Heterogeneity in respiratory electron transfer and adaptive iron utilization in a bacterial biofilm

Mild Tuning of the Microbial Habitat via Titanium-Based Pre-coagulation Mitigates Reverse Osmosis Membrane Fouling

Membrane fouling remains a persistent challenge in reverse osmosis (RO) systems. Devising effective strategies to mitigate membrane fouling has become crucial for sustainable water treatment. Here, we propose a titanium-based pre-coagulation strategy for RO fouling mitigation through regulation of the microbial habitat in RO feed. The pre-coagulation performance of Ti(SO4)2 for desulfurization wastewater and the subsequent RO fouling mechanism were systematically investigated. Our findings revealed that the Ti pre-coagulation induced an acidized environment, maintained a balance between organic and inorganic depositions, and fostered a beneficial microbial community that resisted rapid fouling. The 20 day RO operations in different pre-coagulation scenarios (Ti, Al, and Ctrl) showed that the Ti group membranes maintained the highest normalized flux at 57.15%, outperforming the Ctrl and Al groups by 7.92% and 15.16%, respectively. Microbial community analyses, including taxonomic profiling and metagenomic analysis, demonstrated that Ti-based pre-coagulation reduced the dominance of extracellular polymeric substance (EPS)-secreting genera, such as Sphingopyxis, while promoting Terrimonas and Paenarthrobacter, with acid-tolerance traits and reduced EPS production. This shift mitigated biofouling by enhancing microbial balance and limiting biofilm formation. These results underscored the potential of the Ti pre-coagulation-based microbial habitat tuning strategy in enhancing RO system sustainability, offering a practical solution for improving industrial wastewater treatment.

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.

Antagonism of Bacillus velezensis ZGE166 Against the Pathogenic Fungi Causing Corm Rot Disease in Saffron (Crocus sativus L.)

Saffron can be infected with pathogenic fungi that cause corm rot as it grows and multiplies, which can reduce the quality and yield of saffron. Corm rot has become one of the most serious diseases of saffron. In this study, rhizosphere bacteria were isolated from saffron rhizosphere soil, and bacteria exhibiting antagonistic effects against corm rot pathogenic fungi were screened using in vitro plate co-culture assays and dual-compartment agar plate systems. Selected strains were further evaluated for hydrolase activity determination and PGP potential assessment. Among them, Bacillus velezensis showed the best disease resistance activity. The degradative enzyme production and some beneficial characteristics of Bacillus velezensis for plant growth promotion were evaluated. It was found that Bacillus velezensis possesses nitrogen fixing, NH3-producing, IAA production, and ACC-deaminating enzymes. The whole genome sequence of this strain was annotated and analyzed. The genome of Bacillus velezensis consists of a circular chromosome of 3,908,025 bp base pairs, with a guanine and cytosine content of 46.64%. There are 3737 protein-coding genes, including 86 tRNA genes, 27 rRNA genes, and 85 sRNA genes. The genome also contains four genomic islands, two pre-phages, and one transposon. The prediction of the secondary metabolic accumulation gene cluster demonstrated that the genome sequence of ZGE166 encodes 12 gene clusters involved in the synthesis of secondary metabolites, including macrolactin H, bacillaene, fengycin, difficidin, and bacillibactin. In summary, strain ZGE166 Bacillus velezensis has the potential to be developed as a biological agent.

Development of a safe formulation that induces biofilm formation in probiotic bacteria for controlling Salmonella enteriditis Heidelberg and avian pathogenic Escherichia coli in wood shavings

1. The aim of this study was to develop a formulation that stimulated the spontaneous formation of biofilms by probiotic bacteria, specifically Bacillus velezensis (BV), Bacillus subtilis (BS), or Lactococcus lactis subspecies lactis (LL) for control of Salmonella enteriditis Heidelberg (SH) and avian pathogenic E. coli (APEC).2. A formulation was developed to induce spontaneous biofilm formation of probiotic bacteria (BV, BS and LL) by testing various media containing minerals and polymers on polystyrene plates. The most potent probiotic strains were identified based on their efficacy in inhibiting SH and APEC. The formulation was tested on wood shavings to hinder APEC and SH. The safety and colonisation of the formulation was assessed in chicken embryos (CE) from 19 d of incubation to the broiler chicken stage.3. After evaluating various media, one containing calcium, magnesium, iron and polymers (dextran, chitosan and xylan) was selected. Notably, xylan, a highly sustainable biopolymer, showed outstanding results at a low concentration (27 µg/ml), which led to its selection for conducting inhibition tests on wood shavings against SH and APEC. The B. velezensis demonstrated superior biofilm formation and efficacy in controlling SH and APEC. Consequently, a BV strain was selected and associated with a strain of LL.4. While drying the formulation, maltodextrin was added and the biofilm formed by BV01 and LLL01 on wood shavings could control both SH and APEC species, reducing them by approximately 92.64 to 99.42%. Inoculating the formulation in CE did not result in a delay in hatching, injury, or death for either the CE or chicks. The probiotic bacteria multiplied and colonised the intestine of CE.5. This work successfully developed a formulation that induced spontaneous biofilm formation in BV and LL, significantly controlling SH and APEC while ensuring safety for birds.

Interaction and cross-contamination potential of prepared beef steak isolates Pseudomonas weihenstephanensis and Macrococcus caseolyticus in biofilms of dual-species

This study evaluated the interactions between single or dual-species biofilms formed by dominant spoilage bacteria P. weihenstephanensis and M. caseolyticus isolated from refrigerated, spoilage prepared beef steaks at 4 °C and elucidated the interactive behavior of biofilm development in dual species. In addition, the relationship between biofilm formation capacity and cross-contamination was analyzed by simulating surface to food contact transfer. The results showed that the two species exhibited synergism as biofilms developed, which was the main mode of interaction observed. Under aerobic conditions, Pseudomonas weihenstephanensis and Macrococcus caseolyticus co-cultured for 96 h showed obvious biofilm formation ability, resulting in greater cross-contamination. Scanning electron microscopy and Confocal laser scanning microscopy showed the formation of flattened dense biofilms in the co-culture. The significant increase in Fe content and decrease in siderophore content of the dual-species biofilm as determined by ICP-MS was attributed to respiratory inhibition resulting in a decrease in the transcription of genes regulating the two-component regulatory system of Macrococcus tyrolyticus SrrAB and an increase in the expression of cytoplasmic hydrolase leading to the rupture of the release of hemoglobin to provide a source of iron for P. weihenstephanensis. The increase of heme content in the supernatant of dual-species and the results of RT-qPCR showed that the gene expression of the heme transport system of P. weihenstephanensis was significantly up-regulated and the siderophore gene expression was decreased, which further revealed that P. weihenstephanensis preferentially uses the heme uptake system to take up the iron source provided by M. caseolyticus for P. weihenstephanensis. Overall, our results provide insight into the complex dynamics of biofilms formed by P. weihenstephanensis and M. caseolyticus, emphasizing that the iron reaction pathway may be a key factor influencing the growth of P. weihenstephanensis biofilms, and that these results will provide a theoretical basis for the control of spoilage of refrigerated foods.

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.

Influence of Endogenous Derivatives on the Chemical Sensing Performance of Carbonized Polymer Dots

Endogenous derivatives, inevitably introduced during carbonized polymer dots (CPDs) synthesis, are considered to significantly influence their sensing performance. In this study, comparative studies on CPDs prepared via hydrothermal methods (CPDs-H2O) and airflow-assisted melt polymerization (CPDs-AMP) reveal that CPDs-H2O, containing abundant derivatives, exhibit superior stability and robustness in Fe3+ sensing in both solution and cells compared to derivative-deficient CPDs-AMP. Mechanistic investigations highlight the crucial role of endogenous derivatives in enhancing the intrinsic stability of CPDs polymer frameworks, challenging conventional perceptions and providing valuable insights for designing robust CPDs-based sensors for practical applications.

Ferroptosis in schizophrenia: Mechanisms and therapeutic potentials (Review)

Schizophrenia, a complex psychiatric disorder, presents with multifaceted symptoms and important challenges in treatment, primarily due to its pathophysiological complexity, which involves oxidative stress and aberrant iron metabolism. Recent insights into ferroptosis, a unique form of iron‑dependent cell death characterized by lipid peroxidation and antioxidant system failures, open new avenues for understanding the neurobiological foundation of schizophrenia. The present review explores the interplay between ferroptosis and schizophrenia, emphasizing the potential contributions of disrupted iron homeostasis and oxidative mechanisms to the pathology and progression of this disease. The emerging evidence linking ferroptosis with the oxidative stress observed in schizophrenia provides a compelling narrative for re‑evaluating current therapeutic strategies and exploring novel interventions targeting these molecular pathways, such as the glutathione peroxidase 4 pathway and the ferroptosis suppressor protein 1 pathway. By integrating recent advances in ferroptosis research, the current review highlights innovative therapeutic potentials, including N‑acetylcysteine, selenium, omega‑3 fatty acids and iron chelation therapy, which could address the limitations of existing treatments and improve clinical outcomes for individuals with schizophrenia.

Streptomyces secretes a siderophore that sensitizes competitor bacteria to phage infection

To overtake competitors, microbes produce and secrete secondary metabolites that kill neighbouring cells and sequester nutrients. This metabolite-mediated competition probably evolved in complex microbial communities in the presence of viral pathogens. We therefore hypothesized that microbes secrete natural products that make competitors sensitive to phage infection. We used a binary-interaction screen and chemical characterization to identify a secondary metabolite (coelichelin) produced by Streptomyces sp. that sensitizes its soil competitor Bacillus subtilis to phage infection in vitro. The siderophore coelichelin sensitized B. subtilis to a panel of lytic phages (SPO1, SP10, SP50, Goe2) via iron sequestration, which prevented the activation of B. subtilis Spo0A, the master regulator of the stationary phase and sporulation. Metabolomics analysis revealed that other bacterial natural products may also provide phage-mediated competitive advantages to their producers. Overall, this work reveals that synergy between natural products and phages can shape the outcomes of competition between microbes.

Bioelectronic tools for understanding the universal language of electrical signaling across species and kingdoms

Modern bioelectronic tools are rapidly advancing to detect electric potentials within networks of electrogenic cells, such as cardiomyocytes, neurons, and pancreatic beta cells. However, it is becoming evident that electrical signaling is not limited to the animal kingdom but may be a universal form of cell-cell communication. In this review, we discuss the existing evidence of, and tools used to collect, subcellular, single-cell and network-level electrical signals across kingdoms, including bacteria, plants, fungi, and even viruses. We discuss how cellular networks employ altered electrical "circuitry" and intercellular mechanisms across kingdoms, and we assess the functionality and scalability of cutting-edge nanobioelectronics to collect electrical signatures regardless of cell size, shape, or function. Researchers today aim to design micro- and nano-topographic structures which harness mechanosensitive membrane and cytoskeletal pathways that enable tight electrical coupling to subcellular compartments within high-throughput recording systems. Finally, we identify gaps in current knowledge of inter-species and inter-kingdom electrical signaling and propose critical milestones needed to create a central theory of electrical signaling across kingdoms. Our discussion demonstrates the need for high resolution, high throughput tools which can probe multiple, diverse cell types at once in their native or experimentally-modeled environments. These advancements will not only reveal the underlying biophysical laws governing the universal language of electrical communication, but can enable bidirectional electrical communication and manipulation of biological systems.

Synergistic promotion of microalgal growth and copper removal from synthetic wastewater by nanoscale zero-valent iron particles

The increasing concentrations of heavy metals in livestock wastewater pose a serious threat to the environmental safety and human health, limiting its resource utilisation. In the present study, microalgae and nanoscale zero-valent iron were selected to construct a coupled system for copper-containing wastewater treatment. The addition of 50 mg·L-1 nanoscale zero-valent iron (50 nm) was the optimal value for the experiment, which could significantly increase the biomass of microalgae. In addition, nanoscale zero-valent iron stimulated microalgal secretion of extracellular polymeric substances, increasing the contents of binding sites, organic ligands, and functional groups on the microalgal surfaces and ultimately promoting the settling of microalgae and binding of heavy metals. The coupled system could quickly adapt to copper-containing wastewater of 10 mg·L-1, and the copper removal rate reached 94.99%. Adsorption and uptake by organisms, together with the contribution of zero-valent iron nanoparticles, are the major copper removal pathways. Overall, this work offers a novel technical solution for enhanced treatment of copper-containing livestock wastewater, which will help improve the efficiency and quality of wastewater treatment.

Trojan Horse Bioheterojunction Empowers Adhesive Hydrogel with Robust Antibacterial Activity and Sensing Capacity for Infected Cutaneous Regeneration

Strategic integration of adhesive hydrogels with phototherapy-based antibacterial properties has been extensively leveraged in infected tissue repair. Nevertheless, the interference of bacterial heat shock proteins and antioxidant defense systems attenuates the bactericidal potency of phototherapy. To address this imposing predicament, a Trojan horse bioheterojunction (Th-bioHJ) incorporating liquid metal and copper sulfide is devised to confer an adhesive hydrogel with multimodal and comprehensive antibacterial properties for remedying infectious wounds. Th-bioHJ generates phototherapeutic effects and interrupts the electron transport chain with the Trojan horse strategy, achieving rapid and robust sterilization. Additionally, Th-bioHJ promotes cell migration and angiogenesis. In vivo studies elucidate the remarkable efficacy of Th-bioHJ hydrogel in rapidly eradicating bacteria, promoting angiogenesis and boosting infectious cutaneous regeneration. Meanwhile, the Th-bioHJ hydrogel demonstrates exceptional biointerface adhesion and sensing capabilities for real-time motion monitoring. This study provides groundbreaking insights into the innovative application of an adhesive hydrogel in the management of infected wounds.

Molecular level decontamination of trace quinolones and Serratia marcescens in wastewater via in situ Cu(III) complexes mediated Fenton-like oxidation

Co-pollution caused by antibiotics and antibiotic-resistant bacteria (ARB) in wastewater has led to widespread concerns. Hence, their targeted and synergistic decontamination is urgently required. A homogeneous Fenton-like oxidation system comprising cupric complexes-activated peroxymonosulfate (PMS) was demonstrated to synergistically decontaminate trace quinolones (QNs) and QNs-resistant Serratia marcescens (QRSM) in wastewater. More than 99 % of QNs were degraded within 60 min under alkaline condition, and the degradation efficiency was only slightly influenced by humic acid (up to 1 %) and various anions (up to 20 %), furthermore, the degraded pathway was proposed and the environmental risk after QNs degradation were also reduced. The activation of PMS via cupric complexes coupling in situ Cu(III) complexes generation promoted intramolecular electron transfer (IET) featuring the targeted oxidation of QNs. The produced Cu(III) and •OH played primary and secondary roles in the synergistic inactivation of QRSM by destroying the cell membranes and walls, DNA bases (T, A, C, and G), antibiotic resistance genes (ARGs, including intracellular ARGs and extracellular ARGs), and total DNA (including intracellular DNA and extracellular DNA). This study demonstrates a successful strategy and provides an innovative perspective for the molecular level decontamination of trace antibiotics and ARB using a homogeneous cupric complexes-activated Fenton-like oxidation system from metal ions inherent in breeding wastewater under alkaline condition.

Construction of Bacillus subtilis chassis strain with enhanced α-amylase expression capability based on CRISPRi screening

Bacillus subtilis has been widely used in the expression of recombinant proteins due to its food safe and powerful secretion characteristic, but the current production level cannot meet the increasing industrial needs. To enhance the production of recombinant protein, we first screened target key genes that are directly or indirectly involved in protein synthesis, using CRISPRi technology targeting the whole genome, with industrial valuable Bacillus stearothermophilus α-amylase as the model protein. Then the screened key genes were combined, yielding a chassis strain that owning enhanced protein expression capability. Following overlaying molecular chaperone GroES/L and peptidoglycan glycosyltransferase PonA, α-amylase activity reached 102,893 U/mL in a 3-L fermenter, the highest level reported till now. Finally, transcriptome analysis showed that the enhanced recombinant expression may be due to more rational allocation of energy and resources. These strategies can be well implicated in engineering other microbial cell factories for higher industrial production.

Characterization of Siderophores Produced by Bacillus velezensis YL2021 and Its Application in Controlling Rice Sheath Blight and Rice Blast

Bacillus velezensis YL2021 has extensive antimicrobial activities against phytopathogens, and its genome harbors a catechol-type siderophore biosynthesis gene cluster. Here, we describe the characterization of siderophores produced by strain YL2021 and its antimicrobial activity in vitro and in vivo. A few types of siderophores were detected by chrome azurol S plates coupled with Arnow's test, purified, and identified by reversed-phase high-performance liquid chromatography. We found that strain YL2021 can produce different antimicrobial compounds under low-iron M9 medium or iron-sufficient Luria-Bertani medium, although antimicrobial activities can be easily observed on the two media as described above in vitro. Strain YL2021 can produce at least three catechol-type siderophores in low-iron M9 medium, whereas no siderophores were produced in Luria-Bertani medium. Among them, the main antimicrobial siderophore produced by strain YL2021 was bacillibactin, with m/z 882, based on the liquid chromatography-tandem mass spectrometry analysis, which has broad-spectrum antimicrobial activities against gram-positive and gram-negative bacteria, the oomycete Phytophthora capsici, and phytopathogenic fungi. Moreover, the antifungal activity of siderophores, including bacillibactin, observed in vitro was correlated with control efficacies against rice sheath blight disease caused by Rhizoctonia solani and rice blast disease caused by Magnaporthe oryzae in vivo. Collectively, the results demonstrate that siderophores, including bacillibactin, produced by B. velezensis YL2021 are promising biocontrol agents for application in rice disease control.

Improving Beneficial Traits in Bacillus cabrialesii subsp. cabrialesii TE3T through UV-Induced Genomic Changes

It is essential to hunt for new technologies that promote sustainable practices for agroecosystems; thus, the bioprospecting of beneficial microorganisms complementing with mutation induction techniques to improve their genomic, metabolic, and functional traits is a promising strategy for the development of sustainable microbial inoculants. Bacillus cabrialesii subsp. cabrialesii strain TE3T, a previously recognized plant growth-promoting and biological control agent, was subjected to UV mutation induction to improve these agro-biotechnological traits. Dilutions were made which were spread on Petri dishes and placed under a 20 W UV lamp at 10-min intervals for 60 min. After the UV-induced mutation of this strain, 27 bacterial colonies showed morphological differences compared to the wild-type strain; however, only a strain named TE3T-UV25 showed an improvement in 53.6% of the biocontrol against Bipolaris sorokiniana vs. the wild-type strain, by competition of nutrient and space (only detected in the mutant strain), as well as diffusible metabolites. Furthermore, the ability to promote wheat growth was evaluated by carrying out experiments under specific greenhouse conditions, considering un-inoculated, strain TE3T, and strain TE3T-UV25 treatments. Thus, after 120 days, biometric traits in seedlings were quantified and statistical analyses were performed, which showed that strain TE3T-UV25 maintained its ability to promote wheat growth in comparison with the wild-type strain. On the other hand, using bioinformatics tools such as ANI, GGDC, and TYGS, the Overall Genome Relatedness Index (OGRI) and phylogenomic relationship of mutant strain TE3T-UV25 were performed, confirming that it changed its taxonomic affiliation from B. cabrialesii subsp. cabrialesii to Bacillus subtilis. In addition, genome analysis showed that the mutant, wild-type, and B. subtilis strains shared 3654 orthologous genes; however, a higher number of shared genes (3954) was found between the TE3T-UV25 mutant strain and B. subtilis 168, while the mutant strain shared 3703 genes with the wild-type strain. Genome mining was carried out using the AntiSMASH v7.0 web server and showed that mutant and wild-type strains shared six biosynthetic gene clusters associated with biocontrol but additionally, pulcherriminic acid cluster only was detected in the genome of the mutant strain and Rhizocticin A was exclusively detected in the genome of the wild-type strain. Finally, using the PlaBase tool, differences in the number of genes (17) associated with beneficial functions in agroecosystems were detected in the genome of the mutant vs. wild-type strain, such as biofertilization, bioremediation, colonizing plant system, competitive exclusion, phytohormone, plant immune response stimulation, putative functions, stress control, and biocontrol. Thus, the UV-induced mutation was a successful strategy to improve the bioactivity of B. cabrialesii subsp. cabrialesii TE3T related to the agro-biotecnology applications. The obtained mutant strain, B. subtilis TE3T-UV25, is a promising strain to be further studied as an active ingredient for the bioformulation of bacterial inoculants to migrate sustainable agriculture.

Mechanism and functional verification of genes by virulence factors of P. gingivalis in ferroptosis

OBJECTIVE

Porphyromonas gingivalis (P. gingivalis) is a key etiological agent in periodontitis and functions as a facultative intracellular microorganism and involves many virulence factors. These virulence factors participate in multiple intracellular processes, like ferroptosis, the mechanistic underpinnings remain to be elucidated. Aim of this study was to investigate the effects of virulence factors on the host cells.

DESIGN

Human umbilical vein endothelial cells (HUVECs) were treated with 4% paraformaldehyde-fixed P. gingivalis, and subsequent alterations in gene expression were profiled via RNA-seq. Further, the molecules associated with ferroptosis were quantitatively analyzed using qRT-PCR and Western blot.

RESULTS

A total of 1125 differentially expressed genes (DEGs) were identified, encompassing 225 upregulated and 900 downregulated. Ferroptosis was conspicuously represented in the kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis, with notable upregulation of Heme oxygenase 1 (HMOX1), Ferritin light chain (FTL), and Solute carrier family 3 member 2 (SLC3A2) and downregulation of Scavenger receptor class A member 5 (SCARA5) and glutaminase (GLS). Random selection of DEGs for validation through qRT-PCR corroborated the RNA-Seq data (R2 = 0.93). Kelch like ECH associated protein 1 (Keap1) protein expression decreased after 4 and 8 h, while NFE2 like bZIP transcription factor 2 (Nrf2) and HMOX1 were elevated, with significant nuclear translocation of Nrf2.

CONCLUSIONS

The virulence factors of P. gingivalis may potentially instigating ferroptosis through activation of the Keap1-Nrf2-HMOX1 signaling cascade, in conjunction with modulating the expression of other ferroptosis-associated elements. Further research is necessary to achieve a thorough comprehension of these complex molecular interactions.

Oleanolic Acid Promotes the Formation of Probiotic Escherichia coli Nissle 1917 (EcN) Biofilm by Inhibiting Bacterial Motility

Probiotic biofilms have been beneficial in the fight against infections, restoring the equilibrium of the host's gut microbiota, and enhancing host health. They are considered a novel strategy for probiotic gut colonization. In this case, we evaluated the effects of various active substances from traditional Chinese medicine on Escherichia coli Nissle 1917 (EcN) to determine if they promote biofilm formation. It was shown that 8-64 μg/mL of oleanolic acid increased the development of EcN biofilm. Additionally, we observed that oleanolic acid can effectively suppress biofilm formation in pathogenic bacteria such as Salmonella and Staphylococcus aureus. Next, we assessed the amount of EcN extracellular polysaccharides, the number of live bacteria, their metabolic activity, the hydrophobicity of their surface, and the shape of their biofilms using laser confocal microscopy. Through transcriptome analysis, a total of 349 differentially expressed genes were identified, comprising 134 upregulated and 215 downregulated genes. GO functional enrichment analysis and KEGG pathway enrichment analysis revealed that oleanolic acid functions are through the regulation of bacterial motility, the iron absorption system, the two-component system, and adhesion pathways. These findings suggest that the main effects of oleanolic acid are to prevent bacterial motility, increase initial adhesion, and encourage the development of EcN biofilms. In addition, oleanolic acid interacts with iron absorption to cooperatively control the production of EcN biofilms within an optimal concentration range. Taking these results together, this study suggests that oleanolic acid may enhance probiotic biofilm formation in the intestines, presenting new avenues for probiotic product development.

Colony-Based Electrochemistry Reveals Electron Conduction Mechanisms Mediated by Cytochromes and Flavins in Shewanella oneidensis

Bacteria utilize electron conduction in their communities to drive their metabolism, which has led to the development of various environmental technologies, such as electrochemical microbial systems and anaerobic digestion. It is challenging to measure the conductivity among bacterial cells when they hardly form stable biofilms on electrodes. This makes it difficult to identify the biomolecules involved in electron conduction. In the present study, we aimed to identify c-type cytochromes involved in electron conduction in Shewanella oneidensis MR-1 and examine the molecular mechanisms. We established a colony-based bioelectronic system that quantifies bacterial electrical conductivity, without the need for biofilm formation on electrodes. This system enabled the quantification of the conductivity of gene deletion mutants that scarcely form biofilms on electrodes, demonstrating that c-type cytochromes, MtrC and OmcA, are involved in electron conduction. Furthermore, the use of colonies of gene deletion mutants demonstrated that flavins participate in electron conduction by binding to OmcA, providing insight into the electron conduction pathways at the molecular level. Furthermore, phenazine-based electron transfer in Pseudomonas aeruginosa PAO1 and flavin-based electron transfer in Bacillus subtilis 3610 were confirmed, indicating that this colony-based system can be used for various bacteria, including weak electricigens.

Enterobacterales Biofilm-Specific Genes and Antimicrobial and Anti-Inflammatory Biomarkers in the Blood of Patients with Ischemic Heart Disease

BACKGROUND

Ischemic heart disease (IHD) is the most prevalent type of cardiovascular disease. The main cause of IHD is atherosclerosis, which is a multifactorial inflammatory disease of blood vessels. Studies show that bacteria might have a significant impact on the pathogenesis of atherosclerosis and plaque rupture. This study aimed to evaluate the complexity of interactions between bacteria and the human body concerning metabolites and bacterial genes in patients with ischemic heart disease.

METHODS

Bacterial 16S rDNA and wcaF, papC, and sdhC genes were detected in whole blood using a real-time PCR methodology. An enzyme-linked immunosorbent assay was used to measure the concentration of the LL-37 protein. An analysis of ARA in blood plasma was performed.

RESULTS

Bacterial 16S rDNA was detected in 31% of the study patients, and the genes wcaF and sdhC in 20%. Enterobacterales genes were detected more frequently in patients younger than 65 years than in patients aged 65 years and older (p = 0.018) and in patients with type 2 diabetes (p = 0.048). Concentrations of the human antimicrobial peptide LL-37 and 12S-HETE concentrations were determined to be higher if patients had 16S rDNA and biofilm-specific genes.

CONCLUSIONS

The results of this study enhance the understanding that Enterobacterales bacteria may participate in the pathogenesis of atherosclerosis and IHD. Bacterial DNA and host metabolites in higher concentrations appear to be detected.

DIET-like and MIET-like mutualism of S. oneidensis MR-1 and metal-reducing function microflora boosts Cr(VI) reduction

Microbial treatment of Cr(VI) is an environmentally friendly and low-cost approach. However, the mechanism of mutualism and the role of interspecies electron transfer in Cr(VI) reducing microflora are unclear. Herein, we constructed an intersymbiotic microbial association flora to augment interspecies electron transfer via functionalizing electroactive Shewanella oneidensis MR-1 with metal-reducing microflora, and thus the efficiency of Cr(VI) reduction. The findings suggest that the metal-reducing active microflora could converts glucose into lactic acid and riboflavin for S. oneidensis MR-1 to act as a carbon source and electron mediator. Thus, when adding initial 25 mg/L Cr (VI), this microflora exhibited an outstanding Cr (VI) removal efficiency (100%) at 12 h and elevated Cr (III) immobilization efficiency (80%) at 60 h with the assistance of 25 mg/L Cu(II). A series of electrochemical experiments proved this remarkable removal efficiency were ascribed to the improved interspecies electron transfer efficiency through direct interspecies electron transfer and riboflavin through mediated interspecies electron transfer. Furthermore, the metagenomic analysis revealed the expression level of the electron transport pathway was promoted. Intriguing high abundance of genes participating in the bio-reduction and biotransformation of Cr(VI) was also observed in functional microflora. These outcomes give a novel strategy for enhancing the reduction and fixation of harmful heavy metals by coculturing function microflora with electrogenic microorganisms.

A new ROS response factor YvmB protects Bacillus licheniformis against oxidative stress under adverse environment

Bacillus spp., a class of aerobic bacteria, is widely used as a biocontrol microbe in the world. However, the reactive oxygen species (ROS) will accumulate once the aerobic bacteria are exposed to environmental stresses, which can decrease cell activity or lead to cell death. Hydroxyl radical (·OH), the strongest oxide in the ROS, can damage DNA directly, which is generated through Fenton Reaction by H2O2 and free iron. Here, we proved that the synthesis of pulcherriminic acid (PA), an iron chelator produced by Bacillus spp., could reduce DNA damage to protect cells from oxidative stress by sequestrating excess free iron, which enhanced the cell survival rates in stressful conditions (salt, antibiotic, and high temperature). It was worth noting that the synthesis of PA was found to be increased under oxidative stress. Thus, we demonstrated that the YvmB, a direct negative regulator of PA synthesis cluster yvmC-cypX, could be oxidized at cysteine residue (C57) to form a dimer losing the DNA-binding activity, which led to an improvement in PA production. Collectively, our findings highlight that YvmB senses ROS to regulate PA synthesis is one of the evolved proactive defense systems in bacteria against adverse environments.IMPORTANCEUnder environment stress, the electron transfer chain will be perturbed resulting in the accumulation of H2O2 and rapidly transform to ·OH through Fenton Reaction. How do bacteria deal with oxidative stress? At present, several iron chelators have been reported to decrease the ·OH generation by sequestrating iron, while how bacteria control the synthesis of iron chelators to resist oxidative stress is still unclear. Our study found that the synthesis of iron chelator PA is induced by reactive oxygen species (ROS), which means that the synthesis of iron chelator is a proactive defense mechanism against environment stress. Importantly, YvmB is the first response factor found to protect cells by reducing the ROS generation, which present a new perspective in antioxidation studies.

Root colonization by beneficial rhizobacteria

Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.

Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas marginalis

Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera, like Bacillus and Pseudomonas, siderophores are well known for their biocontrol functions. Here, we explored the functional role of the Bacillus subtilis siderophore bacillibactin (BB) in an antagonistic interaction with Pseudomonas marginalis. The presence of BB strongly influenced the outcome of the interaction in an iron-dependent manner. The BB producer B. subtilis restricts colony spreading of P. marginalis by repressing the transcription of histidine kinase-encoding gene gacS, thereby abolishing production of secondary metabolites such as pyoverdine and viscosin. By contrast, lack of BB restricted B. subtilis colony growth. To explore the specificity of the antagonism, we cocultured B. subtilis with a collection of fluorescent Pseudomonas spp. and found that the Bacillus-Pseudomonas interaction is conserved, expanding our understanding of the interplay between two of the most well-studied genera of soil bacteria.

Word-based GWAS harnesses the rich potential of genomic data for E. coli quinolone resistance

Quinolone resistance presents a growing global health threat. We employed word-based GWAS to explore genomic data, aiming to enhance our understanding of this phenomenon. Unlike traditional variant-based GWAS analyses, this approach simultaneously captures multiple genomic factors, including single and interacting resistance mutations and genes. Analyzing a dataset of 92 genomic E. coli samples from a wastewater treatment plant in Dresden, we identified 54 DNA unitigs significantly associated with quinolone resistance. Remarkably, our analysis not only validated known mutations in gyrA and parC genes and the results of our variant-based GWAS but also revealed new (mutated) genes such as mdfA, the AcrEF-TolC multidrug efflux system, ptrB, and hisI, implicated in antibiotic resistance. Furthermore, our study identified joint mutations in 14 genes including the known gyrA gene, providing insights into potential synergistic effects contributing to quinolone resistance. These findings showcase the exceptional capabilities of word-based GWAS in unraveling the intricate genomic foundations of quinolone resistance.

Iron Competition as an Important Mechanism of Pulcherrimin-Producing Metschnikowia sp. Strains for Controlling Postharvest Fungal Decays on Citrus Fruit

This study identified and tested fruit-isolated Metschnikowia yeasts against three major postharvest citrus pathogens, namely, Penicillium digitatum, Penicillium italicum, and Geotrichum citri-aurantii, and further evaluated the impact of FeCl3 on the biocontrol efficiency of pulcherrimin-producing M. pulcherrima strains. Based on the characterization of the pigmented halo surrounding the colonies and the analysis of the D1/D2 domain of 26S rDNA, a total of 46 Metschnikowia sp. were screened and identified. All 46 Metschnikowia strains significantly inhibited the hyphal growth of Penicillium digitatum, Penicillium italicum, and Geotrichum citri-aurantii, and effectively controlled the development of green mold, blue mold and sour rot of citrus fruit. The introduction of exogenous FeCl3 at certain concentrations did not significantly impact the pulcherriminic acid (PA) production of pigmented M. pulcherrima strains, but notably diminished the size of pigmented zones and the biocontrol efficacy against the three pathogens. Iron deficiency sensitivity experiments revealed that P. digitatum and P. italicum exhibited higher sensitivity compared to G. citri-aurantii, indicating that iron dependence varied among the three pathogens. These results suggested that M. pulcherrima strains, capable of producing high yields of PA, possessed great potential for use as biocontrol agents against postharvest citrus diseases. The biocontrol efficacy of these yeasts is mainly attributed to their ability to competitively deplete iron ions in a shared environment, with the magnitude of their pigmented halo directly correlating to their antagonistic capability. It is worth noting that the level of sensitivity of pathogens to iron deficiency might also affect the biocontrol effect of pulcherrimin-producing M. pulcherrima.

"Sharing the matrix" - a cooperative strategy for survival in Salmonella enterica serovar Typhimurium

BACKGROUND

Bacteria in nature live together in communities called biofilms, where they produce a matrix that protects them from hostile environments. The components of this matrix vary among species, with Salmonella enterica serovar Typhimurium (STm- WT) primarily producing curli and cellulose, which are regulated by the master regulator csgD. Interactions between bacteria can be competitive or cooperative, with cooperation more commonly observed among the kin population. This study refers to STm- WT as the generalist which produces all the matrix components and knockout strains that are defective in either curli or cellulose as the specialists, which produces one of the matrix components but not both. We have asked whether two different specialists will cooperate and share matrix components during biofilm formation to match the ability of the generalist which produces both components.

RESULTS

In this study, the response of the specialists and generalist to physical, chemical, and biological stress during biofilm formation is also studied to assess their abilities to cooperate and produce biofilms like the generalist. STm WT colony biofilm which produces both the major biofilm matrix component were protected from stress whereas the non-matrix producer (∆csgD), the cellulose, and curli alone producers ∆csgA, ∆bcsA respectively were affected. During the exposure to various stresses, the majority of killing occurred in ∆csgD. Whereas the co-culture (∆csgA: ∆bcsA) was able to resist stress like that of the STm WT. Phenotypic and morphological characteristics of the colonies were typed using congo red assay and the Influence of matrix on the architecture of biofilms was confirmed by scanning electron microscopy.

CONCLUSION

Our results show that matrix aids in survival during antibiotic, chlorine, and predatory stress. And possible sharing of the matrix is occurring in co-culture, with one counterbalancing the inability of the other when confronted with stress.

Pulcherrimin protects Bacillus subtilis against oxidative stress during biofilm development

Pulcherrimin is an iron-binding reddish pigment produced by various bacterial and yeast species. In the soil bacterium Bacillus subtilis, this pigment is synthesized intracellularly as the colorless pulcherriminic acid by using two molecules of tRNA-charged leucine as the substrate; pulcherriminic acid molecules are then secreted and bind to ferric iron extracellularly to form the red-colored pigment pulcherrimin. The biological importance of pulcherrimin is not well understood. A previous study showed that secretion of pulcherrimin caused iron depletion in the surroundings and growth arrest on cells located at the edge of a B. subtilis colony biofilm. In this study, we identified that pulcherrimin is primarily produced under biofilm conditions and provides protection to cells in the biofilm against oxidative stress. We presented molecular evidence on how pulcherrimin lowers the level of reactive oxygen species (ROS) and alleviates oxidative stress and DNA damage caused by ROS accumulation in a mature biofilm. We also performed global transcriptome profiling to identify differentially expressed genes in the pulcherrimin-deficient mutant compared with the wild type, and further characterized the regulation of genes by pulcherrimin that are related to iron homeostasis, DNA damage response (DDR), and oxidative stress response. Based on our findings, we propose pulcherrimin as an important antioxidant that modulates B. subtilis biofilm development.

The putative role of the epipeptide EpeX in Bacillus subtilis intra-species competition

Bacteria engage in competitive interactions with neighbours that can either be of the same or different species. Multiple mechanisms are deployed to ensure the desired outcome and one tactic commonly implemented is the production of specialised metabolites. The Gram-positive bacterium Bacillus subtilis uses specialized metabolites as part of its intra-species competition determinants to differentiate between kin and non-kin isolates. It is, however, unknown if the collection of specialized metabolites defines competitive fitness when the two isolates start as a close, interwoven community that grows into a densely packed colony biofilm. Moreover, the identity of specialized metabolites that have an active role in defining the outcome of an intra-species interaction has not been revealed. Here, we determine the competition outcomes that manifest when 21 environmental isolates of B. subtilis are individually co-incubated with the model isolate NCIB 3610 in a colony biofilm. We correlated these data with the suite of specialized metabolite biosynthesis clusters encoded by each isolate. We found that the epeXEPAB gene cluster was primarily present in isolates with a strong competitive phenotype. This cluster is responsible for producing the epipeptide EpeX. We demonstrated that EpeX is a competition determinant of B. subtilis in an otherwise isogenic context for NCBI 3610. However, when we competed the NCIB 3610 EpeX-deficient strain against our suite of environmental isolates we found that the impact of EpeX in competition is isolate-specific, as only one of the 21 isolates showed increased survival when EpeX was lacking. Taken together, we have shown that EpeX is a competition determinant used by B. subtilis that impacts intra-species interactions but only in an isolate-specific manner.

The cellular redox state in Bacillus amyloliquefaciens WH1 affects biofilm formation indirectly in a surfactant direct manner

Surfactin is a signal to trigger biofilm formation against harsh environments. Generally, harsh environments can result in change of the cellular redox state to induce biofilm formation, but we know little about whether the cellular redox state influences biofilm formation via surfactin. Here, the reductant glucose could reduce surfactin and enhance biofilm formation by a surfactin-indirect way. The oxidant H₂ O₂ led to a decrease of surfactin accompanying with weakened biofilm formation. Spx and PerR were both necessary for surfactin production and biofilm formation. H₂ O₂ improved surfactin production but inhibited biofilm formation by a surfactin-indirect manner in Δspx, while it reduced surfactin production without obvious influence on biofilm formation in ΔperR. The ability against H₂ O₂ stress was enhanced in Δspx, but weakened in ΔperR. Thereby, PerR was favorable for resisting oxidative stress, while Spx played a negative role in this action. Knockout and compensation of rex also supported that the cells could form biofilm by a surfactin-indirect way. Collectively, surfactin is not a unique signal to trigger biofilm formation, and the cellular redox state can influence biofilm formation by a surfactin-direct or -indirect way in Bacillus amyloliquefaciens WH1.

Pulcherriminic acid modulates iron availability and protects against oxidative stress during microbial interactions

Siderophores are soluble or membrane-embedded molecules that bind the oxidized form of iron, Fe(III), and play roles in iron acquisition by microorganisms. Fe(III)-bound siderophores bind to specific receptors that allow microbes to acquire iron. However, certain soil microbes release a compound (pulcherriminic acid, PA) that, upon binding to Fe(III), forms a precipitate (pulcherrimin) that apparently functions by reducing iron availability rather than contributing to iron acquisition. Here, we use Bacillus subtilis (PA producer) and Pseudomonas protegens as a competition model to show that PA is involved in a peculiar iron-managing system. The presence of the competitor induces PA production, leading to precipitation of Fe(III) as pulcherrimin, which prevents oxidative stress in B. subtilis by restricting the Fenton reaction and deleterious ROS formation. In addition, B. subtilis uses its known siderophore bacillibactin to retrieve Fe(III) from pulcherrimin. Our findings indicate that PA plays multiple roles by modulating iron availability and conferring protection against oxidative stress during inter-species competition.

Respiration-induced biofilm formation as a driver for bacterial niche colonization

Depending on their physiology and metabolism, bacteria can carry out diverse redox processes for energy acquisition, which facilitates adaptation to environmental or host-associated niches. Of these processes, respiration, using oxygen or alternative terminal electron acceptors, is energetically the most favorable in heterotrophic bacteria. The biofilm lifestyle, a coordinated multicellular behavior, is ubiquitous in bacteria and is regulated by a variety of intrinsic and extrinsic cues. Respiration of distinct electron acceptors has been shown to induce biofilm formation or dispersal. The notion of biofilm formation regulation by electron acceptor availability and respiration has often been considered species-specific. However, recent evidence suggests that this phenomenon can be strain-specific, even in strains sharing the same functional respiratory pathways, thereby implying subtle regulatory mechanisms. On this basis, I argue that induction of biofilm formation by sensing and respiration of electron acceptors might direct subgroups of redox-specialized strains to occupy certain niches. A palette of respiration and electron-transfer-mediated microbial social interactions within biofilms may broaden ecological opportunities. The strain specificity of this phenomenon represents an important opportunity to identify key molecular mechanisms and their ecophysiological significance, which in turn may lay the ground for applications in areas ranging from biotechnology to the prevention of antimicrobial resistance.

Biocontrol endophytes Bacillus subtilis R31 influence the quality, transcriptome and metabolome of sweet corn

During colonization of soil and plants, biocontrol bacteria can effectively regulate the physiological metabolism of plants and induce disease resistance. To illustrate the influence of Bacillus subtilis R31 on the quality, transcriptome and metabolome of sweet corn, field studies were conducted at a corn experimental base in Zhuhai City. The results show that, after application of B. subtilis R31, sweet corn was more fruitful, with a 18.3 cm ear length, 5.0 cm ear diameter, 0.4 bald head, 403.9 g fresh weight of single bud, 272.0 g net weight of single ear, and 16.5 kernels sweetness. Combined transcriptomic and metabolomic analyses indicate that differentially expressed genes related to plant-pathogen interactions, MAPK signaling pathway-plant, phenylpropanoid biosynthesis, and flavonoid biosynthesis were significantly enriched. Moreover, the 110 upregulated DAMs were mainly involved in the flavonoid biosynthesis and flavone and flavonol biosynthesis pathways. Our study provides a foundation for investigating the molecular mechanisms by which biocontrol bacteria enhance crop nutrition and taste through biological means or genetic engineering at the molecular level.

Biofilm: New insights in the biological control of fruits with Bacillus amyloliquefaciens B4

Biofilms are sessile microbial communities growing on surfaces, which are encased in some self-produced extracellular material. Beneficial biofilm could be widely used in agriculture, food, medicine, environment and other fields. As an ideal biocontrol agent, Bacillus amyloliquefaciens B4 can form a strong biofilm under static conditions. In this study, we screened out metal compounds that enhanced or inhibited the biofilm formation ability of B4, established the relationship between the biofilm of B4 strain and its postharvest biocontrol effect, and explored the regulation of metal compounds on the biofilm formation. The results showed 0.5 mmol L^-1 ferric chloride could enhance the biofilm formation and strengthen the antifungal effect of B4, indicating that there was a positive relationship between the growth of biofilm and its biocontrol effect. The enhanced biofilm had a certain biocontrol effect on different fruit, including peach, loquat, Kyoho grape and cherry tomato. Furthermore, the expression of degU and tasA was affected by metal ion treatment, which meant the genes might be essential for the biofilm formation of B4. Our findings suggested that biofilm of B. amyloliquefaciens played an essential role in the process of biocontrol and it might be a novel strategy for managing postharvest fruit decay.

Overexpression of pdeR promotes biofilm formation of Paracoccus denitrificans by promoting ATP production and iron acquisition

Bacterial biofilms are ubiquitous in natural environments and play an essential role in bacteria’s environmental adaptability. Quorum sensing (QS), as the main signaling mechanism bacteria used for cell-to-cell communication, plays a key role in bacterial biofilm formation. However, little is known about the role of QS circuit in the N-transformation type strain, Paracoccus denitrificans, especially for the regulatory protein PdeR. In this study, we found the overexpression of pdeR promoted bacterial aggregation and biofilm formation. Through RNA-seq analysis, we demonstrated that PdeR is a global regulator which could regulate 656 genes expression, involved in multiple metabolic pathways. Combined with transcriptome as well as biochemical experiments, we found the overexpressed pdeR mainly promoted the intracellular degradation of amino acids and fatty acids, as well as siderophore biosynthesis and transportation, thus providing cells enough energy and iron for biofilm development. These results revealed the underlying mechanism for PdeR in biofilm formation of P. denitrificans, adding to our understanding of QS regulation in biofilm development.

Magnetite-Bacillus subtilis synergy on the metabolic selection of products in electrofermentation system

The study examines the role of magnetite (1-150 mg/L) at the interface of Bacillus subtilis-electrode under poised-condition (-0.2 V) for product-formation and catalytic-conduct with the relative-gene-expression encoding lactate dehydrogenase (lctE), pyruvate dehydrogenase (pdhA), acetate kinase (ackA), pyruvate carboxylase (pycA), and NADH dehydrogenase (ndh). The magnetite load of 25 mg/L showed positive influence on acidogenesis resulting in H₂ production of 264.7 mol/mL and fatty acids synthesis of 3.6 g/L. Additionally, this condition showed higher succinic acid productivity (2.8 g/L) which correlates with the upregulated pycA gene and fumarate to succinate redox peak. With 10 mg/L loading, production of higher acetic acid (3.1 g/L) along with H₂ (181.6 mol/mL) was depicted wherein upregulation of pdhA, ackA and ndh genes was observed. In absence of magnetite, lctE gene was upregulated which resulted higher lactate production. The findings suggest that the mutual-interactions between magnetite-active sites of specific enzymes enhances the biocatalytic activity triggering product-formation.

Natural products from mangrove sediments-derived microbes: Structural diversity, bioactivities, biosynthesis, and total synthesis

The mangrove forests are a complex ecosystem, and the microbial communities in mangrove sediments play a critical role in the biogeochemical cycles of mangrove ecosystems. Mangrove sediments-derived microbes (MSM), as a rich reservoir of natural product diversity, could be utilized in the exploration of new antibiotics or drugs. To understand the structural diversity and bioactivities of the metabolites of MSM, this review for the first time provides a comprehensive overview of 519 natural products isolated from MSM with their bioactivities, up to 2021. Most of the structural types of these compounds are alkaloids, lactones, xanthones, quinones, terpenoids, and steroids. Among them, 210 compounds are obtained from bacteria, most of which are from Streptomyces, while 309 compounds are from fungus, especially genus Aspergillus and Penicillium. The pharmacological mechanisms of some representative lead compounds are well studied, revealing that they have important medicinal potentials, such as piericidins with anti-renal cell cancer effects, azalomycins with anti-MRSA activities, and ophiobolins as antineoplastic agents. The biosynthetic pathways of representative natural products from MSM have also been summarized, especially ikarugamycin, piericidins, divergolides, and azalomycins. In addition, the total synthetic strategies of representative secondary metabolites from MSM are also reviewed, such as piericidin A and borrelidin. This review provides an important reference for the research status of natural products isolated from MSM and the lead compounds worthy of further development, and reveals that MSM have important medicinal values and are worthy of further development.

MacAB-TolC Contributes to the Development of Acinetobacter baumannii Biofilm at the Solid–Liquid Interface

Acinetobacter baumannii has emerged as one of the most problematic bacterial pathogens responsible for hospital-acquired and community infections worldwide. Besides its high capacity to acquire antibiotic resistance mechanisms, it also presents high adhesion abilities on inert and living surfaces leading to biofilm development. This lifestyle confers additional protection against various treatments and allows it to persist for long periods in various hospital niches. Due to their remarkable antimicrobial tolerance, A. baumannii biofilms are difficult to control and ultimately eradicate. Further insights into the mechanism of biofilm development will help to overcome this challenge and to develop novel antibiofilm strategies. To unravel critical determinants of this sessile lifestyle, the proteomic profiles of two A. baumannii strains (ATTC17978 and SDF) grown in planktonic stationary phase or in mature solid–liquid (S-L) biofilm were compared using a semiquantitative proteomic study. Of interest, among the 69 common proteins determinants accumulated in the two strains at the S-L interface, we sorted out the MacAB-TolC system. This tripartite efflux pump played a role in A. baumannii biofilm formation as demonstrated by using ΔmacAB-tolC deletion mutant. Complementary approaches allowed us to get an overview of the impact of macAB-tolC deletion in A. baumannii physiology. Indeed, this efflux pump appeared to be involved in the envelope stress response occurring in mature biofilm. It contributes to maintain wild type (WT) membrane rigidity and provides tolerance to high osmolarity conditions. In addition, this system is probably involved in the maintenance of iron and sulfur homeostasis. MacAB-TolC might help this pathogen face and adapt to deleterious conditions occurring in mature biofilms. Increasing our knowledge of A. baumannii biofilm formation will undoubtedly help us develop new therapeutic strategies to tackle this emerging threat to human health.

Direct Visualization of Chemical Cues and Cellular Phenotypes throughout Bacillus subtilis Biofilms

Bacillus subtilis is a soil bacterium that can form biofilms, which are communities of cells encased by an extracellular matrix. In these complex communities, cells perform numerous metabolic processes and undergo differentiation into functionally distinct phenotypes as a survival strategy. Because biofilms are often studied in bulk, it remains unclear how metabolite production spatially correlates with B. subtilis phenotypes within biofilm structures. In many cases, we still do not know where these biological processes are occurring in the biofilm. Here, we developed a method to analyze the localization of molecules within sagittal thin sections of B. subtilis biofilms using high-resolution mass spectrometry imaging. We correlated the organization of specific molecules to the localization of well-studied B. subtilis phenotypic reporters determined by confocal laser scanning fluorescence microscopy within analogous biofilm thin sections. The correlations between these two data sets suggest the role of surfactin as a signal for extracellular matrix gene expression in the biofilm periphery and the role of bacillibactin as an iron-scavenging molecule. Taken together, this method will help us generate hypotheses to discover relationships between metabolites and phenotypic cell states in B. subtilis and other biofilm-forming bacteria. IMPORTANCE Bacterial biofilms are complex and heterogeneous structures. Cells within biofilms carry out numerous metabolic processes in a nuanced and organized manner, details of which are still being discovered. Here, we used multimodal imaging to analyze B. subtilis biofilm processes at the metabolic and gene expression levels in biofilm sagittal thin sections. Often, imaging techniques analyze only the top of the surface of the biofilm and miss the multifaceted interactions that occur deep within the biofilm. Our analysis of the sagittal planes of B. subtilis biofilms revealed the distributions of metabolic processes throughout the depths of these structures and allowed us to draw correlations between metabolites and phenotypically important subpopulations of B. subtilis cells. This technique provides a platform to generate hypotheses about the role of specific molecules and their relationships to B. subtilis subpopulations of cells.

Nitrogen and sulfur co-doped carbon dots with bright fluorescence for intracellular detection of iron ion and thiol

Carbon dots (CDs) have been widely used in recent years because of their excellent water solubility and abundant surface functional groups. However, compared with quantum dots or biological probes, the quantum yield of CDs is lower, and the fluorescence mainly concentrated in the blue-green range, which significantly limits the biological applications of CDs. Heteroatoms doping is the most common method to improve the luminescence of CDs. In this work, nitrogen and sulfur co-doped luminescent CDs were successfully synthesized by microwave assisted method using glutathione (GSH) and p-phenylenediamine (PPD) as raw materials. It can emit bright green fluorescence in ethanol solution, and the maximum emission wavelength is 535 nm when excited at 374 nm, and the absolute quantum yield is as high as 63%. Iron ion (Fe³⁺) can interact with the functional groups on the surface of the CDs to form CDs/Fe³⁺, which is a non-fluorescence complex, and Fe³⁺ can be reduced to ferrous ion (Fe²⁺). In other words, the reaction mechanism of CDs and Fe³⁺ is a combination of dynamic quenching and static quenching. The fluorescence of CDs quenched by Fe³⁺ can be restored by thiol, because there is a stronger binding force between sulfhydryl (-SH) on the surface of thiol and Fe³⁺, which enables CDs to be released. In addition, the CDs has good biocompatibility and stability, indicating that it has excellent potential in bioimaging. This discovery will expand the application of CDs in the fields of biosensing and imaging.

Metschnikowia citriensis FL01 antagonize Geotrichum citri-aurantii in citrus fruit through key action of iron depletion

Metschnikowia citriensis FL01 has great potential for biocontrol applications for its excellent biocontrol efficacy on postharvest diseases of citrus fruit, and the iron depletion by pulcherriminic acid (PA) and then formation of insoluble pigment pulcherrimin had been speculated as an important action mechanism. To identify the genes involved in pulcherrimin synthesis and reutilization in M. citriensis FL01, we de novo assembled the genome of M. citriensis FL01 based on long-read PacBio sequencing. The final assembled genome consisted of 12 contigs with a genome size of 25.74 Mb, G + C content of 49.16% and 9310 protein-coding genes. The genome-wide BLAST of the PUL genes of M. pulcherrima APC 1.2 showed that the four PUL genes were clustered and located on Contig 4 of M. citriensis FL01. In order to further clarify the role of pulcherrimin pigment on biocontrol of M. citriensis FL01, CRISPR/cas9 technology was used to knock out PUL2 gene that was responsible for PA synthesis and the pigmentless mutants with stable phenotype were obtained. The mutant strains of M. citriensis FL01 lost the ability to produce pulcherrimin pigment, and simultaneously lost the ability to inhibit the growth of Geotrichum citri-aurantii in vitro. Moreover, the biocontrol efficacy of pigmentless mutant strains against sour rot was about 80% lower than that of wild-type M. citriensis FL01. These results directly proved that the iron depletion was an important mechanism of M. citriensis FL01.

Engineering membrane asymmetry to increase medium-chain fatty acid tolerance in Saccharomyces cerevisiae

Saccharomyces cerevisiae is an attractive chassis for the production of medium-chain fatty acids, but the toxic effect of these compounds often prevents further improvements in titer, yield, and productivity. To address this issue, Lem3 and Sfk1 were identified from adaptive laboratory evolution mutant strains as membrane asymmetry regulators. Co-overexpression of Lem3 and Sfk1 [Lem3(M)-Sfk1(H) strain] through promoter engineering remodeled the membrane phospholipid distribution, leading to an increased accumulation of phosphatidylethanolamine in the inner leaflet of the plasma membrane. As a result, membrane potential and integrity were increased by 131.5% and 29.2%, respectively; meanwhile, the final OD₆₀₀ in the presence of hexanoic acid, octanoic acid, and decanoic acid was improved by 79.6%, 73.4%, and 57.7%, respectively. In summary, this study shows that membrane asymmetry engineering offers an efficient strategy to enhance medium-chain fatty acids tolerance in S. cerevisiae, thus generating a robust industrial strain for producing high-value biofuels.

The Intertwined Roles of Specialized Metabolites within the Bacillus subtilis Biofilm

Bacteria produce specialized metabolites with a range of functions. In this issue of the Journal of Bacteriology, Schoenborn et al. study the production and role of secondary metabolites during biofilm development and sporulation in Bacillus subtilis (A. A. Schoenborn, S. M. Yannarell, E. D. Wallace, H. Clapper, et al., J Bacteriol 203:e00337-21, 2021, https://doi.org/https://doi.org/10.1128/JB.00337-21). Most metabolites studied are produced during differentiation, and six are required for the development of biofilms and/or spores. The authors propose a model for the timing of production and role in differentiation exerted by each secondary metabolite.

Defining the Expression, Production, and Signaling Roles of Specialized Metabolites during Bacillus subtilis Differentiation

Bacterial specialized (or secondary) metabolites are structurally diverse molecules that mediate intra- and interspecies interactions by altering growth and cellular physiology and differentiation. Bacillus subtilis, a Gram-positive model bacterium commonly used to study biofilm formation and sporulation, has the capacity to produce more than 10 specialized metabolites. Some of these B. subtilis specialized metabolites have been investigated for their role in facilitating cellular differentiation, but only rarely has the behavior of multiple metabolites been simultaneously investigated. In this study, we explored the interconnectivity of differentiation (biofilm and sporulation) and specialized metabolites in B. subtilis. Specifically, we interrogated how development influences specialized metabolites and vice versa. Using the sporulation-inducing medium DSM, we found that the majority of the specialized metabolites examined are expressed and produced during biofilm formation and sporulation. Additionally, we found that six of these metabolites (surfactin, ComX, bacillibactin, bacilysin, subtilosin A, and plipastatin) are necessary signaling molecules for proper progression of B. subtilis differentiation. This study further supports the growing body of work demonstrating that specialized metabolites have essential physiological functions as cell-cell communication signals in bacteria. IMPORTANCE Bacterially produced specialized metabolites are frequently studied for their potential use as antibiotics and antifungals. However, a growing body of work has suggested that the antagonistic potential of specialized metabolites is not their only function. Here, using Bacillus subtilis as our model bacterium, we demonstrated that developmental processes such as biofilm formation and sporulation are tightly linked to specialized metabolite gene expression and production. Additionally, under our differentiation-inducing conditions, six out of the nine specialized metabolites investigated behave as intraspecific signals that impact B. subtilis physiology and influence biofilm formation and sporulation. Our work supports the viewpoint that specialized metabolites have a clear role as cell-cell signaling molecules within differentiated populations of bacteria.

Site-directed mutagenesis of the quorum-sensing transcriptional regulator SinR affects the biosynthesis of menaquinone in Bacillus subtilis

Background

Menaquinone (MK-7) is a highly valuable vitamin K₂ produced by Bacillus subtilis. Common static metabolic engineering approaches for promoting the production of MK-7 have been studied previously. However, these approaches caused an accumulation of toxic substances and reduced product yield. Hence, dynamic regulation by the quorum sensing (QS) system is a promising method for achieving a balance between product synthesis and cell growth.

Results

In this study, the QS transcriptional regulator SinR, which plays a significant role in biofilm formation and MK production simultaneously, was selected, and its site-directed mutants were constructed. Among these mutants, sinR knock out strain (KO-SinR) increased the biofilm biomass by 2.8-fold compared to the wild-type. SinR^quad maximized the yield of MK-7 (102.56 ± 2.84 mg/L). To decipher the mechanism of how this mutant regulates MK-7 synthesis and to find additional potential regulators that enhance MK-7 synthesis, RNA-seq was used to analyze expression changes in the QS system, biofilm formation, and MK-7 synthesis pathway. The results showed that the expressions of tapA, tasA and epsE were up-regulated 9.79-, 0.95-, and 4.42-fold, respectively. Therefore, SinR^quad formed more wrinkly and smoother biofilms than BS168. The upregulated expressions of glpF, glpk, and glpD in this biofilm morphology facilitated the flow of glycerol through the biofilm. In addition, NADH dehydrogenases especially sdhA, sdhB, sdhC and glpD, increased 1.01-, 3.93-, 1.87-, and 1.11-fold, respectively. The increased expression levels of NADH dehydrogenases indicated that more electrons were produced for the electron transport system. Electrical hyperpolarization stimulated the synthesis of the electron transport chain components, such as cytochrome c and MK, to ensure the efficiency of electron transfer. Wrinkly and smooth biofilms formed a network of interconnected channels with a low resistance to liquid flow, which was beneficial for the uptake of glycerol, and facilitated the metabolic flux of four modules of the MK-7 synthesis pathway.

Conclusions

In this study, we report for the first time that SinR^quad has significant effects on MK-7 synthesis by forming wrinkly and smooth biofilms, upregulating the expression level of most NADH dehydrogenases, and providing higher membrane potential to stimulate the accumulation of the components in the electron transport system.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01603-5.

Enhanced biodegradation of chlorobenzene via combined Fe3+ and Zn2+ based on rhamnolipid solubilisation

Biotrickling filters (BTFs) for hydrophobic chlorobenzene (CB) purification are limited by mass transfer and biodegradation. The CB mass transfer rate could be improved by 150 mg/L rhamnolipids. This study evaluated the combined use of Fe³⁺ and Zn²⁺ to enhance biodegradation in a BTF over 35 day. The effects of these trace elements were analysed under different inlet concentrations (250, 600, 900, and 1200 mg/L) and empty bed residence times (EBRTs; 60, 45, and 32 sec). Batch experiments showed that the promoting effects of Fe³⁺/Zn²⁺ on microbial growth and metabolism were highest for 3 mg/L Fe³⁺ and 2 mg/L Zn²⁺, followed by 2 mg/L Zn²⁺, and lowest at 3 mg/L Fe³⁺. Compared to BTF in the absence of Fe³⁺ and Zn²⁺, the average CB elimination capacity and removal efficiency in the presence of Fe³⁺ and Zn²⁺ increased from 61.54 to 65.79 g/(m³⋅hr) and from 80.93% to 89.37%, respectively, at an EBRT of 60 sec. The average removal efficiency at EBRTs of 60, 45, and 32 sec increased by 2.89%, 5.63%, and 11.61%, respectively. The chemical composition (proteins (PN), polysaccharides (PS)) and functional groups of the biofilm were analysed at 60, 81, and 95 day. Fe³⁺ and Zn²⁺ significantly enhanced PN and PS secretion, which may have promoted CB adsorption and biodegradation. High-throughput sequencing revealed the promoting effect of Fe³⁺ and Zn²⁺ on bacterial populations. The combination of Fe³⁺ and Zn²⁺ with rhamnolipids was an efficient method for improving CB biodegradation in BTFs.

Anodic electro-fermentation: Empowering anaerobic production processes via anodic respiration

In nature as well as in industrial microbiology, all microorganisms need to achieve redox balance. Their redox state and energy conservation highly depend on the availability of a terminal electron acceptor, for example oxygen in aerobic production processes. Under anaerobic conditions in the absence of an electron acceptor, redox balance is achieved via the production of reduced carbon-compounds (fermentation). An alternative strategy to artificially stabilize microbial redox and energy state is the use of anodic electro-fermentation (AEF). This emerging biotechnology empowers respiration under anaerobic conditions using the anode of a bioelectrochemical system as an undepletable terminal electron acceptor. Electrochemical control of redox metabolism and energy conservation via AEF can steer the carbon metabolism towards a product of interest and avoid the need for continuous and cost-inefficient supply of oxygen as well as the production of mixed reduced by-products, as is the case in aerobic production and fermentation processes, respectively. The great challenge for AEF is to establish efficient extracellular electron transfer (EET) from the microbe to the anode and link it to central carbon metabolism to enhance the synthesis of a target product. This article reviews the advantages and challenges of AEF, EET mechanisms, microbial energy gain, and discusses the rational choice of substrate-product couple as well as the choice of microbial catalyst. Besides, it discusses the potential of the industrial model-organism Bacillus subtilis as a promising candidate for AEF, which has not been yet considered for such an application. This prospective review contributes to a better understanding of how industrial microbiology can benefit from AEF and analyses key-factors required to successfully implement AEF processes. Overall, this work aims to advance the young research field especially by critically revisiting the fundamental aspects of AEF.