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Jain E, Rose M, Jayapal PK, Singh GP, Ram RJ. Harnessing Raman spectroscopy for the analysis of plant diversity. Sci Rep 2024; 14:12692. [PMID: 38830877 PMCID: PMC11148151 DOI: 10.1038/s41598-024-62932-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
Here, we explore the application of Raman spectroscopy for the assessment of plant biodiversity. Raman spectra from 11 vascular plant species commonly found in forest ecosystems, specifically angiosperms (both monocots and eudicots) and pteridophytes (ferns), were acquired in vivo and in situ using a Raman leaf-clip. We achieved an overall accuracy of 91% for correct classification of a species within a plant group and identified lignin Raman spectral features as a useful discriminator for classification. The results demonstrate the potential of Raman spectroscopy in contributing to plant biodiversity assessment.
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Affiliation(s)
- Ekta Jain
- Disruptive and Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, 1 Create Way, 03-06/07/8 Research Wing, Singapore, 138602, Singapore
| | - Michelle Rose
- Disruptive and Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, 1 Create Way, 03-06/07/8 Research Wing, Singapore, 138602, Singapore
| | - Praveen Kumar Jayapal
- Disruptive and Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, 1 Create Way, 03-06/07/8 Research Wing, Singapore, 138602, Singapore
| | - Gajendra P Singh
- Disruptive and Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, 1 Create Way, 03-06/07/8 Research Wing, Singapore, 138602, Singapore
| | - Rajeev J Ram
- Disruptive and Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, 1 Create Way, 03-06/07/8 Research Wing, Singapore, 138602, Singapore.
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 36-491, Cambridge, MA, 02139, USA.
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Payne TD, Dixon LR, Schmidt FC, Blakeslee JJ, Bennett AE, Schultz ZD. Identification and quantification of pigments in plant leaves using thin layer chromatography-Raman spectroscopy (TLC-Raman). ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:2449-2455. [PMID: 38563199 DOI: 10.1039/d4ay00082j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Carotenoids are yellow, orange, and red pigments commonly found in plants. In leaves, these molecules are essential for photosynthesis, but they also play a major role in plant growth and development. Efficiently monitoring concentrations of specific carotenoids in plant tissues could help to explain plant responses to environmental stressors, infection and disease, fertilization, and other conditions. Previously, Raman methods have been used to demonstrate a correlation between plant fitness and the carotenoid content of leaves. Due to solvatochromatic effects and structural similarities within the carotenoid family, current Raman spectroscopy techniques struggle to assign signals to specific carotenoids with certainty, complicating the determination of amounts of individual carotenoids present in a sample. In this work, we use thin layer chromatography-Raman spectroscopy, or TLC-Raman, to identify and quantify carotenoids extracted from tomato leaves. These quick and accurate methods could be applied to study the relationship between pigment content and a number of factors affecting plant health.
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Affiliation(s)
- Taylor D Payne
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Lily R Dixon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Fiona C Schmidt
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Joshua J Blakeslee
- Department of Horticulture and Crop Sciences, The Ohio State University, Columbus, Ohio 43210, USA
- Laboratory for the Analysis of Metabolites from Plants (LAMP) Metabolomics Facility, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Alison E Bennett
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Zachary D Schultz
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
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Juárez ID, Dou T, Biswas S, Septiningsih EM, Kurouski D. Diagnosing arsenic-mediated biochemical responses in rice cultivars using Raman spectroscopy. FRONTIERS IN PLANT SCIENCE 2024; 15:1371748. [PMID: 38590750 PMCID: PMC10999542 DOI: 10.3389/fpls.2024.1371748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/05/2024] [Indexed: 04/10/2024]
Abstract
Rice (Oryza sativa) is the primary crop for nearly half of the world's population. Groundwater in many rice-growing parts of the world often has elevated levels of arsenite and arsenate. At the same time, rice can accumulate up to 20 times more arsenic compared to other staple crops. This places an enormous amount of people at risk of chronic arsenic poisoning. In this study, we investigated whether Raman spectroscopy (RS) could be used to diagnose arsenic toxicity in rice based on biochemical changes that were induced by arsenic accumulation. We modeled arsenite and arsenate stresses in four different rice cultivars grown in hydroponics over a nine-day window. Our results demonstrate that Raman spectra acquired from rice leaves, coupled with partial least squares-discriminant analysis, enabled accurate detection and identification of arsenic stress with approximately 89% accuracy. We also performed high-performance liquid chromatography (HPLC)-analysis of rice leaves to identify the key molecular analytes sensed by RS in confirming arsenic poisoning. We found that RS primarily detected a decrease in the concentration of lutein and an increase in the concentration of vanillic and ferulic acids due to the accumulation of arsenite and arsenate in rice. This showed that these molecules are detectable indicators of biochemical response to arsenic accumulation. Finally, a cross-correlation of RS with HPLC and ICP-MS demonstrated RS's potential for a label-free, non-invasive, and non-destructive quantification of arsenic accumulation in rice.
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Affiliation(s)
- Isaac D. Juárez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, TX, United States
| | - Tianyi Dou
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Sudip Biswas
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, TX, United States
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Juárez ID, Steczkowski MX, Chinnaiah S, Rodriguez A, Gadhave KR, Kurouski D. Using Raman spectroscopy for early detection of resistance-breaking strains of tomato spotted wilt orthotospovirus in tomatoes. FRONTIERS IN PLANT SCIENCE 2024; 14:1283399. [PMID: 38235194 PMCID: PMC10791937 DOI: 10.3389/fpls.2023.1283399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 12/08/2023] [Indexed: 01/19/2024]
Abstract
Tomato spotted wilt (TSW) disease caused by tomato spotted wilt orthotospovirus (TSWV, Orthotospovirus tomatomaculae) poses a significant threat to specialty and staple crops worldwide by causing over a billion dollars in crop losses annually. Current strategies for TSWV diagnosis heavily rely on nucleic acid or protein-based techniques which require significant technical expertise, and are invasive, time-consuming, and expensive, thereby catalyzing the search for better alternatives. In this study, we explored the potential of Raman spectroscopy (RS) in early detection of TSW in a non-invasive and non-destructive manner. Specifically, we investigated whether RS could be used to detect strain specific TSW symptoms associated with four TSWV strains infecting three differentially resistant tomato cultivars. In the acquired spectra, we observed notable reductions in the intensity of vibrational peaks associated with carotenoids. Using high-performance liquid chromatography (HPLC), we confirmed that TSWV caused a substantial decrease in the concentration of lutein that was detected by RS. Finally, we demonstrated that Partial Least Squares-Discriminant Analysis (PLS-DA) could be used to differentiate strain-specific TSW symptoms across all tested cultivars. These results demonstrate that RS can be a promising solution for early diagnosis of TSW, enabling timely disease intervention and thereby mitigating crop losses inflicted by TSWV.
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Affiliation(s)
- Isaac D. Juárez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, TX, United States
| | | | | | - Axell Rodriguez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, TX, United States
| | - Kiran R. Gadhave
- Department of Entomology, Texas A&M University, College Station, Texas, TX, United States
- Texas A&M AgriLife Research, Amarillo, Texas, TX, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, TX, United States
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Holman AP, Goff NK, Juárez ID, Higgins S, Rodriguez A, Bagavathiannan M, Kurouski D, Subramanian N. Elucidation of sex from mature Palmer amaranth ( Amaranthus palmeri) leaves using a portable Raman spectrometer. RSC Adv 2024; 14:1833-1837. [PMID: 38192310 PMCID: PMC10772952 DOI: 10.1039/d3ra06368b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/01/2024] [Indexed: 01/10/2024] Open
Abstract
Palmer amaranth (Amaranthus palmeri) is a pervasive and troublesome weed species that poses significant challenges to agriculture in the United States. Identifying the sex of Palmer amaranth plants is crucial for developing tailored control measures due to the distinct characteristics and reproductive strategies exhibited by male and female plants. Traditional methods for sex determination are expensive and time-consuming, but recent advancements in spectroscopic techniques offer new possibilities. This study explores the potential of portable Raman spectroscopy for determining the sex of mature Palmer amaranth plants in-field. Raman analysis of the plant leaves reveals spectral differences associated with nitrate salts, lipids, carotenoids, and terpenoids, allowing for high accuracy and reliable identification of the plant's sex; male plants had higher concentrations of these compounds compared to females. It was also found that male plants had higher concentrations of these compounds compared to the females. Raman spectra were analyzed using a machine learning tool, partial least squares discriminant analysis (PLS-DA), to generate accuracies of no less than 83.7% when elucidating sex from acquired spectra. These findings provide insights into the sex-specific characteristics of Palmer amaranth and suggest that Raman analysis, combined with PLS-DA, can be a promising, non-destructive, and efficient method for sex determination in field settings. This approach has implications for developing sex-specific management strategies to monitor and control this invasive weed in real-world environments, benefiting farmers, agronomists, researchers, and master gardeners.
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Affiliation(s)
- Aidan P Holman
- Department of Entomology, Texas A&M University College Station Texas 77843 USA
- Department of Biochemistry and Biophysics, Texas A&M University College Station Texas 77843 USA
| | - Nicolas K Goff
- Department of Biochemistry and Biophysics, Texas A&M University College Station Texas 77843 USA
- The University of Texas at Austin Dell Medical School Austin Texas 78712 USA
| | - Isaac D Juárez
- Department of Biochemistry and Biophysics, Texas A&M University College Station Texas 77843 USA
| | - Samantha Higgins
- Department of Biochemistry and Biophysics, Texas A&M University College Station Texas 77843 USA
| | - Axell Rodriguez
- Department of Biochemistry and Biophysics, Texas A&M University College Station Texas 77843 USA
| | | | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University College Station Texas 77843 USA
- Institute for Advancing Health Through Agriculture College Station Texas 77843 USA
| | - Nithya Subramanian
- Department of Soil and Crop Sciences, Texas A&M University College Station Texas 77843 USA
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Steczkowski M, McClellan K, Jessup R, Kurouski D. Raman-based diagnostics of drought, heat and light-induced stresses in three different varieties of hemp. PLANTA 2023; 259:21. [PMID: 38091099 DOI: 10.1007/s00425-023-04299-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023]
Abstract
MAIN CONCLUSION Hand-held Raman spectroscopy can be used for highly accurate differentiation between drought, heat and light-triggered stresses in hemp. The differentiation is based on the changes in the biochemistry of plants caused by such stresses. Hemp farming is a rapidly growing industry. This dioecious plant is primarily cultivated for its fibers, seeds, and cannabinoid-rich oils. The yield of these materials can be drastically lowered by many abiotic stresses, such as drought, heat and light. It becomes critically important to develop robust and reliable approaches that can be used to diagnose such abiotic stresses in hemp. In this study, we investigate the accuracy of Raman spectroscopy, an emerging tool within crop monitoring, in the confirmatory identification of drought, heat, and light-induced stresses in three varieties of hemp. Our results showed that mono, double and triple stresses uniquely alter plant biochemistry that results in small spectroscopic changes detected in the Raman spectra acquired from the hemp leaves. These changes could be used for the 80-100% accurate identification of individual abiotic stresses and their combinations in plants. These results demonstrate that a hand-held Raman spectrometer can be used for highly accurate, non-invasive, non-destructive, and label-free diagnostics of hemp stresses directly in the greenhouse or in the field.
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Affiliation(s)
- Mackenzi Steczkowski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Kyle McClellan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Russell Jessup
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA.
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA.
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Higgins S, Joshi R, Juarez I, Bennett JS, Holman AP, Kolomiets M, Kurouski D. Non-invasive identification of combined salinity stress and stalk rot disease caused by Colletotrichum graminicola in maize using Raman spectroscopy. Sci Rep 2023; 13:7661. [PMID: 37169839 PMCID: PMC10175297 DOI: 10.1038/s41598-023-34937-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 05/10/2023] [Indexed: 05/13/2023] Open
Abstract
Food security is an emerging problem that is faced by our civilization. There are millions of people around the world suffering from various kinds of malnutrition. The number of people that starve will only increase considering the continuous growth of the world's population. The problem of food security can be addressed by timely detection and identification biotic and abiotic stresses in plants that drastically reduce the crop yield. A growing body of evidence suggests that Raman spectroscopy (RS), an emerging analytical technique, can be used for the confirmatory and non-invasive diagnostics of plant stresses. However, it remains unclear whether RS can efficiently disentangle biotic and abiotic stresses, as well as detect both of them simultaneously in plants. In this work, we modeled a stalk rot disease in corn by inoculating the plant stalks with Colletotrichum graminicola. In parallel, we subjected plants to salt stress, as well as challenging plants with both stalk rot disease and salinity stress simultaneously. After the stresses were introduced, Raman spectra were collected from the stalks to reveal stress-specific changes in the plant biochemistry. We found that RS was able to differentiate between stalk rot disease and salinity stresses with 100% accuracy, as well as predict presence of both of those stresses in plants on early and late stages. These results demonstrate that RS is a robust and reliable approach that can be used for confirmatory, non-destructive and label-free diagnostics of biotic and abiotic stresses in plants.
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Affiliation(s)
- Samantha Higgins
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Ritu Joshi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Isaac Juarez
- Department of Toxicology, Texas A&M University, College Station, TX, 77843, USA
| | - John S Bennett
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Aidan P Holman
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Michael Kolomiets
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
- Department of Toxicology, Texas A&M University, College Station, TX, 77843, USA.
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843, USA.
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