A synchrotron FTIR microspectroscopy investigation of fungal hyphae grown under optimal and stressed conditions

Extraction of polysaccharide fraction from cadamba (Neolamarckia cadamba) fruits and evaluation of its in vitro and in vivo antioxidant activities

In this study, polysaccharide fraction (PFFNC) derived from Neolamarckia cadamba fruits showed remarkable antioxidant activity. The PFFNC was successfully extracted from the fruits by the hot water extraction process, followed by decolorization, defatting, and deproteinization. The chemical composition of PFFNC was effectively characterized by the use of UV-Vis, FT-IR, CHN, GC-MS, and 13C NMR spectroscopy. The findings indicated that PFFNC had an average molecular weight of 292 kDa and was predominantly composed of carbohydrates (76 %), with notable contributions from uronic acids (37.22 %) and proteins (12.35 %). The primary components of the sugar content were glucose (19.24 %), galactose (10.19 %), mannose (4.09 %), and glucuronic acid (2.8 %). The tertiary structural study verified the existence of a triple-helical structure. PFFNC exhibited a strong reducing power in vitro as determined by ABTS (IC50: 121 ± 0.12 μg/mL), DPPH (IC50: 146.065 ± 0.54 μg/mL), FRAP (677.788 ± 24.189 mM Fe (II)/g), hydroxyl radical scavenging (IC50: 78.736 ± 0.32 μg/mL), and phosphomolybdate assay (90.7 ± 0.43 mg AAE/g). In addition, the PFFNC furthermore showed significant in vivo antioxidant capacity, as determined using the brine shrimp (Bsmp) (Artemia salina Leach) model. The PFFNC exhibits significant antioxidant potential, suggesting broad spectrum applications in pharmaceuticals, nutraceuticals, and oxidative stress-related disorders.

Saccharomyces cerevisiae CellWall Remodeling in the Absence of Knr4 and Kre6 Revealed by Nano-FourierTransform Infrared Spectroscopy

The cell wall integrity (CWI) signaling pathway regulates yeast cell wall biosynthesis, cell division, and responses to external stress. The cell wall, comprised of a dense network of chitin, β-1,3- and β-1,6- glucans, and mannoproteins, is very thin, <100 nm. Alterations in cell wall composition may activate the CWI pathway. Saccharomyces cerevisiae, a model yeast, was used to study the role of individual wall components in altering the structure and biophysical properties of the yeast cell wall. Near-field Fourier transform infrared spectroscopy (nano-FT-IR) was used for the first direct, spectrochemical identification of cell wall composition in a background (wild-type) strain and two deletion mutants from the yeast knock-out collection: kre6Δ and knr4Δ. Killer toxin resistant 6 (Kre6) is an integral membrane protein required for biosynthesis of β-1,6-glucan, while Knr4 is a cell signaling protein involved in the control of cell wall biosynthesis, in particular, biosynthesis and deposition of chitin. Complementary spectral data were obtained with far-field (FF)-FT-IR, in transmission, and with attenuated total reflectance (ATR) spectromicroscopy with 3-10 μm wavelength-dependent spatial resolution. The FF-FT-IR spectra of cells and spectra of isolated cell wall components showed that components of the cell body dominated transmission spectra and were still evident in ATR spectra. In contrast, the nano-FT-IR at ∼25 nm spatial resolution could be used to characterize the yeast wall chemical structure. Our results show that the β-1,6-glucan content is decreased in kre6Δ, while all glucan content is decreased in the knr4Δ cell wall. The latter may be thinner than in wild type, since not only are mannan and chitin detectable by nano-FT-IR, but also lipid membranes and protein, indicative of cell interior.

Conditions for CaCO3 Biomineralization by Trichoderma Reesei with the Perspective of Developing Fungi-Mediated Self-Healing Concrete

Concrete, a widely used building material, often suffers from cracks that lead to corrosion and degradation. A promising solution to enhance its durability is the use of fungi as self-healing agents, specifically by harnessing their ability to promote calcium carbonate (CaCO3) precipitation on their cell walls. However, the ideal conditions for CaCO3 precipitation by the filamentous fungal species Trichoderma reesei are still unclear. In this study, the biomineralization properties of T. reesei in liquid media are investigated. Two different calcium sources, calcium chloride (CaCl2) and calcium lactate are tested, at varying concentrations and in the presence of different nutritional sources that support growth of T. reesei. This study also explores the effects on fungal growth upon adding cement to the medium. Calcium lactate promotes greater fungal biomass production, although less crystals are formed as compared to samples with CaCl2. An increasing calcium concentration positively influences fungal growth and precipitation, but this effect is hindered upon the addition of cement. The highest amounts of biomass and calcium carbonate precipitation are achieved with potato dextrose broth as a nutritional source. By identifying the optimal conditions for CaCO3 precipitation by T. reesei, this study highlights its potential as a self-healing agent in concrete.

Arbuscular Mycorrhizal Fungi Drive Organo-Mineral Association in Iron Ore Tailings: Unravelling Microstructure at the Submicron Scale by Synchrotron-Based FTIR and STXM-NEXAFS

Arbuscular mycorrhizal (AM) fungi play an important role in organic matter (OM) stabilization in Fe ore tailings for eco-engineered soil formation. However, little has been understood about the AM fungi-derived organic signature and organo-mineral interactions in situ at the submicron scale. In this study, a compartmentalized cultivation system was used to investigate the role of AM fungi in OM formation and stabilization in tailings. Particularly, microspectroscopic analyses including synchrotron-based transmission Fourier transform infrared (FTIR) and scanning transmission X-ray microspectroscopy combined with near-edge X-ray absorption fine structure spectroscopy (STXM-NEXAFS) were employed to characterize the chemical signatures at the AM fungal-mineral and mineral-OM interfaces at the submicron scale. The results indicated that AM fungal mycelia developed well in the tailings and entangled mineral particles for aggregation. AM fungal colonization enhanced N-rich OM stabilization through organo-mineral association. Bulk spectroscopic analysis together with FTIR mapping revealed that fungi-derived lipids, proteins, and carbohydrates were associated with Fe/Si minerals. Furthermore, STXM-NEXAFS analysis revealed that AM fungi-derived aromatic, aliphatic, and carboxylic/amide compounds were heterogeneously distributed and trapped by Fe(II)/Fe(III)-bearing minerals originating from biotite-like minerals weathering. These findings imply that AM fungi can stimulate mineral weathering and provide organic substances to associate with minerals, contributing to OM stabilization and aggregate formation as key processes for eco-engineered soil formation in tailings.

Carbon availability affects already large species-specific differences in chemical composition of ectomycorrhizal fungal mycelia in pure culture

Although ectomycorrhizal (ECM) contribution to soil organic matter processes receives increased attention, little is known about fundamental differences in chemical composition among species, and how that may be affected by carbon (C) availability. Here, we study how 16 species (incl. 19 isolates) grown in pure culture at three different C:N ratios (10:1, 20:1, and 40:1) vary in chemical structure, using Fourier transform infrared (FTIR) spectroscopy. We hypothesized that C availability impacts directly on chemical composition, expecting increased C availability to lead to more carbohydrates and less proteins in the mycelia. There were strong and significant effects of ECM species (R2 = 0.873 and P = 0.001) and large species-specific differences in chemical composition. Chemical composition also changed significantly with C availability, and increased C led to more polysaccharides and less proteins for many species, but not all. Understanding how chemical composition change with altered C availability is a first step towards understanding their role in organic matter accumulation and decomposition.

Lignin Nanoparticles with Entrapped Thymus spp. Essential Oils for the Control of Wood-Rot Fungi

After decades of utilization of fossil-based and environmentally hazardous compounds for wood preservation against fungal attack, there is a strong need to substitute those compounds with bio-based bioactive solutions, such as essential oils. In this work, lignin nanoparticles containing four essential oils from thyme species (Thymus capitatus, Coridothymus capitatus, T. vulgaris, and T. vulgaris Demeter) were applied as biocides in in vitro experiments to test their anti-fungal effect against two white-rot fungi (Trametes versicolor and Pleurotus ostreatus) and two brown-rot fungi (Poria monticola and Gloeophyllum trabeum). Entrapment of essential oils provided a delayed release over a time frame of 7 days from the lignin carrier matrix and resulted in lower minimum inhibitory concentrations of the essential oils against the brown-rot fungi (0.30-0.60 mg/mL), while for the white-rot fungi, identical concentrations were determined compared with free essential oils (0.05-0.30 mg/mL). Fourier Transform infrared (FTIR) spectroscopy was used to assess the fungal cell wall changes in the presence of essential oils in the growth medium. The results regarding brown-rot fungi present a promising approach for a more effective and sustainable utilization of essential oils against this class of wood-rot fungi. In the case of white-rot fungi, lignin nanoparticles, as essential oils delivery vehicles, still need optimization in their efficacy.

Screening of Native Trichoderma Species for Nickel and Copper Bioremediation Potential Determined by FTIR and XRF

Soil pollution with heavy metals is a serious threat to the environment. However, soils polluted with heavy metals are considered good sources of native metal-resistant Trichoderma strains. Trichoderma spp. are free-living fungi commonly isolated from different ecosystems, establishing endophytic associations with plants. They have important ecological and biotechnological roles due to their production of a wide range of secondary metabolites, thus regulating plant growth and development or inducing resistance to plant pathogens. In this work we used indigenous Trichoderma strains that were previously isolated from different soil types to determine their tolerance to increased copper and nickel concentrations as well as mechanisms of metal removal. The concentrations of bioavailable metal concentrations were determined after extraction with diethylene-triamine pentaacetate (DTPA)-extractable metals (Cd, Cr, Co, Cu, Pb, Mn, Ni, and Zn) from the soil samples by inductively coupled plasma-optical emission spectrometry (ICP-OES). Two indigenous T. harzianum strains were selected for copper tolerance, and three indigenous T. longibrachiatum strains were selected for nickel tolerance tests. Strains were isolated from the soils with the highest and among the lowest DTPA-extractable metal concentrations to determine whether the adaptation to different concentrations of metals affects the mechanisms of remediation. Mechanisms of metal removal were determined using Fourier-transform infrared spectroscopy (FTIR) and X-ray fluorescence spectroscopy (XRF), non-destructive methods characterized by high measurement speed with little or no need for sample preparation and very low costs. Increased DTPA-extractable metal content for nickel and copper was detected in the soil samples above the target value (TV), and for nickel above the soil remediation intervention values (SRIVs), for total metal concentrations which were previously determined. The SRIV is a threshold of metal concentrations indicating a serious soil contamination, thus confirming the need for soil remediation. The use of FTIR and XRF methods revealed that the presence of both biosorption and accumulation of metals in the Trichoderma cells, providing good bioremediation potential for Ni and Cu.

Synergistic Antifungal Interactions between Antibiotic Amphotericin B and Selected 1,3,4-thiadiazole Derivatives, Determined by Microbiological, Cytochemical, and Molecular Spectroscopic Studies

In recent years, drug-resistant and multidrug-resistant fungal strains have been more frequently isolated in clinical practice. This phenomenon is responsible for difficulties in the treatment of infections. Therefore, the development of new antifungal drugs is an extremely important challenge. Combinations of selected 1,3,4-thiadiazole derivatives with amphotericin B showing strong synergic antifungal interactions are promising candidates for such formulas. In the study, microbiological, cytochemical, and molecular spectroscopy methods were used to investigate the antifungal synergy mechanisms associated with the aforementioned combinations. The present results indicate that two derivatives, i.e., C1 and NTBD, demonstrate strong synergistic interactions with AmB against some Candida species. The ATR-FTIR analysis showed that yeasts treated with the C1 + AmB and NTBD + AmB compositions, compared with those treated with single compounds, exhibited more pronounced abnormalities in the biomolecular content, suggesting that the main mechanism of the synergistic antifungal activity of the compounds is related to a disturbance in cell wall integrity. The analysis of the electron absorption and fluorescence spectra revealed that the biophysical mechanism underlying the observed synergy is associated with disaggregation of AmB molecules induced by the 1,3,4-thiadiazole derivatives. Such observations suggest the possibility of the successful application of thiadiazole derivatives combined with AmB in the therapy of fungal infections.

Metabolomic and Proteomic Changes in Candida albicans Biofilm in Response to Zosteric Acid Treatment

Zosteric acid (ZA) is a secondary metabolite of the seagrass Zostera marina, with antibiofilm activity against fungi. Information concerning its mechanisms of action is lacking and this limits the development of more potent derivatives based on the same target and activity structure. The aim of this work was to investigate the ZA mode of action by analyzing the metabolic status of Candida albicans biofilm and its protein expression profile upon ZA treatment. Fourier-Transform Infrared Spectroscopy confirmed that ZA modified the metabolomic response of treated cells, showing changes in the spectral regions, mainly related to the protein compartment. Nano Liquid Chromatography-High-Resolution Mass Spectrometry highlighted that 10 proteins were differentially expressed in the C. albicans proteome upon ZA treatment. Proteins involved in the biogenesis, structure and integrity of cell walls as well as adhesion and stable attachment of hyphae were found downregulated, whereas some proteins involved in the stress response were found overexpressed. Additionally, ZA was involved in the modulation of non-DNA-based epigenetic regulatory mechanisms triggered by reactive oxygen species. These results partially clarified the ZA mechanism of action against fungi and provided insight into the major C. albicans pathways responsible for biofilm formation.

Consortium Growth of Filamentous Fungi and Microalgae: Evaluation of Different Cultivation Strategies to Optimize Cell Harvesting and Lipid Accumulation

This study aims to evaluate the potential of consortium biomass formation between Mucor circinelloides, an oleaginous filamentous fungal species, and Chlorella vulgaris, in order to promote a straightforward approach to harvest microalgal cells and to evaluate the lipid production in the consortium system. A synthetic medium with glucose (2 g·L−1) and mineral nutrients essential for both fungi and algae was selected. Four different inoculation strategies were assessed, considering the effect of simultaneous vs. separate development of fungal spores and algae cells, and the presence of a supporting matrix aiming at the higher recovery of algae cell rates. The results were evaluated in terms of consortium biomass composition, demonstrating that the strategy using a mature fungal mycelium with a higher algae count may provide biomass samples with up to 79% of their dry weight as algae, still promoting recovery rates greater than 97%. The findings demonstrate a synergistic effect on the lipid accumulation by the fungal strain, at around a fourfold increase when compared to the axenic control, with values in the range of 23% of dry biomass weight. Furthermore, the fatty acid profile from the samples presents a balance between saturated and unsaturated fatty acids that is likely to present an adequate balance for applications such as biodiesel production.

Extended multiplicative signal correction for FTIR spectral quality test and pre-processing of infrared imaging data

Spectral quality control is an important step in the analysis of infrared spectral data, however, often neglected in scientific literature. A frequently used quality test that was originally developed for infrared spectra of bacteria is provided by OPUS software from Bruker Optik GmbH. In this study, the OPUS quality test is applied to a large number of spectra of bacteria, yeasts and moulds and hyperspectral images of microorganisms. It is shown that the use of strict thresholds for parameters of the OPUS quality test leads to discarding too many spectra. A strategy for optimizing parameters thresholds of the OPUS quality test is provided and a novel approach for spectral quality testing based on extended multiplicative signal correction (EMSC) is suggested. For all the data sets considered in our study, the EMSC quality test is shown to be the best among different alternatives of OPUS quality test provided.

Molecular identification of fungi microfossils in a Neoproterozoic shale rock

Precambrian fossils of fungi are sparse, and the knowledge of their early evolution and the role they played in the colonization of land surface are limited. Here, we report the discovery of fungi fossils in a 810 to 715 million year old dolomitic shale from the Mbuji-Mayi Supergroup, Democratic Republic of Congo. Syngenetically preserved in a transitional, subaerially exposed paleoenvironment, these carbonaceous filaments of ~5 μm in width exhibit low-frequency septation (pseudosepta) and high-angle branching that can form dense interconnected mycelium-like structures. Using an array of microscopic (SEM, TEM, and confocal laser scanning fluorescence microscopy) and spectroscopic techniques (Raman, FTIR, and XANES), we demonstrated the presence of vestigial chitin in these fossil filaments and document the eukaryotic nature of their precursor. Based on those combined evidences, these fossil filaments and mycelium-like structures are identified as remnants of fungal networks and represent the oldest, molecularly identified remains of Fungi.

Antifungal effects of a 1,3,4-thiadiazole derivative determined by cytochemical and vibrational spectroscopic studies

Compounds belonging to the group of 5-substituted 4-(1,3,4-thiadiazol-2-yl) benzene-1,3-diols exhibit a broad spectrum of biological activity, including antibacterial, antifungal, and anticancer properties. The mechanism of the antifungal activity of compounds from this group has not been described to date. Among the large group of 5-substituted 4-(1,3,4-thiadiazol-2-yl) benzene-1,3-diol derivatives, the compound 4-(5-methyl-1,3,4-thiadiazole-2-yl) benzene-1,3-diol, abbreviated as C1, was revealed to be one of the most active agents against pathogenic fungi, simultaneously with the lowest toxicity to human cells. The C1 compound is a potent antifungal agent against different Candida species, including isolates resistant to azoles, and molds, with MIC100 values ranging from 8 to 96 μg/ml. The antifungal activity of the C1 compound involves disruption of the cell wall biogenesis, as evidenced by the inability of cells treated with C1 to maintain their characteristic cell shape, increase in size, form giant cells and flocculate. C1-treated cells were also unable to withstand internal turgor pressure causing protoplast material to leak out, exhibited reduced osmotic resistance and formed buds that were not covered with chitin. Disturbances in the chitin septum in the neck region of budding cells was observed, as well as an uneven distribution of chitin and β(1→3) glucan, and increased sensitivity to substances interacting with wall polymerization. The ATR-FTIR spectral shifts in cell walls extracted from C. albicans cells treated with the C1 compound suggested weakened interactions between the molecules of β(1→3) glucans and β(1→6) glucans, which may be the cause of impaired cell wall integrity. Significant spectral changes in the C1-treated cells were also observed in bands characteristic for chitin. The C1 compound did not affect the ergosterol content in Candida cells. Given the low cytotoxicity of the C1 compound to normal human dermal fibroblasts (NHDF), it is possible to use this compound as a therapeutic agent in the treatment of surface and gastrointestinal tract mycoses.

Vanadium-basidiomycete fungi interaction and its impact on vanadium biogeochemistry

Fungi are well known to strongly interact with metals, thereby influencing metal biogeochemistry in the terrestrial environment. To assess and quantify potential fungi-vanadium (V) interactions, Amanita muscaria, Armillaria cepistipes, Xerocomus badius and Bjerkandera adusta were cultured in media containing soluble V (VOSO₄ or NaVO₃) or solid-phase V of different chemical forms and oxidation state (V₂O₃, VO₂, V₂O₅, or V-Ti magnetite slag). All fungi underwent physiological and structural changes, as revealed by alterations in FT-IR peak positions and intensities relative to the control, and morphological changes of mycelia, as observed by scanning electron microscopy. The diametric growth size generally decreased with decreasing oxidation state of V and with increasing concentrations of VOSO₄ and NaVO₃, implying that V toxicity is dependent on V speciation. The tolerance index, the ratio of treated and control mycelium (dry weight), shows different tendencies, suggesting additional factors influencing fungi weight, such as the formation of extrahyphal crystals. Vanadium accumulation from VOSO₄ and NaVO₃ medium in all fungi (up to 51.3 mg g^-1) shows the potential of fungi to immobilise soluble V, thereby reducing its impacts on environmental and human health. Uptake and accumulation of V in slag was insignificant, reflecting the association of slag V with insoluble crystalline materials. The fungal accumulation of V in medium amended with V-oxides demonstrates the ability of fungi to solubilise solid-phase V compounds, thereby introducing previously immobile V into the V biogeochemical cycle and into the food chain where it may impact ecological and human health. A.muscaria lowered the pH of the medium substantially during cultivation, indicating acidolysis and complexolysis via excretion of organic acids (e.g. oxalic acid). Oxidation of VOSO₄ was observed by a colour change of the medium to yellow during B. adusta cultivation, revealing the role of fungally-mediated redox transformation in V (im)mobilisation. The calculated removal efficiencies of soluble V were 40-90% for A. cepistipes and X. badius, but a much lower recovery (0-20%) was observed from V oxides and slag (0-20%) by all fungi. This suggests the probable application of fungi for bio-remediation of mobile/soluble V in contaminated soils but not of V incorporated in the lattice of soil minerals.

Spectroscopic Characterization of Bovine, Avian and Johnin Purified Protein Derivative (PPD) with High-Throughput Fourier Transform InfraRed-Based Method

Tuberculins purified protein derivatives (PPDs) are obtained by precipitation from heat treated mycobacteria. PPDs are used in diagnosis of mycobacterial infections in humans and animals. Bovine PPD (PPDB) is obtained from Mycobacterium bovis (Mycobacterium tuberculosis complex), while Avian PPD (PPDA) and Johnin PPD (PPDJ) are extracted, respectively, from Mycobacterium avium and M. avium subsp. paratuberculosis (M. avium complex). PPDB and PPDA are used for bovine tuberculosis diagnosis, while PPDJ is experimentally used in the immunodiagnosis of paratuberculosis. Although PPDs date back to the 19th Century, limited knowledge about their composition is currently available. The goal of our study was to evaluate Fourier Transform InfraRed (FTIR) spectroscopy as a tool to differentiate PPDB, PPDA, and three PPDJs. The results highlighted that the three PPDs have specific profiles, correlated with phylogenetic characteristics of mycobacteria used for their production. This analysis is eligible as a specific tool for different PPDs batches characterization and for the assessment of their composition. The entire PPD production may be efficiently controlled, since the N content of each preparation is related to IR spectra, with a reference spectrum for each PPD and a standardized analysis protocol.

Extended Multiplicative Signal Correction for Infrared Microspectroscopy of Heterogeneous Samples with Cylindrical Domains

Optical scattering corrections are invoked to computationally distinguish between scattering and absorption contributions to recorded data in infrared (IR) microscopy, with a goal to obtain an absorption spectrum that is relatively free of the effects of sample morphology. Here, we present a modification of the extended multiplicative signal correction (EMSC) approach that allows for spectral recovery from fibers and cylindrical domains in heterogeneous samples. The developed theoretical approach is based on exact Mie theory for infinite cylinders. Although rigorous Mie theory implies utilization of comprehensive and time-consuming calculations, we propose to change the workflow of the original EMSC algorithm to minimize extensive calculations for each recorded spectrum at each iteration step. This makes the modified EMSC approach practical for routine use. First, we tested our approach using synthetic data derived from a rigorous model of scattering from cylinders in an IR microscope. Second, we applied the approach to Fourier transform IR (FT-IR) microspectroscopy data recorded from filamentous fungal and cellulose samples with pronounced fiber-like shapes. While the corrected spectra show greatly reduced baseline offsets and consistency, strongly absorbing regions of the spectrum require further refinement. The modified EMSC algorithm broadly mitigates the effects of scattering, offering a practical approach to more consistent and accurate spectra from cylindrical objects or heterogeneous samples with cylindrical domains.

Ultrastructural and SINS analysis of the cell wall integrity response of Aspergillus nidulans to the absence of galactofuranose

With lethal opportunistic fungal infections on the rise, it is imperative to explore new methods to examine virulence mechanisms. The fungal cell wall is crucial for both the virulence and viability of Aspergillus nidulans. One wall component, Galf, has been shown to contribute to important fungal processes, integrity of the cell wall and pathogenesis. Here, we explore gene deletion strains lacking the penultimate enzyme in Galf biosynthesis (ugmAΔ) and the protein that transports Galf for incorporation into the cell wall (ugtAΔ). In applying gene deletion technology to the problem of cell wall integrity, we have employed multiple micro- and nano-scale imaging tools, including confocal fluorescence microscopy, electron microscopy, X-Ray fluorescence and atomic force microscopy. Atomic force microscopy allows quantification of ultrastructural cell wall architecture while near-field infrared spectroscopy provides spatially resolved chemical signatures, both at the nanoscale. Here, for the first time, we demonstrate correlative data collection with these two emerging modalities for the multiplexed in situ study of the nanoscale architecture and chemical composition of fungal cell walls.

FTIR spectroscopy of whole cells for the monitoring of yeast apoptosis mediated by p53 over-expression and its suppression by Nigella sativa extracts

p53 over expression in yeast results in cell death with typical markers of apoptosis such as DNA fragmentation and phosphatidylserine externalization. We aimed to substitute/supplement classical fluorescent techniques (TUNEL, Annexin V, ROS detection) usually used to detect biochemical changes occurring during yeast apoptosis mediated by p53 over expression and the effect of anti-apoptotic purified molecules from Nigel (Nigella sativa) extracts on these same yeasts by the label free technique of FTIR spectroscopy. The comparison of the entire IR spectra highlighted clear modifications between apoptotic p53-expressing yeasts and normal ones. More precisely, DNA damage was detected by the decrease of band intensities at 1079 and 1048 cm^-1. While phosphatidylserine exposure was followed by the increase of νsCH₂ and νasCH₂ bands of unsaturated fatty acids that were exhibited at 2855 and 2926 cm^-1, and the appearance of the C = O ester functional group band at 1740 cm^-1. In a second step, this FTIR approach was used to estimate the effect of a purified fraction of the Nigel extract. The modulation of band intensities specific to DNA and membrane status was in agreement with apoptosis supression in presence of the Nigel extracts. FTIR spectroscopy is thus proven to be a very reliable technique to monitor the apoptotic cell death in yeast and to be used as a means of evaluating the biomolecules effect on yeast survival.

Current and Future Perspectives on the Structural Identification of Small Molecules in Biological Systems

Although significant advances have been made in recent years, the structural elucidation of small molecules continues to remain a challenging issue for metabolite profiling. Many metabolomic studies feature unknown compounds; sometimes even in the list of features identified as "statistically significant" in the study. Such metabolic "dark matter" means that much of the potential information collected by metabolomics studies is lost. Accurate structure elucidation allows researchers to identify these compounds. This in turn, facilitates downstream metabolite pathway analysis, and a better understanding of the underlying biology of the system under investigation. This review covers a range of methods for the structural elucidation of individual compounds, including those based on gas and liquid chromatography hyphenated to mass spectrometry, single and multi-dimensional nuclear magnetic resonance spectroscopy, and high-resolution mass spectrometry and includes discussion of data standardization. Future perspectives in structure elucidation are also discussed; with a focus on the potential development of instruments and techniques, in both nuclear magnetic resonance spectroscopy and mass spectrometry that, may help solve some of the current issues that are hampering the complete identification of metabolite structure and function.

Microfluidic approaches to synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy of living biosystems

A long-standing desire in biological and biomedical sciences is to be able to probe cellular chemistry as biological processes are happening inside living cells. Synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy is a label-free and nondestructive analytical technique that can provide spatiotemporal distributions and relative abundances of biomolecules of a specimen by their characteristic vibrational modes. Despite great progress in recent years, SR-FTIR imaging of living biological systems remains challenging because of the demanding requirements on environmental control and strong infrared absorption of water. To meet this challenge, microfluidic devices have emerged as a method to control the water thickness while providing a hospitable environment to measure cellular processes and responses over many hours or days. This paper will provide an overview of microfluidic device development for SR-FTIR imaging of living biological systems, provide contrast between the various techniques including closed and open-channel designs, and discuss future directions of development within this area. Even as the fundamental science and technological demonstrations develop, other ongoing issues must be addressed; for example, choosing applications whose experimental requirements closely match device capabilities, and developing strategies to efficiently complete the cycle of development. These will require imagination, ingenuity and collaboration.

Screening of Astaxanthin-Hyperproducing Haematococcus pluvialis Using Fourier Transform Infrared (FT-IR) and Raman Microspectroscopy

Haematococcus pluvialis has promising applications owing to its ability to accumulate astaxanthin under stress conditions. In order to acquire higher astaxanthin productivity from H. pluvialis, it is critical not only to develop efficient mutagenesis techniques, but also to establish rapid and effective screening methods which are highly demanded in current research and application practice. In this work, we therefore attempted to develop a new approach to screening the astaxanthin-hyperproducing strains based on spectroscopic tools. Using Fourier transform infrared (FT-IR) and Raman microspectroscopy, we have achieved rapid and quantitative analysis of the algal cells in terms of astaxanthin, β-carotene, proteins, lipids, and carbohydrates. In particular, we have found that the ratio of the IR absorption band at 1740 cm^-1 to the band at 1156 cm^-1 can be utilized for identifying astaxanthin-hyperproducing strains. This work may therefore open a new avenue for developing high-throughput screening methods necessary for the microbial mutant breeding industry.

Effects of cadmium on bioaccumulation and biochemical stress response in rice (Oryza sativa L.)

This study investigated the effects of various Cd concentrations on the bioaccumulation, antioxidative defense, and stress responses of rice (Oryza sativa L.). The distribution characteristics of Cd in rice were in the following order: roots>stems>grains. The bioconcentration factor values of Cd increased at concentrations lower than 3.00 mg Cd/kg and approximately decreased to a constant value at concentrations higher than 3.00 mg Cd/kg. Rice showed a higher Cd accumulation potential at low Cd concentrations than at high Cd concentrations. The Freundlich isotherm model described well the adsorption isotherms of Cd in rice roots. The biosorption mechanism of rice roots was determined to be cooperative adsorption. The malondialdehyde (MDA) content increased at a concentration range of 0.00-5.00 mg/L, indicating the enhancement of lipid peroxidation. By contrast, the MDA content slightly decreased at concentrations higher than 5.00 mg/L. Peroxidase (POD) activity exhibited active response to oxidative stress at concentrations lower than 5.00 mg/L but was inhibited at concentrations higher than 5.00 mg/L. The response to Cd stress of the N-H, O-H and C-O functional groups in rice shoots was observed via Fourier transform infrared spectroscopy.

Understanding the cryotolerance of lactic acid bacteria using combined synchrotron infrared and fluorescence microscopies

Freezing is widely used for preserving different types of cells. Frozen concentrates of lactic acid bacteria (LAB) are extensively used for manufacturing food, probiotic products and for green chemistry and medical applications. However, the freezing and thawing processes cause cell injuries that result in significant cell death. Producing homogeneous bacterial populations with high cryotolerance remains a real challenge. Our objective was to investigate the biochemical and physiological changes in a LAB model at the cell scale following fermentation and freezing in order to identify cellular biomarkers of cryotolerance. Infrared spectra of individual bacteria produced by applying different fermentation and freezing conditions were acquired using synchrotron radiation-based Fourier-transform infrared (SR-FTIR) microspectroscopy to achieve sub-cellular spatial resolution. Fluorescent microscopy was concomitantly assessed, thus making possible to simultaneously analyse the biochemistry and physiological state of a single cell for the first time. Principal component analysis was used to evaluate changes in cell composition, with particular focus on lipids, proteins and polysaccharides. SR-FTIR results indicated that before freezing, freeze-resistant cells grown in a rich medium presented a high content of CH3 groups from lipid chains, of cell proteins in an α-helix secondary structure and of charged polymers such as teichoic and lipoteichoic acids that constitute the Gram-positive bacterial wall. Moreover, SR-FTIR microspectroscopy made it possible to reveal cell heterogeneity within the cluster of resistant cells, which was ascribed to the diversity of potential substrates in the growth medium. Freezing and thawing processes induced losses of membrane integrity and cell viability in more than 90% of the freeze-sensitive bacterial population. These damages leading to cell death were ascribed to biochemical modification of cell membrane phospholipids, in particular a rigidification of the cytoplasmic membrane following freezing. Furthermore the freeze-resistant cells remained viable after freezing and thawing but a modification of protein secondary structure was detected by SR-FTIR analysis. These results highlighted the potential application of bimodal analysis by SR-FTIR and fluorescence microscopy to increase our knowledge about mechanisms related to cell damage.

Uranium Binding Mechanisms of the Acid-Tolerant Fungus Coniochaeta fodinicola

The uptake and binding of uranium [as (UO2)(2+)] by a moderately acidophilic fungus, Coniochaeta fodinicola, recently isolated from a uranium mine site, is examined in this work in order to better understand the potential impact of organisms such as this on uranium sequestration in hydrometallurgical systems. Our results show that the viability of the fungal biomass is critical to their capacity to remove uranium from solution. Indeed, live biomass (viable cells based on vital staining) were capable of removing ∼16 mg U/g dry weight in contrast with dead biomass (autoclaved) which removed ∼45 mg U/g dry weight after 2 h. Furthermore, the uranium binds with different strength, with a fraction ranging from ∼20-50% being easily leached from the exposed biomass by a 10 min acid wash. Results from X-ray absorption spectroscopy measurements show that the strength of uranium binding is strongly influenced by cell viability, with live cells showing a more well-ordered uranium bonding environment, while the distance to carbon or phosphorus second neighbors is similar in all samples. When coupled with time-resolved laser fluorescence and Fourier transformed infrared measurements, the importance of organic acids, phosphates, and polysaccharides, likely released with fungal cell death, appear to be the primary determinants of uranium binding in this system. These results provide an important progression to our understanding with regard to uranium sequestration in hydrometallurgical applications with implications to the unwanted retention of uranium in biofilms and/or its mobility in a remediation context.

FTIR metabolomic fingerprint reveals different modes of action exerted by structural variants of N-alkyltropinium bromide surfactants on Escherichia coli and Listeria innocua cells

Surfactants are extremely important agents to clean and sanitize various environments. Their biocidal activity is a key factor determined by the interactions between amphiphile structure and the target microbial cells. The object of this study was to analyze the interactions between four structural variants of N-alkyltropinium bromide surfactants with the Gram negative Escherichia coli and the Gram positive Listeria innocua bacteria. Microbiological and conductometric methods with a previously described FTIR bioassay were used to assess the metabolomic damage exerted by these compounds. All surfactants tested showed more biocidal activity in L. innocua than in E. coli. N-tetradecyltropinium bromide was the most effective compound against both species, while all the other variants had a reduced efficacy as biocides, mainly against E. coli cells. In general, the most prominent metabolomic response was observed for the constituents of the cell envelope in the fatty acids (W1) and amides (W2) regions and at the wavenumbers referred to peptidoglycan (W2 and W3 regions). This response was particularly strong and negative in L. innocua, when cells were challenged by N-tetradecyltropinium bromide, and by the variant with a smaller head and a 12C tail (N-dodecylquinuclidinium bromide). Tail length was critical for microbial inhibition especially when acting against E. coli, maybe due the complex nature of Gram negative cell envelope. Statistical analysis allowed us to correlate the induced mortality with the metabolomic cell response, highlighting two different modes of action. In general, gaining insights in the interactions between fine structural properties of surfactants and the microbial diversity can allow tailoring these compounds for the various operative conditions.

FTIR spectroscopic evaluation of changes in the cellular biochemical composition of the phytopathogenic fungus Alternaria alternata induced by extracts of some Greek medicinal and aromatic plants

In this study, the biological activity of aquatic extracts of selected Greek medicinal and aromatic plants to the phytopathogenic fungus Alternaria alternata was investigated. Lamiaceae species (Hyssopus officinalis L., Melissa officinalis L., Origanum dictamnus L., Origanum vulgare L. and Salvia officinalis L.) were found to enhance significantly the mycelium growth whereas Crocus sativus appears to inhibit it slightly. M. officinalis and S. officinalis caused the highest stimulation in mycelium growth (+97%) and conidia production (+65%) respectively. In order to further investigate the bioactivity of plant extracts to A. alternata, we employed Fourier Transform Infrared Spectroscopy (FTIR). Differences of original spectra were assigned mainly to amides of proteins. The second derivative transformation of spectra revealed changes in spectral regions corresponding to absorptions of the major cellular constituents such as cell membrane and proteins. Principal component analysis of the second derivative transformed spectra confirmed that fatty acids of the cell membranes, amides of proteins and polysaccharides of the cell wall had the major contribution to data variation. FTIR band area ratios were found to correlate with fungal mycelium growth.

Ectomycorrhizal identification in environmental samples of tree roots by Fourier-transform infrared (FTIR) spectroscopy

Roots of forest trees are associated with various ectomycorrhizal (ECM) fungal species that are involved in nutrient exchange between host plant and the soil compartment. The identification of ECM fungi in small environmental samples is difficult. The present study tested the feasibility of attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy followed by hierarchical cluster analysis (HCA) to discriminate in situ collected ECM fungal species. Root tips colonized by distinct ECM fungal species, i.e., Amanita rubescens, Cenococcum geophilum, Lactarius subdulcis, Russula ochroleuca, and Xerocomus pruinatus were collected in mono-specific beech (Fagus sylvatica) and mixed deciduous forests in different geographic areas to investigate the environmental variability of the ECM FTIR signatures. A clear HCA discrimination was obtained for ECM fungal species independent of individual provenance. Environmental variability neither limited the discrimination between fungal species nor provided sufficient resolution to discern species sub-clusters for different sites. However, the de-convoluted FTIR spectra contained site-related spectral information for fungi with wide nutrient ranges, but not for Lactarius subdulcis, a fungus residing only in the litter layer. Specific markers for distinct ECM were identified in spectral regions associated with carbohydrates (i.e., mannans), lipids, and secondary protein structures. The present results support that FTIR spectroscopy coupled with multivariate analysis is a reliable and fast method to identify ECM fungal species in minute environmental samples. Moreover, our data suggest that the FTIR spectral signatures contain information on physiological and functional traits of ECM fungi.

Root exudate-induced alterations in Bacillus cereus cell wall contribute to root colonization and plant growth promotion

The outcome of an interaction between plant growth promoting rhizobacteria and plants may depend on the chemical composition of root exudates (REs). We report the colonization of tobacco, and not groundnut, roots by a non-rhizospheric Bacillus cereus (MTCC 430). There was a differential alteration in the cell wall components of B. cereus in response to the REs from tobacco and groundnut. Attenuated total reflectance infrared spectroscopy revealed a split in amide I region of B. cereus cells exposed to tobacco-root exudates (TRE), compared to those exposed to groundnut-root exudates (GRE). In addition, changes in exopolysaccharides and lipid-packing were observed in B. cereus grown in TRE-amended minimal media that were not detectable in GRE-amended media. Cell-wall proteome analyses revealed upregulation of oxidative stress-related alkyl hydroperoxide reductase, and DNA-protecting protein chain (Dlp-2), in response to GRE and TRE, respectively. Metabolism-related enzymes like 2-amino-3-ketobutyrate coenzyme A ligase and 2-methylcitrate dehydratase and a 60 kDa chaperonin were up-regulated in response to TRE and GRE. In response to B. cereus, the plant roots altered their exudate-chemodiversity with respect to carbohydrates, organic acids, alkanes, and polyols. TRE-induced changes in surface components of B. cereus may contribute to successful root colonization and subsequent plant growth promotion.

Toxicity of organic and inorganic nanoparticles to four species of white-rot fungi

The rapid development of nanoparticles (NP) for industrial applications and large-volume manufacturing, with its subsequent release into the environment, raised the need to understand and characterize the potential effects of NP to biota. Accordingly, this work aimed to assess sublethal effects of five NP to the white-rot fungi species Trametes versicolor, Lentinus sajor caju, Pleurotus ostreatus, and Phanerochaete chrysosporium. Each species was exposed to serial dilutions of the following NP: organic-vesicles of SDS/DDAB and of Mo/NaO; gold-NP, quantum dot CdSe/ZnS, and Fe/Co. Fungi growth rate was monitored every day, and at the end of assay the mycelium from each replicate was collected to evaluate possible changes in its chemical composition. For all NP-suspensions the following parameters were characterized: hydrodynamic diameter, surface charge, aggregation index, zeta potential, and conductivity. All tested NP tended to aggregate when suspended in aqueous media. The obtained results showed that gold-NP, CdSe/ZnS, Mo/NaO, and SDS/DDAB significantly inhibited the growth of fungi with effects on the mycelium chemical composition. Among the tested NP, gold-NP and CdSe/ZnS were the ones exerting a higher effect on the four fungi. Finally to our knowledge, this is the first study reporting that different types of NP induce changes in the chemical composition of fungi mycelium.

High spatial resolution infrared micro-spectroscopy reveals the mechanism of leaf lignin decomposition by aquatic fungi

Organic carbon is a critical component of aquatic systems, providing energy storage and transfer between organisms. Fungi are a major decomposer group in the aquatic carbon cycle, and are one of few groups thought to be capable of breaking down woody (lignified) tissue. In this work we have used high spatial resolution (synchrotron light source) infrared micro-spectroscopy to study the interaction between aquatic fungi and lignified leaf vein material (xylem) from River Redgum trees (E. camaldulensis) endemic to the lowland rivers of South-Eastern Australia. The work provides spatially explicit evidence that fungal colonisation of leaf litter involves the oxidative breakdown of lignin immediately adjacent to the fungal tissue and depletion of the lignin-bound cellulose. Cellulose depletion occurs over relatively short length scales (5–15 µm) and highlights the likely importance of mechanical breakdown in accessing the carbohydrate content of this resource. Low bioavailability compounds (oxidized lignin and polyphenols of plant origin) remain in colonised leaves, even after fungal activity diminishes, and suggests a possible pathway for the sequestration of carbon in wetlands. The work shows that fungi likely have a critical role in the partitioning of lignified material into a biodegradable fraction that can re-enter the aquatic carbon cycle, and a recalcitrant fraction that enters long-term storage in sediments or contribute to the formation of dissolved organic carbon in the water column.

Synchrotron FTIR microspectroscopy of Escherichia coli at single-cell scale under silver-induced stress conditions

The present work was focused on elucidating biochemical changes in the model bacterium Escherichia coli exposed to ionic silver mediated stress, at a single-cell scale. In order to achieve this, in situ synchrotron Fourier-transform infrared (sFTIR) microspectroscopy was performed, for the first time, on individual cells by attenuated total reflectance (ATR) combined with the use of zinc-selenide hemisphere for high spatial resolution. In a first part, the potential of the method was evaluated on bacteria subjected to a lethal 100 μM AgNO(3) concentration for 2 h compared to untreated 100 % viable cells. Differences in cell composition were assessed for the C-H stretching and protein spectral regions, indicating that the inhibitory action was targeted against both fatty acids and proteins. Transmission electron microscopy (TEM) confirmed morphological damages of the cell ultrastructure. The relevance of ATR-sFTIR microspectroscopy for highlighting the heterogeneity in Ag(+)-mediated effects within a given bacterial population was also pointed out. In a second part, cells were exposed to sub-lethal Ag(+) concentrations (<10 μM AgNO(3)) tested under "dynamic" growth mode: early addition vs. pulse in the mid-exponential phase, and compared to simultaneously batch-grown untreated bacteria or cells sampled just before the pulse, respectively. sFTIR microspectroscopy and TEM imaging were performed in close relation with growth kinetics characterization. No significant effect of the Ag(+) pulses was detected, in accordance with macrokinetics data. For early-treated cells, effects on fatty acid composition were shown, although no major alteration of protein secondary structure was noticed. These partial effects were consistent with TEM observations and growth kinetics.

Characterization of mannitol in Curvularia protuberata hyphae by FTIR and Raman spectromicroscopy

FTIR and Raman spectromicroscopy were used to characterize the composition of Curvularia protuberata hyphae, and to compare a strain isolated from plants inhabiting geothermal soils with a non-geothermal isolate. Thermal IR source images of hyphae have been acquired with a 64 × 64 element focal plane array detector; single point IR spectra have been obtained with synchrotron source light. In some C. protuberata hyphae, we have discovered the spectral signature of crystalline mannitol, a fungal polyol with complex protective roles. With FTIR-FPA imaging, we have determined that the protein content in cells remains fairly constant throughout the length of a hypha, whereas the mannitol is found at discrete, irregular locations. This is the first direct observation of mannitol in intact fungal hyphae. Since the concentration of mannitol in cells varies with respect to position and is not present in all hyphae, this discovery may be related to habitat adaptation, fungal structure and growth stages.

Influence of cell geometry and number of replicas in the reproducibility of whole cell FTIR analysis

Fourier Transform InfraRed (FTIR) spectroscopy is an increasingly used technique in biology, especially for whole cell metabolomic fingerprint. The reproducibility of this technique is influenced by a large number of factors such as the physiological state of cells, sample manipulation and growth conditions. Evidence exists suggesting that the cell shape and dimension can be further elements to consider in whole cell FTIR analysis. In this study we aimed to address the effect of cell geometry on the FTIR spectra and to define the extent of variability occurring between machine and biological replicas with a standardized protocol. The yeast species Saccharomyces cerevisiae (large oval-shaped cells) and Debaryomyces hansenii (small round shaped cells) were employed for their different morphology. Thirty machine replicas of each were analyzed separately and after averaging in groups of three, showing a three to four-fold reduction of the variability. Similarly, a two-fold reduction of variability was observed when thirty biological replicas of the two yeast species were analyzed. The optimal number of replicas to average was then estimated with a bootstrap-like procedure in which biological and machine replicas were randomly resampled 2000 times and averaged in groups spanning from 2 to 12 replicas. This simulation has shown that little if any advantage can be obtained by increasing the number of replicas over five and that the variability exhibited by the small regular cells of D. hansenii was always roughly half of that displayed by the large S. cerevisiae cells, confirming the results obtained with standard non-bootstrapped averages.