Optimization of fixation methods for observation of bacterial cell morphology and surface ultrastructures by atomic force microscopy

Distinctive toxic repercussions of polystyrene nano plastic towards aquatic non target species Nitrobacter vulgaris, Scenedesmus sp and Daphnia magna

The widespread application of plastics and its eventual degradation to micro-sized or nano-sized plastics has led to several environmental concerns. Moreover, nanoplastics can easily cascade through the food chain accumulating in the aquatic organisms. Thus, our study focussed on investigating the hazardous impact of nano-sized plastics on aquatic species including Nitrobacter vulgaris, Scenedesmus sp, and Daphnia magna. Various concentrations of polystyrene nanoplastics ranging from 0.01 mg/L to 100 mg/L were tested against Nitrobacter vulgaris, Scenedesmus sp, and Daphnia magna. The minimum inhibitory concentration of polystyrene nanoplastics in Nitrobacter vulgaris was found to be 25 mg/L, and in Daphnia magna, the median lethal concentration 50 was observed to be 64.02 mg/L. Exposure of Scenedesmus sp with increasing nanoplastic concentrations showed a significant decrease in total protein (p < 0.001), and chlorophyll content (p < 0.01), whereas the lipid peroxidation increased (p < 0.001) significantly. Similarly, Nitrobacter vulgaris and Daphnia magna showed a significant decrease in catalase activity (p < 0.001) and an increase in lipid peroxidation levels (p < 0.01). Concomitant with lipid peroxidation results, decreased superoxide dismutase levels (p < 0.01) and protein concentrations (p < 0.01) were observed in Daphnia magna. Besides, the increasing concentration of polystyrene nanoplastics displayed an elevated mortality rate in Scenedesmus sp (p < 0.001) and Nitrobacter vulgaris (p < 0.01). Further, scanning electron microscopy analysis substantiated the morphological alterations in Nitrobacter vulgaris and Scenedesmus sp on exposure to polystyrene nanoplastics.

In Vivo Quantification of Surfactin Nonribosomal Peptide Synthetase Complexes in Bacillus subtilis

Surfactin, a potent biosurfactant produced by Bacillus subtilis, is synthesized using a non-ribosomal peptide synthetase (NRPS) encoded by the srfAA-AD operon. Despite its association with quorum sensing via the ComX pheromone, the dynamic behavior and in vivo quantification of the NRPS complex remain underexplored. This study established an in vivo quantification system using fluorescence labeling to monitor the availability of surfactin-forming NRPS subunits (SrfAA, SrfAB, SrfAC, and SrfAD) during bioprocesses. Four Bacillus subtilis sensor strains were constructed by fusing these subunits with the megfp gene, resulting in strains BMV25, BMV26, BMV27, and BMV28. These strains displayed growth and surfactin productivity similar to those of the parental strain, BMV9. Fluorescence signals indicated varying NRPS availability, with BMV27 showing the highest and BMV25 showing the lowest relative fluorescence units (RFUs). RFUs were converted to the relative number of NRPS molecules using open-source FPCountR package. During bioprocesses, NRPS availability peaked at the end of the exponential growth phase and declined in the stationary phase, suggesting reduced NRPS productivity under nutrient-limited conditions and potential post-translational regulation. This study provides a quantitative framework for monitoring NRPS dynamics in vivo, offering insights into optimizing surfactin production. The established sensor strains and quantification system enable the real-time monitoring of NRPS availability, aiding bioprocess optimization for industrial applications of surfactin and potentially other non-ribosomal peptides.

Biostasis: A Roadmap for Research in Preservation and Potential Revival of Humans

Human biostasis, the preservation of a human when all other contemporary options for extension of quality life are exhausted, offers the speculative potential for survival via continuation of life in the future. While provably reversible preservation, also known as suspended animation, is not yet possible for humans, the primary justification for contemporary biostasis is the preservation of the brain, which is broadly considered the seat of memories, personality, and identity. By preserving the information contained within the brain's structures, it may be possible to resuscitate a healthy whole individual using advanced future technologies. There are numerous challenges in biostasis, including inadequacies in current preservation techniques, methods to evaluate the quality of preservation, and potential future revival technologies. In this report, we describe a roadmap that attempts to delineate research directions that could improve the field of biostasis, focusing on optimizing preservation protocols and establishing metrics for querying preservation quality, as well as pre- and post-cardiac arrest factors, stabilization strategies, and methods for long-term preservation. We acknowledge the highly theoretical nature of future revival technologies and the importance of achieving high-fidelity brain preservation to maximize the potential of future repair technologies. We plan to update the research roadmap biennially. Our goal is to encourage multidisciplinary communication and collaboration in this field.

Protocol for comparing ribosomal levels in single bacterial cells at different growth stages using rRNA-FISH

Ribosome quantification in single cells is typically achieved through fluorescence tagging of ribosomal proteins. Here, we present a protocol for comparing ribosomal levels in bacteria at different growth stages using fluorescence in situ hybridization of rRNA (rRNA-FISH), eliminating the need for genetic engineering of the strain of interest. We detail the steps for preparing bacterial samples, staining with fluorescent probes, and acquiring data using flow cytometry and microscopy. Furthermore, we provide guidelines on controlling for proper labeling through signal localization analysis. For complete details on the use and execution of this protocol, please refer to Ciolli Mattioli et al.1.

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.

Microbeads as carriers for Bacillus pumilus: a biofertilizer focus on auxin production

The study aimed to develop a solid biofertilizer using Bacillus pumilus, focusing on auxin production to enhance plant drought tolerance. Methods involved immobilising B. pumilus in alginate-starch beads, focusing on microbial concentration, biopolymer types, and environmental conditions. The optimal formulation showed a diameter of 3.58 mm ± 0.18, a uniform size distribution after 15 h of drying at 30 °C, a stable bacterial concentration (1.99 × 109 CFU g-1 ± 1.03 × 109 over 180 days at room temperature), a high auxin production (748.8 µg g-1 ± 10.3 of IAA in 7 days), and a water retention capacity of 37% ± 4.07. In conclusion, this new formulation of alginate + starch + L-tryptophan + B. pumilus has the potential for use in crops due to its compelling water retention, high viability in storage at room temperature, and high auxin production, which provides commercial advantages.

Single-Molecule Fluorescent In Situ Hybridization (smFISH) for RNA Detection in Bacteria

In this chapter, we describe in detail how to perform a successful smFISH experiment and how to quantify mRNA transcripts in bacterial cells. The flexibility of the method allows for straightforward adaptation to different bacterial species and experimental conditions. Thanks to the feasibility of the approach, the method can easily be adapted by other laboratories. Finally, we believe that this method has a great potential to generate insights into the complicated life of bacteria.

The Role of Chlorine in the Formation and Development of Tap Water Biofilms under Different Flow Regimes

Water companies make efforts to reduce the risk of microbial contamination in drinking water. A widely used strategy is to introduce chlorine into the drinking water distribution system (DWDS). A subtle potential risk is that non-lethal chlorine residuals may select for chlorine resistant species in the biofilms that reside in DWDS. Here, we quantify the thickness, density, and coverage of naturally occurring multi-species biofilms grown on slides in tap water with and without chlorine, using fluorescence microscopy. We then place the slides in an annular rotating reactor and expose them to fluid-wall shears, which are redolent of those on pipe walls in DWDS. We found that biofilms in chlorine experiment were thicker, denser and with higher coverage than in non-chlorine conditions under all flow regimes and during incubation. This suggests that the formation and development of biofilms was promoted by chlorine. Surprisingly, for both chlorinated and non-chlorinated conditions, biofilm thickness, density and coverage were all positively correlated with shear stress. More differences were detected in biofilms under the different flow regimes in non-chlorine than in chlorine experiments. This suggests a more robust biofilm under chlorine conditions. While this might imply less mobilization of biofilms in high shear events in pipe networks, it might also provide refuge from chlorine residuals for pathogens.

Engineering nanowires in bacteria to elucidate electron transport structural-functional relationships

Bacterial pilin nanowires are protein complexes, suggested to possess electroactive capabilities forming part of the cells' bioenergetic programming. Their role is thought to be linked to facilitating electron transfer between cells and the external environment to permit metabolism and cell-to-cell communication. There is a significant debate, with varying hypotheses as to the nature of the proteins currently lying between type-IV pilin-based nanowires and polymerised cytochrome-based filaments. Importantly, to date, there is a very limited structure-function analysis of these structures within whole bacteria. In this work, we engineered Cupriavidus necator H16, a model autotrophic organism to express differing aromatic modifications of type-IV pilus proteins to establish structure-function relationships on conductivity and the effects this has on pili structure. This was achieved via a combination of high-resolution PeakForce tunnelling atomic force microscopy (PeakForce TUNA™) technology, alongside conventional electrochemical approaches enabling the elucidation of conductive nanowires emanating from whole bacterial cells. This work is the first example of functional type-IV pili protein nanowires produced under aerobic conditions using a Cupriavidus necator chassis. This work has far-reaching consequences in understanding the basis of bio-electrical communication between cells and with their external environment.

Characterizing Intraindividual Podocyte Morphology In Vitro with Different Innovative Microscopic and Spectroscopic Techniques

Podocytes are critical components of the glomerular filtration barrier, sitting on the outside of the glomerular basement membrane. Primary and secondary foot processes are characteristic for podocytes, but cell processes that develop in culture were not studied much in the past. Moreover, protocols for diverse visualization methods mostly can only be used for one technique, due to differences in fixation, drying and handling. However, we detected by single-cell RNA sequencing (scRNAseq) analysis that cells reveal high variability in genes involved in cell type-specific morphology, even within one cell culture dish, highlighting the need for a compatible protocol that allows measuring the same cell with different methods. Here, we developed a new serial and correlative approach by using a combination of a wide variety of microscopic and spectroscopic techniques in the same cell for a better understanding of podocyte morphology. In detail, the protocol allowed for the sequential analysis of identical cells with light microscopy (LM), Raman spectroscopy, scanning electron microscopy (SEM) and atomic force microscopy (AFM). Skipping the fixation and drying process, the protocol was also compatible with scanning ion-conductance microscopy (SICM), allowing the determination of podocyte surface topography of nanometer-range in living cells. With the help of nanoGPS Oxyo^®, tracking concordant regions of interest of untreated podocytes and podocytes stressed with TGF-β were analyzed with LM, SEM, Raman spectroscopy, AFM and SICM, and revealed significant morphological alterations, including retraction of podocyte process, changes in cell surface morphology and loss of cell-cell contacts, as well as variations in lipid and protein content in TGF-β treated cells. The combination of these consecutive techniques on the same cells provides a comprehensive understanding of podocyte morphology. Additionally, the results can also be used to train automated intelligence networks to predict various outcomes related to podocyte injury in the future.

Effect of manganese oxides on arsenic speciation and mobilization in different arsenic-adsorbed iron-minerals under microbially-reducing conditions

The oxidation and immobilization of arsenic (As) by manganese oxides have been shown to reduce As toxicity and bioavailability under abiotic conditions. In this study, we investigate the impact of manganese oxide (δ-MnO₂) on the fate of different Fe-minerals-adsorbed As in the presence of As(V)-reducing bacteria Bacillus sp. JQ. Results showed that in the absence of δ-MnO₂, As release in goethite was much higher than in ferrihydrite and hematite during microbial reduction. Adding 3.1 mM Mn reduced As release by 0.3%, 46.3%, and 6.7% in the ferrihydrite, goethite, and hematite groups, respectively. However, aqueous As was dominated by As(III) in the end, because the oxidation effect of δ-MnO₂ was limited and short-lived. Additionally, the fraction of solid-phase As(V) increased by 9.8% in ferrihydrite, 39.4% in goethite, and 7.4% in hematite in the high-Mn treatments, indicating that δ-MnO₂ had the most significant oxidation and immobilization effect on goethite-adsorbed As. This was achieved because goethite particles were evenly distributed on δ-MnO₂ surface, which supported As(III) oxidation by δ-MnO₂; while ferrihydrite strongly aggregated, which hindered the oxidation of As(III). Our study shows that As-oxidation and immobilization by manganese oxides cannot easily be assessed without considering the mineral composition and microbial conditions of soils.

Nanovesicle and extracellular polymeric substance synthesis from the remediation of heavy metal ions from soil

Heavy metal toxicity affects aquatic plants and animals, disturbing biodiversity and ecological balance causing bioaccumulation of heavy metals. Industrialization and urbanization are inevitable in modern-day life, and control and detoxification methods need to be accorded to meet the hazardous environment. Microorganisms and plants have been widely used in the bioremediation of heavy metals. Sporosarcina pasteurii, a gram-positive bacterium that is widely known for its calcite precipitation property in bio-cementing applications has been explored in the study for its metal tolerance ability for the first time. S. pasteurii SRMNP1 (KF214757) can tolerate silver stress to form nanoparticles and can remediate multiple heavy metals to promote the growth of various plants. This astounding property of the isolate warranted extensive examinations to comprehend the physiological changes during an external heavy metal stress condition. The present study aimed to understand various physiological responses occurring in S. pasteuriiSRMNP1 during the metal tolerance phenomenon using electron microscopy. The isolate was subjected to heavy metal stress, and a transmission electron microscope examination was used to analyze the physiological changes in bacteria to evade the metal stress. S. pasteurii SRMNP1 was tolerant against a wide range of heavy metal ions and can withstand a broad pH range (5-9). Transmission Electron Microscopy (TEM) examination of S. pasteurii SRMNP1 followed by 5 mM nickel sulfate treatment revealed the presence of nanovesicles encapsulating nanosized particles in intra and extracellular spaces. This suggests that the bacteria evade the metal stress by converting the metal ions into nanosized particles and encapsulating them within nanovesicles to efflux them through the vesicle budding mechanism. Moreover, the TEM images revealed an excessive secretion of extracellular polymeric substances by the strain to discharge the metal particles outside the bacterial system. S. pasteurii can be foreseen as an effective bioremediation agent with the potential to produce nanosized particles, nanovesicles, and extracellular polymeric substances. This study provides physiological evidence that, besides calcium precipitation applications, S. pasteurii can further be explored for its multidimensional roles in the fields of drug delivery and environmental engineering.

Development and validation of a flow cytometry antibody test for Lawsonia intracellularis

Lawsonia intracellularis is the etiologic agent of porcine proliferative enteropathy (PPE), an inflammatory bowel disease with a major economic impact on the pig industry. The serological diagnosis of PPE can be performed using Blocking or Indirect ELISA, Immunoperoxidase Monolayer Assay (IPMA) and Indirect Fluorescence Antibody Test (IFAT). Here, we designed a most sophisticated immunological method for the detection of porcine anti-L. intracellularis IgGs, named Flow Cytometry Antibody Test - FCAT. This assay uses whole, live-attenuated L. intracellularis bacteria derived from a commercial vaccine. For the assay, we set up the optimal antigen concentration (10⁶ bacterium/assay), primary antibody dilution (1:100), time of incubation (20 min), antigen stability (15 days), precision (coefficient of variation - CV < 10%), reproducibility (CV ≤ 13%) and Receiver Operating Characteristic (ROC). When using a cut-off of >15.15% for FCAT, we determined that it showed a sensitivity of 98.8% and specificity of 100%. The rate of agreement with IPMA was 84.09% with a kappa index of 0.66. FCAT was used to screen 1,000 sera from non-vaccinated pigs housed in 22 different farms and we found that 730 pigs (73%) from 16 farms (72.7%) had L. intracellularis IgG. This high prevalence confirms that L. intracellularis is endemic on Brazilian pig farms. Finally, we determined that FCAT is an easy to perform diagnostic assay and we would highly recommend it for: i) seroepidemiological studies; ii) evaluation of infection dynamics; and iii) characterization of the humoral response profile induced by vaccines.

Copper and nanostructured anatase rutile and carbon coatings induce adaptive antibiotic resistance

Contaminated surfaces are vehicles for the spread of infectious disease-causing microorganisms. A strategy to prevent their spread is applying antimicrobial coatings to surfaces. Both nanostructured anatase rutile and carbon (NsARC), a TiO₂ formulation, and copper are examples of antimicrobial agents that are used in making or coating door handles and similar surfaces, to reduce microbial loads. Antimicrobial surfaces have been extensively tested for antimicrobial activity but not sublethal effects, such as exposure-associated multiple antibiotic resistance phenotypes usually caused by induction of efflux pump genes. The possibility of NsARC and copper inducing indicative efflux pump pathways was investigated by monitoring the expression of mScarlet fluorescent protein (FP) in two reporter strains of Escherichia coli. There was an increase in the expression of FP in the reporter strains exposed to NsARC and copper relative to the inert control composed of stainless steel. Furthermore we tested E. coli and Staphylococcus aureus following 8 h of exposure to NsARC for changes in resistance to selected antibiotics. E. coli that were exposed to NsARC became more susceptible to kanamycin but there was no significant change in susceptibility of S. aureus to any tested antibiotics. These findings suggests that even though NsARC and copper are antimicrobial, they also have some potential to cause unintended phenotypes.

New antimicrobial material NsARC based on TiO₂ compared to copper.

Both NsARC and copper induce efflux pump gene transcription.

Species-specific changes in antibiotic resistance from exposure to antimicrobial surface coatings.

A microfluidic-based analysis of 3D macrophage migration after stimulation by Mycobacterium, Salmonella and Escherichia

Macrophages play an essential role in the process of recognition and containment of microbial infections. These immune cells are recruited to infectious sites to reach and phagocytose pathogens. Specifically, in this article, bacteria from the genus Mycobacterium, Salmonella and Escherichia, were selected to study the directional macrophage movement towards different bacterial fractions. We recreated a three-dimensional environment in a microfluidic device, using a collagen-based hydrogel that simulates the mechanical microarchitecture associated to the Extra Cellular Matrix (ECM). First, we showed that macrophage migration is affected by the collagen concentration of their environment, migrating greater distances at higher velocities with decreasing collagen concentrations. To recreate the infectious microenvironment, macrophages were exposed to lateral gradients of bacterial fractions obtained from the intracellular pathogens M. tuberculosis and S. typhimurium. Our results showed that macrophages migrated directionally, and in a concentration-dependent manner, towards the sites where bacterial fractions are located, suggesting the presence of attractants molecules in all the samples. We confirmed that purified M. tuberculosis antigens, as ESAT-6 and CFP-10, stimulated macrophage recruitment in our device. Finally, we also observed that macrophages migrate towards fractions from non-pathogenic bacteria, such as M. smegmatis and Escherichia coli. In conclusion, our microfluidic device is a useful tool which opens new perspectives to study the recognition of specific antigens by innate immune cells.

Measurement of the low-frequency charge noise of bacteria

Bacteria meticulously regulate their intracellular ion concentrations and create ionic concentration gradients across the bacterial membrane. These ionic concentration gradients provide free energy for many cellular processes and are maintained by transmembrane transport. Given the physical dimensions of a bacterium and the stochasticity in transmembrane transport, intracellular ion concentrations and hence the charge state of a bacterium are bound to fluctuate. Here we investigate the charge noise of hundreds of nonmotile bacteria by combining electrical measurement techniques from condensed matter physics with microfluidics. In our experiments, bacteria in a microchannel generate charge density fluctuations in the embedding electrolyte due to random influx and efflux of ions. Detected as electrical resistance noise, these charge density fluctuations display a power spectral density proportional to 1/f^{2} for frequencies 0.05Hz≤f≤1Hz. Fits to a simple noise model suggest that the steady-state charge of a bacterium fluctuates by ±1.30×10^{6}e(e≈1.60×10^{-19}C), indicating that bacterial ion homeostasis is highly dynamic and dominated by strong charge noise. The rms charge noise can then be used to estimate the fluctuations in the membrane potential; however, the estimates are unreliable due to our limited understanding of the intracellular concentration gradients.

The role of shear dynamics in biofilm formation

There is growing evidence that individual bacteria sense and respond to changes in mechanical loading. However, the subtle responses of multispecies biofilms to dynamic fluid shear stress are not well documented because experiments often fail to disentangle any beneficial effects of shear stress from those delivered by convective transport of vital nutrients. We observed the development of biofilms with lognormally distributed microcolony sizes in drinking water on the walls of flow channels underflow regimes of increasing complexity. First, where regular vortices induced oscillating wall shear and simultaneously enhanced mass transport, which produced the thickest most extensive biofilms. Second, where unsteady uniform flow imposed an oscillating wall shear, with no enhanced transport, and where the biomass and coverage were only 20% smaller. Finally, for uniform steady flows with constant wall shear where the extent, thickness, and density of the biofilms were on average 60% smaller. Thus, the dynamics of shear stress played a significant role in promoting biofilm development, over and above its magnitude or mass transfer effects, and therefore, mechanosensing may prevail in complex multispecies biofilms which could open up new ways of controlling biofilm structure.

Development of a fixative protocol using formadehyde and gluteradehyde for preservation of microbial art on agar plates

Aims

Agar art bridges the gap between science and art using microbes instead of paint. Afterwards, the art can change in response to microbial fluctuation, meaning preservation of the original art is essential. Here, formaldehyde and glutaraldehyde were investigated as preservatives, involving techniques used in healthcare settings to preserve samples.

Methods and Results

Formaldehyde was tested at 1.0%, 2.0% and 3.7%, w/v, whereas glutaraldehyde was tested at 1% and 2.5%, w/v. Both compounds and respective concentrations were tested for different time periods. Escherichia coli, Serratia marcescens, Staphlococcus aureus and Micrococcus luteus were used as bacteria for “drawing” the works of art. The effectiveness of fixation was determined using integrated densities and visual assessment. Initially, both compounds showed potential promise, albeit with a loss of bacteria. Ser. marcescens was prone to colour changes and glutaraldehyde caused discolouration of agar and bacteria. These could be caused by a pH decrease in the agar, due to residual free aldehyde groups. Reduction of this was tested using 300 mM sodium metabisulfite to neutralize excess aldehydes. This initially led to reduced bacterial loss and avoided colour changes, however measurements 24 h post‐fixation showed colour loss to some bacterial clusters.

Conclusions

Here, at least 2% formaldehyde for a short fixation period, typically 1 min, depending on the species, was most promising for the preservation of art. Given the success of this with different bacteria, it would make a good starting combination for anyone trying to fix agar art, although methodology refinement may be needed for optimisation depending on the bacterial species used.

Significance and Impact of Study

This study shows, for the first time, successful fixation and preservation of different bacterial species on agar. The impact of this is to preserve agar art while making it safe and non‐infective to those in contact with the microbial art.

Fusobacterium nucleatum Subspecies Differ in Biofilm Forming Ability in vitro

Development of dysbiosis in complex multispecies bacterial biofilms forming on teeth, known as dental plaque, is one of the factors causing periodontitis. Fusobacterium nucleatum (F. nucleatum) is recognised as a key microorganism in subgingival dental plaque, and is linked to periodontitis as well as colorectal cancer and systemic diseases. Five subspecies of F. nucleatum have been identified: animalis, fusiforme, nucleatum, polymorphum, and vincentii. Differential integration of subspecies into multispecies biofilm models has been reported, however, biofilm forming ability of individual F. nucleatum subspecies is largely unknown. The aim of this study was to determine the single-subspecies biofilm forming abilities of F. nucleatum ATCC type strains. Static single subspecies F. nucleatum biofilms were grown anaerobically for 3 days on untreated or surface-modified (sandblasting, artificial saliva, fibronectin, gelatin, or poly-L-lysine coating) plastic and glass coverslips. Biofilm mass was quantified using crystal violet (CV) staining. Biofilm architecture and thickness were analysed by scanning electron microscopy and confocal laser scanning microscopy. Bioinformatic analysis was performed to identify orthologues of known adhesion proteins in F. nucleatum subspecies. Surface type and treatment significantly influenced single-subspecies biofilm formation. Biofilm formation was overall highest on poly-L-lysine coated surfaces and sandblasted glass surfaces. Biofilm thickness and stability, as well as architecture, varied amongst the subspecies. Interestingly, F. nucleatum ssp. polymorphum did not form a detectable, continuous layer of biofilm on any of the tested substrates. Consistent with limited biofilm forming ability in vitro, F. nucleatum ssp. polymorphum showed the least conservation of the adhesion proteins CmpA and Fap2 in silico. Here, we show that biofilm formation by F. nucleatum in vitro is subspecies- and substrate-specific. Additionally, F. nucleatum ssp. polymorphum does not appear to form stable single-subspecies continuous layers of biofilm in vitro. Understanding the differences in F. nucleatum single-subspecies biofilm formation may shed light on multi-species biofilm formation mechanisms and may reveal new virulence factors as novel therapeutic targets for prevention and treatment of F. nucleatum-mediated infections and diseases.

Bimolecular fluorescence complementation assay to explore protein-protein interactions of the Yersinia virulence factor YopM

Yersinia outer protein M (YopM) is one of the effector proteins and essential for virulence. YopM is delivered by the Yersinia type III secretion system (T3SS) into the host cell, where it shows immunosuppressive effect through interaction with host proteins. Therefore, protein-protein interactions of YopM is significant to understand its molecular mechanism. In this study, we aimed to explore protein-protein interactions of YopM with the two components of T3SS, namely LcrV and LcrG. We used bimolecular fluorescence complementation (BiFC) assay and monitored the reassembly of green fluorescence protein in Escherichia coli. As an indicator of the protein-protein interaction, we monitored the in vivo reconstitution of fluorescence by measuring fluorescence intensity and imaging the cells under fluorescence microscope. We showed, for the first time, that YopM interacts with LcrG, but not with LcrV. Here, we propose BiFC assay as a simple method to screen novel interaction partners of YopM.

A simple, quantitative assay for the detection of viable but non-culturable (VBNC) bacteria

This protocol determines the fraction of a bacterial population that is viable and culturable, viable and non-culturable, or non-viable (dead). Each population is detected by isolating colonies on agar plates, performing direct counts, and staining for live or dead cells. Its application is limited to bacteria that are stainable and when permissible growth conditions are known. The quantitative data extracted allow for the detection of a viable but non-culturable (alive and non-dividing) population from a liquid culture.

For complete details on the use and execution of this protocol, please refer to Stott et al. (2015).

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Liquid cultures are spread onto agar plates to quantify CFU/mL

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Direct counting is performed to determine the total number of bacteria per mL

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Fluorescence microscopy is used to distinguish between live and dead bacteria

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In sum, the protocol can reveal VBNC populations in a culture

Engineering the permeability of Halomonas bluephagenesis enhanced its chassis properties

Bacterial outer membrane (OM), an asymmetric lipid bilayer functioning as a self-protective barrier with reduced permeability for Gram-negative bacteria, yet wasting nutrients and energy to synthesize, has not been studied for its effect on bioproduction. Here we construct several OM-defected halophile Halomonas bluephagenesis strains to investigate the effects of OM on bioproduction. We achieve enhanced chassis properties of H. bluephagenesis based on positive cellular properties among several OM-defected strains. The OM-defected H. bluephagenesis WZY09 demonstrates better adaptation to lower salinity, increasing 28%, 30% and 12% on dry cell mass (DCM), poly(3-hydroxybutyrate) (PHB) accumulation and glucose to PHB conversion rate, respectively, including enlarged cell sizes and 21-folds reduced endotoxin. Interestingly, a poly(3-hydroxybutyrate-co-21mol%4-hydroxybutyrate) (P(3HB-co-21mol%4HB)) is produced by H. bluephagenesis WZY09 derivate WZY249, increasing 60% and 260% on polyhydroxyalkanoate (PHA) production and 4HB content, respectively. Furthermore, increased electroporation efficiency, more sensitive isopropyl β-D-1-thio-galactopyranoside (IPTG) induction, better oxygen uptake, enhanced antibiotics sensitivity and ectoine secretion due to better membrane permeability are observed if OM defected, demonstrating significant OM defection impacts for further metabolic engineering, synthetic biology studies and industrial applications.

Comparison and optimization of nanoscale extracellular vesicle imaging by scanning electron microscopy for accurate size-based profiling and morphological analysis

Nanosized extracellular vesicles (EVs) have been found to play a key role in intercellular communication, offering opportunities for both disease diagnostics and therapeutics. However, lying below the diffraction limit and also being highly heterogeneous in their size, morphology and abundance, these vesicles pose significant challenges for physical characterization. Here, we present a direct visual approach for their accurate morphological and size-based profiling by using scanning electron microscopy (SEM). To achieve that, we methodically examined various process steps and developed a protocol to improve the throughput, conformity and image quality while preserving the shape of EVs. The study was performed with small EVs (sEVs) isolated from a non-small-cell lung cancer (NSCLC) cell line as well as from human serum, and the results were compared with those obtained from nanoparticle tracking analysis (NTA). While the comparison of the sEV size distributions showed good agreement between the two methods for large sEVs (diameter > 70 nm), the microscopy based approach showed a better capacity for analyses of smaller vesicles, with higher sEV counts compared to NTA. In addition, we demonstrated the possibility of identifying non-EV particles based on size and morphological features. The study also showed process steps that can generate artifacts bearing resemblance with sEVs. The results therefore present a simple way to use a widely available microscopy tool for accurate and high throughput physical characterization of EVs.

Effects of fixation on bacterial cellular dimensions and integrity

Fixation facilitates imaging of subcellular localization and cell morphology, yet it remains unknown how fixation affects cellular dimensions and intracellular fluorescence patterns, particularly during long-term storage. Here, we characterized the effects of multiple fixatives on several bacterial species. Fixation generally reduced cell length by 5-15%; single-cell tracking in microfluidics revealed that the length decrease was an aggregate effect of many steps in the fixation protocol and that fluorescence of cytoplasmic GFP but not membrane-bound MreB-msfGFP was rapidly lost with formaldehyde-based fixatives. Cellular dimensions were preserved in formaldehyde-based fixatives for ≥4 days, but methanol caused length to decrease. Although methanol preserved cytoplasmic fluorescence better than formaldehyde-based fixatives, some Escherichia coli cells were able to grow directly after fixation. Moreover, methanol fixation caused lysis in a subpopulation of cells, with virtually all Bacillus subtilis cells lysing after one day. These findings highlight tradeoffs between maintenance of fluorescence and membrane integrity for future applications of fixation.

Antimicrobial and biofilm-disrupting nanostructured TiO2 coating demonstrating photoactivity and dark activity

Antimicrobial materials are tools used to reduce the transmission of infectious microorganisms. Photo-illuminated titania (TiO2) is a known antimicrobial material. Used as a coating on door handles and similar surfaces, it may reduce viability and colonization by pathogens and limit their spread. We tested the survival of Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Saccharomyces cerevisiae on a nano-structured TiO2-based thin film, called 'NsARC', and on stainless steel under a variety of light wavelengths and intensities. There was significantly less survival (P <0.001) of all the organisms tested on NsARC compared to inert uncoated stainless steel under all conditions. NsARC was active in the dark and possible mechanisms for this are suggested. NsARC inhibited biofilm formation as confirmed by scanning electron microscopy. These results suggest that NsARC can be used as a self-cleaning and self-sterilizing antimicrobial surface coating for the prevention and reduction in the spread of potentially infectious microbes.

Production of inactivated gram-positive and gram-negative species with preserved cellular morphology and integrity

There are many approaches available to produce inactive bacteria by termination of growth, each with a different efficacy, impact on cell integrity, and potential for application in standardized inactivation protocols. The aim of this study was to compare these approaches and develop a standardized protocol for generation of inactivated Gram-positive and Gram-negative bacteria, yielding cells that are metabolically dead with retained cellular integrity i.e., preserving the surface and limited leakage of intracellular proteins and DNA. These inactivated bacteria are required for various applications, for instance, when investigating receptor-triggered signaling or bacterial contact-dependent analysis of cell lines requiring long incubation times. We inactivated eight different bacterial strains of different species by treatment with beta-propiolactone, ethanol, formalin, sodium hydroxide, and pasteurization. Inactivation efficacy was determined by culturing, and cell wall integrity assessed by quantifying released DNA, bacterial membrane and intracellular DNA staining, and visualization by scanning electron microscopy. Based on these results, we discuss the bacterial inactivation methods, and their advantages and disadvantages to study host-microbe interactions with inactivated bacteria.

An updated toolkit for exploring bacterial cell wall structure and dynamics

The bacterial cell wall is made primarily from peptidoglycan, a complex biomolecule which forms a bag-like exoskeleton that envelops the cell. As it is unique to bacteria and typically essential for their growth and survival, it represents one of the most successful targets for antibiotics. Although peptidoglycan has been studied intensively for over 50 years, the past decade has seen major steps in our understanding of this molecule because of the advent of new analytical and imaging methods. Here, we outline the most recent developments in tools that have helped to elucidate peptidoglycan structure and dynamics.

The histone demethylase KDM6B fine-tunes the host response to Streptococcus pneumoniae

Streptococcus pneumoniae is a natural colonizer of the human respiratory tract and an opportunistic pathogen. Although epithelial cells are among the first to encounter pneumococci, the cellular processes and contribution of epithelial cells to the host response are poorly understood. Here, we show that a S. pneumoniae serotype 6B ST90 strain, which does not cause disease in a murine infection model, induces a unique NF-κB signature response distinct from an invasive-disease-causing isolate of serotype 4 (TIGR4). This signature is characterized by activation of p65 and requires a histone demethylase KDM6B. We show, molecularly, that the interaction of the 6B strain with epithelial cells leads to chromatin remodelling within the IL-11 promoter in a KDM6B-dependent manner, where KDM6B specifically demethylates histone H3 lysine 27 dimethyl. Remodelling of the IL-11 locus facilitates p65 access to three NF-κB sites that are otherwise inaccessible when stimulated by IL-1β or TIGR4. Finally, we demonstrate through chemical inhibition of KDM6B with GSK-J4 inhibitor and through exogenous addition of IL-11 that the host responses to the 6B ST90 and TIGR4 strains can be interchanged both in vitro and in a murine model of infection in vivo. Our studies therefore reveal how a chromatin modifier governs cellular responses during infection.

Detection of human-associated bacteria in water from Akiyoshi-do Cave, Japan

Akiyoshi-do Cave is one of the oldest and the largest show caves in Japan. Environmental alterations induced by tourism impacts have been suggested; however, only a few previous studies have investigated the impacts of tourism on the cave. In this study, enrichment culture procedures were applied to detect human-associated bacteria (HAB) including Escherichia coli, Staphylococcus aureus, and thermo-tolerant Bacillus spp. in cave water. Physical and bacterial parameters of water including total nitrogen, ammonia, phosphate, total number of bacteria, and total number of viable bacteria were collected as environmental factors. Escherichia coli was absent at all sites, but increased levels of total bacteria, viable bacteria, S. aureus, and thermo-tolerant Bacillus spp. were present at high-impact sites. Examination of the origin tracking of HAB suggested that cave tourists could be a source of HAB contamination, but other causes related to the surface land use could also contribute to HAB contamination. © 2020 Water Environment Federation PRACTITIONER POINTS: Detection of HAB was performed for the first time in Japanese show caves to consider tourism impacts. The greater number of HAB was detected from the tourist area than the nontourist area in the cave. It was suggested that the origin of HAB may not be limited to tourists, but may also include the surface.

A novel cell permeability assay for macromolecules

BACKGROUND

Many cell permeabilisation methods to mediate internalisation of various molecules to mammalian or bacterial cells have been developed. However, no size-specific permeability assay suitable for both cell types exists.

RESULTS

We report the use of intrinsically biotinylated cell components as the target for reporter molecules for assessing permeabilisation. Due to its well-described biotin binding activity, we developed an assay using Streptavidin (SAv) as a molecular weight marker for assessing eukaryotic and prokaryotic cell internalisation, using flow cytometry as a readout. This concept was tested here as part of the development of host DNA depletion strategies for microbiome analysis of formalin-fixed (FF) samples. Host depletion (HD) strategies require differential cell permeabilisation, where mammalian cells but not bacterial cells are permeabilised, and are subsequently treated with a nuclease. Here, the internalisation of a SAv-conjugate was used as a reference for nucleases of similar dimensions. With this assay, it was possible to demonstrate that formalin fixation does not generate pores which allow the introduction of 60 KDa molecules in mammalian or bacterial membranes/envelopes. Among surfactants tested, Saponin derived from Quillaja bark showed the best selectivity for mammalian cell permeabilisation, which, when coupled with Benzonase nuclease, provided the best results for host DNA depletion, representing a new HD strategy for formalin fixed samples.

CONCLUSION

The assay presented provides researchers with a sensitive and accessible tool for discerning membrane/cell envelop permeability for different size macromolecules.

Fixed versus live endothelial cells: The effect of glutaraldehyde fixation manifested by characteristic bands on the Raman spectra of cells

This work shows an impact of glutaraldehyde (GA) fixation on endothelial cells. Raman spectroscopy imaging was used as a method to monitor biochemical content of the cells due to GA fixation since this is an approach frequently used for studying cells by means of Raman imaging. To get a deeper insight into the changes and to understand them better the measurements of live and fixed cells were performed using two lasers, i.e. 488 and 532 nm. It has been demonstrated that GA fixation affects lipids, proteins, nucleic acid and carbohydrates to small extent. The application of 488 nm laser line seems to be more efficient for live cells due to the small impact of cytochrome resonance on Raman spectra, however 532 nm line is more beneficial for fixed cells due to higher quantum efficiency of the detector, thus leading to higher intensity of Raman bands. Generally, the changes due to fixation are not pronounced but cannot be ignored and the knowledge about them can help in a proper interpretation of data collected for fixed versus live cells.

Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

BACKGROUND

Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over 3 months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing.

RESULTS

While the bacterial community recovered mostly over 3 months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared 3 months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrated in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate.

CONCLUSIONS

We demonstrated that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition. Video abstract.

The Anti-Microbial Peptide (Lin-SB056-1)2-K Reduces Pro-Inflammatory Cytokine Release through Interaction with Pseudomonas aeruginosa Lipopolysaccharide

The ability of many anti-microbial peptides (AMPs) to modulate the host immune response has highlighted their possible therapeutic use to reduce uncontrolled inflammation during chronic infections. In the present study, we examined the anti-inflammatory potential of the semi-synthetic peptide lin-SB056-1 and its dendrimeric derivative (lin-SB056-1)₂-K, which were previously found to have anti-microbial activity against Pseudomonas aeruginosa in in vivo-like models mimicking the challenging environment of chronically infected lungs (i.e., artificial sputum medium and 3-D lung mucosa model). The dendrimeric derivative exerted a stronger anti-inflammatory activity than its monomeric counterpart towards lung epithelial- and macrophage-cell lines stimulated with P. aeruginosa lipopolysaccharide (LPS), based on a marked decrease (up to 80%) in the LPS-induced production of different pro-inflammatory cytokines (i.e., IL-1β, IL-6 and IL-8). Accordingly, (lin-SB056-1)₂-K exhibited a stronger LPS-binding affinity than its monomeric counterpart, thereby suggesting a role of peptide/LPS neutralizing interactions in the observed anti-inflammatory effect. Along with the anti-bacterial and anti-biofilm properties, the anti-inflammatory activity of (lin-SB056-1)₂-K broadens its therapeutic potential in the context of chronic (biofilm-associated) infections.

Modified Papanicolaou staining for oral swab samples stored long term

Pathologists collect swab samples for Papanicolaou (Pap) staining to diagnose various diseases including cancer and HIV. Time constraints and limited resources, may preclude staining a sample immediately. To re-confirm results, samples must be frozen for later analysis. We present a method for Pap staining cells that have been stored long term. An effective method for Pap staining of frozen cells should enable flexibility for processing samples.

Role of adhesion forces in mechanosensitive channel gating in Staphylococcus aureus adhering to surfaces

Mechanosensitive channels in bacterial membranes open or close in response to environmental changes to allow transmembrane transport, including antibiotic uptake and solute efflux. In this paper, we hypothesize that gating of mechanosensitive channels is stimulated by forces through which bacteria adhere to surfaces. Hereto, channel gating is related with adhesion forces to different surfaces of a Staphylococcus aureus strain and its isogenic ΔmscL mutant, deficient in MscL (large) channel gating. Staphylococci becoming fluorescent due to uptake of calcein, increased with adhesion force and were higher in the parent strain (66% when adhering with an adhesion force above 4.0 nN) than in the ΔmscL mutant (40% above 1.2 nN). This suggests that MscL channels open at a higher critical adhesion force than at which physically different, MscS (small) channels open and contribute to transmembrane transport. Uptake of the antibiotic dihydrostreptomycin was monitored by staphylococcal killing. The parent strain exposed to dihydrostreptomycin yielded a CFU reduction of 2.3 log-units when adhering with an adhesion force above 3.5 nN, but CFU reduction remained low (1.0 log-unit) in the mutant, independent of adhesion force. This confirms that large channels open at a higher critical adhesion-force than small channels, as also concluded from calcein transmembrane transport. Collectively, these observations support our hypothesis that adhesion forces to surfaces play an important role, next to other established driving forces, in staphylococcal channel gating. This provides an interesting extension of our understanding of transmembrane antibiotic uptake and solute efflux in infectious staphylococcal biofilms in which bacteria experience adhesion forces from a wide variety of surfaces, like those of other bacteria, tissue cells, or implanted biomaterials.

Enzyme-targeted fluorescent small-molecule probes for bacterial imaging

Molecular imaging methods to visualize myriad biochemical processes in bacteria have traditionally been dependent upon molecular biology techniques to incorporate fluorescent biomolecules (e.g., fusion proteins). Such methods have been instrumental in our understanding of how bacteria function but are not without drawbacks, including potential perturbation to native protein expression and function. To overcome these limitations, the use of fluorescent small-molecule probes has gained much attention. Here, we highlight examples from the recent literature that showcase the utility of small-molecule probes for the fluorescence imaging of bacterial cells, including electrophilic, metabolic, and enzyme-activated probes. Although the use of these types of compounds for bacterial imaging is still relatively new, the selected examples demonstrate the exciting potential of these critical tools in the exploration of bacterial physiology.

Rectinema subterraneum sp. nov, a chemotrophic spirochaete isolated from the deep terrestrial subsurface

A novel, obligately anaerobic bacterium (strain SURF-ANA1^T) was isolated from deep continental subsurface fluids at a depth of 1500 m below surface in the former Homestake Gold Mine (now Sanford Underground Research Facility, in Lead, South Dakota, USA). Cells of strain SURF-ANA1^T were Gram-negative, helical, non-spore-forming and were 0.25-0.55×5.0-75.0 µm with a wavelength of 0.5-0.62 µm. Strain SURF-ANA1^T grew at 15-50 °C (optimally at 40 °C), at pH 4.8-9.0 (pH 7.2) and in 1.0-40.0 g l^-1 NaCl (10 g l^-1 NaCl). The strain grew chemoheterotrophically with hydrogen or mono-, di- and polysaccharides as electron donors. The major cellular fatty acids in order of decreasing abundance (comprising >5% of total) were 10-methyl C_16:0, iso-C_15:0, C_18:2 and C_18:0 dimethyl acetal (DMA) and C_20:0 methylene-nonadecanoic acid. Phylogenetic analysis based on the 16S rRNA gene sequence of strain SURF-ANA1^T indicated a closest relationship with the recently characterized Rectinema cohabitans (99%). Despite high sequence identity, because of its distinct physiology, morphology and fatty acid profile, strain SURF-ANA1^T is considered to represent a novel species within the genus Rectinema, for which the name Rectinema subterraneum sp. nov. is proposed. To our knowledge, this is the first report of an isolate within the phylum Spirochaetes from the deep (>100 m) terrestrial subsurface. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and genomic sequences of strain SURF-ANA1^T are KU359248 and GCF 009768935.1, respectively. The type strain of Rectinema subterraneum is SURF-ANA1^T (=ATCC TSD-67=JCM 32656).

The Antimicrobial Peptide Human Beta-Defensin 2 Inhibits Biofilm Production of Pseudomonas aeruginosa Without Compromising Metabolic Activity

Biofilm production is a key virulence factor that facilitates bacterial colonization on host surfaces and is regulated by complex pathways, including quorum sensing, that also control pigment production, among others. To limit colonization, epithelial cells, as part of the first line of defense, utilize a variety of antimicrobial peptides (AMPs) including defensins. Pore formation is the best investigated mechanism for the bactericidal activity of AMPs. Considering the induction of human beta-defensin 2 (HBD2) secretion to the epithelial surface in response to bacteria and the importance of biofilm in microbial infection, we hypothesized that HBD2 has biofilm inhibitory activity. We assessed the viability and biofilm formation of a pyorubin-producing Pseudomonas aeruginosa strain in the presence and absence of HBD2 in comparison to the highly bactericidal HBD3. At nanomolar concentrations, HBD2 - independent of its chiral state - significantly reduced biofilm formation but not metabolic activity, unlike HBD3, which reduced biofilm and metabolic activity to the same degree. A similar discrepancy between biofilm inhibition and maintenance of metabolic activity was also observed in HBD2 treated Acinetobacter baumannii, another Gram-negative bacterium. There was no evidence for HBD2 interference with the regulation of biofilm production. The expression of biofilm-related genes and the extracellular accumulation of pyorubin pigment, another quorum sensing controlled product, did not differ significantly between HBD2 treated and control bacteria, and in silico modeling did not support direct binding of HBD2 to quorum sensing molecules. However, alterations in the outer membrane protein profile accompanied by surface topology changes, documented by atomic force microscopy, was observed after HBD2 treatment. This suggests that HBD2 induces structural changes that interfere with the transport of biofilm precursors into the extracellular space. Taken together, these data support a novel mechanism of biofilm inhibition by nanomolar concentrations of HBD2 that is independent of biofilm regulatory pathways.

Antibacterial activity of chlorogenic acid-loaded SiO2 nanoparticles caused by accumulation of reactive oxygen species

Diseases caused by pathogenic bacilli pose an increasing threat to human health. A common feature of these bacteria is a complete cell wall; therefore, drugs that can penetrate this protective barrier could be used as a novel approach for treating these infections. Here we present a simple method for synthesizing a silica mesoporous material loaded with cadmium selenide (CdSe) and chlorogenic acid. Using UV-visible, fluorescence, and infrared imaging in combination with transmission electron microscopy, it was shown that CdSe and chlorogenic acid could be successfully embedded in the mesopores of silica nanoparticles (CSC NPs), and these NPs presented with a strong fluorescence, uniform size, and good dispersion. Additionally, the results of these analyses indicated that the fluorescence of the CSC NPs was localized within the cells of Escherichia coli and Bacillus subtilis, signifying that these NPs could breach the cell wall and enter the cells of these two bacilli. Additional assessments found that these CSC NPs inhibited the proliferation of the bacteria by disrupting the cell wall, and this was most likely due to the overproduction of reactive oxygen species induced by chlorogenic acid. Importantly, histopathology analysis indicated that the CSC NPs had limited side effects and high biocompatibility.

Simultaneous cleanup of Reactive Black 5 and cadmium by a desert soil bacterium

Multi-contaminated industrial wastewaters pose serious environmental risks due to high toxicity and non-biodegradability. The work reported here evaluated the ability of Pseudomonas aeruginosa strain Gb30 isolated from desert soil to simultaneously remove cadmium (Cd) and Reactive Black 5 (RB5), both common contaminants in various industrial effluents. The strain was able to grow normally and decolorize 50 mg L^-1 RB5 within 24 h of incubation in the presence of 0.629 m mol L^-1 of Cd²⁺. In order to evaluate strain performance in RB5 detoxification, a cytotoxicity test using Human Embryonic Kidney cells (HEK293) was used. Cadmium removal from culture media was determined using atomic adsorption. Even in presence of (0.115 + 0.157 + 0.401 + 0.381) m mol L^-1, respectively, of Cr⁶⁺, Cd²⁺, Cu²⁺ and Zn²⁺ in the growth medium, strain Gb30 successfully removed 35% of RB5 and 44%, 36%, 59% and 97%, respectively, of introduced Zn²⁺, Cu²⁺, Cr⁶⁺ and Cd²⁺, simultaneously. In order to understand the mechanism of Cd removal used by P. aeruginosa strain Gb30, biosorption and bioaccumulation abilities were examined. The strain was preferentially biosorbing Cd on the cell surface, as opposed to intracellular bioaccumulation. Microscopic investigations using AFM, SEM and FTIR analysis of the bacterial biomass confirmed the presence of various structural features, which enabled the strain to interact with metal ions. The study suggests that Pseudomonas aeruginosa Gb30 is a potential candidate for bioremediation of textile effluents in the presence of complex dye-metal contamination.

A new approach for repeated tip-sample relocation for AFM imaging of nano and micro sized particles and cells in liquid environment

The ability to repeatedly find exact the same nano region-of-interest (nROI) is essential for atomic force microscopy (AFM) studies of heterogeneous environmental samples. The large variety of methods makes it difficult to find the most suitable one for a specific research question. We thus conducted a literature research for nROI relocation methods and organized the found references in order to give an overview over relocation methods including the advantages, limitations and documented applications. This survey of nROI relocation methods and their key information facilitates the selection of appropriate methods with respect to a specific research question. Based on this survey, we developed a new AFM relocation approach urgently needed for the study of nano and micro sized particles and cells in air and aqueous environment. This approach uses commercially available TEM grids fully embedded in a semitransparent resin as a glue body on top of which particles and cells are fixed. Relocation of nROI within one grid is based on easily recognizable sample features in micro and nanometer scale. The stable sticking of the studied mineral particles and bacterial cells allows repeated measurements of the same nROI with differently functionalized tips in air as well as in water. Our simple, fast, and cost-effective method allows relocation with an accuracy of 10-40 nm and enables the implementation of AFM/ESEM correlative microscopy.

Endomembrane Protein Trafficking Regulated by a TvCyP2 Cyclophilin in the Protozoan Parasite, Trichomonas vaginalis

In Trichomonas vaginalis, the TvCyP1-catalyzed conformational switches of two glycinyl-prolyl imide bonds in Myb3 were previously shown to regulate the trafficking of Myb3 from cytoplasmic membrane compartments towards the nucleus. In this study, TvCyP2 was identified as a second cyclophilin that binds to Myb3 at the same dipeptide motifs. The enzymatic proficiency of TvCyP2, but not its binding to Myb3, was aborted by a mutation of Arg⁷⁵ in the catalytic domain. TvCyP2 was localized to the endoplasmic reticulum with a weak signal that extensively extends into the cytoplasm as well as to the plasma membrane according to an immunofluorescence assay. Moreover, TvCyP2 was co-enriched with TvCyP1 and Myb3 in various membrane fractions purified by differential and gradient centrifugation. TvCyP2 was found to proficiently enzymatically regulate the distribution of TvCyP1 and Myb3 among purified membrane fractions, and to localize TvCyP1 in hydrogenosomes and on plasma membranes. Protein complexes immunoprecipitated from lysates of cells overexpressing TvCyP1 and TvCyP2 were found to share some common components, like TvCyP1, TvCyP2, TvBip, Myb3, TvHSP72, and the hydrogenosomal heat shock protein 70 (HSP70). Direct interaction between TvCyP1 and TvCyP2 was confirmed by a GST pull-down assay. Fusion of vesicles with hydrogenosomes was observed by transmission electron microscopy, whereas TvCyP1, TvCyP2, and Myb3 were each detected at the fusion junction by immunoelectron microscopy. These observations suggest that T. vaginalis may have evolved a novel protein trafficking pathway to deliver proteins among the endomembrane compartments, hydrogenosomes and plasma membranes.

Probing the surface ultrastructure of Brevibacillus laterosporus using atomic force microscopy

One of the main obstacles to studying the surface ultrastructure of microbial cells by atomic force microscopy (AFM) is determining how to immobilize live cells on the AFM substrates. Each method has its own advantages and disadvantages. The aim of this study was to characterize a new simple and inexpensive method using two types of polyethersulfone (PES) membrane filters that differ in pore size (micropore and nanopore) to immobilize live and dead Brevibacillus laterosporus for AFM imaging. B. laterosporus was easily trapped by the microporous PES membrane, facilitating the successful AFM scanning of the bacterial surface ultrastructure. In addition, B. laterosporus strongly attached to the nanoporous membranes and withstood the pulling forces exerted by the AFM tip during scanning. These methods of immobilization did not affect the cell viability. The nanostructure and roughness of the bacterial surface were also observed for live, fixed, and air-dried cells. Live and dead bacteria displayed similar morphologies at low resolution, while at high resolution, live bacteria displayed a more convoluted surface ("brain-like structure").

Insignificant Impact of Chemotactic Responses of Pseudomonas aeruginosa on the Bacterial Attachment to Organic Pre-Conditioned RO Membranes

We investigated the impact of conditioning compositions on the way bacteria move and adhere to reverse osmosis (RO) membranes that have been pre-conditioned by organic compounds. We used humic acid (HA), bovine serum albumin (BSA), and sodium alginate (SA) to simulate conditioning layers on the RO membranes. First, we investigated the chemotactic responses of Pseudomonas aeruginosa PAO1 to the organic substances and the impact of changes in physicochemical characteristics of pre-conditioned membranes on bacterial attachment. Second, we observed bacterial attachment under the presence or absence of nutrients or microbial metabolic activity. Results showed that there was no relationship between the chemotactic response of P. aeruginosa PAO1 and the organic substances, and the changes in hydrophobicity, surface free energy, and surface charge resulting from changing the composition of the conditioning layer did not seem to affect bacterial attachment, whereas changing the roughness of the conditioned membrane exponentially did (exponential correlation coefficient, R² = 0.85). We found that the initial bacterial attachment on the membrane surface is influenced by (i) the nutrients in the feed solution and (ii) the microbial metabolic activity, whereas the chemotaxis response has a negligible impact. This study would help to establish a suitable strategy to manage bacterial attachment.

Cell-Penetrating And Antibacterial BUF-II Nanobioconjugates: Enhanced Potency Via Immobilization On Polyetheramine-Modified Magnetite Nanoparticles

Introduction

Controlled delivery of therapeutic molecules in a localized manner has become an area of interest due to its potential to reduce drug exposure to healthy tissues and consequently to minimize undesirable side effects. We have recently introduced novel cell-penetrating vehicles by immobilizing the antimicrobial peptide Buforin II (BUF-II) on magnetite nanoparticles (MPNPs). Despite the potent translocating abilities of such nanobioconjugates, they failed to preserve the antimicrobial activity of native BUF-II. In this work, we explored immobilization on MNPs with the aid of polymer surface spacers, which has been considered as an attractive alternative for the highly efficient conjugation of various biomolecules.

Methods

Here, we immobilized BUF-II on polyetheramine-modified magnetite nanoparticles to preserve its structural integrity. As a result, for the obtained nanobioconjugates the lost antimicrobial activity against gram-positive and gram-negative bacteria was only 50% with respect to the native BUF-II. The nanobioconjugates were also characterized via FTIR, DLS, TEM, and TGA. Delivery on THP-1, HaCaT, HFF, and Escherichia coli cells was conducted to confirm capability for cell membrane translocation.

Results

Colocalization with Lysotracker showed an endosomal escape efficiency of about 73∓12% in THP-1 cells. Avoidance of endocytic pathways of internalization was qualitatively confirmed by a delivery assay at low temperature. Nuclear penetration of the nanobioconjugates was corroborated via confocal microscopy and showed high biocompatibility as demonstrated by hemolysis levels below 5% and acute cytotoxicity of around 15%.

Conclusion

The obtained nanobioconjugates were capable of translocating the cell membrane and nuclei of different normal and cancerous cell lines without significantly decreasing viability. This makes the vehicle addressable for a number of applications ranging from antimicrobial topical treatments to the delivery of nucleotides and therapeutic molecules with difficulties to bypass cell membranes.