Analysis of Bacteria on Steel Surfaces Using Reflectance Micro-Fourier Transform Infrared Spectroscopy

Microbial Seafloor Weathering of Hydrothermal Sulfides: Insights from an 18-Month In Situ Incubation at the Wocan-1 Hydrothermal Field

The weathering of seafloor hydrothermal sulfides is facilitated by microbial activities, yet the specific mechanisms of different sulfide types are not well understood. Previous studies have primarily been carried out under laboratory conditions, making it difficult to accurately replicate the complex in situ conditions of deep-sea hydrothermal fields. Herein, we deployed two well-characterized pyrite (Py)-dominated and chalcopyrite (Ccp)-dominated sulfide slices, which were placed 300 m from an active venting site in the Wocan-1 hydrothermal field (Carlsberg Ridge, Northwest Indian Ocean) for an 18-month in situ incubation experiment. Microscopic observations and organic matter analyses were conducted on the recovered sulfide slices to investigate the microbial weathering features of different sulfide types. Our results demonstrated that the weathering of the Py-dominated sulfide sample was primarily mediated by extracellular polymeric substances (EPSs) through indirect interactions, whereas the Ccp-dominated sulfide sample exhibited both direct microbial dissolution, resulting in the formation of distinct dissolution pits, and indirect EPS-mediated interactions. Four distinct phases of microbe-sulfide interactions were identified: approach, adsorption, stable attachment, and extensive colonization. Furthermore, the weathering products and biomineralization structures differed significantly between the two sulfide types, reflecting their different microbial colonization processes. Our study confirms that microorganisms are crucial in seafloor sulfide weathering. These findings advance our understanding of microbial-driven processes in sulfide mineral transformations and their role in marine ecosystems. Our findings are also valuable for future research on biogeochemical cycles and for developing bioremediation strategies for deep-sea mining.

A novel protein corona-induced aggregation-ECL strategy based on poly-l-cys/Cu NCs for detecting microplastics in water

To address the health risks posed by microplastics (MPs), this work developed a poly-l-cysteine (poly-L-cys)-based electrochemiluminescence (ECL) sensor for detecting MPs in water environments. The porous structure of poly-L-cys film can regulate the generation of copper nanoclusters (Cu NCs) in the pores, effectively limiting the migration and aggregation of nanopaticles. In addition, poly-L-cys film also acted as co-reactant promoters, promoting electron transfer and effectively enhancing ECL signal of Cu NCs. Therefore, Cu NCs in the poly-L-cys porous membrane has been used as luminescent probes. Furthermore, the poly-L-cys/Cu NC-based ECL sensor was constructed with the protein corona induced aggregation effect (PCIAE) to determine the concentration of MP. Due to the strong binding affinity of PCIAE, MP can adsorb strongly to biomolecule surfaces as a protein crown. So, the modified BSA on the poly-L-cys film was removed by MP, resulting in the ECL signal enhancement. The PCIAE-ECL sensor has been successfully applied to measure MP in lakes with excellent recovery rates (90.7-106.0 %). The PCIAE-ECL sensor provided a new analytical method for detecting MPs in water environments.

Spectroscopic and Microscopic Characterization of Microbial Biofouling on Aircraft Fuel Tanks

Avoiding microbial contamination and biofilm formation on the surfaces of aircraft fuel tanks is a major challenge in the aviation industry. The inevitable presence of water in fuel systems and nutrients provided by the fuel makes an ideal environment for bacteria, fungi, and yeast to grow. Understanding how microbes grow on different fuel tank materials is the first step to control biofilm formation in aviation fuel systems. In this study, biofilms of Pseudomonas putida, a model Gram-negative bacterium previously found in aircraft fuel tanks, were characterized on aluminum 7075-T6 surfaces, which is an alloy used by the aviation industry due to favorable properties including high strength and fatigue resistance. Scanning electron microscopy (SEM) coupled with energy-dispersive X-ray (EDX) showed that extracellular polymeric substances (EPS) produced by P. putida were important components of biofilms with a likely role in biofilm stability and adhesion to the surfaces. EDX analysis showed that the proportion of phosphorus with respect to nitrogen is higher in the EPS than in the bacterial cells. Additionally, different morphologies in biofilm formation were observed in the fuel phase compared to the water phase. Micro-Fourier transform infrared spectroscopy (micro-FTIR) analysis suggested that phosphoryl and carboxyl functional groups are fundamental for the irreversible attachment between the EPS of bacteria and the aluminum surface, by the formation of hydrogen bonds and inner-sphere complexes between the macromolecules and the aluminum surface. Based on the hypothesis that nucleic acids (particularly DNA) are an important component of EPS in P. putida biofilms, the impact of degrading extracellular DNA was tested. Treatment with the enzyme DNase I affected both water and fuel phase biofilms─with the cell structure disrupted in the aqueous phase, but cells remained attached to the aluminum coupons.

Interactions between microplastics and contaminants: A review focusing on the effect of aging process

Microplastics (MPs) in the environment are a major global concern due to their persistent nature and wide distribution. The aging of MPs is influenced by several processes including photodegradation, thermal degradation, biodegradation and mechanical fragmentation, which affect their interaction with contaminants. This comprehensive review aims to summarize the aging process of MPs and the factors that impact their aging, and to discuss the effects of aging on the interaction of MPs with contaminants. A range of characterization methods that can effectively elucidate the mechanistic processes of these interactions are outlined. The rate and extent of MPs aging are influenced by their physicochemical properties and other environmental factors, which ultimately affect the adsorption and aggregation of aged MPs with environmental contaminants. Pollutants such as heavy metals, organic matter and microorganisms have a tendency to accumulate on MPs through adsorption and the interactions between them impact their environmental behavior. Aging enhances the specific surface area and oxygen-containing functional groups of MPs, thereby affecting the mechanism of interaction between MPs and contaminants. To obtain a more comprehensive understanding of how aging affects the interactions, this review also provides an overview of the mechanisms by which MPs interact with contaminants. In the future, there should be further in-depth studies of the potential hazards of aged MPs in different environments e.g., soil, sediment, aquatic environment, and effects of their interaction with environmental pollutants on human health and ecology.

Development of Forensically Important Sarcophaga peregrina (Diptera: Sarcophagidae) and Intra-Puparial Age Estimation Utilizing Multiple Methods at Constant and Fluctuating Temperatures

Sarcophaga peregrina (Robineau-Desvoidy, 1830) has the potential to estimate the minimum postmortem interval (PMI_min). Development data and intra-puparial age estimation are significant for PMI_min estimation. Previous research has focused on constant temperatures, although fluctuating temperatures are a more real scenario at a crime scene. The current study examined the growth patterns of S. peregrina under constant (25.75 °C) and fluctuating temperatures (18-36 °C; 22-30 °C). Furthermore, differentially expressed genes, attenuated total reflectance Fourier-transform infrared spectroscopy, and cuticular hydrocarbons of S. peregrina during the intra-puparial period were used to estimate age. The results indicated that S. peregrina at fluctuating temperatures took longer to develop and had a lower pupariation rate, eclosion rate, and pupal weight than the group at constant temperatures did. Moreover, we found that six DEG expression profiles and ATR-FTIR technology, CHCs detection methods, and chemometrics can potentially estimate the intra-puparial age of S. peregrina at both constant and fluctuating temperatures. The findings of the study support the use of S. peregrina for PMI_min estimation and encourage the use of entomological evidence in forensic practice.

Plastic packaging-associated chemicals and their hazards - An overview of reviews

Plastic packaging contains residues from substances used during manufacturing, such as solvents, as well as non-intentionally added substances (NIAS), such as impurities, oligomers, or degradation products. By searching peer-reviewed literature, we found that at least 10,259 chemicals were related to plastic packaging materials, which include chemicals used during manufacturing and/or present in final packaging items. We then summarized and discussed their chemical structures, analytical instruments, migration characteristics, and hazard categories where possible. For plastic packaging chemicals, examination of the literature reveals gas and liquid chromatography hyphenated to a variety of accurate mass analyzers based on the use of high-resolution mass spectrometry is usually used for the identification of unknown migrants coming from plastic packaging. Chemical migration from food packaging is affected by several parameters, including the nature and complexity of the food, contact time, temperature of the system, type of packaging contact layer, and properties of the migrants. A review of the literature reveals that information on adverse effects is only available for approximately 1600 substances. Among them, it appears that additives are more toxic than monomers to wildlife and humans. Neurotoxicity accounted for the highest proportion of toxicity of all types of chemicals, while benzenoids, organic acids, and derivatives were the most toxic types of chemicals. Furthermore, studies have demonstrated that hydrocarbon derivatives, organic nitrogen compounds, and organometallic compounds have the highest proportions of dermatotoxicity, and organohalogen compounds have the highest proportions of hepatotoxicity. The main contributors to skin sensitization are organic salts. This study provides a basis for comprehensively publicizing information on chemicals in plastics, and could be helpful to better understand their potential risks to the environment and humans.

Micro- and nanoplastic contamination in livestock production: Entry pathways, potential effects and analytical challenges

The abundant and widespread presence of particulate plastics in the environment is considered an area of increasing environmental, animal and human health concern. Despite the abundance and the potential to cause deleterious biological effects, studies related to the impact of micro and nanoplastics (MNPs) on livestock animals are limited. This review evaluates the sources and entry pathways of particulate plastics in all the types of livestock production systems. The potential health effects of MNPs on mouse models, ruminant animals and a few other livestock animals are discussed. Since evaluation of MNPs in almost all types of matrices in hindered by analytical challenges, this review also evaluates the commonly used methods, emerging techniques, and quality control/quality assurance (QC/QA) procedures. Plastic mulching, fragmentation of plastic wastes and stream water runoff have been identified as major routes of MNPs entry in grazing-based and mixed livestock production systems. Notwithstanding the controlled indoor environment and relatively efficient waste management, MNPs have been detected in industrial livestock systems. The bioaccumulation and biomagnification of chemical toxicants can exacerbate the adverse effects of MNPs on higher trophic level species. Although there are several methods for the analysis of MNPs, dearth of standardized methods, certified reference materials, MPs standards, and global database libraries are major impediments. The adverse effects of MNPs on the internal organs of different livestock animals have to be studied using large sample sizes and without raising ethical concerns. Importantly, investigations on the accurate quantification of MNPs and its adverse effects in various livestock animals using rapid, cost-effective and robust analytical methods are required.

Distribution Characteristics and Source Analysis of Microplastics in Urban Freshwater Lakes: A Case Study in Songshan Lake of Dongguan, China

Current studies on microplastic pollution mainly focus on marine systems. However, few studies have investigated microplastics in an urban lake. This research intends to use an urban lake (Songshan Lake) as an example to explore the pollution characteristics of microplastics and use the principal component as well as the heat map analysis to discuss the relationships between different shapes of microplastics. According to this study, the average abundance of microplastics in the surface water and surface sediments of Songshan Lake were, respectively, 2.29 ± 0.98 items/m3 and 244 ± 121 items/kg; thin films were the major microplastics in both media; transparent this type of color has the most microplastic content. The particle size of microplastics was mainly 0.18–0.6 mm (43.3%) in surface water and 1–2 mm (48.3%) in surface sediments. The composition included five polymers: polyethylene (PE), polypropylene (PP), polypropylene–polyethylene copolymer (PP–PE copolymer), polystyrene (PS), and polyvinyl chloride (PVC), among which PE (47%) and PP (36%) were the main components. Principal component analysis (PCA) showed that there was a positive correlation among the four shapes of microplastics: films, fragments, foams, and fibers. The heat map analysis showed that the same category of shape distribution features may be similar for each sampling site.

Microplastics: An overview on separation, identification and characterization of microplastics

At present plastic residues has become grave threat to the environment. Microplastics are plastic residues with a size <5 mm, due to their small size it is very difficult to remove them from water bodies, sediments and air with available techniques. Nanoplastics are different in size range as nanoplastics are smaller than 1 μm in size. This review is an attempt to gather an insight towards microplastic and its associated point of concerns. The review will highlight some of the methods appropriate for microplastics sampling and techniques for its identification in environmental samples. Some of the sampling methods include sieving, filtration, visual sorting, digestion, density separation. While, identification techniques in practice are SEM-EDS, FTIR, NIR, Raman, NMR spectroscopy, etc. Still there is a need and scope for development of more economical and portable techniques in this direction.

The importance of the bacterial cell wall in uranium(VI) biosorption

The bacterial cell envelope, in particular the cell wall, is considered the main controlling factor in the biosorption of aqueous uranium(vi) by microorganisms. However, the specific roles of the cell wall, associated biomolecules, and other components of the cell envelope are not well defined. Here we report findings on the biosorption of uranium by isolated cell envelope components and associated biomolecules, with P. putida 33015 and B. subtilis 168 investigated as representative strains for the differences in Gram-negative and Gram-positive cell envelope architecture, respectively. The cell wall and cell surface membrane were isolated from intact cells and characterised by X-ray Photoelectron Spectroscopy (XPS) and Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FT-IR) spectroscopy; revealing variations in the abundance of functional moieties and biomolecules associated with components of the cell envelope. Uranium biosorption was investigated as a function of cell envelope component and pH, comparing with intact cells. The isolated cell wall from both strains exhibited the greatest uranium biosorption capacity. Deprotonation of favourable functional groups on the biomass as the pH increased from 3 to 5.5 increased their uranium biosorption capacity by approximately 3 fold. The results from ATR-FT-IR indicated that uranium(vi) biosorption was mediated by phosphate and carboxyl groups associated with proteins and phosphorylated biopolymers of the cell envelope. This includes outer membrane phospholipids and LPS of Gram-negative bacteria and teichoic acids, surface proteins and peptidoglycan from Gram-positive bacteria. As a result, the biosorption process of uranium(vi) to microorganisms is controlled by surface interactions, resulting in higher accumulation of uranium in the cell envelope. This demonstrates the importance of bacterial cell wall as the key mediator of uranium biosorption with microorganisms.

Optimized microplastic analysis based on size fractionation, density separation and μ-FTIR

Microplastic particles have been recognized as global hazardous pollutants in the last few decades pointing to the importance of analyzing and monitoring microplastics, especially in soils and sediments. This study focused on a multi-step approach for microplastic analysis combining grain size fractionation, density separation and identification by μ-FTIR-spectroscopy. Eight widely used polymers (polyethylene (PE), polypropylene (PP), polyvinylchloride (PVC), polystyrol (PS), polyethylenterephthalate (PET), polymethylmethacrylate (PMMA), polyurethane (PU) and polyamide (PA)) were fractionated into four groups of grain sizes (0.1-5 mm). Thereafter, sea sand was spiked with these particles to test a ZnCl₂-based density separation for the polymer types and the various grain sizes. The obtained recovery rates were close to 100% showing that ZnCl₂-based density separation is suitable to separate the polymer particles from a sandy matrix. This approach was extended on three further environmental matrices and recovery rates for two of them (sandy-silty and fine-grained sediment) also provided reliable values (94-106%). Lastly, the developed multi-step approach was verified by analyzing an environmental sample (sediment from river Tiranë, Albania) characterized by smaller grain size and moderate organic matter content. Identification of two polymer types in different grain size classes verified the suitability of the developed approach for microplastic analyses on particulate matter such as soils and sediments.

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.

Characterization of Microbial Communities Associated with Ceramic Raw Materials as Potential Contributors for the Improvement of Ceramic Rheological Properties

Technical ceramics are being widely employed in the electric power, medical and engineering industries because of their thermal and mechanical properties, as well as their high resistance qualities. The manufacture of technical ceramic components involves complex processes, including milling and stirring of raw materials in aqueous solutions, spray drying and dry pressing. In general, the spray-dried powders exhibit an important degree of variability in their performance when subjected to dry-pressing, which affects the efficiency of the manufacturing process. Commercial additives, such as deflocculants, biocides, antifoam agents, binders, lubricants and plasticizers are thus applied to ceramic slips. Several bacterial and fungal species naturally occurring in ceramic raw materials, such as Sphingomonas, Aspergillus and Aureobasidium, are known to produce exopolysaccharides. These extracellular polymeric substances (EPS) may confer unique and potentially interesting properties on ceramic slips, including viscosity control, gelation, and flocculation. In this study, the microbial communities present in clay raw materials were identified by both culture methods and DNA-based analyses to select potential EPS producers based on the scientific literature for further assays based on the use of EPS for enhancing the performance of technical ceramics. Potential exopolysaccharide producers were identified in all samples, such as Sphingomonas sp., Pseudomonas xanthomarina, P. stutzeri, P. koreensis, Acinetobacter lwoffi, Bacillus altitudinis and Micrococcus luteus, among bacteria. Five fungi (Penicillium citrinum, Aspergillus niger, Fusarium oxysporum, Acremonium persicinum and Rhodotorula mucilaginosa) were also identified as potential EPS producers.

Microplastics and associated PAHs in surface water from the Feilaixia Reservoir in the Beijiang River, China

Microplastics have been a prevalent and persistent contamination problem in the global aquatic environment. In particular, microplastics that can adsorb persistent organic pollutants (POPs) and therefore transfer these POPs to organisms in the aquatic environment have received much attention. In this study, an investigation of microplastics in the surface water of the Feilaixia Reservoir (Guangdong Province, China), which is an important part of people's daily lives in Guangdong Province was carried out, mainly focusing on the characteristics and spatial distribution of microplastics, as well as microplastics and their adsorded PAHs in the surface water of the Feilaixia Reservoir were investigated. The average abundance of microplastics in the surface water of the Feilaixia Reservoir was 0.56 ± 0.45 items/m³. Six kinds of polymers, including polyethylene (PE), polypropylene (PP), polystyrene (PS), expanded polystyrene (EPS), polyvinyl chloride (PVC) and polyethylene terephthalate (PET), were identified, among which PP (52.31%) and PE (27.39%) were the major compositions. Four shapes of microplastics, i.e., foams, films, fragments and fibers were found, and films (37.78%) being the main shape. The most common typical size of the plastic particles ranged from 0.6 to 2 mm (41.36%). The total concentration of the sixteen PAHs carried on the EPS, PE and PP microplastics ranged from 282.4 to 427.3 ng/g; chrysene, benzo [ghi] perylene, and phenanthrene were abundant in the samples, at concentrations of 39.5-89.6 ng/g, 34.6-56.8 ng/g and 25.6-45.6 ng/g, respectively. Based on the ratios of the PAH isomers (Flut/Py < 1 and Phe/Ant >10), it was speculated that the source of the PAHs may be derived from the imperfect combustion of fossil fuels.

Characteristic of microplastics in the atmospheric fallout from Dongguan city, China: preliminary research and first evidence

Microplastic pollution has exhibited a global distribution, including seas, lakes, rivers, and terrestrial environment in recent years. However, little attention was paid on the atmospheric environment, though the fact that plastic debris can escape as wind-blown debris was previously reported. Thus, characteristics of microplastics in the atmospheric fallout from Dongguan city were preliminarily studied. Microplastics of three different polymers, i.e., PE, PP, and PS, were identified. Diverse shapes of microplastics including fiber, foam, fragment, and film were found, and fiber was the dominant shape of the microplastics. SEM images illustrated that adhering particles, grooves, pits, fractures, and flakes were the common patterns of degradation. The concentrations of non-fibrous microplastics and fibers ranged from 175 to 313 particles/m²/day in the atmospheric fallout. Thus, dust emission and deposition between atmosphere, land surface, and aquatic environment were associated with the transportation of microplastics.

Influence of l-amino acids on aggregation and biofilm formation in Azotobacter chroococcum and Trichoderma viride

AIM

The effects of l-amino acids on growth and biofilm formation in Azotobacter chroococcum (Az) and Trichoderma viride (Tv) as single (Az, Tv) and staggered inoculated cultures (Az-Tv, Tv-Az) were investigated.

METHODS AND RESULTS

A preliminary study using a set of 20 l-amino acids, identified 6 amino acids (l-Glu, l-Gln, l-His, l-Ser, l-Thr and l-Trp) which significantly enhanced growth and biofilm formation. Supplementation of these amino acids at different concentrations revealed that 40 mmol l^-1 was most effective. l-Glu and l-Gln favoured planktonic growth in both single and in staggered inoculated cultures, while l-Trp and l-Thr, enhanced aggregation and biofilm formation. Addition of l-Glu or l-Gln increased carbohydrate content and planktonic population. Principal component analysis revealed the significant role of proteins in growth and biofilm formation, particularly with supplementation of l-Trp, l-Thr and l-Ser. Azotobacter was found to function better as biofilm under staggered inoculated culture with Trichoderma.

CONCLUSIONS

The results illustrate that amino acids play crucial roles in microbial biofilm formation, by influencing growth, aggregation and carbohydrates synthesized.

SIGNIFICANCE AND IMPACT OF THE STUDY

The differential and specific roles of amino acids on biofilm formation are of significance for agriculturally important micro-organisms that grow as biofilms, colonize and benefit the plants more effectively.

Vibrational Spectroscopy for Imaging Single Microbial Cells in Complex Biological Samples

Vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of the samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of single-cell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.

Can Near-infrared Spectroscopy Detect and Differentiate Implant-associated Biofilms?

BACKGROUND

Established bacterial diagnostic techniques for orthopaedic-related infections rely on a combination of imperfect tests that often can lead to negative culture results. Spectroscopy is a tool that potentially could aid in rapid detection and differentiation of bacteria in implant-associated infections.

QUESTIONS/PURPOSES

We asked: (1) Can principal component analysis explain variation in spectral curves for biofilm obtained from Staphylococcus aureus, Staphylococcus epidermidis, and Pseudomonas aeruginosa? (2) What is the accuracy of Fourier transformed-near infrared (FT-NIR)/multivariate data analysis in identifying the specific species associated with biofilm?

METHODS

Three clinical isolates, S aureus, S epidermidis, and P aeruginosa were cultured to create biofilm on surgical grade stainless steel. At least 52 samples were analyzed per group using a FT-NIR spectrometer. Multivariate and principal component analyses were performed on the spectral data to allow for modeling and identification of the bacterial species.

RESULTS

Spectral analysis was able to correctly identify 86% (37/43) of S aureus, 89% (16/18) of S epidermidis, and 70% (28/40) of P aeruginosa samples with minimal error. Overall, models developed using spectral data preprocessed using a combination of standard normal variant and first-derivative transformations performed much better than models developed with the raw spectral data in discriminating between the three classes of bacteria because of its low Type 1 error and large intermodel distinction.

CONCLUSIONS

The use of spectroscopic methods to identify and classify bacterial biofilms on orthopaedic implant material is possible and improves with advanced modeling that can be obtained rapidly with little error. The sensitivity for identification was 97% for S aureus (95% CI, 88-99%), 100% for S epidermidis (95% CI, 95-100%), and 77% for P aeruginosa (95% CI, 65-86%). The specificity of the S aureus was 86% (95% CI, 3-93%), S epidermidis was 89% (95% CI, 67-97%), and P aeruginosa was 70% (95% CI, 55-82%).

CLINICAL RELEVANCE

This technique of spectral data acquisition and advanced modeling should continue to be explored as a method for bacterial biofilm identification. A spectral databank of bacterial and potentially contaminating tissues should be acquired initially through an in vivo animal model and quickly transition to explanted devices and the clinical arena.

Combination of synchrotron radiation-based Fourier transforms infrared microspectroscopy and confocal laser scanning microscopy to understand spatial heterogeneity in aquatic multispecies biofilms

Understanding the spatial heterogeneity within environmental biofilms can provide an insight into compartmentalization of different functions in biofilm communities. We used a non-destructive and label-free method by combining Synchrotron Radiation-based Fourier Transform Infrared Microspectroscopy (SR-FTIR) with Confocal Laser Scanning Microscopy (CLSM) to distinguish the spatial chemical changes within multispecies biofilms grown from natural storm waters in flow cells. Among the different surfaces tested for biofilm growth and optimal imaging, mylar membranes were most suited and it enabled successful spatial infrared imaging of natural biofilms for obtaining reliable and interpretable FTIR spectra. Time series analysis of biofilm growth showed that influx of water during biofilm growth, results in significant changes in biofilm formation. Early biofilms showed active nutrient acquisition and desiccation tolerance mechanisms corresponding with accumulation of secreted proteins. Statistical approach used for the evaluation of chemical spectra allowed for clustering and classification of various regions of the biofilm. Microheterogeneity was observed in the polymeric components of the biofilm matrix, including cellulose, glycocalyx and dextran-like molecules. Fructan and glycan-rich regions were distinguishable and glycocalyx was abundant in the strongly adhering peripheral regions of biofilms. Inner core showed coexistence of oxygen dimers and ferrihydrite that will likely support growth of Fe (II)-oxidising bacteria. The combined SR-FTIR microspectroscopy and CSLM approach for complex natural biofilms described here will be useful both in understanding heterogeneity of matrix components and in correlating functions of juxtaposed microbial species in complex natural biofilms with physicochemical microenvironment to which they are exposed.

Quantitative determination of polyphosphate in sediments using Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy and partial least squares regression

Phosphorus (P) is a major cause of eutrophication and subsequent loss of water quality in freshwater ecosystems. A major part of the flux of P to eutrophic lake sediments is organically bound or of biogenic origin. Despite the broad relevance of polyphosphate (Poly-P) in bioremediation and P release processes in the environment, its quantification is not yet well developed for sediment samples. Current methods possess significant disadvantages because of the difficulties associated with using a single extractant to extract a specific P compound without altering others. A fast and reliable method to estimate the quantitative contribution of microorganisms to sediment P release processes is needed, especially when an excessive P accumulation in the form of polyphosphate (Poly-P) occurs. Development of novel approaches for application of emerging spectroscopic techniques to complex environmental matrices such as sediments significantly contributes to the speciation models of P mobilization, biogeochemical nutrient cycling and development of nutrient models. In this study, for the first time Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy in combination with partial least squares (PLS) was used to quantify Poly-P in sediments. To reduce the high absorption matrix components in sediments such as silica, a physical extraction method was developed to separate sediment biological materials from abiotic particles. The aim was to achieve optimal separation of the biological materials from sediment abiotic particles with minimum chemical change in the sample matrix prior to ATR-FTIR analysis. Using a calibration set of 60 samples for the PLS prediction models in the Poly-P concentration range of 0-1 mg g(-1) d.w. (dry weight of sediment) (R(2) = 0.984 and root mean square error of prediction RMSEP = 0.041 at Factor-1) Poly-P could be detected at less than 50 μg g(-l) d.w. Using this technique, there is no solvent extraction or chemical treatment required, sample preparation is minimal and simple, and the analysis time is greatly reduced. The results from this study demonstrated the potential of ATR FT-IR spectroscopy as an alternative method to study Poly-P in sediments.

Bacteriogenic Fe(III) (oxyhydr)oxides characterized by synchrotron microprobe coupled with spatially resolved phylogenetic analysis

Ubiquitous presence of microbes in aquatic systems and their inherent ability of biomineralization make them extremely important agents in the geochemical cycling of inorganic elements. However, the detailed mechanisms of environmental biomineralization (e.g., the actual reaction rates, the temporal and spatial dynamics of these processes) are largely unknown, because there are few adequate analytical techniques to observe the biogenic oxidation/reduction reactions in situ. Here, we report a novel technical approach to characterize specific biominerals associated with a target microbe on high spatial resolution. The technique was developed by combining directly in situ phylogenetic analysis, fluorescence in situ hybridization (FISH), with a synchrotron microprobe method, micro X-ray absorption fine structure spectroscopy (μ-XAFS), and was applied to iron mineral deposition by iron(II)-oxidizing bacteria (IOB) in environmental samples. In situ visualization of microbes revealed that in natural iron mats, Betaproteobacteria dominated by IOB were dominantly localized within 10 μm of the surface. Furthermore, in situ chemical speciation by the synchrotron microprobe suggested that the Fe local structure at the IOB accumulating parts was dominantly composed of short-ordered Fe-O(6) linkage, which is not observed in bulk iron mat samples. The present study indicates that coupled XAFS-FISH could be a potential technique to provide direct information on specific biogenic reaction mediated by target microorganism.

The applicability of reflectance micro-Fourier-transform infrared spectroscopy for the detection of synthetic microplastics in marine sediments

Synthetic microplastics (≤5-mm fragments) are globally distributed contaminants within coastal sediments that may transport organic pollutants and additives into food webs. Although micro-Fourier-transform infrared (micro-FT-IR) spectroscopy represents an ideal method for detecting microplastics in sediments, this technique lacks a standardized operating protocol. Herein, an optimized method for the micro-FT-IR analysis of microplastics in vacuum-filtered sediment retentates was developed. Reflectance micro-FT-IR analyses of polyethylene (PE) were compared with attenuated total reflectance FT-IR (ATR-FT-IR) measurements. Molecular mapping as a precursor to the imaging of microplastics was explored in the presence and absence of 150-μm PE fragments, added to sediment at concentrations of 10, 100, 500 and 1000ppm. Subsequently, polymer spectra were assessed across plastic-spiked sediments from fifteen offshore sites. While all spectra obtained of evenly shaped plastics were typical to PE, reflectance micro-FT-IR measurements of irregularly shaped materials must account for refractive error. Additionally, we provide the first evidence that mapping successfully detects microplastics without their visual selection for characterization, despite this technique relying on spectra from small and spatially separated locations. Flotation of microplastics from sediments only enabled a fragment recovery rate of 61 (±31 S.D.) %. However, mapping 3-mm(2) areas (within 47-mm filters) detected PE at spiking concentrations of 100ppm and above, displaying 69 (±12 S.D.) % of the fragments in these locations. Additionally, mapping detected a potential PE fragment in a non-spiked retentate. These data have important implications for research into the imaging of microplastics. Specifically, the sensitivity and spatial resolution of the present protocol may be improved by visualizing the entire filter with high-throughput detection techniques (e.g., focal plane array-based imaging). Additionally, since micro-FT-IR analyses depend on methods of sample collection, our results emphasize the urgency of developing efficient and reproducible techniques to separate microplastics from sediments.

Fourier transform infrared spectroscopy for molecular analysis of microbial cells

A rapid and inexpensive method to characterise chemical cell properties and identify the functional groups present in the cell wall is Fourier transform infrared spectroscopy (FTIR). Infrared spectroscopy is a well-established technique to identify functional groups in organic molecules based on their vibration modes at different infrared wave numbers. The presence or absence of functional groups, their protonation states, or any changes due to new interactions can be monitored by analysing the position and intensity of the different infrared absorption bands. Additionally, infrared spectroscopy is non-destructive and can be used to monitor the chemistry of living cells. Despite the complexity of the spectra, the elucidation of functional groups on Gram-negative and Gram-positive bacteria has been already well documented in the literature. Recent advances in detector sensitivity have allowed the use of micro-FTIR spectroscopy as an important analytical tool to analyse biofilm samples without the need of previous treatment. Using FTIR spectroscopy, the infrared bands corresponding to proteins, lipids, polysaccharides, polyphosphate groups, and other carbohydrate functional groups on the bacterial cells can now be identified and compared along different conditions. Despite some differences in FTIR spectra among bacterial strains, experimental conditions, or changes in microbiological parameters, the IR absorption bands between approximately 4,000 and 400 cm(-1) are mainly due to fundamental vibrational modes and can often be assigned to the same particular functional groups. In this chapter, an overview covering the different sample preparation protocols for infrared analysis of bacterial cells is given, alongside the basic principles of the technique, the procedures for calculating vibrational frequencies based on simple harmonic motion, and the advantages and disadvantages of FTIR spectroscopy for the analysis of microorganisms.

Quantitative protein expression and cell surface characteristics of Escherichia coli MG1655 biofilms

Cell surface physicochemical characterization techniques were combined with quantitative changes in protein expression, to investigate the biological and biophysical changes of Escherichia coli MG1655 cells when grown as a biofilm (BIO). The overall surface charge of BIO cells was found to be less negative, highlighting the need for a lower electrophoretic mobility for attachment to occur. Comparison of the chemical functional groups on the cell surface showed similar profiles, with the absorbance intensity higher for proteins and carbohydrates in the BIO cells. Quantitative proteomic analysis demonstrated that 3 proteins were significantly increased, and 9 proteins significantly decreased in abundance, in cells grown as a BIO compared to their planktonic counterparts, with 7 of these total 12 proteins unique to this study. Proteins showing significant increased or decreased abundance include proteins involved in acid resistance, DNA protection and binding and ABC transporters. Further predictive analysis of the metabolic pathways showed an increased abundance of the amino acid metabolism and tricarboxylic acid (TCA) cycle, with a decrease in expression within the pentose phosphate and glycolysis pathways. It is therefore hypothesized that cells grown as a BIO are still energetically viable potentially using amino acids as an indirect carbon backbone source into the TCA cycle.