1
|
Raman Method in Identification of Species and Varieties, Assessment of Plant Maturity and Crop Quality—A Review. Molecules 2022; 27:molecules27144454. [PMID: 35889327 PMCID: PMC9322835 DOI: 10.3390/molecules27144454] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023] Open
Abstract
The present review covers reports discussing potential applications of the specificity of Raman techniques in the advancement of digital farming, in line with an assumption of yield maximisation with minimum environmental impact of agriculture. Raman is an optical spectroscopy method which can be used to perform immediate, label-free detection and quantification of key compounds without destroying the sample. The authors particularly focused on the reports discussing the use of Raman spectroscopy in monitoring the physiological status of plants, assessing crop maturity and quality, plant pathology and ripening, and identifying plant species and their varieties. In recent years, research reports have presented evidence confirming the effectiveness of Raman spectroscopy in identifying biotic and abiotic stresses in plants as well as in phenotyping and digital selection of plants in farming. Raman techniques used in precision agriculture can significantly improve capacities for farming management, crop quality assessment, as well as biological and chemical contaminant detection, thereby contributing to food safety as well as the productivity and profitability of agriculture. This review aims to increase the awareness of the growing potential of Raman spectroscopy in agriculture among plant breeders, geneticists, farmers and engineers.
Collapse
|
2
|
Saletnik A, Saletnik B, Puchalski C. Overview of Popular Techniques of Raman Spectroscopy and Their Potential in the Study of Plant Tissues. Molecules 2021; 26:1537. [PMID: 33799702 PMCID: PMC7999012 DOI: 10.3390/molecules26061537] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 01/15/2023] Open
Abstract
Raman spectroscopy is one of the main analytical techniques used in optical metrology. It is a vibration, marker-free technique that provides insight into the structure and composition of tissues and cells at the molecular level. Raman spectroscopy is an outstanding material identification technique. It provides spatial information of vibrations from complex biological samples which renders it a very accurate tool for the analysis of highly complex plant tissues. Raman spectra can be used as a fingerprint tool for a very wide range of compounds. Raman spectroscopy enables all the polymers that build the cell walls of plants to be tracked simultaneously; it facilitates the analysis of both the molecular composition and the molecular structure of cell walls. Due to its high sensitivity to even minute structural changes, this method is used for comparative tests. The introduction of new and improved Raman techniques by scientists as well as the constant technological development of the apparatus has resulted in an increased importance of Raman spectroscopy in the discovery and defining of tissues and the processes taking place in them.
Collapse
Affiliation(s)
| | - Bogdan Saletnik
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszów, Ćwiklińskiej 2D, 35-601 Rzeszów, Poland; (A.S.); (C.P.)
| | | |
Collapse
|
3
|
Korinth F, Mondol AS, Stiebing C, Schie IW, Krafft C, Popp J. New methodology to process shifted excitation Raman difference spectroscopy data: a case study of pollen classification. Sci Rep 2020; 10:11215. [PMID: 32641779 PMCID: PMC7343813 DOI: 10.1038/s41598-020-67897-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/15/2020] [Indexed: 02/07/2023] Open
Abstract
Shifted excitation Raman difference spectroscopy (SERDS) is a background correction method for Raman spectroscopy. Here, the difference spectra were directly used as input for SERDS-based classification after an optimization procedure to correct for photobleaching of the autofluorescence. Further processing included a principal component analysis to compensate for the reduced signal to noise ratio of the difference spectra and subsequent classification by linear discriminant analysis. As a case study 6,028 Raman spectra of single pollen originating from plants of eight different genera and four different growth habits were automatically recorded at excitation wavelengths 784 and 786 nm using a high-throughput screening Raman system. Different pollen were distinguished according to their growth habit, i.e. tree versus non-tree with an accuracy of 95.9%. Furthermore, all pollen were separated according to their genus, providing also insight into similarities based on their families. Classification results were compared using spectra reconstructed from the differences and raw spectra after state-of-art baseline correction as input. Similar sensitivities, specificities, accuracies and precisions were found for all spectra with moderately background. Advantages of SERDS are expected in scenarios where Raman spectra are affected by variations due to detector etaloning, ambient light, and high background.
Collapse
Affiliation(s)
- F Korinth
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - A S Mondol
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - C Stiebing
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - I W Schie
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745, Jena, Germany.,Department of Medical Engineering and Biotechnology, University of Applied Sciences, Carl-Zeiss-Promenade 2, 07745, Jena, Germany
| | - C Krafft
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745, Jena, Germany.
| | - J Popp
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745, Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
| |
Collapse
|
4
|
Kenđel A, Zimmermann B. Chemical Analysis of Pollen by FT-Raman and FTIR Spectroscopies. FRONTIERS IN PLANT SCIENCE 2020; 11:352. [PMID: 32296453 PMCID: PMC7136416 DOI: 10.3389/fpls.2020.00352] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/10/2020] [Indexed: 05/13/2023]
Abstract
Pollen studies are important for the assessment of present and past environment, including biodiversity, sexual reproduction of plants and plant-pollinator interactions, monitoring of aeroallergens, and impact of climate and pollution on wild communities and cultivated crops. Although information on chemical composition of pollen is of importance in all of those research areas, pollen chemistry has been rarely measured due to complex and time-consuming analyses. Vibrational spectroscopies, coupled with multivariate data analysis, have shown great potential for rapid chemical characterization, identification and classification of pollen. This study, comprising 219 species from all principal taxa of seed plants, has demonstrated that high-quality Raman spectra of pollen can be obtained by Fourier transform (FT) Raman spectroscopy. In combination with Fourier transform infrared spectroscopy (FTIR), FT-Raman spectroscopy is obtaining comprehensive information on pollen chemistry. Presence of all the main biochemical constituents of pollen, such as proteins, lipids, carbohydrates, carotenoids and sporopollenins, have been identified and detected in the spectra, and the study shows approaches to measure relative and absolute content of these constituents. The results show that FT-Raman spectroscopy has clear advantage over standard dispersive Raman measurements, in particular for measurement of pollen samples with high pigment content. FT-Raman spectra are strongly biased toward chemical composition of pollen wall constituents, namely sporopollenins and pigments. This makes Raman spectra complementary to FTIR spectra, which over-represent chemical constituents of the grain interior, such as lipids and carbohydrates. The results show a large variability in pollen chemistry for families, genera and even congeneric species, revealing wide range of reproductive strategies, from storage of nutrients to variation in carotenoids and phenylpropanoids. The information on pollen's chemical patterns for major plant taxa should be of outstanding value for various studies in plant biology and ecology, including aerobiology, palaeoecology, forensics, community ecology, plant-pollinator interactions, and climate effects on plants.
Collapse
Affiliation(s)
- Adriana Kenđel
- Division of Analytical Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Boris Zimmermann
- Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| |
Collapse
|
5
|
Mondol AS, Patel MD, Rüger J, Stiebing C, Kleiber A, Henkel T, Popp J, Schie IW. Application of High-Throughput Screening Raman Spectroscopy (HTS-RS) for Label-Free Identification and Molecular Characterization of Pollen. SENSORS 2019; 19:s19204428. [PMID: 31614861 PMCID: PMC6832956 DOI: 10.3390/s19204428] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/23/2019] [Accepted: 10/10/2019] [Indexed: 12/26/2022]
Abstract
Pollen studies play a critical role in various fields of science. In the last couple of decades, replacement of manual identification of pollen by image-based methods using pollen morphological features was a great leap forward, but challenges for pollen with similar morphology remain, and additional approaches are required. Spectroscopy approaches for identification of pollen, such as Raman spectroscopy has potential benefits over traditional methods, due to the investigation of the intrinsic molecular composition of a sample. However, current Raman-based characterization of pollen is complex and time-consuming, resulting in low throughput and limiting the statistical significance of the acquired data. Previously demonstrated high-throughput screening Raman spectroscopy (HTS-RS) eliminates the complexity as well as human interaction by incorporation full automation of the data acquisition process. Here, we present a customization of HTS-RS for pollen identification, enabling sampling of a large number of pollen in comparison to other state-of-the-art Raman pollen investigations. We show that using Raman spectra we are able to provide a preliminary estimation of pollen types based on growth habits using hierarchical cluster analysis (HCA) as well as good taxonomy of 37 different Pollen using principal component analysis-support vector machine (PCA-SVM) with good accuracy even for the pollen specimens sharing similar morphological features. Our results suggest that HTS-RS platform meets the demands for automated pollen detection making it an alternative method for research concerning pollen.
Collapse
Affiliation(s)
- Abdullah S Mondol
- Leibniz Institute of Photonic Technology, Albert Einstein Str. 9, 07745 Jena, Germany.
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany.
| | - Milind D Patel
- Leibniz Institute of Photonic Technology, Albert Einstein Str. 9, 07745 Jena, Germany.
| | - Jan Rüger
- Leibniz Institute of Photonic Technology, Albert Einstein Str. 9, 07745 Jena, Germany.
| | - Clara Stiebing
- Leibniz Institute of Photonic Technology, Albert Einstein Str. 9, 07745 Jena, Germany.
| | - Andreas Kleiber
- Leibniz Institute of Photonic Technology, Albert Einstein Str. 9, 07745 Jena, Germany.
| | - Thomas Henkel
- Leibniz Institute of Photonic Technology, Albert Einstein Str. 9, 07745 Jena, Germany.
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology, Albert Einstein Str. 9, 07745 Jena, Germany.
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany.
| | - Iwan W Schie
- Leibniz Institute of Photonic Technology, Albert Einstein Str. 9, 07745 Jena, Germany.
- Department of Medical Engineering and Biotechnology, University of Applied Sciences - Jena, Carl-Zeiss Promenade 2, 07745 Jena, Germany.
| |
Collapse
|
6
|
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) shows adaptation of grass pollen composition. Sci Rep 2018; 8:16591. [PMID: 30409982 PMCID: PMC6224550 DOI: 10.1038/s41598-018-34800-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/22/2018] [Indexed: 11/22/2022] Open
Abstract
MALDI time-of-flight mass spectrometry (MALDI-TOF MS) has become a widely used tool for the classification of biological samples. The complex chemical composition of pollen grains leads to highly specific, fingerprint-like mass spectra, with respect to the pollen species. Beyond the species-specific composition, the variances in pollen chemistry can be hierarchically structured, including the level of different populations, of environmental conditions or different genotypes. We demonstrate here the sensitivity of MALDI-TOF MS regarding the adaption of the chemical composition of three Poaceae (grass) pollen for different populations of parent plants by analyzing the mass spectra with partial least squares discriminant analysis (PLS-DA) and principal component analysis (PCA). Thereby, variances in species, population and specific growth conditions of the plants were observed simultaneously. In particular, the chemical pattern revealed by the MALDI spectra enabled discrimination of the different populations of one species. Specifically, the role of environmental changes and their effect on the pollen chemistry of three different grass species is discussed. Analysis of the group formation within the respective populations showed a varying influence of plant genotype on the classification, depending on the species, and permits conclusions regarding the respective rigidity or plasticity towards environmental changes.
Collapse
|
7
|
Lauer F, Diehn S, Seifert S, Kneipp J, Sauerland V, Barahona C, Weidner S. Multivariate Analysis of MALDI Imaging Mass Spectrometry Data of Mixtures of Single Pollen Grains. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2237-2247. [PMID: 30043358 DOI: 10.1007/s13361-018-2036-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/26/2018] [Accepted: 07/09/2018] [Indexed: 05/09/2023]
Abstract
Mixtures of pollen grains of three different species (Corylus avellana, Alnus cordata, and Pinus sylvestris) were investigated by matrix-assisted laser desorption/ionization time-of-flight imaging mass spectrometry (MALDI-TOF imaging MS). The amount of pollen grains was reduced stepwise from > 10 to single pollen grains. For sample pretreatment, we modified a previously applied approach, where any additional extraction steps were omitted. Our results show that characteristic pollen MALDI mass spectra can be obtained from a single pollen grain, which is the prerequisite for a reliable pollen classification in practical applications. MALDI imaging of laterally resolved pollen grains provides additional information by reducing the complexity of the MS spectra of mixtures, where frequently peak discrimination is observed. Combined with multivariate statistical analyses, such as principal component analysis (PCA), our approach offers the chance for a fast and reliable identification of individual pollen grains by mass spectrometry. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Franziska Lauer
- Bundesanstalt für Materialforschung und-prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany
- Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Sabrina Diehn
- Bundesanstalt für Materialforschung und-prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany
- Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Stephan Seifert
- Bundesanstalt für Materialforschung und-prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany
- Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Janina Kneipp
- Bundesanstalt für Materialforschung und-prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany
- Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Volker Sauerland
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Cesar Barahona
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Steffen Weidner
- Bundesanstalt für Materialforschung und-prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany.
| |
Collapse
|
8
|
Heiner Z, Zeise I, Elbaum R, Kneipp J. Insight into plant cell wall chemistry and structure by combination of multiphoton microscopy with Raman imaging. JOURNAL OF BIOPHOTONICS 2018; 11:e201700164. [PMID: 29024576 DOI: 10.1002/jbio.201700164] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/08/2017] [Accepted: 10/10/2017] [Indexed: 06/07/2023]
Abstract
Spontaneous Raman scattering microspectroscopy, second harmonic generation (SHG) and 2-photon excited fluorescence (2PF) were used in combination to characterize the morphology together with the chemical composition of the cell wall in native plant tissues. As the data obtained with unstained sections of Sorghum bicolor root and leaf tissues illustrate, nonresonant as well as pre-resonant Raman microscopy in combination with hyperspectral analysis reveals details about the distribution and composition of the major cell wall constituents. Multivariate analysis of the Raman data allows separation of different tissue regions, specifically the endodermis, xylem and lumen. The orientation of cellulose microfibrils is obtained from polarization-resolved SHG signals. Furthermore, 2-photon autofluorescence images can be used to image lignification. The combined compositional, morphological and orientational information in the proposed coupling of SHG, Raman imaging and 2PF presents an extension of existing vibrational microspectroscopic imaging and multiphoton microscopic approaches not only for plant tissues.
Collapse
Affiliation(s)
- Zsuzsanna Heiner
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
- SALSA School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ingrid Zeise
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Rivka Elbaum
- The Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Janina Kneipp
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
- SALSA School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
9
|
Zeise I, Heiner Z, Holz S, Joester M, Büttner C, Kneipp J. Raman Imaging of Plant Cell Walls in Sections of Cucumis sativus. PLANTS 2018; 7:plants7010007. [PMID: 29370089 PMCID: PMC5874596 DOI: 10.3390/plants7010007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/19/2018] [Accepted: 01/23/2018] [Indexed: 12/25/2022]
Abstract
Raman microspectra combine information on chemical composition of plant tissues with spatial information. The contributions from the building blocks of the cell walls in the Raman spectra of plant tissues can vary in the microscopic sub-structures of the tissue. Here, we discuss the analysis of 55 Raman maps of root, stem, and leaf tissues of Cucumis sativus, using different spectral contributions from cellulose and lignin in both univariate and multivariate imaging methods. Imaging based on hierarchical cluster analysis (HCA) and principal component analysis (PCA) indicates different substructures in the xylem cell walls of the different tissues. Using specific signals from the cell wall spectra, analysis of the whole set of different tissue sections based on the Raman images reveals differences in xylem tissue morphology. Due to the specifics of excitation of the Raman spectra in the visible wavelength range (532 nm), which is, e.g., in resonance with carotenoid species, effects of photobleaching and the possibility of exploiting depletion difference spectra for molecular characterization in Raman imaging of plants are discussed. The reported results provide both, specific information on the molecular composition of cucumber tissue Raman spectra, and general directions for future imaging studies in plant tissues.
Collapse
Affiliation(s)
- Ingrid Zeise
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Zsuzsanna Heiner
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
- School of Analytical Sciences Adlershof SALSA, Humboldt-Universität zu Berlin, Albert-Einstein-Str. 5-9, 12489 Berlin, Germany.
| | - Sabine Holz
- Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55/57, 14195 Berlin, Germany.
| | - Maike Joester
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
- BAM Federal Institute for Materials Research and Testing, Richard-Willstatter-Straße 11, 12489 Berlin, Germany.
| | - Carmen Büttner
- Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55/57, 14195 Berlin, Germany.
| | - Janina Kneipp
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
- School of Analytical Sciences Adlershof SALSA, Humboldt-Universität zu Berlin, Albert-Einstein-Str. 5-9, 12489 Berlin, Germany.
| |
Collapse
|
10
|
Joester M, Seifert S, Emmerling F, Kneipp J. Physiological influence of silica on germinating pollen as shown by Raman spectroscopy. JOURNAL OF BIOPHOTONICS 2017; 10:542-552. [PMID: 27174545 DOI: 10.1002/jbio.201600011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/22/2016] [Accepted: 04/22/2016] [Indexed: 05/09/2023]
Abstract
The process of silicification in plants and the biochemical effects of silica in plant tissues are largely unknown. To study the molecular changes occurring in growing cells that are exposed to higher than normal concentration of silicic acid, Raman spectra of germinating pollen grains of three species (Pinus nigra, Picea omorika, and Camellia japonica) were analyzed in a multivariate classification approach that takes into account the variation of biochemical composition due to species, plant tissue structure, and germination condition. The results of principal component analyses of the Raman spectra indicate differences in the utilization of stored lipids, a changed mobilization of storage carbohydrates in the pollen grain bodies, and altered composition and/or structure of cellulose of the developing pollen tube cell walls. These biochemical changes vary in the different species.
Collapse
Affiliation(s)
- Maike Joester
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Stephan Seifert
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Franziska Emmerling
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Janina Kneipp
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| |
Collapse
|
11
|
Seifert S, Merk V, Kneipp J. Identification of aqueous pollen extracts using surface enhanced Raman scattering (SERS) and pattern recognition methods. JOURNAL OF BIOPHOTONICS 2016; 9:181-9. [PMID: 26249322 DOI: 10.1002/jbio.201500176] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/09/2015] [Accepted: 07/09/2015] [Indexed: 05/09/2023]
Abstract
Aqueous pollen extracts of varying taxonomic relations were analyzed with surface enhanced Raman scattering (SERS) by using gold nanoparticles in aqueous suspensions as SERS substrate. This enables a selective vibrational characterization of the pollen water soluble fraction (mostly cellular components) devoid of the spectral contributions from the insoluble sporopollenin outer layer. The spectra of the pollen extracts are species-specific, and the chemical fingerprints can be exploited to achieve a classification that can distinguish between different species of the same genus. In the simple experimental procedure, several thousands of spectra per species are generated. Using an artificial neural network (ANN), it is demonstrated that analysis of the intrinsic biochemical information of the pollen cells in the SERS data enables the identification of pollen from different plant species at high accuracy. The ANN extracts the taxonomically-relevant information from the data in spite of high intra-species spectral variation caused by signal fluctuations and preparation specifics. The results show that SERS can be used for the reliable characterization and identification of pollen samples. They have implications for improved investigation of pollen physiology and for allergy warning.
Collapse
Affiliation(s)
- Stephan Seifert
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Straße 2, 12489, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Virginia Merk
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Janina Kneipp
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Straße 2, 12489, Berlin, Germany.
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany.
| |
Collapse
|
12
|
Zimmermann B, Bağcıoğlu M, Sandt C, Kohler A. Vibrational microspectroscopy enables chemical characterization of single pollen grains as well as comparative analysis of plant species based on pollen ultrastructure. PLANTA 2015; 242:1237-50. [PMID: 26289829 DOI: 10.1007/s00425-015-2380-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 08/07/2015] [Indexed: 05/27/2023]
Abstract
Chemical imaging of pollen by vibrational microspectroscopy enables characterization of pollen ultrastructure, in particular phenylpropanoid components in grain wall for comparative study of extant and extinct plant species. A detailed characterization of conifer (Pinales) pollen by vibrational microspectroscopy is presented. The main problems that arise during vibrational measurements were scatter and saturation issues in Fourier transform infrared (FTIR), and fluorescence and penetration depth issues in Raman. Single pollen grains larger than approx. 15 µm can be measured by FTIR microspectroscopy using conventional light sources, while smaller grains may be measured by employing synchrotron light sources. Pollen grains that were larger than 50 µm were too thick for FTIR imaging since the grain constituents absorbed almost all infrared light. Chemical images of pollen were obtained on sectioned samples, unveiling the distribution and concentration of proteins, carbohydrates, sporopollenins and lipids within pollen substructures. The comparative analysis of pollen species revealed that, compared with other Pinales pollens, Cedrus atlantica has a higher relative amount of lipid nutrients, as well as different chemical composition of grain wall sporopollenin. The pre-processing and data analysis, namely extended multiplicative signal correction and principal component analysis, offer simple estimate of imaging spectral data and indirect estimation of physical properties of pollen. The vibrational microspectroscopy study demonstrates that detailed chemical characterization of pollen can be obtained by measurement of an individual grain and pollen ultrastructure. Measurement of phenylpropanoid components in pollen grain wall could be used, not only for the reconstruction of past environments, but for assessment of diversity of plant species as well. Therefore, analysis of extant and extinct pollen species by vibrational spectroscopies is suggested as a valuable tool in biology, ecology and palaeosciences.
Collapse
Affiliation(s)
- Boris Zimmermann
- Department of Mathematical Sciences and Technology, Faculty of Environmental Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, 1430, Ås, Norway.
| | - Murat Bağcıoğlu
- Department of Mathematical Sciences and Technology, Faculty of Environmental Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, 1430, Ås, Norway.
| | - Christophe Sandt
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France.
| | - Achim Kohler
- Department of Mathematical Sciences and Technology, Faculty of Environmental Science and Technology, Norwegian University of Life Sciences, Drøbakveien 31, 1430, Ås, Norway.
- Nofima AS, Osloveien 1, 1430, Ås, Norway.
| |
Collapse
|
13
|
Seifert S, Weidner SM, Panne U, Kneipp J. Taxonomic relationships of pollens from matrix-assisted laser desorption/ionization time-of-flight mass spectrometry data using multivariate statistics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1145-54. [PMID: 25981545 DOI: 10.1002/rcm.7207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/01/2015] [Accepted: 04/01/2015] [Indexed: 05/09/2023]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been suggested as a promising tool for the investigation of pollen, but the usefulness of this approach for classification and identification of pollen species has to be proven by an application to samples of varying taxonomic relations. METHOD MALDI-MS in combination with hierarchical cluster analysis (HCA) and principal component analysis (PCA) was used to delineate taxonomic relations between plants based on pollen biochemistry. To assess the robustness of the approach, pollen of 74 species of the plant orders Fagales and Coniferales were probed. RESULTS Discrimination at the levels of plant order and genus were achieved using the whole spectral range. In many cases, different species of the same genus could be distinguished. The sources of the spectral/chemical differences at the genus level can be understood using PCA. Specifically, typical mass regions for exact genus detection were identified. CONCLUSIONS Our results indicate that the chemical information represented by MALDI-TOFMS data is useful for reconstructing taxonomic relationships and is complementary to other chemical information on pollen from other spectroscopic data.
Collapse
Affiliation(s)
- Stephan Seifert
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Straße 2, 12489, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Steffen M Weidner
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Ulrich Panne
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Straße 2, 12489, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Janina Kneipp
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor-Straße 2, 12489, Berlin, Germany
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| |
Collapse
|
14
|
Zimmermann B, Kohler A. Infrared spectroscopy of pollen identifies plant species and genus as well as environmental conditions. PLoS One 2014; 9:e95417. [PMID: 24748390 PMCID: PMC3991668 DOI: 10.1371/journal.pone.0095417] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 03/27/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND It is imperative to have reliable and timely methodologies for analysis and monitoring of seed plants in order to determine climate-related plant processes. Moreover, impact of environment on plant fitness is predominantly based on studies of female functions, while the contribution of male gametophytes is mostly ignored due to missing data on pollen quality. We explored the use of infrared spectroscopy of pollen for an inexpensive and rapid characterization of plants. METHODOLOGY The study was based on measurement of pollen samples by two Fourier transform infrared techniques: single reflectance attenuated total reflectance and transmission measurement of sample pellets. The experimental set, with a total of 813 samples, included five pollination seasons and 300 different plant species belonging to all principal spermatophyte clades (conifers, monocotyledons, eudicots, and magnoliids). RESULTS The spectroscopic-based methodology enables detection of phylogenetic variations, including the separation of confamiliar and congeneric species. Furthermore, the methodology enables measurement of phenotypic plasticity by the detection of inter-annual variations within the populations. The spectral differences related to environment and taxonomy are interpreted biochemically, specifically variations of pollen lipids, proteins, carbohydrates, and sporopollenins. The study shows large variations of absolute content of nutrients for congenital species pollinating in the same environmental conditions. Moreover, clear correlation between carbohydrate-to-protein ratio and pollination strategy has been detected. Infrared spectral database with respect to biochemical variation among the range of species, climate and biogeography will significantly improve comprehension of plant-environment interactions, including impact of global climate change on plant communities.
Collapse
Affiliation(s)
- Boris Zimmermann
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Achim Kohler
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway
| |
Collapse
|
15
|
Weidner S, Schultze RD, Enthaler B. Matrix-assisted laser desorption/ionization imaging mass spectrometry of pollen grains and their mixtures. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:896-903. [PMID: 23495059 DOI: 10.1002/rcm.6523] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 01/22/2013] [Accepted: 01/28/2013] [Indexed: 05/24/2023]
Abstract
RATIONALE The fast and univocal identification of different species in mixtures of pollen grains is still a challenge. Apart from microscopic evaluation and Raman spectroscopy, no other techniques are available. METHODS Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry was applied to the analysis of extracts of single pollen grains and pollen mixtures. Pollen grains were fixed, treated and covered with matrix directly on the MALDI target. RESULTS Clearly resolved MALDI ion intensity images could be obtained enabling the identification of single pollen grains in a mixture. CONCLUSIONS Our results demonstrate the potential and the suitability of MALDI imaging mass spectrometry as an additional method for the identification of pollen mixtures.
Collapse
Affiliation(s)
- Steffen Weidner
- BAM-Federal Institute for Materials Research and Testing, Richard Willstaetter-Strasse 11, D-12489, Berlin, Germany.
| | | | | |
Collapse
|
16
|
Krause B, Seifert S, Panne U, Kneipp J, Weidner SM. Matrix-assisted laser desorption/ionization mass spectrometric investigation of pollen and their classification by multivariate statistics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1032-8. [PMID: 22467452 DOI: 10.1002/rcm.6202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
RATIONALE A fast and reliable online identification of pollen is not yet available. The identification of pollen is based mainly on the evaluation of morphological data obtained by microscopic methods. METHODS Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) was applied to the analysis of extracts and milled pollen samples. The obtained MALDI data were explored for characteristic peak patterns which could be subjected to a multivariate statistical analysis. RESULTS Two sample preparation methods are presented, which require only minimal or no chemical extraction of the pollen. MALDI pollen spectra could be recorded showing various peak patterns. A multivariate statistics approach allowed the classification of pollen into clusters indicating similarities and differences between various species. CONCLUSIONS These results demonstrate the potential and the reliability of MALDI-TOF MS for the identification and, in combination with multivariate statistics, also for the classification of pollen.
Collapse
Affiliation(s)
- Benjamin Krause
- BAM Federal Institute for Materials Research and Testing, Analytical Chemistry, Richard-Willstätter-Str. 11, D-12489, Berlin, Germany
| | | | | | | | | |
Collapse
|
17
|
Drescher D, Kneipp J. Nanomaterials in complex biological systems: insights from Raman spectroscopy. Chem Soc Rev 2012; 41:5780-99. [DOI: 10.1039/c2cs35127g] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|