Differentiation of mesophilic and thermophilic bacteria with fourier transform infrared spectroscopy

Ignited competition: Impact of bioactive extracellular compounds on organelle functions and photosynthetic systems in harmful algal blooms

Prevalent interactions among marine phytoplankton triggered by long-range climatic stressors are well-known environmental disturbers of community structure. Dynamic response of phytoplankton physiology is likely to come from interspecies interactions rather than direct climatic effect on single species. However, studies on enigmatic interactions among interspecies, which are induced by bioactive extracellular compounds (BECs), especially between related harmful algae sharing similar shellfish toxins, are scarce. Here, we investigated how BECs provoke the interactions between two notorious algae, Alexandrium minutum and Gymnodinium catenatum, which have similar paralytic shellfish toxin (PST) profiles. Using techniques including electron microscopy and transcriptome analysis, marked disruptions in G. catenatum intracellular microenvironment were observed under BECs pressure, encompassing thylakoid membrane deformations, pyrenoid matrix shrinkage and starch sheaths disappearance. In addition, the upregulation of gene clusters responsible for photosystem-I Lhca1/4 and Rubisco were determined, leading to weaken photon captures and CO2 assimilation. The redistribution of lipids and proteins occurred at the subcellular level based on in situ focal plane array FTIR imaging approved the damages. Our findings illuminated an intense but underestimated interspecies interaction triggered by BECs, which is responsible for dysregulating photosynthesis and organelle function in inferior algae and may potentially account for fitness alteration in phytoplankton community.

Synergizing Bacillus halotolerans, Pseudomonas sihuiensis and Bacillus atrophaeus with folic acid for enhanced drought resistance in wheat by metabolites and antioxidants

Drought stress imposes a serious challenge to cultivate wheat, restricting its growth. Drought reduces the capability of plant to uptake essential nutrients. This causes stunted growth, development and yield. Traditional ways to increase wheat growth under drought stress have shortcomings. Using plant-growth-promoting rhizobacteria (PGPR) has proved feasible and eco-friendly way to enhance wheat growth even under the drought stress. Combining PGPR in consortiums further boosts up their effects. In this study, we have checked the efficacy of drought-tolerant Bacillus halotolerans, Pseudomonas sihuiensis and Bacillus atrophaeus in combination. These strains were allowed to grow on PEG 6000 with concentrations (-0.15, -0.49, -0.73 and - 1.2) Mega Pascal (MPa) alone and in combination. Furthermore, Fourier transmission infrared (FTIR) spectroscopy and scanning electron microscopy (SEM) were used. Their biochemical traits such as solubilization of K, P and Zn and the synthesis of siderophore, indole acetic acid (IAA), protease, amylase, hydrogen cyanide (HCN) and 1-aminocyclopropane-1-carboxylate (ACC) deaminase were done. In addition to this, we investigated the optimum folic acid concentration i.e 150 ppm for wheat against drought stress. We conducted a pot experiment to check the growth-enhancing and drought-mitigating effects of consortium and folic acid alone and in combination. As a result, we found a significantly increased wheat biomass, relative water content (RWC), chlorophyll content, antioxidants including glutathione reductase and total soluble sugars and protein content under all treatments. However, the combined treatment of bacterial consortium and folic acid showed maximum potential to boost wheat growth and survival even under drought. We also investigated the minerals uptake by wheat after the treatments and found maximum nutrient uptake under the co-effect of folic acid and bacterial consortium We believe this is the first study that has investigated the optimal dose of folic acid for wheat. Our research is also novel in that we seek to investigate the effects of folic acid along with a bacterial consortium comprising Bacillus halotolerans, Pseudomonas sihuiensis and Bacillus atrophaeus on wheat grown under the drought stress.

Global biochemical profiling of fast-growing Antarctic bacteria isolated from meltwater ponds by high-throughput FTIR spectroscopy

Fourier transform infrared (FTIR) spectroscopy is a biophysical technique used for non-destructive biochemical profiling of biological samples. It can provide comprehensive information about the total cellular biochemical profile of microbial cells. In this study, FTIR spectroscopy was used to perform biochemical characterization of twenty-nine bacterial strains isolated from the Antarctic meltwater ponds. The bacteria were grown on two forms of brain heart infusion (BHI) medium: agar at six different temperatures (4, 10, 18, 25, 30, and 37°C) and on broth at 18°C. Multivariate data analysis approaches such as principal component analysis (PCA) and correlation analysis were used to study the difference in biochemical profiles induced by the cultivation conditions. The observed results indicated a strong correlation between FTIR spectra and the phylogenetic relationships among the studied bacteria. The most accurate taxonomy-aligned clustering was achieved with bacteria cultivated on agar. Cultivation on two forms of BHI medium provided biochemically different bacterial biomass. The impact of temperature on the total cellular biochemical profile of the studied bacteria was species-specific, however, similarly for all bacteria, lipid spectral region was the least affected while polysaccharide region was the most affected by different temperatures. The biggest temperature-triggered changes of the cell chemistry were detected for bacteria with a wide temperature tolerance such Pseudomonas lundensis strains and Acinetobacter lwoffii BIM B-1558.

Characterization of biofilm formation by Exiguobacterium strains in response to arsenic exposure

IMPORTANCE

In this work, we characterized the composition, structure, and functional potential for biofilm formation of Exiguobacterium strains isolated from the Salar de Huasco in Chile in the presence of arsenic, an abundant metalloid in the Salar that exists in different oxidation states. Our results showed that the Exiguobacterium strains tested exhibit a significant capacity to form biofilms when exposed to arsenic, which would contribute to their resistance to the metalloid. The results highlight the importance of biofilm formation and the presence of specific resistance mechanisms in the ability of microorganisms to survive and thrive under adverse conditions.

An experimental study of the effects of bacteria on asphaltene adsorption and wettability alteration of dolomite and quartz

The adsorption of asphaltene on the rock surface and the changes in its wettability are very relevant issues in flow assurance and oil recovery studies, and for carbonate reservoirs, they are even more important. During microbial enhanced oil recovery (MEOR) processes, wettability alteration is considered a crucial mechanism leading to improved oil recovery. Therefore, it is essential to understand the mechanisms of surface wettability changes by bacteria and biosurfactants and find new and reliable methods to prevent asphaltene adsorption. Hence, the main aim of this research was to investigate the effect of a mixture of thiobacillus thiooxidans and thiobacillus ferooxidans microorganisms with an optimum effective temperature of around 30 °C (referred to as mesophilic bacteria), as well as a mixture of two moderate thermophiles Sulfobacillus thermosulfidooxidans for operating temperatures around 50 °C (referred to as moderately thermophilic bacteria) on the adsorption of asphaltene samples isolated from two different crude oils onto main reservoir minerals (i.e., quartz and dolomite). The results indicated that after two weeks of mineral aging in moderate thermophilic bacteria, the adsorption of asphaltene on both minerals increased between 180 and 290%. Fourier-transform infrared spectroscopy (FTIR) analysis for quartz and dolomite samples demonstrated that after aging in bacterial solution, bonds related to the adsorption of bacterial cells and biosurfactant production appear, which are the main factors of change in wettability. Alteration in wettability towards hydrophilicity expands hydrogen bonds on the surface, thus improving asphaltene adsorption due to polar interaction. Asphaltene 1 changed the contact angle of dolomite from 53.85° to 90.51° and asphaltene 2 from 53.85° to 100.41°. However, both strains of bacteria caused a strong water-wetting effect on the dolomite rock samples. The influence of moderate thermophilic bacteria on surface wettability is more significant than that of mesophilic bacteria, which may be caused by the high protein content of these bacteria, which expands hydrogen bonding with the surface. Adsorption of asphaltenes on dolomite rocks previously aged with bacteria showed that the wetted rock samples retained their water-wet state. This study highlights the dual impact of the used microorganisms. On one hand, they significantly reduce contact angles and shift wettability towards a strongly water-wet condition, a crucial positive factor for MEOR. On the other hand, these microorganisms can elevate the adsorption of asphaltenes on reservoir rock minerals, posing a potential challenge in the form of formation damage, particularly in low-permeability reservoirs.

Enhancement of Cr(VI) reduction by indigenous bacterial consortia using natural pyrite: A detailed study to elucidate the mechanisms involved in the highly efficient and possible sustainable system

Pyrite was applied to Cr(VI) bioremediation as an inorganic electron donor due to the ability to provide electrons, while the role of pyrite in Cr(VI) bioremediation where organics as electron donors remains unknown. Herein a pyrite-based Cr(VI) bioreduction process in the sediment system containing lactate was demonstrated to be effective to detoxify Cr(VI): over 2200 mg L^-1 Cr(VI) was continuously removed within 210 h with high reactivity (10.5 mg/(L·h)) all along. High-throughput 16S rDNA gene sequencing indicated that the pyrite could shape a functioning community that electrochemically active bacteria dominated (such as Fusibacter sp. and Rhodobacteraceae) instead of iron-oxidizing bacteria and sulfur-oxidizing bacteria. Mineralogy analysis results indicated that Fe(III), S₂^2- and S⁰ formed on the pyrite surface after the oxidation of Cr(VI) might serve as the electron acceptor of microflora, then the S^2- and Fe(II) with strong Cr(VI) reduction ability were formed by microbial reduction to enhance the removal of Cr(VI). This study provides new insights into thoroughly understanding the role of pyrite in the practical application of Cr(VI) bioreduction.

Tapioca Starch Modulates Cellular Events in Oral Probiotic Streptococcus salivarius Strains

Considering the implications of microbiota in health, scientists are in search of microbiota-oriented strategies for the effective prevention and/or treatment of a wide variety of serious diseases. A microbiota comprises diverse microorganisms with either probiotic or pathogenic properties. The fermentation of prebiotic carbohydrates by probiotic bacteria can affect host metabolism. Therefore, understanding the prebiotic-mediated metabolic modulations in probiotics is crucial to develop functional foods for the improvement of disturbed microbiota. Studies have emphasized the importance of prebiotics in probiotic therapies for mucosal diseases and highlighted the need for extensive research on oral bacteria. In the present study, the cellular events have been studied in batch cultures of probiotic Streptococcus salivarius exposed to the natural prebiotic, tapioca starch (TS). TS modulated the keystone metabolic events in Streptococcus salivarius in a dose-dependent manner. Besides increasing the live cell counts and altering the colony morphologies, TS affected the protein metabolism in terms of cellular expression and conformational changes in protein secondary structures. After treatment with TS, the nucleic acid synthesis increased and B-DNA was more than A- and Z-DNA, together with the diminished fatty acids and increased polysaccharide synthesis. The study results can be considered for the assessment of functional foods and probiotics in oral health.

Biodegradation and physiological response mechanism of a bacterial strain to 2,4,6-trinitrotoluene contamination

The aim of this study was to reveal the biodegradation characteristics and physiological response mechanism of a newly isolated bacterium to 2,4,6-trinitrotoluene (TNT) contamination. A Klebsiella variicola strain with high efficiency of TNT degradation was used as the test strain to analyze the changes in cell growth, morphology, and functional groups under different TNT concentrations (0, 100 mg⋅L^-1) and the effects of TNT stress on the metabolic profile as revealed by non-targeted metabonomics. A TNT concentration of 100 mg L^-1 caused a significant increase in the 5-day biochemical oxygen demand (BOD₅) to 950 mg L^-1, while the degradation rate of TNT reached 100% within 30 h after inoculation with Klebsiella variicola. Fourier transform infrared spectroscopy (FTIR) analysis showed changes in the characteristic peak of triamide by TNT treatment. Non-targeted metabonomics identified a total of 544 differentially produced metabolites under TNT treatment (252 upregulated and 292 downregulated), mainly lipids and lipid-like molecules. The metabolic pathways associated with amino acid biosynthesis and metabolism were the most significantly enriched pathways, and simultaneous detection showed that TNT was degraded to 4-amino-2,6-dinitrotoluene (DNT), 2-hydroxylamino-4,6-DNT, 2-amino-4,6-DNT, 2-amino-4-nitrotoluene, and 2,4-DNT. These results confirmed that Klebsiella variicola has a high tolerance to TNT and efficiently degrades it. The degradation mechanism involves TNT-induced accelerated amino acid biosynthesis, production of a protease to catalyze the TNT transformation, and the participation of the transformed TNT products in cell metabolism.

Novel application of isolated Micrococcus luteus and Bacillus pumilus for Li+ ion biosorption: a comparative study

In this study, Li⁺ biosorption profiles of Micrococcus luteus and Bacillus pumilus bacterial strains were investigated. Comparative surface characterization of the biomasses revealed that B. pumilus had a significantly greater surface negativity than the other, which had a direct positive effect on the ability to attract the Li⁺ ions. Biosorption experiments showed that B. pumilus cell had more efficient performance at all pH and initial Li⁺ concentration values in the ranges of 3.0-10.0 and 2.5-20.0 mg/L, respectively. The maximum adsorption capacities obtained at initial Li⁺ concentration of 20.0 mg/L and pH 9.0 were 1.160 mg Li⁺/g (167.1 µmol/g) and 2.280 mg Li⁺/g (328.5 µmol/g) for M. luteus and B. pumilus, respectively. For all the cases studied, the biosorption equilibrium was reached very quickly, suggesting that physical interaction dominated this process. Experimental data were found to be compatible with both Langmuir and Freundlich models under the studied experimental conditions. This study highlights the idea that B. pumilus bacterial strain will be a new and preferred biosorbent for Li⁺ ions by providing a low cost, rapid and quite efficient process.

Studies on the Neuromodulatory Effects of Ginkgo biloba on Alterations in Lipid Composition and Membrane Integrity of Rat Brain Following Aluminium Neurotoxicity

Brain contains the highest lipid content involved in various structural and physiological activities such as structural development, neurogenesis, synaptogenesis, signal transduction and myelin sheath formation. Lipids bilayer is essential to maintain the structural integrity for the physiological functions of protein. Impairments in lipid metabolism and its composition can lead to the progression of various brain ailments such as neurodegenerative and neuropsychiatric disorders. Aluminium (Al), the potent neurotoxin has been linked to Alzheimer's disease (AD) like pathology. Al can bind to biomembrane and influence oligomerization and conformational changes of proteins by acting as cross-linkers. The present study evaluated the influence of Ginkgo biloba (GBE) on the lipid profile alterations induced by Al lactate in hippocampal and cortical regions using FTIR spectroscopy. Rats were exposed with 10 mg/kg b.w. (intraperitoneal) of Al lactate for 6 weeks. This was followed by a treatment protocol of GBE (100 mg/kg b.w.) both preexposure (2 weeks) and conjunctive (6 weeks) exposure. A self recovery group was also included, where Al withdrawal was done for 2 weeks post Al exposure. A significant decrease in peak areas of cholesterol, sphingolipids and phospholipids was observed in Al treated groups. Further, polyunsaturated fatty acids and membrane fluidity has also decreased, as revealed by olefinic and methyl asymmetric stretching bands. Al treatment significantly increased the fluorescence polarization, anisotropy and order parameter, which however were normalized following GBE supplementation. Results also showed that pretreatment with GBE provided more beneficial effects on the adverse changes following Al in membrane composition and behavioral outcome.

Aerobic biodegradation of bio-based plastics in the seawater/sediment interface (sublittoral) marine environment of the coastal zone - Test method under controlled laboratory conditions

Pollution of the seas due to plastic litter is a rapidly growing environmental problem. Among several actions, legal and technological, undertaken to alleviate this problem, included are the control of single use conventional plastics and the replacement of conventional non-biodegradable plastics with innovative biodegradable-in-the-sea polymers, both aiming at the mitigation of marine litter accumulation. Laboratory tests have been used to characterize plastics regarding their biodegradation in various environments. Biodegradation of plastics depends on the inherent characteristics of the polymer and the particular marine habitat conditions. In the present work, the international standard test method ISO 19679 (2016) for determining the aerobic biodegradation of non-floating plastic materials in a seawater-sediment interface of the coastal marine zone under laboratory simulated conditions is evaluated. Modifications are proposed to improve the reliability of this test method in some aspects. Agitation of the seawater surface in the bioreactor was found to enhance the continuous availability of oxygen at the seawater-sediment interface, thus assuring aerobic biodegradation conditions throughout the test simulating real sublittoral conditions. Additional recommended improvements include the use of larger samples and supplementary nutrients to optimise biodegradation conditions. The laboratory measurements were validated by field experiments. The proposed modifications and refinements optimise the robustness and reliability of the test method for determining aerobic biodegradation of plastic materials in a simulated seawater-sediment interface of the coastal zone.

Size-Dependent Antibacterial Activity of Silver Nanoparticle-Loaded Graphene Oxide Nanosheets

A series of graphene oxide (GO) suspensions with different particle sizes (<100 nm, ~100 nm, ~1 µm and >1 µm) were successfully fabricated after 0, 30, 60 and 120 min of sonication, respectively. The antibacterial properties of GO suspensions showed that >1 µm GO size resulted in a loss of nearly 50% of bacterial viability, which was higher than treatment by ~100 nm GO size (25%) towards Escherichia coli (E. coli). Complete entrapment of bacteria by the larger GO was observed in transmission electron microscopy (TEM). Silver nanoparticles (Ag NPs) were doped onto GO samples with different lateral sizes to form GO-Ag NP composites. Resulting larger GO-Ag NPs showed higher antibacterial activity than smaller GO-Ag NPs. As observed by Fourier transform infrared spectroscopy (FTIR), the interaction between E. coli and GO occurred mainly at the outer membrane, where membrane amino acids interact with hydroxyl and epoxy groups. The reactive oxygen species (ROS) and the considerable penetration of released Ag⁺ into the inner bacterial cell membrane result in loss of membrane integrity and damaged morphology. The present work improves the combined action of GO size effect with constant Ag loadings for potential antibacterial activity.

The mechanism for inhibiting acidification of variable charge soils by adhered Pseudomonas fluorescens

Acidification in variable charge soils is on the rise due to increased acid deposition and use of nitrogenous fertilizers. The associated low pH and cation exchange capacity make the soils prone to depleted base cations and increased levels of Al³⁺. Consequently, Al toxicity to plants and soil infertility decrease crop yield. This study was designed to investigate the effect of Pseudomonas fluorescens on the acidification of two Ultisols. The simulated acidification experiment demonstrated that the pH of bacteria-treated soil was higher than that of control under similar conditions, suggesting that the adhered bacteria inhibited soil acidification. This observation was attributed to the association of organic anions (RCOO^- or RO^-) on bacteria with H⁺ to form neutral molecules (RCOOH or ROH) and reducing the activity of H⁺ in solution. The bacteria also inhibited the increase in soil soluble Al and exchangeable Al during soil acidification. The adhesion of bacteria on the soils increased soil effective cation exchange capacity (ECEC) and exchangeable base cations at each pH compared to control. The release of exchangeable base cations from bacteria-treated soil, and the decrease in soil ECEC and exchangeable base cations with decreasing pH confirmed that protonation of organic anions on adhered bacteria was mainly responsible for the inhibition of soil acidification. The change of zeta potential of the bacteria with pH and the ART-FTIR analysis at various pH provided more evidence for this mechanism. Therefore, the bacteria in variable charge soils played an important role in retarding soil acidification.

Deciphering the biodegradation of petroleum hydrocarbons using FTIR spectroscopy: application to a contaminated site

The chemical composition of groundwater in a petroleum-contaminated site is determined by the present functional groups and these play a vital role in a feasibility remediation technique. Based on the in situ investigation of a contaminated shallow groundwater in an oilfield, Fourier transform infrared (FTIR) spectroscopy associated with chemometric treatments, principal component analysis (PCA), and simple-to-use interactive self-modeling mixture analysis (SIMPLISMA), were used to decipher the biodegradation process by analyzing the conversion of functional groups. Environmental factors that can influence microbial metabolism were also evaluated for a comprehensive explanation. FTIR spectroscopy and PCA results showed that the contamination in the study area can be divided into three parts based on FTIR spectra: (1) regular contamination plume distribution and biodegradation level to fresh oil, (2) moderate biodegradation area, and (3) intensive biodegradation area. FTIR spectra further revealed the present functional groups as aliphatic, aromatic, and polar family compounds. SIMPLISMA was used to discuss the degree of biodegradation along the flow path quantitatively and qualitatively and elucidated that the aliphatic and aromatic compounds were mainly metabolized into polar compounds with nitrogen, sulfur, and oxygen via microbes. During metabolism, microbial indices, such as the Shannon-Weaver, Simpson, and Pielou indices, indicated that microbial diversity did not greatly change; hence, hydrocarbons were constantly consumed to feed dominant microbes. Dissolved oxygen concentrations decreased from 4.58 ± 0.31 mg/L (in monitoring well Z1) to 3.21 ± 0.26 mg/L (in monitoring well Z16) and then became constant in the down-gradient area, demonstrating that aerobic biodegradation was the dominant process at the up-gradient plume. Results were in accordance with the oxidation index, which continuously increased from 0.028 ± 0.013 (in monitoring well Z1) to 0.669 ± 0.047 (in monitoring well Z10), showing that oxygen was consumed along the flow path. Similarly, concentration changes in Fe²⁺, Mn²⁺, and SO₄ ^2- proved that the down-gradient area was in reduction condition.

Investigation of the effect of different environmental conditions on biofilm structure of Salmonella enterica serotype Virchow via FTIR spectroscopy

This study aims to describe the content of polymeric matrix components under different incubation temperatures and pH levels. Optimal biofilm production of 15 S. Virchow isolates occurred following the incubation in LB^-NaCl for 72 h, at pH 6.6 and 20 °C. The expression of csgA, csgD, adrA and bcsA genes at 20 °C, 25 °C and 30 °C in S. Virchow DMC18 was analyzed, and it was discovered that the maximum production of cellulose and curli fimbriae occurred at 20 °C. The physical characteristics of pellicle structure of S. Virchow DMC18 was determined as rigid at 20 °C, while becoming fragile at higher temperatures. FTIR analyses confirmed the obtained molecular findings. The intensities of the 16 different peaks originating from carbohydrate, protein, and nucleic acid in the spectra of biofilm samples significantly diminished (p < 0.05) with the increasing temperature. The highest intensities of lipids and carbohydrates were observed at 20 °C indicating the changes in cell surface properties.

Graphene oxide exhibits differential mechanistic action towards Gram-positive and Gram-negative bacteria

The antibacterial nature of graphene oxide (GO) has stimulated wide interest in the medical field. Although the antibacterial activity of GO towards bacteria has been well studied, a deeper understanding of the mechanism of action of GO is still lacking. The objective of the study was to elucidate the difference in the interactions of GO towards Gram-positive and Gram-negative bacteria. The synthesized GO was characterized by Ultraviolet-visible spectroscopy (UV-vis), Raman and Attenuated Total Reflectance-Fourier-transform infrared spectroscopy (ATR-FTIR). Viability, time-kill and Lactose Dehydrogenase (LDH) release assays were carried out along with FESEM, TEM and ATR-FTIR analysis of GO treated bacterial cells. Characterizations of synthesized GO confirmed the transition of graphene to GO and the antibacterial activity of GO was concentration and time-dependent. Loss of membrane integrity in bacteria was enhanced with increasing GO concentrations and this corresponded to the elevated release of LDH in the reaction medium. Surface morphology of GO treated bacterial culture showed apparent differences in the mechanism of action of GO towards Gram-positive and Gram-negative bacteria where cell entrapment was mainly observed for Gram-positive Staphylococcus aureus and Enterococcus faecalis whereas membrane disruption due to physical contact was noted for Gram-negative Escherichia coli and Pseudomonas aeruginosa. ATR-FTIR characterizations of the GO treated bacterial cells showed changes in the fatty acids, amide I and amide II of proteins, peptides and amino acid regions compared to untreated bacterial cells. Therefore, the data generated further enhance our understanding of the antibacterial activity of GO towards bacteria.

Differentiation in MALDI-TOF MS and FTIR spectra between two pathovars of Xanthomonas oryzae

Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc) strains are closely related phenotypically and genetically, which make it difficult to differentiate between the two pathovars based on phenotypic and DNA-based methods. In this study, a fast and accurate method was developed based on the differences in MALDI-TOF MS and FTIR spectra between the two pathovars. MALDI-TOF MS analysis revealed that 9 and 10 peaks are specific to Xoo and Xoc, respectively, which can be used as biomarkers to identify and differentiate the two closely related pathovars. Furthermore, FTIR analysis showed that there is a significant difference in both the band frequencies and absorption intensity of various functional groups between the two pathovars. In particular, the 6 peaks at 3433, 2867, 1273, 1065, 983 and 951cm(-1) were specific to the Xoo strains, while one peak at 1572cm(-1) was specific to the Xoc strains. Overall, this study gives the first attempt to identify and differentiate the two pathovars of X. oryzae based on mass and FTIR spectra, which will be helpful for the early detection and prevention of the two rice diseases caused by both X. oryzae pathovars.

A small heat shock protein enables Escherichia coli to grow at a lethal temperature of 50°C conceivably by maintaining cell envelope integrity

It is essential for organisms to adapt to fluctuating growth temperatures. Escherichia coli, a model bacterium commonly used in research and industry, has been reported to grow at a temperature lower than 46.5°C. Here we report that the heterologous expression of the 17-kDa small heat shock protein from the nematode Caenorhabditis elegans, CeHSP17, enables E. coli cells to grow at 50°C, which is their highest growth temperature ever reported. Strikingly, CeHSP17 also rescues the thermal lethality of an E. coli mutant deficient in degP, which encodes a protein quality control factor localized in the periplasmic space. Mechanistically, we show that CeHSP17 is partially localized in the periplasmic space and associated with the inner membrane of E. coli, and it helps to maintain the cell envelope integrity of the E. coli cells at the lethal temperatures. Together, our data indicate that maintaining the cell envelope integrity is crucial for the E. coli cells to grow at high temperatures and also shed new light on the development of thermophilic bacteria for industrial application.

Multiple metabolomics of uropathogenic E. coli reveal different information content in terms of metabolic potential compared to virulence factors

No single analytical method can cover the whole metabolome and the choice of which platform to use may inadvertently introduce chemical selectivity.

Infrared (IR) spectral markers of bronchial epithelia in victims of fatal burns

Changes in the infrared spectra of bronchial epithelia in victims of fatal burns were investigated. The mechanism of spectral changes on the basis of cellular morphological changes was considered. The ability of spectral parameters to diagnose fatal burns was assessed. Ten cases of fatal burns and 20 control cases were selected. Their lung tissues were removed, and sections were cut and mounted on glass and barium fluoride slides. Spectra of polarized bronchial epithelia were obtained by microscopy based on their morphological changes. In the spectra, 16 major absorbance bands were evaluated to determine their ability to act as positive markers for exposure to fire. Compared with the control group, the bronchial epithelia of the fatal burn victims showed three spectral results. (1) The absorbance of 16 major bands from the spectra of polarized bronchial epithelia in fatal burn victims significantly increased. (2) For the same cell number, the absorbance at 2850, 2920, 2959, and 3084 cm(-1) decreased. (3) The degree of increased or decreased absorbance of bands is related to the degree of polarization. These spectral results suggest that there is a vital reaction induced by the inhalation of hot fumes that includes an increase in the number of bronchial epithelia and a polarization effect. Overall, Fourier transform infrared (FT-IR) microspectroscopy was shown to be a convenient and reliable method to provide objective spectral markers to assist the diagnosis of fatal burns by simultaneously monitoring several specific parameters, although these observations have yet to be applied at forensic scenes.

High-throughput phenotyping of uropathogenic E. coli isolates with Fourier transform infrared spectroscopy

Fourier transform infrared (FT-IR) spectroscopy is an established rapid whole-organism fingerprinting method that generates metabolic fingerprints from bacteria that reflect the phenotype of the microorganism under investigation. However, whilst FT-IR spectroscopy is fast (typically 10 s to 1 min per sample), the approaches for microbial sample preparation can be time consuming as plate culture or shake flasks are used for growth of the organism. We report a new approach that allows micro-cultivation of bacteria from low volumes (typically 200 μL) to be coupled with FT-IR spectroscopy. This approach is fast and easy to perform and gives equivalent data to the lengthier and more expensive shake flask cultivations (sample volume = 20 mL). With this micro-culture approach we also demonstrate high reproducibility of the metabolic fingerprints. The approach allowed separation of different isolates of Escherichia coli involved in urinary tract infection, including members of the globally disseminated ST131 clone, with respect to both genotype and resistance or otherwise to the antibiotic Ciprofloxacin.

Aluminium induced structural, metabolic alterations and protective effects of desferrioxamine in the brain tissue of mice: an FTIR study

In this study, we intended to made a new approach to evaluate aluminium induced metabolic changes in mice brain tissue using Fourier transform infrared spectroscopy. Results demonstrate that FTIR can successfully indicate the molecular changes that occur in all groups. The overall findings demonstrate the alterations on the major biochemical constituents, such as lipids, proteins and nucleic acids of the brain tissues of mice. The significant decrease in the area value of amide A peak and Olefinic = CH stretching band suggests an alteration in the protein profile and lipid levels due to aluminium exposure, respectively. The significant shift in the amide I and amide II protein peaks may indicate the progression of aluminium induced Alzheimer's disease. Further the administration of DFO significantly improved the level of protein and brought back the amide I and II peaks nearer to the control value. Histopathological results also revealed impairment of Aluminium induced alterations in brain tissue. The results of the FTIR study were found to be in agreement with biochemical studies.

Differentiation in MALDI-TOF MS and FTIR spectra between two closely related species Acidovorax oryzae and Acidovorax citrulli

BACKGROUND

Two important plant pathogenic bacteria Acidovorax oryzae and Acidovorax citrulli are closely related and often not easy to be differentiated from each other, which often resulted in a false identification between them based on traditional methods such as carbon source utilization profile, fatty acid methyl esters, and ELISA detection tests. MALDI-TOF MS and Fourier transform infrared (FTIR) spectra have recently been successfully applied in bacterial identification and classification, which provide an alternate method for differentiating the two species.

RESULTS

Characterization and comparison of the 10 A. oryzae strains and 10 A. citrulli strains were performed based on traditional bacteriological methods, MALDI-TOF MS, and FTIR spectroscopy. Our results showed that the identity of the two closely related plant pathogenic bacteria A. oryzae and A. citrulli was able to be confirmed by both pathogenicity tests and species-specific PCR, but the two species were difficult to be differentiated based on Biolog and FAME profile as well as 16 S rRNA sequence analysis. However, there were significant differences in MALDI-TOF MS and FTIR spectra between the two species of Acidovorax. MALDI-TOF MS revealed that 22 and 18 peaks were specific to A. oryzae and A. citrulli, respectively, while FTIR spectra of the two species of Acidovorax have the specific peaks at 1738, 1311, 1128, 1078, 989 cm(-1) and at 1337, 968, 933, 916, 786 cm(-1), respectively.

CONCLUSIONS

This study indicated that MALDI-TOF MS and FTIR spectra may give a new strategy for rapid bacterial identification and differentiation of the two closely related species of Acidovorax.

Characterization of Xenorhabdus and Photorhabdus bacteria by Fourier transform mid-infrared spectroscopy with attenuated total reflection (FT-IR/ATR)

The use of Fourier transform mid-infrared spectroscopy with attenuated total reflection for characterizing entomopathogenic bacteria from genera Xenorhabdus and Photorhabdus is evaluated for the first time. The resulting spectra of Xenorhabdus poinarii and Photorhabdus luminiscens were compared with the spectrum of Escherichia coli samples. The absorption spectra generated by the bacteria samples, were very different at the region below 1400cm(-1) which represents the stretching vibrations of phosphate and carbohydrates. Star diagrams of the fingerprint section of nematodes spectra (between 1,350 and 1,650 cm(-1)) for separation between spectra was used and showed to be a useful tool for classification purposes.

Bone marrow mesenchymal stem cells in patients with beta thalassemia major: molecular analysis with attenuated total reflection-Fourier transform infrared spectroscopy study as a novel method

Bone marrow mesenchymal stem cells (BM-MSCs) are the main cellular components of the bone marrow, providing a supportive cellular microenvironment to maintain healthy hematopoiesis. β-thalassemia major (β-TM) is characterized by anemia that is caused by a genetic defect in hemoglobin synthesis and results in ineffective erythropoiesis (IE). The alterations in the microenvironment in thalassemic bone marrow during IE can cause changes in BM-MSCs. This study aimed to investigate global structural and compositional changes in BM-MSCs in β-TM that may provide a basis in understanding interactions of hematopoietic stem cells (HSCs)-MSCs in such a pathological bone marrow microenvironment. Following characterization of morphological, immunophenotypical, and differentiation properties, the changes in healthy and thalassemic BM-MSCs before and after bone marrow transplantation (BMT) were examined by attenuated total reflection-Fourier transform infrared (ATR-FTIR). The significant increase in lipid, protein, glycogen, and nucleic acid contents in thalassemic BM-MSCs with respect to healthy BM-MSCs was attributed to enhanced cell proliferation and BM activity during IE. The significant decreases in the content of mentioned macromolecules in post-transplant group BM-MSCs versus pre-transplant BM-MSCs was interpreted as restoring effect of BMT therapy on IE and defective BM microenvironment. These alterations were also supported by ELISA results of erythropoietin (EPO) and growth differentiation factor (GDF15) in bone marrow plasma samples as a reflection of IE and by MTT proliferation assay on BM-MSCs. Based on these changes, sampling groups were discriminated by cluster analysis. These results provide information for the studies that concentrate on interactions between HSCs-MSCs in bone marrow.

Characterization of microRNA-125b expression in MCF7 breast cancer cells by ATR-FTIR spectroscopy

MicroRNAs (miRNAs), are ~22 nucleotides long, non-coding RNAs that control gene expression post-transcriptionally by binding to their target mRNA's 3'UTRs (untranslated regions). Due to their roles in various important regulatory processes and pathways, miRNAs have been implicated in disease mechanisms such as tumorigenesis when their expression is deregulated. To date, a significant number of miRNAs and their target messenger RNAs (mRNAs) have been identified and verified. It is generally accepted that miRNAs can potentially bind to many mRNAs, which brings the requirement of validation of these interactions. While understanding that such individual interactions is crucial to delineate the role of a specific miRNA, we took a holistic approach and analyzed global changes in the cell due to expression of a miRNA in a model cell line system. Our model consisted of MCF7 cells stably transfected with miR-125b (MCF7-125b) and empty vector (MCF7-EV). MiR-125b is one of the known down-regulated miRNAs in breast cancers. In this study we examined the global structural changes in MCF7 cells lacking and expressing miR-125b by Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) Spectroscopy and investigated the dynamic changes by more sensitive spin-labelling Electron Spin Resonance (ESR) spectroscopy. Our results revealed less RNA, protein, lipid, and glycogen content in MCF7-125b compared to MCF7-EV cells. Membrane fluidity and proliferation rate were shown to be lower in MCF7-125b cells. Based on these changes, MCF7-125b and MCF7-EV cells were discriminated successfully by cluster analysis. Here, we provide a novel means to understand the global effects of miRNAs in cells. Potential applications of this approach are not only limited to research purposes. Such a strategy is also promising to pioneer the development of future diagnostic tools for deregulated miRNA expression in patient samples.

Attenuated total reflection Fourier transform infrared spectroscopic investigation of the postmortem metabolic process in rat and human kidney cortex

Attenuated total reflection (ATR) Fourier transform infrared (FT-IR) spectroscopy has been applied to study the short and long term postmortem metabolic processes in rat and human kidney cortexes. The goals of this project were as follows: (1) to investigate the changes of ATR spectra in different rat and human tissues after death, (2) to explore the best mathematical model with different band absorption ratio changes to determine the postmortem interval (PMI), and (3) to establish a preliminary human postmortem ATR spectra database. There were three different types of metabolic changes after death based on the spectral results: (1) the intensities of some bands increased continuously (e.g., C-H stretching region), (2) the intensities of other bands decreased continuously (e.g., PO(2)(-) symmetric stretching), and (3) other bands remained relatively stable (e.g., C-OH bending, CO-O-C antisymmetric stretching). The band absorbance ratios for rats were found to display either a significant increase or decrease with increasing time after death. Of the absorbance ratios of the various bands investigated to find the best fit with the cubic model function in rats, the A(1652)/A(1396) ratio showed the strongest correlation (R(2) = 0.937). Comparison of the rat kidney cortex spectra with selected human postmortem cases showed similar postmortem metabolic changes. In conclusion, ATR FT-IR spectroscopy was shown to be a convenient and reliable method of determining short and long term postmortem intervals by simultaneously monitoring several specific parameters, although these observations have yet to be applied at forensic scenes by further field studies.

Determination of simvastatin-induced changes in bone composition and structure by Fourier transform infrared spectroscopy in rat animal model

Simvastatin is a hypolipidemic drug which is used to control hypercholesterolemia and to prevent cardiovascular disease. In the current study, the effects of high and low doses of simvastatin treatment on tibia of healthy rats were investigated. Wistar rats were used for the control, 20mg and 50mg simvastatin-treated groups. Molecular investigations were performed using Fourier transform infrared spectroscopy. In the bones of the two groups of simvastatin-treated rats, the relative mineral/matrix ratio (p<0.001), relative carbonate content (p<0.001), carbonate/amide I ratio (p<0.001) and crystallinity (p<0.001) decreased significantly compared to the control group. Low dose of simvastatin treatment is more effective in reducing the relative carbonate content indicating the amount of carbonate substitution for phosphate in the mineral crystal. The olefinic band almost disappeared in the high dose of simvastatin-treated group which implies a decrease in unsaturation and an increase in lipid peroxidation. The higher frequency value and the bandwidth of CH(2) asymmetric stretching band for the 50mg treated group imply more disordered (p<0.001) and fluid (p<0.001) membrane structure. Low dose of simvastatin is more effective in strengthening the bone than high dose simvastatin treatment. High dose simvastatin treatment induces lipid peroxidation and changes the lipid composition and concentration, which are known to affect membrane physical properties.

Classification of select category A and B bacteria by Fourier transform infrared spectroscopy

Fourier transform infrared (FT-IR) spectroscopy historically is a powerful tool for the taxonomic classification of bacteria by genus, species, and strain when they are grown under carefully controlled conditions. Relatively few reports have investigated the determination and classification of pathogens such as the National Institute of Allergy and Infectious Diseases (NIAID) Category A Bacillus anthracis spores and cells (BA), Yersinia species, Francisella tularensis (FT), and Category B Brucella species from FT-IR spectra. We investigated the multivariate statistics classification ability of the FT-IR spectra of viable pathogenic and non-pathogenic NIAID Category A and B bacteria. The impact of different growth media, growth time and temperature, rolling circle filter of the data, and wavelength range were investigated for their microorganism differentiation capability. Viability of the bacteria was confirmed by agar plate growth after the FT-IR experimental procedures were performed. Principal component analysis (PCA) was reduced to maps of two PC vectors in order to distill the FT-IR spectral features into manageable, visual presentations. The PCA results of the strains of BA, FT, Brucella, and Yersinia spectra from conditions of varying growth media and culture time were readily separable in two-dimensional (2D) PC plots. FT spectra were separated from those of the three other genera. The BA pathogenic spore strains 1029, LA1, and Ames were clearly differentiated from the rest of the dataset. Yersinia rhodei, Y. enterocolitica, and Y. pestis species were distinctly separated from the remaining dataset and could also be classified by growth media. Different growth media produced distinct subsets in the FT, BA, and Yersinia spp. regions in the 2D PC plots. Various 2D PC plots provided differential degrees of separation with respect to the four viable bacterial genera including the BA sub-categories of pathogenic spores, vegetative cells, and nonpathogenic vegetative cells. This work provided evidence that FT-IR spectroscopy can indeed separate the four major pathogenic bacterial genera of NIAID Category A and B biological threat agents including details according to the growth conditions and statistical parameters.

The characterization and differentiation of higher plants by fourier transform infrared spectroscopy

Several techniques have been used to identify and classify plants. We proposed Fourier transform infrared (FT-IR) spectroscopy, together with hierarchical cluster analysis, as a rapid and noninvasive technique to differentiate plants based on their leaf fragments. We applied this technique to three different genera, namely, Ranunculus (Ranunculaceae), Acantholimon (Plumbaginaceae), and Astragalus (Leguminoseae). All of these genera are angiosperms and include a large number of species in Turkey. Ranunculus and Acantholimon have ornamental importance, while Astragalus is an important pharmaceutical genus. The FT-IR spectra revealed dramatic differences, which indicated the variations in lipid metabolism, carbohydrate composition, and protein conformation of the genera. Moreover, cell wall polysaccharides including diverse groups could be identified for each genus. Acantholimon was found to have the highest hydrogen capacity in its polysaccharide and proteins. A higher lignin content and a lower occurrence of decarboxylation and pectin esterification reactions were appointed for Ranunculus and Astragalus compared to Acantholimon. All these results suggested that FT-IR spectroscopy can be successfully applied to differentiate genera, as demonstrated here with Ranunculus, Astragalus, and Acantholimon. In addition, we used this technique to identify the same species from different geographical regions. In conclusion, the current FT-IR study presents a novel method for rapid and accurate molecular characterization and identification of plants based on the compositional and structural differences in their macromolecules.