Fourier transform infrared spectroscopy as a metabolite fingerprinting tool for monitoring the phenotypic changes in complex bacterial communities capable of degrading phenol

Bacterial discrimination by Fourier transform infrared spectroscopy, MALDI-mass spectrometry and whole-genome sequencing

Aim: Proof-of-concept study, highlighting the clinical diagnostic ability of FT-IR compared with MALDI-TOF MS, combined with WGS. Materials & methods: 104 pathogenic isolates of Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus were analyzed. Results: Overall prediction accuracy was 99.6% in FT-IR and 95.8% in MALDI-TOF-MS. Analysis of N. meningitidis serogroups was superior in FT-IR compared with MALDI-TOF-MS. Phylogenetic relationship of S. pyogenes was similar by FT-IR and WGS, but not S. aureus or S. pneumoniae. Clinical severity was associated with the zinc ABC transporter and DNA repair genes in S. pneumoniae and cell wall proteins (biofilm formation, antibiotic and complement permeability) in S. aureus via WGS. Conclusion: FT-IR warrants further clinical evaluation as a promising diagnostic tool.

Biodegradation of Reactive Yellow-145 azo dye using bacterial consortium: A deterministic analysis based on degradable Metabolite, phytotoxicity and genotoxicity study

Azo dyes are used at larger-scale as coloring agent in the textile industry. It generates a huge amount of dye containing wastewater and its toxicity threatens all kinds of life and also impacts human beings. At present, more impetus is being given to the biological treatment of dye effluent because of its azoreductase enzyme action to break down azo bond which leads to decolorization and degradation of dye. Bacterial consortium of E. asburiae and E. cloacae (1:1 ratio) was used for degradation and decolorization of Reactive Yellow-145 (RY-145) dye. The optimization of dye concentration, temperature, pH, and media has been carried out to determine the conditions required for maximum degradation and decolorization. The mixed consortium (10%) has shown 98.78% decolorization of RY-145 dye under static condition at 500 mgL^-1 concentration, 35 °C and pH 7.0 at 12 h contact period. FTIR analysis showed formation of new functional groups in the treated dye, such as O-H stretch at 1361 cm^-1, C-H stretch at 890 cm^-1, N-H stretch at 1598 cm^-1 and aromatic C-H at 671 cm^-1 revealing degradation of dye. Biodegraded metabolites of RY-145 dye were identified through GC-MS analysis that includes 2-Cyclohexen-1-ol, 5-Nitroso-2, 4, 6-triaminopyrimidine, Octahydroquinoline-9-hydroxyperoxide, Tetramethyl-2-hexadecen-1-ol, 9-Octadecanoic acid, methyl ester and Hexadecanoic acid, methyl ester, respectively which have industrial applications. Cyclohexane was used in gasoline and adhesive while Octahydroquinoline-9-hydroxyperoxide and 5-Nitroso-2, 4, 6-triaminopyrimidine were used in manufacturing drugs. Tetramethyl-2-hexadecen-1-ol, 9-Octadecanoic acid, methyl ester and Hexadecanoic acid, methyl ester are antimicrobial and antioxidant. Phytotoxicity test also showed non-toxic effects of treated dye on germination of Cicer arietinum and Vigna radiata seeds. Similarly, genotoxicity study indicated less toxic effects of biodegraded dye products on Mitotic index (MI) and cell division of Allium cepa.

An ensemble approach to the structure-function problem in microbial communities

The metabolic activity of microbial communities plays a primary role in the flow of essential nutrients throughout the biosphere. Molecular genetics has revealed the metabolic pathways that model organisms utilize to generate energy and biomass, but we understand little about how the metabolism of diverse, natural communities emerges from the collective action of its constituents. We propose that quantifying and mapping metabolic fluxes to sequencing measurements of genomic, taxonomic, or transcriptional variation across an ensemble of diverse communities, either in the laboratory or in the wild, can reveal low-dimensional descriptions of community structure that can explain or predict their emergent metabolic activity. We survey the types of communities for which this approach might be best suited, review the analytical techniques available for quantifying metabolite fluxes in communities, and discuss what types of data analysis approaches might be lucrative for learning the structure-function mapping in communities from these data.

Metabolism in action: stable isotope probing using vibrational spectroscopy and SIMS reveals kinetic and metabolic flux of key substrates

Microbial communities play essential functions which drive various ecosystems supporting animal and aquatic life. However, linking bacteria with specific metabolic functions is difficult, since microbial communities consist of numerous and phylogenetically diverse microbes. Stable isotope probing (SIP) combined with single-cell tools has emerged as a novel culture-independent strategy for unravelling microbial metabolic roles and intertwined interactions in complex communities. In this study, we applied Raman and Fourier-transform infrared (FT-IR) spectroscopies, secondary ion mass spectrometry (SIMS) with SIP to probe the rate of ¹³C incorporation in Escherichia coli at 37 and 25 °C. Our results indicate quantitative enrichment and flow of ¹³C into E. coli at various time points. Multivariate and univariate analyses of Raman and FT-IR data demonstrated distinctive ¹³C concentration-dependent trends that were due to vibrational bands shifting to lower frequencies and these shifts were a result of incubation time and metabolic rate. SIMS results were in complete agreement with the spectroscopy findings, and confirmed the detected levels of ¹³C incorporation into microbial biomass at the investigated conditions. Having established that FT-IR and Raman spectroscopy with SIP can measure metabolism kinetics in this simple system, we have applied the kinetics concept to study the metabolism of phenol by Pseudomonas putida and metabolic interactions within a two-species consortia with E. coli that could not degrade phenol. Raman spectroscopy combined with SIP identified quantitative shifts in P. putida due to temporal assimilation of phenol. Although E. coli was unable to grow on phenol, in co-culture with P. putida, general metabolic probing using deuterated water for SIP revealed that E. coli displayed increasing metabolic activity, presumably due to cross feeding from metabolites generated by P. putida. This study clearly demonstrates that Raman and FT-IR combined with SIP provide rapid and sensitive detection of carbon incorporation rates and microbial interactions. These novel findings may guide the identification of primary substrate consumers in complex microbial communities in situ, which is a key step towards the characterisation of novel genes, enzymes and metabolic flux analysis in microbial consortia.

In situ spectroscopic analysis of Lactobacillus rhamnosus GG flow on an abiotic surface reveals a role for nutrients in biofilm development

In this work, infrared spectroscopy was used to monitor the changes in the biochemical composition of biofilms of the probiotic bacterium Lactobacillus rhamnosus GG (LGG) in three nutritive media (10-fold diluted MRS, AOAC, and mTSB), in situ and under flow conditions. Epifluorescence microscopy was used to observe the shape of LGG cells and their distribution on the surface. Spectroscopic fingerprints recorded as a function of time revealed a medium-dependent content of nucleic acids, phospholipids and polysaccharides in the biofilms. In addition, time-dependent synthesis of lactic acid was observed in MRS/10 and AOAC/10. Polysaccharides were produced to the highest extent in mTSB/10, and the biofilms obtained were the densest in this medium. The rod shape of the cells was preserved in MRS/10, whereas acidic stress induced in AOAC/10 and the nutritional quality of mTSB/10 led to strong morphological changes. These alterations due to the nutritive environment are important to consider in research and use of LGG biofilms.

Rapid, accurate, and comparative differentiation of clinically and industrially relevant microorganisms via multiple vibrational spectroscopic fingerprinting

Despite the fact that various microorganisms (e.g., bacteria, fungi, viruses, etc.) have been linked with infectious diseases, their crucial role towards sustaining life on Earth is undeniable. The huge biodiversity, combined with the wide range of biochemical capabilities of these organisms, have always been the driving force behind their large number of current, and, as of yet, undiscovered future applications. The presence of such diversity could be said to expedite the need for the development of rapid, accurate and sensitive techniques which allow for the detection, differentiation, identification and classification of such organisms. In this study, we employed Fourier transform infrared (FT-IR), Raman, and surface enhanced Raman scattering (SERS) spectroscopies, as molecular whole-organism fingerprinting techniques, combined with multivariate statistical analysis approaches for the classification of a range of industrial, environmental or clinically relevant bacteria (P. aeruginosa, P. putida, E. coli, E. faecium, S. lividans, B. subtilis, B. cereus) and yeast (S. cerevisiae). Principal components-discriminant function analysis (PC-DFA) scores plots of the spectral data collected from all three techniques allowed for the clear differentiation of all the samples down to sub-species level. The partial least squares-discriminant analysis (PLS-DA) models generated using the SERS spectral data displayed lower accuracy (74.9%) when compared to those obtained from conventional Raman (97.8%) and FT-IR (96.2%) analyses. In addition, whilst background fluorescence was detected in Raman spectra for S. cerevisiae, this fluorescence was quenched when applying SERS to the same species, and conversely SERS appeared to introduce strong fluorescence when analysing P. putida. It is also worth noting that FT-IR analysis provided spectral data of high quality and reproducibility for the whole sample set, suggesting its applicability to a wider range of samples, and perhaps the most suitable for the analysis of mixed cultures in future studies. Furthermore, our results suggest that while each of these spectroscopic approaches may favour different organisms (sample types), when combined, they would provide complementary and more in-depth knowledge (structural and/or metabolic state) of biological systems. To the best of our knowledge, this is the first time that such a comparative and combined spectroscopic study (using FT-IR, Raman and SERS) has been carried out on microbial samples.

Preparation and application of magnetic superhydrophobic polydivinylbenzene nanofibers for oil adsorption in wastewater

Superhydrophobic materials have an excellent performance in oil adsorption. In this study, a novel magnetic polydivinylbenzene (PDVB) nanofiber was synthesized by the method of cation polymerization to adsorb oil from water. The magnetic PDVB was hollow nanofiber with Fe₃O₄ nanoparticles embedded in its structure. The synthesis condition was optimized that the ratio of divinylbenzene (DVB) to boron fluoride ethyl ether (BFEE) was 10:1 (v/v), and the Fe₃O₄ dosage was 0.175 g/g of DVB. The material showed an excellent oil adsorption performance in wastewater, and the oil concentration could be reduced from 2000 to 92.2 mg/L within 5 min. The magnetic PDVB had relatively high adsorption capacity (12 g/g) for oil, which could be attributed to its super hydrophobicity and one-dimensional nanostructure with high crosslinking degree. The isotherm study indicated that the magnetic PDVB adsorbed oil was an asymmetric or multilayer adsorption process. The material could be regenerated by simple squeeze and maintain its adsorption capacity after it has been used for 10 recycles. In real coking wastewater, the magnetic PDVB kept a good oil adsorption performance without the interference of various pollutants, indicating a wide prospect in practical use.

Qualitative analysis of activated sludge using FT-IR technique

The ability to measure and control the composition of activated sludge is an important issue, aiming at evaluating the effectiveness of changes occurring in the sludge, what determines its usefulness to treat wastewater. In this research, diffuse reflectance infrared Fourier transform (FTIR–DRIFT) technique was used, which relies on measuring the reflectance of the powdered substance’s surface layer and capturing spectra in range of infrared wave. First, spectra correlation table of the substances mostly occurring in wastewater was developed to assess the main components of the tested samples of activated sludge. The simplest compounds containing functional groups characteristic for particular chemical classes were chosen: peptides (peptone and albumin), fats (glycerin and fatty acids), carbohydrates (glucose and sucrose), nitrogen compounds (NaNO₃ and NH₄SO₄), sulfur compounds (Na₂SO₄ and Na₂S₂O₃), silicate, etc. The spectra of those substances were captured and characteristic absorption bands for respective bonds in the function groups were assigned. Second, samples of activated sludge from lab-scale membrane bioreactors (MBRs), which purifies petroleum wastewater, were taken. Samples were properly prepared (lyophilization and homogenization) and their spectra were captured. During spectra analysis, previously developed correlation table was used. In obtained spectra of activated sludge, absorption bonds characteristic for amides, peptides, carbohydrates, fats, and aliphatic was identified. The spectra profile of the sludge sample from MBR feed with petroleum wastewater was slightly different from the control MBR sample’s spectra. Intensity of bands in the area characteristic for aliphatic compounds and phenols was clearly higher. This study proves the usefulness of FT-IR technique to observe changes in the chemical composition of activated sludge.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Metabolic Profiling of Geobacter sulfurreducens during Industrial Bioprocess Scale-Up

During the industrial scale-up of bioprocesses it is important to establish that the biological system has not changed significantly when moving from small laboratory-scale shake flasks or culturing bottles to an industrially relevant production level. Therefore, during upscaling of biomass production for a range of metal transformations, including the production of biogenic magnetite nanoparticles by Geobacter sulfurreducens, from 100-ml bench-scale to 5-liter fermentors, we applied Fourier transform infrared (FTIR) spectroscopy as a metabolic fingerprinting approach followed by the analysis of bacterial cell extracts by gas chromatography-mass spectrometry (GC-MS) for metabolic profiling. FTIR results clearly differentiated between the phenotypic changes associated with different growth phases as well as the two culturing conditions. Furthermore, the clustering patterns displayed by multivariate analysis were in agreement with the turbidimetric measurements, which displayed an extended lag phase for cells grown in a 5-liter bioreactor (24 h) compared to those grown in 100-ml serum bottles (6 h). GC-MS analysis of the cell extracts demonstrated an overall accumulation of fumarate during the lag phase under both culturing conditions, coinciding with the detected concentrations of oxaloacetate, pyruvate, nicotinamide, and glycerol-3-phosphate being at their lowest levels compared to other growth phases. These metabolites were overlaid onto a metabolic network of G. sulfurreducens, and taking into account the levels of these metabolites throughout the fermentation process, the limited availability of oxaloacetate and nicotinamide would seem to be the main metabolic bottleneck resulting from this scale-up process. Additional metabolite-feeding experiments were carried out to validate the above hypothesis. Nicotinamide supplementation (1 mM) did not display any significant effects on the lag phase of G. sulfurreducens cells grown in the 100-ml serum bottles. However, it significantly improved the growth behavior of cells grown in the 5-liter bioreactor by reducing the lag phase from 24 h to 6 h, while providing higher yield than in the 100-ml serum bottles.

Comparative study of toxicity of azo dye Procion Red MX-5B following biosorption and biodegradation treatments with the fungi Aspergillus niger and Aspergillus terreus

Azo dyes are an important class of environmental contaminants and are characterized by the presence of one or more azo bonds (-N=N-) in their molecular structure. Effluents containing these compounds resist many types of treatments due to their molecular complexity. Therefore, alternative treatments, such as biosorption and biodegradation, have been widely studied to solve the problems caused by these substances, such as their harmful effects on the environment and organisms. The aim of the present study was to evaluate biosorption and biodegradation of the azo dye Procion Red MX-5B in solutions with the filamentous fungi Aspergillus niger and Aspergillus terreus. Decolorization tests were performed, followed by acute toxicity tests using Lactuca sativa seeds and Artemia salina larvae. Thirty percent dye removal of the solutions was achieved after 3 h of biosorption. UV-Vis spectroscopy revealed that removal of the dye molecules occurred without major molecular changes. The acute toxicity tests confirmed lack of molecular degradation following biosorption with A. niger, as toxicity to L. sativa seed reduced from 5% to 0%. For A. salina larvae, the solutions were nontoxic before and after treatment. In the biodegradation study with the fungus A. terreus, UV-Vis and FTIR spectroscopy revealed molecular degradation and the formation of secondary metabolites, such as primary and secondary amines. The biodegradation of the dye molecules was evaluated after 24, 240 and 336 h of treatment. The fungal biomass demonstrated considerable affinity for Procion Red MX-5B, achieving approximately 100% decolorization of the solutions by the end of treatment. However, the solutions resulting from this treatment exhibited a significant increase in toxicity, inhibiting the growth of L. sativa seeds by 43% and leading to a 100% mortality rate among the A. salina larvae. Based on the present findings, biodegradation was effective in the decolorization of the samples, but generated toxic metabolites, while biosorption was effective in both decolorization and reducing the toxicity of the solutions.

Waste gas biofiltration: advances and limitations of current approaches in microbiology

As confidence in gas biofiltration efficacy grows, ever more complex malodorant and toxic molecules are ameliorated. In parallel, for many countries, emission control legislation becomes increasingly stringent to accommodate both public health and climate change imperatives. Effective gas biofiltration in biofilters and biotrickling filters depends on three key bioreactor variables: the support medium; gas molecule solubilization; and the catabolic population. Organic and inorganic support media, singly or in combination, have been employed and their key criteria are considered by critical appraisal of one, char. Catabolic species have included fungal and bacterial monocultures and, to a lesser extent, microbial communities. In the absence of organic support medium (soil, compost, sewage sludge, etc.) inoculum provision, a targeted enrichment and isolation program must be undertaken followed, possibly, by culture efficacy improvement. Microbial community process enhancement can then be gained by comprehensive characterization of the culturable and total populations. For all species, support medium attachment is critical and this is considered prior to filtration optimization by water content, pH, temperature, loadings, and nutrients manipulation. Finally, to negate discharge of fungal spores, and/or archaeal and/or bacterial cells, capture/destruction technologies are required to enable exploitation of the mineralization product CO(2).

Research Spotlight: Biospectroscopy at the Manchester Interdisciplinary Biocentre

The Manchester Interdisciplinary Biocentre (MIB) at The University of Manchester (UK), is a large research facility located in central Manchester. The research undertaken in the MIB is said to address a number of grand challenges, including industrial biotechnology, energy and biofuels, and biomedical healthcare. These are realized via four main research themes: biomolecular mechanism and catalysis; synthetic and chemical biology; systems biology; and enabling technologies. This research spotlight focuses on biospectroscopy in the MIB, namely vibrational spectroscopies. This is just one area of research across just three of the many research groups in the MIB, which could be said to exemplify the fundamental and applied aspects of this field, its interdisciplinary nature and also the way it realizes several of the research themes and grand challenges already mentioned, with cutting edge and innovative research.