Abstract
This chapter will begin with the basic principles of Fourier transform infrared (FTIR) spectroscopy, microscopy and imaging followed by highlighted examples of applications.
FTIR imaging is an excellent tool to directly study the spatially resolved chemical composition of fungal material without requiring labels. Areas or band heights of selected spectral ranges can be calculated and colour-coded for each image pixel to visualise the spatial distribution of the corresponding chemical substance within samples. Although the size of single hyphae is close to the wavelength-dependent resolution limit, modern FTIR microscopes are capable of spatially resolved chemical imaging of single hyphae. Multivariate statistics can be used to reveal pattern differences of spectra within the sample or between various samples. The main spectral differences can be identified and their chemical nature concluded from the wavelength/wavenumber of absorption without prior knowledge of their chemical basis. Thus, it is possible, for example, to image the distribution of fungal mycelium within growth substrates such as wood.
FTIR analysis, by comparing spectral pattern differences, enables discrimination of fungi at various taxonomic levels . Discriminating a limited number of fungi with distinct spectral features is very simple, but distinguishing many taxa having spectral similarity requires more sophisticated statistical discrimination models.
In addition to imaging fungal material and discriminating fungal taxa, it is also possible to detect changes in chemical composition due to biotic interactions . Good examples examine the effect of wood-degrading fungi on lignin and cellulose/polysaccharide distribution within wood or the interactions of fungi and living organisms.
Finally, the future potential of FTIR microscopy is discussed.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abramović B, Jajić I, Abramović B, Ćosić J, Jurić V (2007) Detection of deoxynivalenol in wheat by Fourier transform infrared spectroscopy. Acta Chim Slov 54:859–867
Alcantara GB, Honda NK, Ferreira MMC, Ferreira AG (2007) Chemometric analysis applied in 1 H HR-MAS NMR and FT-IR data for chemotaxonomic distinction of intact lichen samples. Anal Chim Acta 595:3–8
Allwood JW, Ellis DI, Goodacre R (2008) Metabolomic technologies and their application to the study of plants and plant-host interactions. Physiol Plant 132:117–135
Allwood JW, Ellis DI, Heald JK, Goodacre R, Mur LAJ (2006) Metabolomic approaches reveal that phosphatidic and phosphatidyl glycerol phospholipids are major discriminatory non-polar metabolites in responses by Brachypodium distachyon to challenge by Magnaporthe grisea. Plant J 46:351–368
Andrade LHC, Freitas PG, Mantovani BG, Figueiredo MS, Lima RA, Lima SM et al (2008) Detection of soybean rust contamination in soy leaves by FTIR photoacoustic spectroscopy. Eur Phys J Spec Top 153:539–541
Chalmers JM, Griffiths PR (2002) Handbook of vibrational spectroscopy, vol 1–5. Wiley, Chichester
Cheli F, Battaglia D, Pinotti L, Baldi A (2012) State of the art in feedstuff analysis: a technique-oriented perspective. J Agric Food Chem 60:9529–9542
Commission Regulation (EC) No (1881/2006 of 19 December 2006). Setting maximum levels for certain contaminants in foodstuffs. Off J Eur Union L364:5–24
Ergin Ç, İlkit M, Gök Y, Özel MZ, Çon AH, Kabay N et al (2013) Fourier transform infrared spectral evaluation for the differentiation of clinically relevant Trichophyton species. J Microbiol Methods 93:218–223
Erukhimovitch V, Tsror (Lahkim) L, Hazanovsky M, Talyshinsky M, Souprun Y, Huleihel M (2007) Early and rapid detection of potato’s fungal infection by Fourier transform infrared microscopy. Appl Spectrosc 61:1052–1056
Erukhimovitch V, Tsror (Lahkim) L, Hazanovsky M, Huleihel M (2010) Direct identification of potato’s fungal phyto-pathogens by Fourier-transform infrared (FTIR) microscopy. Spectroscopy 24:609–619
Erukhimovitch V, Huleihil M, Huleihel M (2013) Identification of contaminated cells with viruses, bacteria, or fungi by Fourier transform infrared microspectroscopy. J Spectrosc 317458:1–6
Fackler K, Schwanninger M (2012) How spectroscopy and microspectroscopy of degraded wood contribute to understand fungal wood decay. Appl Microbiol Biotechnol 96:587–599
Fackler K, Thygesen LG (2013) Microspectroscopy as applied to the study of wood molecular structure. Wood Sci Technol 47:203–222
Fackler K, Stevanic JS, Ters T, Hinterstoisser B, Schwanninger M, Salmén L (2010) Localisation and characterisation of incipient brown-rot decay within spruce wood cell walls using FT-IR imaging microscopy. Enzyme Microb Technol 47:257–267
Fackler K, Stevanic JS, Ters T, Hinterstoisser B, Schwanninger M, Salmén L (2011) FT-IR imaging microscopy to localise and characterise simultaneous and selective white-rot decay within spruce wood cells. Holzforschung 65:411–420
Fischer G, Braun S, Thissen R, Dott W (2006) FT-IR spectroscopy as a tool for rapid identification and intra-species characterization of airborne filamentous fungi. J Microbiol Methods 64:63–77
Gierlinger N, Goswami L, Schmidt M, Burgert I, Coutand C, Rogge T, Schwanninger M (2008) In situ FT-IR microscopic study on enzymatic treatment of poplar wood cross-sections. Biomacromolecules 9:2194–2201
Gordon SH, Green RV, Wheeler BC, James C (1993) Multivariate FTIR analysis of substrates for protein, polysaccharide, lipid and microbe content: potential for solid-state fermentations. Biotechnol Adv 11:665–675
Gordon SH, Schudy RB, Wheeler BC, Wicklow DT, Greene RV (1997) Identification of Fourier transform infrared photoacoustic spectral features for detection of Aspergillus flavus infection in corn. Int J Food Microbiol 35:179–186
Günzler G, Gremlich H-U (2002) IR spectroscopy. Wiley-VCH, Weinheim
Haberhauer G, Rafferty B, Strebl F, Gerzabek MH (1998) Comparison of the composition of forest soil litter derived from three different sites at various decompositional stages using FTIR spectroscopy. Geoderma 83:331–342
Helm D, Labischinski H, Naumann D (1991) Elaboration of a procedure for identification of bacteria using Fourier-transform IR spectral libraries: a stepwise correlation approach. J Microbiol Methods 14:127–142
Irudayaraj J, Yang H, Sakhamuri S (2002) Differentiation and detection of microorganisms using Fourier transform infrared photoacoustic spectroscopy. J Mol Struct 606:181–188
Isenor M, Kaminskyj SGW, Rodriguez RJ, Redmance RS, Gough KM (2010) Characterization of mannitol in Curvularia protuberata hyphae by FTIR and Raman spectromicroscopy. Analyst 135:3249–3254
Jilkine K, Gough KM, Julian R, Kaminskyj SGW (2008) A sensitive method for examining whole-cell biochemical composition in single cells of filamentous fungi using synchrotron FTIR spectromicroscopy. J Inorg Biochem 102:540–546
Kaminskyj S, Jilkine K, Szeghalmi A, Gough K (2008) High spatial resolution analysis of fungal cell biochemistry—bridging the analytical gap using synchrotron FTIR spectromicroscopy. FEMS Microbiol Lett 284:1–8
Kazarian SG, Chan KLA (2010) Micro- and macro-attenuated total reflection Fourier transform infrared spectroscopic imaging. Appl Spectrosc 64:135–152
Kos G, Lohninger H, Krska R (2002) Fourier transform infrared spectroscopy with attenuated total reflection (FT-IR/ATR) as a tool for the detection of Fusarium fungi on maize. Vib Spectrosc 29:115–119
Kos G, Lohninger H, Krska R (2003) Validation of chemometric models for the determination of deoxynivalenol on maize by mid-infrared spectroscopy. Mycotoxin Res 19:149–153
Krafft C, Steiner G, Beleites C, Salzer R (2009) Disease recognition by infrared and Raman spectroscopy. J Biophoton 2:13–28
Kümmerle M, Scherer S, Seiler H (1998) Rapid and reliable identification of food-borne yeasts by Fourier-transform infrared spectroscopy. Appl Environ Microbiol 64:2207–2214
Lecellier A, Mounier J, Gaydou V, Castrec L, Barbier G, Ablain W, Manfait M, Toubas D, Sockalingum GD (2014) Differentiation and identification of filamentous fungi by high-throughput FTIR spectroscopic analysis of mycelia. Int J Food Microbiol 168–169:32–41
Lecellier A, Gaydou V, Mounier J, Hermet A, Castrec L, Barbier G, Ablain W, Manfait M, Toubas D, Sockalingum GD (2015) Implementation of an FTIR spectral library of 486 filamentous fungi strains for rapid identification of molds. Food Microbiol 45:126–143
Linker R, Tsror (Lahkim) L (2008) Discrimination of soil-borne fungi using Fourier transform infrared attenuated total reflection spectroscopy. Appl Spectrosc 62:302–305
Liu J, Qi Z, Huang Q, Wei X, Ke Z, Fang Y, Tian Y, Yu Z (2013) Study of energetic-particle-irradiation induced biological effect on Rhizopus oryzae through synchrotron-FTIR micro-spectroscopy. J Mol Struct 1031:1–8
Lloyd AJ, Allwood WJ, Winder CL, Dunn WB, Heald JK, Cristescu SM, Sivakumaran A, Harren FJM, Mulema J, Denby K, Goodacre R, Smith AR, Mur LAJ (2011) Metabolomic approaches reveal that cell wall modifications play a major role in ethylene-mediated resistance against Botrytis cinerea. Plant J 67:852–868
Lyng F, Gazi E, Gardner P (2011) Preparation of tissues and cells for infrared and Raman spectroscopy and imaging. In: Moss D (ed) Biomedical applications of synchrotron infrared microspectroscopy. Royal Society of Chemistry, Cambridge, p 145–189
Mariey L, Signolle JP, Amiel C, Travert J (2001) Discrimination, classification, identification of microorganisms using FTIR spectroscopy and chemometrics. Vib Spectrosc 26:151–159
Martín JA, Solla A, Woodward S, Gil L (2005) Fourier transform infrared spectroscopy as a new method for evaluating host resistance in Dutch elm disease complex. Tree Physiol 25:1331–1338
Martín JA, Solla A, Woodward S, Gil L (2007) Detection of differential changes in lignin composition of elm tissues inoculated with Ophiostoma novo-ulmi using Fourier transform infrared spectroscopy. For Pathol 37:187–191
Michell AJ, Higgins HG (2002) Infrared spectroscopy in Australian forest products research. CSIRO forestry and forestry products, Melbourne
Mohaček-Grošev V, Božac R, Puppels GJ (2001) Vibrational spectroscopic characterization of wild growing mushrooms and toadstools. Spectrochim Acta A 57:2815–2829
Morato EM, Morais GR, Sato F, Medina AN, Svidinski TI, Baesso ML et al (2013) Morphological and structural changes in lung tissue infected by Paracoccidioides brasiliensis: FTIR photoacoustic spectroscopy and histological analysis. Photochem Photobiol 89:1170–1175
Mounier J, Goerges S, Gelsomino R, Vancanneyt M, Vandemeulebroecke K, Hoste B, Brennan NM, Scherer S, Swings J, Fitzgerald GF, Cogan TM (2006) Sources of the adventitious microflora of a smear-ripened cheese. J Appl Microbiol 101:668–681
Movasaghi Z, Rehman S, Rehman I (2008) Fourier transform infrared (FTIR) spectroscopy of biological tissues. Appl Spectrosc Rev 43:134–179
Naumann D (2000) Infrared spectroscopy in microbioloy. In: Meyers RA (ed) Encyclopedia of analytical chemistry. Wiley, Chichester, pp 102–131
Naumann A (2009) A novel procedure for strain classification of fungal mycelium by cluster analysis and artificial neural network analysis of Fourier transform infrared (FTIR) spectra. Analyst 134:1215–1223
Naumann D, Helm D, Labischinski H (1991) Microbiological characterizations by FT-IR spectroscopy. Nature 351:81–82
Naumann A, Navarro-González M, Peddireddi S, Kües U, Polle A (2005) Fourier transform infrared microscopy and imaging: detection of fungi in wood. Fungal Genet Biol 42:829–835
Naumann A, Peddireddi S, Kües U, Polle A (2007) Fourier transform infrared microscopy in wood analysis. In: Kües U (ed) Wood production, wood technology and biotechnological impacts. Universitätsverlag Göttingen, Göttingen, pp 179–196
Naumann A, Stephan I, Noll M (2012a) Material resistance of weathered wood-plastic composites against fungal decay. Int Biodeterior Biodegradation 75:28–35
Naumann A, Seefeldt H, Stephan I, Braun U, Noll M (2012b) Material degradation of flame retarded wood-plastic composites against fire and fungal decay. Polymer Degrad Stab 97:1189–1196
Ngo Thi NA, Kirschner C, Naumann D (2000) FT-IR microspectrometry: a new tool for characterizing micro-organisms. Proc SPIE 3918:36–44
Ngo Thi NA, Kirschner C, Naumann D (2003) Characterization and identification of microorganisms by FT-IR microspectrometry. J Mol Struct 661–2:371–380
Nie M, Zhang WQ, Xiao M, Luo JL, Bao K, Chen JK, Li B (2007) FT-IR spectroscopy and artificial neural network identification of Fusarium species. J Phytopathol 155:364–367
NIST Chemistry WebBook (2014) NIST Chemistry WebBook. National Institute of Standards and Technology, Gaithersburg. http://webbook.nist.gov/chemistry/. Accessed 10 April 2014
Oberle-Kilic J, Dighton J, Arbuckle-Keil G (2013) Atomic force microscopy and micro-ATR-FT-IR imaging reveals fungal enzyme activity at the hyphal scale of resolution. Mycology 4:44–53
Pachler KGR, Matlok F, Gremlich H-U (1988) Merck FT-IR atlas. Wiley, Weinheim
Pallua JD, Recheis W, Pöder R, Pfaller K, Pezzei C, Hahn H, Huck-Pezzei V, Bittner LK, Schaefer G, Steiner E, Andre G, Hutwimmer S, Felber S, Pallua AK, Pallua AF, Bonn GK, Huck CW (2012) Morphological and tissue characterization of the medicinal fungus Hericium coralloides by a structural and molecular imaging platform. Analyst 137:1584–1595
Pandey KK, Pitman AJ (2003) FTIR studies of changes in wood chemistry following decay by brown-rot and white-rot fungi. Int Biodeterior Biodegradation 52:151–160
Peiris KHS, Bockus WW, Dowell FE (2012) Infrared spectral properties of germ, pericarp, and endosperm sections of sound wheat kernels and those damaged by Fusarium graminearum. Appl Spectrosc 66:1053–1060
Pena R, Lang C, Naumann A, Polle A (2014) Ectomycorrhizal identification in environmental samples of tree roots by Fourier-transform infrared (FTIR) spectroscopy. Front Plant Sci 229:1–9
Posch AE, Koch C, Helmel M, Marchetti-Deschmann M, Macfelda K, Lendl B, Allmaier G, Herwig C (2013) Combining light microscopy, dielectric spectroscopy, MALDI intact cell mass spectroscopy, FTIR spectromicroscopy and multivariate data mining for morphological and physiological bioprocess characterization of filamentous organisms. Fungl Genet Biol 51:1–11
Raab TK, Vogel JP (2004) Ecological and agricultural applications of synchrotron IR microscopy. Infrared Phys Technol 45:393–402
Rowlette J, Weida M, Bird B, Arnone D, Barre M, Day T (2014) High confidence, high-throughput screening with high-def IR microspectroscopy. BioOptics World 34–37. http://www.bioopticsworld.com/articles/print/volume-7/issue-2/features/clinical-pathology-drug-development-live-cell-imaging-high-confidence-high-throughput-screening-with-high-def-ir-microspectroscopy.html
Salem EZ, Shahin IMI, Mohammed YF, Abdo HM, Abdel Hamid MF, Emam HE et al (2010) Applicability of Fourier transform infrared (FT-IR) spectroscopy for rapid identification of some yeasts and dermatophytes isolated from superficial fungal infections. J Egypt Women Dermatol Soc 7:105–110
Salman A, Pomerantz A, Tsror L, Lapidot I, Zwielly A, Moreh R, Mordechai S, Huleihel M (2011) Distinction of Fusarium oxysporum fungal isolates (strains) using FTIR-ATR spectroscopy and advanced statistical methods. Analyst 136:988–995
Salman A, Pomerantz A, Tsror L, Lapidot I, Moreh R, Mordechai S, Huleihel M (2012) Utilizing FTIR-ATR spectroscopy for classification and relative spectral similarity evaluation of different Colletotrichum coccodes isolates. Analyst 137:3558–3564
Salzer R, Siesler HW (eds) (2009) Infrared and Raman spectroscopic imaging, 1st edn. Wiley, Weinheim
Salzer R, Siesler HW (eds) (2014) Infrared and Raman spectroscopic imaging, 2nd edn. Wiley, Weinheim
Salzer R, Steiner G, Mantsch HH, Mansfield J, Lewis EN (2000) Infrared and Raman imaging of biological and biomimetic samples. Fresenius J Anal Chem 366:712–726
Santos C, Fraga ME, Kozakiewicz Z, Lima N (2010) Fourier transform infrared as a powerful technique for the identification and characterization of filamentous fungi and yeasts. Res Microbiol 161:168–175
Schulz H, Baranska M (2007) Identification and quantification of valuable plant substances by IR and Raman spectroscopy. Vib Spectrosc 43:13–25
Schulz H, Krähmer A, Naumann A, Gudi G (2014) Infrared and Raman spectroscopic mapping and imaging of plant materials. In: Salzer R, Siesler HW (eds) Infrared and Raman spectroscopic imaging. Wiley, Weinheim, pp 227–293
Schwarze FWMR (2007) Wood decay under the microscope. Fungal Biol Rev 21:133–170
Shapaval V, Schmitt J, Møretrø T, Suso HP, Skaar I, Åsli AW, Lillehaug D, Kohler A (2012) Characterization of food spoilage fungi by FTIR spectroscopy. J Appl Microbiol 114:788–796
Singh CB, Jayas DS, Borondics F, White NDG (2011) Synchrotron based infrared imaging study of compositional changes in stored wheat due to infection with Aspergillus glaucus. J Stored Prod Res 47:372–7
Szeghalmi A, Kaminskyj S, Gough KG (2007) A synchrotron FTIR microspectroscopy investigation of fungal hyphae grown under optimal and stressed conditions. Anal Bioanal Chem 387:1779–1789
Timmins ÉM, Howell SA, Alsberg BK, Noble WC, Goodacre R (1998) Rapid differentiation of closely related Candida species and strains by pyrolysis-mass spectrometry and Fourier transform-infrared spectroscopy. J Clin Microbiol 36:367–374
Toubas D, Essendoubi M, Adt I, Pinon J-M, Manfait M, Sockalingum GD (2007) FTIR spectroscopy in medical mycology: applications to the differentiation and typing of Candida. Anal Bioanal Chem 387:1729–1737
Vongsvivut J, Heraud P, Gupta A, Puri M, McNaughton D, Barrow CJ (2013) FTIR microspectroscopy for rapid screening and monitoring of polyunsaturated fatty acid production in commercially valuable marine yeasts and protists. Analyst 138:6016–6031
Weißhaupt P, Naumann A, Pritzkow W, Noll M (2013) Nitrogen uptake of Hypholoma fasciculare and coexisting bacteria. Mycol Prog 12:283–290
Wenning M, Seiler H, Scherer S (2002) Fourier-transform infrared microspectroscopy, a novel and rapid tool for identification of yeasts. Appl Environ Microbiol 68:4717–4721
Zervakis GI, Bekiaris G, Tarantilis PA, Pappas CS (2012) Rapid strain classification and taxa delimitation within the edible mushroom genus Pleurotus through the use of diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy. Fungal Biol 116:715–728
Acknowledgements
AN thanks the reviewer Susan Kaminskyj, the editor Tanya Dahms, Susanne Wurst, and Hartwig Schulz for critical reading of the manuscript and valuable comments that improved the manuscript. Work related to publications labelled with superscript 1 was conducted by AN during 2010–2012 at BAM Federal Institute for Materials Research and Testing in division 4.1, Biology in Materials Protection and Environmental Issues, and division 6.3, Durability of Polymers.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Naumann, A. (2015). Fourier Transform Infrared (FTIR) Microscopy and Imaging of Fungi. In: Dahms, T., Czymmek, K. (eds) Advanced Microscopy in Mycology. Fungal Biology. Springer, Cham. https://doi.org/10.1007/978-3-319-22437-4_4
Download citation
DOI: https://doi.org/10.1007/978-3-319-22437-4_4
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-22436-7
Online ISBN: 978-3-319-22437-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)