function as a motility apparatus but appears to alter its function to that of cell aggregation/adhesion. We speculate that the genotype-specific aggregation of cells producing HagA259T flagella could have increased representation in a batch-culture experiment by allowing similar cells to go through a transfer together and also that this mutation could serve as an early step to evolve sociality in the natural world.IMPORTANCEThe first life forms on this planet were prokaryotic, and the earliest environments were aquatic, and from these relatively simple starting conditions, complex communities of microbes and ultimately multicellular organisms were able to evolve. Usually, motile cells in aqueous environments swim as individuals but become social by giving up motility and secreting extracellular substances to become a biofilm. Here, we identify a single point mutation in the flagellum that is sufficient to allow cells containing this mutation to specifically form large, suspended groups of cells. The specific change in the flagellar filament protein subunits causes a unique change in the flagellar structure. This could represent a distinct way for closely related cells to associate as an early precursor to sociality.

Taxonomy of Pseudomonas spp. determines interactions with Bacillus subtilis

Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil and frequently co-isolated. Isolates from these two genera are frequently used as plant beneficial microorganisms; therefore, their interaction in the plant rhizosphere is relevant for agricultural applications. Despite this, no systematic approach has been employed to assess the coexistence of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on Bacillus subtilis pellicle formation in two types of media and found a predictor for interaction outcome in Pseudomonas taxonomy. Interactions were context-dependent, and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with Pseudomonas capeferrum, Pseudomonas entomophila, and Pseudomonas protegens, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of B. subtilis. Non-inhibiting strains were closely related to Pseudomonas trivialis and Pseudomonas lini. Using such a non-inhibiting isolate, Pseudomonas P9_31, which increased B. subtilis pellicle formation demonstrated that the two species were spatially segregated in cocultures. Our study is the first one to propose an overall negative outcome from pairwise interactions between B. subtilis and fluorescent pseudomonads; hence, cocultures comprising members from these groups are likely to require additional microorganisms for coexistence.

IMPORTANCE

There is a strong interest in the microbial ecology field to predict interaction among microorganisms, whether two microbial isolates will promote each other's growth or compete for resources. Numerous studies have been performed based on surveying the available literature or testing phylogenetically diverse sets of species in synthetic communities. Here, a high throughput screening has been performed using 720 Pseudomonas isolates, and their impact on the biofilm formation of Bacillus subtilis was tested. The aim was to determine whether a majority of Pseudomonas will promote or inhibit the biofilms of B. subtilis in the co-cultures. This study reports that Pseudomonas taxonomy is a good predictor of interaction outcome, and only a minority of Pseudomonas isolates promote Bacillus biofilm establishment.

Bacillus subtilis EpsA-O: A novel exopolysaccharide structure acting as an efficient adhesive in biofilms

Extracellular polysaccharides are crucial components for biofilm development. Although Bacillus subtilis is one of the most characterized Gram-positive biofilm model system, the structure-function of its exopolysaccharide, EpsA-O, remains to be elucidated. By combining chemical analysis, NMR spectroscopy, rheology, and molecular modeling, high-resolution data of EpsA-O structure from atom to supramolecular scale was obtained. The repeating unit is composed of the trisaccharide backbone [→3)-β-D-QuipNAc4NAc-(1→3)-β-D-GalpNAc-(1→3)-α-D-GlcpNAc-(1]n, and the side chain β-D-Galp(3,4-S-Pyr)-(1→6)-β-D-Galp(3,4-S-Pyr)-(1→6)-α-D-Galp-(1→ linked to C4 of GalNAc. Close agreement between the primary structure and rheological behavior allowed us to model EpsA-O macromolecular and supramolecular solution structure, which can span the intercellular space forming a gel that leads to a complex 3D biofilm network as corroborated by a mutant strain with impaired ability to produce EpsA-O. This is a comprehensive structure-function investigation of the essential biofilm adhesive exopolysaccharide that will serve as a useful guide for future studies in biofilm architecture formation.

Bacillaene, sharp objects consist in the arsenal of antibiotics produced by Bacillus

Bacillus species act as plant growth-promoting rhizobacteria (PGPR) that can produce a large number of bioactive metabolites. Bacillaene, a linear polyketide/nonribosomal peptide produced by Bacillus strains, is synthesized by the trans-acyltransferase polyketide synthetase. The complexity of the chemical structure, particularity of biosynthesis, potent bioactivity, and the important role of competition make Bacillus an ideal antibiotic weapon to resist other microbes and maintain the optimal rhizosphere environment. This review provides an updated view of the structural features, biological activity, biosynthetic regulators of biosynthetic pathways, and the important competitive role of bacillaene during Bacillus survival.

Dynamic in situ detection in iRhizo-Chip reveals diurnal fluctuations of Bacillus subtilis in the rhizosphere

Effective colonization by microbe in the rhizosphere is critical for establishing a beneficial symbiotic relationship with the host plant. Bacillus subtilis, a soil-dwelling bacterium that is commonly found in association with plants and their rhizosphere, has garnered interest for its potential to enhance plant growth, suppress pathogens, and contribute to sustainable agricultural practices. However, research on the dynamic distribution of B. subtilis within the rhizosphere and its interaction mechanisms with plant roots remains insufficient due to limitations in existing in situ detection methodologies. To achieve dynamic in situ detection of the rhizosphere environment, we established iRhizo-Chip, a microfluidics-based platform. Using this device to investigate microbial behavior within the rhizosphere, we found obvious diurnal fluctuations in the growth of B. subtilis in the rhizosphere. Temporal dynamic analysis of rhizosphere dissolved oxygen (DO), pH, dissolved organic carbon, and reactive oxygen species showed that diurnal fluctuations in the growth of B. subtilis are potentially related to a variety of environmental factors. Spatial dynamic analysis also showed that the spatial distribution changes of B. subtilis and DO and pH were similar. Subsequently, through in vitro control experiments, we proved that rhizosphere DO and pH are the main driving forces for diurnal fluctuations in the growth of B. subtilis. Our results show that the growth of B. subtilis is driven by rhizosphere DO and pH, resulting in diurnal fluctuations, and iRhizo-Chip is a valuable tool for studying plant rhizosphere dynamics.

Bacterial epigenetics and its implication for agriculture, probiotics development, and biotechnology design

In their natural habitats, organisms encounter numerous external stimuli and must be able to sense and adapt to those stimuli to survive. Unlike mutations, epigenetic changes do not alter the underlying DNA sequence. Instead, they create modifications that promote or silence gene expression. Bacillus subtilis has long been a model organism in studying genetics and development. It is beneficial for numerous biotechnological applications where it is included as a probiotic, in fermentation, or in bio-concrete design. This bacterium has also emerged recently as a model organism for studying bacterial epigenetic adaptation. In this review, we examine the evolving knowledge of epigenetic regulation (restriction-modification systems (RM), orphan methyltransferases, and chromosome condensation) in B. subtilis and related bacteria, and utilize it as a case study to test their potential roles and future applications in genetic engineering and microbial biotechnology. Finally, we suggest how the implementation of these fundamental findings promotes the design of synthetic epigenetic memory circuits and their future applications in agriculture, medicine, and biotechnology.