Model Microbe Research Articles

Chronic Response of Waste Activated Sludge Fermentation to Titanium Dioxide Nanoparticles

Due to the large-scale production and wide applications, many nanoparticles (NPs) enter wastewater treatment plants and accumulate in activated sludge. It is reported that titanium dioxide (TiO2) NPs show severe damage to many model microbes. However, it is still unknown whether the long-term (e.g., 100d) presence of TiO2 NPs would affect the performance of sludge fermentation. In this study, long-term exposure experiments (105d) were conducted to investigate the potential risk of TiO2 NPs to sludge fermentation system. It is found that the presence of environmentally relevant [6mg·(gTSS)−1] and higher [150mg·(gTSS)−1] concentrations of TiO2 NPs does not affect methane production from sludge fermentation. The analysis of fluorescence in situ hybridization indicates that these concentrations of TiO2 NPs present marginal influences on abundances of bacteria and methanogenic archaea in sludge fermentation system. The viability of sludge microorganisms and activities of key enzymes related to methane production such as protease, acetate kinase, and coenzyme F420 are unchanged by the long-term presence of 6 and 150mg·(gTSS)−1 of TiO2 NPs. Further investigations reveal that the insolubility of NPs and the protection role of sludge extracellular polymeric substances are the main reasons for the marginal influence of TiO2 NPs on sludge fermentation.

Phylobiochemical characterization of class-Ib aspartate/prephenate aminotransferases reveals evolution of the plant arogenate phenylalanine pathway.

The aromatic amino acid Phe is required for protein synthesis and serves as the precursor of abundant phenylpropanoid plant natural products. While Phe is synthesized from prephenate exclusively via a phenylpyruvate intermediate in model microbes, the alternative pathway via arogenate is predominant in plant Phe biosynthesis. However, the molecular and biochemical evolution of the plant arogenate pathway is currently unknown. Here, we conducted phylogenetically informed biochemical characterization of prephenate aminotransferases (PPA-ATs) that belong to class-Ib aspartate aminotransferases (AspAT Ibs) and catalyze the first committed step of the arogenate pathway in plants. Plant PPA-ATs and succeeding arogenate dehydratases (ADTs) were found to be most closely related to homologs from Chlorobi/Bacteroidetes bacteria. The Chlorobium tepidum PPA-AT and ADT homologs indeed efficiently converted prephenate and arogenate into arogenate and Phe, respectively. A subset of AspAT Ib enzymes exhibiting PPA-AT activity was further identified from both Plantae and prokaryotes and, together with site-directed mutagenesis, showed that Thr-84 and Lys-169 play key roles in specific recognition of dicarboxylic keto (prephenate) and amino (aspartate) acid substrates. The results suggest that, along with ADT, a gene encoding prephenate-specific PPA-AT was transferred from a Chlorobi/Bacteroidetes ancestor to a eukaryotic ancestor of Plantae, allowing efficient Phe and phenylpropanoid production via arogenate in plants today.

The binary protein-protein interaction landscape of Escherichia coli

Efforts to map the Escherichia coli interactome have identified several hundred macromolecular complexes, but direct binary protein-protein interactions (PPIs) have not been surveyed on a large scale. Here we performed yeast two-hybrid screens of 3,305 baits against 3,606 preys (~70% of the E. coli proteome) in duplicate to generate a map of 2,234 interactions, approximately doubling the number of known binary PPIs in E. coli. Integration of binary PPIs and genetic interactions revealed functional dependencies among components involved in cellular processes, including envelope integrity, flagellum assembly and protein quality control. Many of the binary interactions that could be mapped within multi-protein complexes were informative regarding internal topology and indicated that interactions within complexes are significantly more conserved than those interactions connecting different complexes. This resource will be useful for inferring bacterial gene function and provides a draft reference of the basic physical wiring network of this evolutionarily significant model microbe.

Effects of Background Fluid on the Efficiency of Inactivating Yeast with Non-Thermal Atmospheric Pressure Plasma

Non-thermal plasma at atmospheric pressure has been actively applied to sterilization. However, its efficiency for inactivating microorganisms often varies depending on microbial species and environments surrounding the microorganisms. We investigated the influence of environmental factors (surrounding media) on the efficiency of microbial inactivation by plasma using an eukaryotic model microbe, Saccharomyces cerevisiae, to elucidate the mechanisms for differential efficiency of sterilization by plasma. Yeast cells treated with plasma in water showed the most severe damage in viability and cell morphology as well as damage to membrane lipids, and genomic DNA. Cells in saline were less damaged compared to those in water, and those in YPD (Yeast extract, Peptone, Dextrose) were least impaired. HOG1 mitogen activated protein kinase was activated in cells exposed to plasma in water and saline. Inactivation of yeast cells in water and saline was due to the acidification of the solutions by plasma, but higher survival of yeast cells treated in saline may have resulted from the additional effect related to salt strength. Levels of hydroxyl radical (OH.) produced by plasma were the highest in water and the lowest in YPD. This may have resulted in differential inactivation of yeast cells in water, saline, and YPD by plasma. Taken together, our data suggest that the surrounding media (environment) can crucially affect the outcomes of yeast cell plasma treatment because plasma modulates vital properties of media, and the toxic nature of plasma can also be altered by the surrounding media.

Recyclable and stable silver deposited magnetic nanoparticles with poly (vinyl pyrrolidone)-catechol coated iron oxide for antimicrobial activity

This paper introduces a facile method to make highly stable and recyclable antimicrobial magnetic nanoparticles (NPs). Initially, magnetic iron oxide nanoparticles (IONPs) were coated with poly (vinyl pyrrolidone) conjugated catechol (PVP-CCDP). Afterward, silver nanoparticles (Ag0) were deposited onto PVP-CCDP coated IONPs using remain catechol. The prepared nanoparticles showed long term (~4weeks) colloidal stability and redispersibility, respectively, against external magnetic field and over a broad range of pH (4–12). The NPs were characterized by UV–vis, SEM, XPS, and XRD measurements. TEM and DLS analyses showed that the mean particle size of PVP-CCDP coated IONPs/Ag0 were about 72nm. The recyclable magnetic NPs possessed a high antibacterial effect against the model microbes Staphylococcus aureus and Escherichia coli and could be separated easily using magnet following antibacterial test for repeated uses and maintained 100% antibacterial efficiency during three cycles. In MTT assay, the magnetic nanoparticles possessed no measureable cytotoxicity to live cells.

Hydrothermal synthesis, characterization, and bactericidal activities of hybrid from cellulose and TiO2

The purpose of this study was to explore a new strategy to improve the high value-added applications of biomass. Hybrid from cellulose and titanium dioxide (TiO2) was successfully prepared by using tetra-n-butyl titanate and cellulose solution via a hydrothermal method at 180°C for 24h. The phase, microstructure, morphology, and thermal stability of the hybrid were characterized by X-ray powder diffraction (XRD), Fourier transform infrared spectrometry (FT-IR), thermogravimetric analysis (TGA), differential thermal analysis (DTA), and scanning electron microscopy (SEM). The influences of the tetra-n-butyl titanate concentration and the types of solvent on the products were investigated. The TiO2 nanoparticles were dispersed on the surface of cellulose and/or in the cellulose matrix. The hybrid possessed an antimicrobial activity against the model microbes Escherichia coli (Gram-negative) and Staphylococcus aureus (Gram-positive), and were a promising antimicrobial material for the applications in the biomedical field.

Nanofibrillated cellulose as the support and reductant for the facile synthesis of Fe3O4/Ag nanocomposites with catalytic and antibacterial activity

In this paper, we have demonstrated a facile and environmentally friendly approach to prepare Fe3O4/Ag@nanofibrillated cellulose (NFC) nanocomposites which enables tunability from highly porous, flexible aerogels to solid and stiff films. In the procedure, NFC acts as (i) a biocompatible support for the magnetic silver nanoparticles and (ii) a reducing agent for the silver ions. Neither additional reducing agents nor toxic organic solvents were used during the preparation process. The Fe3O4/Ag@NFC nanocomposite aerogel exhibited excellent catalytic properties (both in efficiency and recyclability) for the reduction of 4-nitrophenol. Moreover, both the Fe3O4/Ag@NFC nanocomposite aerogel and film can be actuated by a small household magnet, and both possess high antibacterial activity against the model microbe S. aureus.

A Membrane-Based Sample Preparation Kit for Waterborne Pathogens: Design and Manufacture

Membrane-based microfluidic devices have been demonstrated in recent literature to show a significant potential in developing low-cost but high-efficient analytical devices. Usually, the step of sampling and sample preparation is the most importance processes in the whole analytical experiments. This study designed and manufactured a low-cost kit for water sampling and sample preparation of waterborne pathogens, especially protozoan parasites. Subsequently, Saccharomyces cerevisiae was employed as the model microbe to verify the function of kit. The concepts of green design and agile manufacturing were reflected throughout this work. In the devices, membrane filters were fixed and locked in a pair of disposable filter holders, and then the filter set would be assembled with a volumetric sample container to filter the microorganism in water samples. After the sampling process, the used filter holder with microbes on the membrane would be taken out and conserved in a preservation buffer, which could protect the DNA/RNA molecules inside the cells. When these filter holders were transported to a remote laboratory, the sample preparation cassette will be used in the on-site extraction of the DNA/RNA from the cells on the membrane. At last, the eluate was made for further identification, i.e. NASBA tests. Eight kinds of candidate membrane filters were evaluated in the kit, and the function of the kit was verified.

Preparation of single-walled carbon nanotubes/polyvinylchloride membrane and its antibacterial property

Polyvinylchloride (PVC) ultrafiltration membranes were modified by blending with single-walled carbon nanotubes (SWCNTs) to improve the membranes' antibacterial property. Both modified and control samples were characterized for pore structure, roughness, hydrophilicity, permeability and mechanical properties. The membranes' antibacterial property was accessed with Escherichia coli as the model microbes by several methods. It was found that, after being blended with SWCNTs, the surface roughness of the modified membrane increased. Also, the surface hydrophilicity was improved. The membrane flux increased accordingly. But the membrane elongation decreased obviously with the SWCNTs addition. The modified membranes did not show the antibacterial property as expected in this research. There was no bacterial inhibition circle around the SWCNTs/PVC membrane coupons in the culture plates. There were no morphological differences of the cells on the control and the modified membranes. Hoechst 33342/propidium iodide stain test showed that there were more than 90% living bacterial cells which could grow on the SWCNTs/PVC membranes. This study suggests that the polymer wrapping may reduce the SWCNTs' antibacterial property greatly.

Paper modified with ZnO nanorods – antimicrobial studies

Paper with antimicrobial properties was developed through in situ growth of ZnO nanorods. The targeted application for this type of paper is in health centers as wallpaper, writing paper, facemasks, tissue paper, etc. The paper was tested on three model microbes, Gram-positive bacteria Staphylococcus aureus, Gram-negative bacteria Escherichia coli and common airborne fungus Aspergillus niger. No viable bacterial colonies or fungal spores could be detected in the areas surrounding test samples of the antimicrobial paper. Gram-negative bacteria Escherichia coli were found to be inhibited in an area that is 239% and 163% the area of the paper sample under different room lighting conditions, i.e., halogen and fluorescent lamp illumination, respectively. For Gram-positive bacteria Staphylococcus aureus the zones of inhibition surrounding the paper samples are 102% and 70%, and for Aspergillus niger, 224% and 183% of the sample area, under similar lighting conditions.

Development of a novel method for simultaneous concentration of viruses and protozoa from a single water sample

A novel method, electronegative membrane-vortex (EMV) method, was developed for simultaneous concentration of viruses and protozoa from a single water sample. Viruses and protozoa in a water sample were mixed with a cation solution and adsorbed on an electronegative membrane. Concentrated virus and protozoa samples were obtained as supernatant and pellet fractions, respectively, by vigorous vortex mixing of the membrane and centrifugation of the eluted material. The highest recovery efficiencies of model microbes from river water and tap water by this EMV method were obtained using a mixed cellulose ester membrane with a pore size of 0.45 μm (Millipore) as the electronegative membrane and MgCl(2) as the cation solution. The recovery was 27.7-86.5% for poliovirus, 25.7-68.3% for coliphage Qβ, 28.0-60.0% for Cryptosporidium oocysts, and 35.0-53.0% for Giardia cysts. The EMV method detected successfully indigenous viruses and protozoa in wastewater and river water samples from the Kofu basin, Japan, showing an overall positive rate of 100% (43/43) for human adenovirus, 79% (34/43) for norovirus GI, 65% (28/43) for norovirus GII, 23% (10/43) for Cryptosporidium oocysts, and 60% (26/43) for Giardia cysts. By direct DNA sequencing, a total of four genotypes (AI, AII, B, and G) of Giardia intestinalis were identified in the water samples, indicating that the river water was contaminated with feces from various mammals, including humans.

Study of Energetic Particle Induced Biological Effect through FTIR and Raman Micro-Spectroscopy

Energetic particles exist ubiquitously in nature and may cause varied biological effects which have been found useful applications such as radiotherapy of human cancers and mutation breeding of crops and microbes by means of ion-beam technology. However, the underlying mechanism for the energetic particle induced biological effects is still elusive because the interacting system involves radiolysis of different biomolecules such as DNA, proteins, sugar and lipids, and moreover, there are cross-correlations among these varied substances due to their interactions and signal transductions in living cells. A new trend of research is therefore to investigate the interaction between energetic particles and organisms with consideration of the entire cellar micro-environment and the entangled processes occurring in a whole cell, and to scrutinize the changes of cellular structure and compositions on the micro-scale and also monitor the dynamic and kinetic processes for the interactions. In this context, it is very useful and powful to apply micro-spectral imaging technology such as FTIR and Raman confocal microscopy because it can provide not only good time and spatial resolution, but also non-invasive measurement. In this work, we utilized the high spatial resolution FTIR and Raman microscopy to study the cellular changes of some model microbes and cells by mapping and monitoring the fingerprint bands of the cellular components such as lipids, carbohydrates, polyunsaturated fatty acids, proteins and nucleic acids under the irradiation of energetic particles. Correspondingly, the cell activity, the intracellular content of ROS, the level of MDA and GSH, the activity of CAT and SOD were measured to explain the biological effect induced by energetic particles. This work is supported by NSFC (No. 10975152, No. 11175204), CAS Innovative Project (KJX2-YW-N34-1) and Hundred Talents Program of CAS, China.

Effect of low-concentration chlorine dioxide gas against bacteria and viruses on a glass surface in wet environments

Aims: To evaluate the efficacy of low‐concentration chlorine dioxide (ClO2) gas against model microbes in the wet state on a glass surface. Methods and Results: We set up a test room (39 m3) and the ClO2 gas was produced by a ClO2 gas generator that continuously releases a constant low‐concentration ClO2 gas. Influenza A virus (Flu‐A), feline calicivirus (FCV), Staphylococcus aureus and Escherichia coli were chosen as the model microbes. The low‐concentration ClO2 gas (mean 0·05 ppmv, 0·14 mg m−3) inactivated Flu‐A and E. coli (>5 log10 reductions) and FCV and S. aureus (>2 log10 reductions) in the wet state on glass dishes within 5 h. Conclusions: The treatment of wet environments in the presence of human activity such as kitchens and bathrooms with the low‐concentration ClO2 gas would be useful for reducing the risk of infection by bacteria and viruses residing on the environmental hard surfaces without adverse effects. Significance and Impact of the Study: This study demonstrates that the low‐concentration ClO2 gas (mean 0·05 ppmv) inactivates various kinds of microbes such as Gram‐positive and Gram‐negative bacteria, enveloped and nonenveloped viruses in the wet state.

Large-scale preparation of strawberry-like, AgNP-dopedSiO2 microspheres using the electrospraying method

In this paper, we report on a novel strategy for the preparation of silver nanoparticle-dopedSiO2 microspheres (Ag-SMSs) with an interesting strawberry-like morphology using a simple andefficient electrospraying method. SEM (scanning electron microscopy), TEM (transmissionelectron microscopy), XRD (x-ray diffraction), EDS (energy-dispersive spectroscopy) andUV–vis spectra (ultraviolet–visible spectra) were applied to investigate the morphology,structure, composition and optical properties of the hybrid microspheres, and E. coli(Escherichia coli) was used as a model microbe to evaluate their antibacterial ability. Theresults showed that the Ag-SMSs were environmentally stable and washing resistant. TheAg-SMSs exhibited effective inhibition against proliferation of E. coli, and theirantibacterial ability could be well preserved for a long time. The environmental stability,washing resistance, efficient antibacterial ability and simple but productive preparationmethod endowed the Ag-SMSs with great potential for practical biomedical applications.

Mapping the Iron Binding Site(s) on the Small Tetraheme Cytochrome ofShewanella oneidensisMR-1

In the model microbe Shewanella oneidensis, multi-heme proteins are utilized for respiratory metabolism where metals serve as the terminal electron acceptor. Among those is the periplasm-localized small tetraheme cytochrome (STC). STC has been extensively characterized structurally and electrochemically to which electron flow in and out of the protein has been modeled. However, until the present work, no kinetic studies have been performed to probe the route of electron flow or to determine the iron-binding site on STC. Using iron chelated by EDTA, NTA, or citrate, we have used chemical modification, site-directed mutagenesis along with isothermal titration calorimetry (ITC), and stopped-flow measurements to identify the iron binding site of STC. Chemical modifications of STC revealed that carboxyl groups on STC are involved in binding of EDTA-Fe(3+). Scanning mutagenesis was performed on Asp and Glu to probe the putative iron-binding site on STC. Two STC mutants (D21N; D80N) showed ∼70% decrease in observed electron transfer rate constant with EDTA-Fe(3+) from transient-state kinetic measurements. The impaired reactivity of STC (D80N/D21N) with EDTA-Fe(3+) was further confirmed by a significant decrease (>10-fold) in iron binding affinity.

Cellulose–silver nanocomposites: Microwave-assisted synthesis, characterization, their thermal stability, and antimicrobial property

A facile microwave-assisted method was developed to fabricate cellulose–silver nanocomposites by reducing silver nitrate in ethylene glycol (EG). EG acts as a solvent, a reducing reagent, and a microwave absorber in the whole system, thus no additional reductant is needed. The influences of the heating time and heating temperature on the products were investigated. The products were characterized by X-ray diffraction (XRD), Fourier transform infrared (FT-IR), and scanning electron microscope (SEM). The thermal stability of cellulose–silver nanocomposites in nitrogen and air was studied using thermogravimetric analysis (TG) and differential scanning calorimetric analysis (DSC). Also, the cellulose–silver nanocomposites possess a high antimicrobial activity against the model microbes Escherichia coli (Gram-negative) and Staphylococcus aureus (Gram-positive). It is expected that the cellulose–silver nanocomposites are a promising material for the application in the biomedical field.

Zinc oxide nanorod mediated visible light photoinactivation of model microbes inwater

The inactivation of model microbes in aqueous matrix by visible light photocatalysisas mediated by ZnO nanorods was investigated. ZnO nanorods were grown onglass substrate following a hydrothermal route and employed in the inactivationof gram-negative Escherichia coli and gram-positive Bacillus subtilis inMilliQ water. Theconcentration of Zn2 + ions in the aqueous matrix, bacterial cell membrane damage, and DNAdegradation at post-exposure were also studied. The inactivation efficiencies forboth organisms under light conditions were about two times higher than underdark conditions across the cell concentrations assayed. Anomalies in supernatantZn2 + concentration were observed under both conditions as compared to control treatments, whilecell membrane damage and DNA degradation were observed only under light conditions.Inactivation under dark conditions was hence attributed to the bactericidal effect ofZn2 + ions, while inactivation under light conditions was due to the combined effects ofZn2 + ions and photocatalytically mediated electron injection. The reduction of pathogenicbacterial densities by the photocatalytically active ZnO nanorods in the presence of visiblelight implies potential ex situ application in water decontamination at ambient conditionsunder sunlight.

Zinc oxide nanorod mediated visible light photoinactivation of model microbes in water

Zinc oxide nanorod mediated visible light photoinactivation of model microbes in water

Systems-Level Metabolic Flux Profiling Elucidates a Complete, Bifurcated Tricarboxylic Acid Cycle in Clostridium acetobutylicum

Obligatory anaerobic bacteria are major contributors to the overall metabolism of soil and the human gut. The metabolic pathways of these bacteria remain, however, poorly understood. Using isotope tracers, mass spectrometry, and quantitative flux modeling, here we directly map the metabolic pathways of Clostridium acetobutylicum, a soil bacterium whose major fermentation products include the biofuels butanol and hydrogen. While genome annotation suggests the absence of most tricarboxylic acid (TCA) cycle enzymes, our results demonstrate that this bacterium has a complete, albeit bifurcated, TCA cycle; oxaloacetate flows to succinate both through citrate/alpha-ketoglutarate and via malate/fumarate. Our investigations also yielded insights into the pathways utilized for glucose catabolism and amino acid biosynthesis and revealed that the organism's one-carbon metabolism is distinct from that of model microbes, involving reversible pyruvate decarboxylation and the use of pyruvate as the one-carbon donor for biosynthetic reactions. This study represents the first in vivo characterization of the TCA cycle and central metabolism of C. acetobutylicum. Our results establish a role for the full TCA cycle in an obligatory anaerobic organism and demonstrate the importance of complementing genome annotation with isotope tracer studies for determining the metabolic pathways of diverse microbes.

A life cycle of branched aerial mycelium- and multiple budding spore-forming bacterium Thermosporothrix hazakensis belonging to the phylum Chloroflexi

As far as known, sporulation modes in prokaryotes include formation of endospores exemplified by Firmicutes bacteria, myxospores by myxobacteria and arthrospores by actinomycetes. Here we describe Thermosporothrix hazakensis strain SK20-1(T) belonging to the phylum Chloroflexi with a life cycle including a novel prokaryotic sporulation mode. Microscopic observations showed that strain SK20-1(T) formed multiple exospores per mother cell by budding in branched aerial mycelia. Although branched aerial mycelia are characteristic of actinomycetes, multiple budding sporulation has not been previously described in prokaryotes. The strain SK20-1(T) could be a model microbe for cellular differentiation with multiple budding spore formation.