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Liu Y, Wu H, Shu Y, Hua Y, Fu P. Symbiodiniaceae and Ruegeria sp. Co-Cultivation to Enhance Nutrient Exchanges in Coral Holobiont. Microorganisms 2024; 12:1217. [PMID: 38930599 PMCID: PMC11205819 DOI: 10.3390/microorganisms12061217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
The symbiotic relationship between corals and their associated microorganisms is crucial for the health of coral reef eco-environmental systems. Recently, there has been a growing interest in unraveling how the manipulation of symbiont nutrient cycling affects the stress tolerance in the holobiont of coral reefs. However, most studies have primarily focused on coral-Symbiodiniaceae-bacterial interactions as a whole, neglecting the interactions between Symbiodiniaceae and bacteria, which remain largely unexplored. In this study, we proposed a hypothesis that there exists an inner symbiotic loop of Symbiodiniaceae and bacteria within the coral symbiotic loop. We conducted experiments to demonstrate how metabolic exchanges between Symbiodiniaceae and bacteria facilitate the nutritional supply necessary for cellular growth. It was seen that the beneficial bacterium, Ruegeria sp., supplied a nitrogen source to the Symbiodiniaceae strain Durusdinium sp., allowing this dinoflagellate to thrive in a nitrogen-free medium. The Ruegeria sp.-Durusdinium sp. interaction was confirmed through 15N-stable isotope probing-single cell Raman spectroscopy, in which 15N infiltrated into the bacterial cells for intracellular metabolism, and eventually the labeled nitrogen source was traced within the macromolecules of Symbiodiniaceae cells. The investigation into Symbiodiniaceae loop interactions validates our hypothesis and contributes to a comprehensive understanding of the intricate coral holobiont. These findings have the potential to enhance the health of coral reefs in the face of global climate change.
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Affiliation(s)
| | | | | | | | - Pengcheng Fu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; (Y.L.); (H.W.); (Y.S.); (Y.H.)
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2
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Park Y, Noda I, Jung YM. Diverse Applications of Two-Dimensional Correlation Spectroscopy (2D-COS). APPLIED SPECTROSCOPY 2024:37028241256397. [PMID: 38835153 DOI: 10.1177/00037028241256397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
This second of the two-part series of a comprehensive survey review provides the diverse applications of two-dimensional correlation spectroscopy (2D-COS) covering different probes, perturbations, and systems in the last two years. Infrared spectroscopy has maintained its top popularity in 2D-COS over the past two years. Fluorescence spectroscopy is the second most frequently used analytical method, which has been heavily applied to the analysis of heavy metal binding, environmental, and solution systems. Various other analytical methods including laser-induced breakdown spectroscopy, dynamic mechanical analysis, differential scanning calorimetry, capillary electrophoresis, seismologic, and so on, have also been reported. In the last two years, concentration, composition, and pH are the main effects of perturbation used in the 2D-COS fields, as well as temperature. Environmental science is especially heavily studied using 2D-COS. This comprehensive survey review shows that 2D-COS undergoes continuous evolution and growth, marked by novel developments and successful applications across diverse scientific fields.
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Affiliation(s)
- Yeonju Park
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, and Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon, Korea
| | - Isao Noda
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, USA
| | - Young Mee Jung
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, and Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon, Korea
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3
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Yuan Q, Gu B, Liu W, Wen X, Wang J, Tang J, Usman M, Liu S, Tang Y, Wang L. Rapid discrimination of four Salmonella enterica serovars: A performance comparison between benchtop and handheld Raman spectrometers. J Cell Mol Med 2024; 28:e18292. [PMID: 38652116 PMCID: PMC11037414 DOI: 10.1111/jcmm.18292] [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: 01/12/2024] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
Foodborne illnesses, particularly those caused by Salmonella enterica with its extensive array of over 2600 serovars, present a significant public health challenge. Therefore, prompt and precise identification of S. enterica serovars is essential for clinical relevance, which facilitates the understanding of S. enterica transmission routes and the determination of outbreak sources. Classical serotyping methods via molecular subtyping and genomic markers currently suffer from various limitations, such as labour intensiveness, time consumption, etc. Therefore, there is a pressing need to develop new diagnostic techniques. Surface-enhanced Raman spectroscopy (SERS) is a non-invasive diagnostic technique that can generate Raman spectra, based on which rapid and accurate discrimination of bacterial pathogens could be achieved. To generate SERS spectra, a Raman spectrometer is needed to detect and collect signals, which are divided into two types: the expensive benchtop spectrometer and the inexpensive handheld spectrometer. In this study, we compared the performance of two Raman spectrometers to discriminate four closely associated S. enterica serovars, that is, S. enterica subsp. enterica serovar dublin, enteritidis, typhi and typhimurium. Six machine learning algorithms were applied to analyse these SERS spectra. The support vector machine (SVM) model showed the highest accuracy for both handheld (99.97%) and benchtop (99.38%) Raman spectrometers. This study demonstrated that handheld Raman spectrometers achieved similar prediction accuracy as benchtop spectrometers when combined with machine learning models, providing an effective solution for rapid, accurate and cost-effective identification of closely associated S. enterica serovars.
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Affiliation(s)
- Quan Yuan
- School of Medical Informatics and EngineeringXuzhou Medical UniversityXuzhouChina
| | - Bin Gu
- School of Medical Informatics and EngineeringXuzhou Medical UniversityXuzhouChina
| | - Wei Liu
- School of Medical Informatics and EngineeringXuzhou Medical UniversityXuzhouChina
| | - Xin‐Ru Wen
- School of Medical Informatics and EngineeringXuzhou Medical UniversityXuzhouChina
| | - Ji‐Liang Wang
- Department of Laboratory MedicineShengli Oilfield Central HospitalDongyingChina
| | - Jia‐Wei Tang
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Muhammad Usman
- School of Medical Informatics and EngineeringXuzhou Medical UniversityXuzhouChina
| | - Su‐Ling Liu
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Yu‐Rong Tang
- Department of Laboratory MedicineShengli Oilfield Central HospitalDongyingChina
| | - Liang Wang
- School of Medical Informatics and EngineeringXuzhou Medical UniversityXuzhouChina
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
- Division of Microbiology and Immunology, School of Biomedical SciencesThe University of Western AustraliaCrawleyWestern AustraliaAustralia
- School of Agriculture and Food SustainabilityUniversity of QueenslandBrisbaneQueenslandAustralia
- Centre for Precision Health, School of Medical and Health SciencesEdith Cowan UniversityPerthWestern AustraliaAustralia
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4
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Frempong SB, Salbreiter M, Mostafapour S, Pistiki A, Bocklitz TW, Rösch P, Popp J. Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms. Molecules 2024; 29:1077. [PMID: 38474589 DOI: 10.3390/molecules29051077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
Raman spectroscopy is an emerging method for the identification of bacteria. Nevertheless, a lot of different parameters need to be considered to establish a reliable database capable of identifying real-world samples such as medical or environmental probes. In this review, the establishment of such reliable databases with the proper design in microbiological Raman studies is demonstrated, shining a light into all the parts that require attention. Aspects such as the strain selection, sample preparation and isolation requirements, the phenotypic influence, measurement strategies, as well as the statistical approaches for discrimination of bacteria, are presented. Furthermore, the influence of these aspects on spectra quality, result accuracy, and read-out are discussed. The aim of this review is to serve as a guide for the design of microbiological Raman studies that can support the establishment of this method in different fields.
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Affiliation(s)
- Sandra Baaba Frempong
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Markus Salbreiter
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Sara Mostafapour
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Aikaterini Pistiki
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Thomas W Bocklitz
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
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5
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Karlo J, Dhillon AK, Siddhanta S, Singh SP. Monitoring of microbial proteome dynamics using Raman stable isotope probing. JOURNAL OF BIOPHOTONICS 2023; 16:e202200341. [PMID: 36527375 DOI: 10.1002/jbio.202200341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Abnormal protein kinetics could be a cause of several diseases associated with essential life processes. An accurate understanding of protein dynamics and turnover is essential for developing diagnostic or therapeutic tools to monitor these changes. Raman spectroscopy in combination with stable isotope probes (SIP) such as carbon-13, and deuterium has been a breakthrough in the qualitative and quantitative study of various metabolites. In this work, we are reporting the utility of Raman-SIP for monitoring dynamic changes in the proteome at the community level. We have used 13 C-labeled glucose as the only carbon source in the medium and verified its incorporation in the microbial biomass in a time-dependent manner. A visible redshift in the Raman spectral vibrations of major biomolecules such as nucleic acids, phenylalanine, tyrosine, amide I, and amide III were observed. Temporal changes in the intensity of these bands demonstrating the feasibility of protein turnover monitoring were also verified. Kanamycin, a protein synthesis inhibitor was used to assess the feasibility of identifying effects on protein turnover in the cells. Successful application of this work can provide an alternate/adjunct tool for monitoring proteome-level changes in an objective and nondestructive manner.
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Affiliation(s)
- Jiro Karlo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | | | - Soumik Siddhanta
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Surya Pratap Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
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6
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Pistiki A, Ryabchykov O, Bocklitz TW, Rösch P, Popp J. Use of polymers as wavenumber calibration standards in deep-UVRR. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 287:122062. [PMID: 36351311 DOI: 10.1016/j.saa.2022.122062] [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: 06/27/2022] [Revised: 10/10/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Deep-UV resonance Raman spectroscopy (UVRR) allows the classification of bacterial species with high accuracy and is a promising tool to be developed for clinical application. For this attempt, the optimization of the wavenumber calibration is required to correct the overtime changes of the Raman setup. In the present study, different polymers were investigated as potential calibration agents. The ones with many sharp bands within the spectral range 400-1900 cm-1 were selected and used for wavenumber calibration of bacterial spectra. Classification models were built using a training cross-validation dataset that was then evaluated with an independent test dataset obtained after 4 months. Without calibration, the training cross-validation dataset provided an accuracy for differentiation above 99 % that dropped to 51.2 % after test evaluation. Applying the test evaluation with PET and Teflon calibration allowed correct assignment of all spectra of Gram-positive isolates. Calibration with PS and PEI leads to misclassifications that could be overcome with majority voting. Concerning the very closely related and similar in genome and cell biochemistry Enterobacteriaceae species, all spectra of the training cross-validation dataset were correctly classified but were misclassified in test evaluation. These results show the importance of selecting the most suitable calibration agent in the classification of bacterial species and help in the optimization of the deep-UVRR technique.
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Affiliation(s)
- Aikaterini Pistiki
- Leibniz Institute of Photonic Technology Jena, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Oleg Ryabchykov
- Leibniz Institute of Photonic Technology Jena, Albert-Einstein-Str. 9, 07745 Jena, Germany; Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Lessingstraße 10, 07743 Jena, Germany
| | - Thomas W Bocklitz
- Leibniz Institute of Photonic Technology Jena, Albert-Einstein-Str. 9, 07745 Jena, Germany; Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Lessingstraße 10, 07743 Jena, Germany
| | - Petra Rösch
- InfectoGnostics Research Campus Jena, Philosophenweg 7, 07743 Jena, Germany; Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Lessingstraße 10, 07743 Jena, Germany.
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology Jena, Albert-Einstein-Str. 9, 07745 Jena, Germany; InfectoGnostics Research Campus Jena, Philosophenweg 7, 07743 Jena, Germany; Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Lessingstraße 10, 07743 Jena, Germany; Jena Biophotonics and Imaging Laboratory, Albert-Einstein-Str. 9, 07745 Jena, Germany; Center for Sepsis Control and Care, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
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7
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Park Y, Jin S, Noda I, Jung YM. Continuing progress in the field of two-dimensional correlation spectroscopy (2D-COS): Part III. Versatile applications. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 284:121636. [PMID: 36229084 DOI: 10.1016/j.saa.2022.121636] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/30/2022] [Accepted: 07/12/2022] [Indexed: 06/16/2023]
Abstract
In this review, the comprehensive summary of two-dimensional correlation spectroscopy (2D-COS) for the last two years is covered. The remarkable applications of 2D-COS in diverse fields using many types of probes and perturbations for the last two years are highlighted. IR spectroscopy is still the most popular probe in 2D-COS during the last two years. Applications in fluorescence and Raman spectroscopy are also very popularly used. In the external perturbations applied in 2D-COS, variations in concentration, pH, and relative compositions are dramatically increased during the last two years. Temperature is still the most used effect, but it is slightly decreased compared to two years ago. 2D-COS has been applied to diverse systems, such as environments, natural products, polymers, food, proteins and peptides, solutions, mixtures, nano materials, pharmaceuticals, and others. Especially, biological and environmental applications have significantly emerged. This survey review paper shows that 2D-COS is an actively evolving and expanding field.
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Affiliation(s)
- Yeonju Park
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sila Jin
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Isao Noda
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA.
| | - Young Mee Jung
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Republic of Korea; Department of Chemistry, and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea.
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8
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Weng J, Müller K, Morgaienko O, Elsner M, Ivleva NP. Multi-element stable isotope Raman microspectroscopy of bacterial carotenoids unravels rare signal shift patterns and single-cell phenotypic heterogeneity. Analyst 2023; 148:128-136. [DOI: 10.1039/d2an01603f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Investigation of bacteria with D-carotenoids reveals unique Raman signatures, inclusive unexpected blue-shift. Simultaneous monitoring of 13C & D of carotenoids provides complementary information on cell growth and metabolic activity, respectively.
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Affiliation(s)
- Julian Weng
- Technical University of Munich, Institute of Water Chemistry, Chair for Analytical Chemistry and Water Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Kara Müller
- Technical University of Munich, Institute of Water Chemistry, Chair for Analytical Chemistry and Water Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Oleksii Morgaienko
- Technical University of Munich, Institute of Water Chemistry, Chair for Analytical Chemistry and Water Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Martin Elsner
- Technical University of Munich, Institute of Water Chemistry, Chair for Analytical Chemistry and Water Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Natalia P. Ivleva
- Technical University of Munich, Institute of Water Chemistry, Chair for Analytical Chemistry and Water Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
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9
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Jayan H, Pu H, Sun DW. Analyzing macromolecular composition of E. Coli O157:H7 using Raman-stable isotope probing. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 276:121217. [PMID: 35427921 DOI: 10.1016/j.saa.2022.121217] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Metabolic dynamics of bacterial cells is needed for understanding the correlation between changes in environmental conditions and cell metabolic activity. In this study, Raman spectroscopy combined with deuterium labelling was used to analyze the metabolic activity of a single Escherichia coli O157:H7 cell. The incorporation of deuterium from heavy water into cellular biomolecules resulted in the formation of carbon-deuterium (CD) peaks in the Raman spectra, indicating the cell metabolic activity. The broad vibrational peaks corresponding to CD and CH peaks encompassed different specific shifts of macromolecules such as protein, lipids, and nucleic acid. The utilization of tryptophan and oleic acid by the cell as the sole carbon source led to changes in cell lipid composition, as indicated by new peaks in the second derivative spectra. Thus, the proposed method could semi-quantitatively determine total metabolic activity, macromolecule specific identification, and lipid and protein metabolism in a single cell.
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Affiliation(s)
- Heera Jayan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Hongbin Pu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Food Refrigeration and Computerized Food Technology (FRCFT), Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Belfield, Dublin 4, Ireland.
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10
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Azemtsop Matanfack G, Taubert M, Reilly-Schott V, Küsel K, Rösch P, Popp J. Phenotypic Differentiation of Autotrophic and Heterotrophic Bacterial Cells Using Raman-D 2O Labeling. Anal Chem 2022; 94:7759-7766. [PMID: 35608509 DOI: 10.1021/acs.analchem.1c04097] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbon cycling is one of the major biogeochemical processes driven by bacteria. Autotrophic bacteria convert carbon dioxide (CO2) into organic compounds that are used by heterotrophs. Mixotrophic bacteria can employ both autotrophy and heterotrophy for growth. The characterization of the lifestyle of individual cells is essential to understand the microbial activity and thus reveal the implication of bacteria in the carbon flux. In this study, we used groundwater bacteria to investigate the potential of Raman-D2O labeling in combination with chemometrics to identify the carbon assimilation strategies of bacteria. Classification models were built using principal component analysis (PCA) followed by linear discriminant analysis (LDA). Autotrophs assimilated a significantly higher amount (mean C-D ratio between 16.63 and 21.69%) of deuterium than heterotrophs. The C-D signal only provides information about the activity since it appears in the Raman-silent region, where no interference with the taxonomic information is expected. The classification between autotrophs and heterotrophs achieved an overall accuracy of 96.3%. In the validation step with an independent dataset containing species not included in the model, the PCA-LDA model achieved 100% accuracy. This demonstrated that the C-D signal contributed to the identification of autotrophic and heterotrophic bacterial cells. This work reports a robust, rapid, and nondestructive approach for the identification of single cells based on their carbon acquisition strategies. The present study foresees the potential of Raman-D2O labeling as a promising method for automated discrimination of in situ functional activities of bacteria in environmental systems.
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Affiliation(s)
- Georgette Azemtsop Matanfack
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany.,Research Campus Infectognostics e.V., 07743 Jena, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Vincent Reilly-Schott
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Research Campus Infectognostics e.V., 07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany.,Research Campus Infectognostics e.V., 07743 Jena, Germany
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11
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Raman Stable Isotope Probing of Bacteria in Visible and Deep UV-Ranges. Life (Basel) 2021; 11:life11101003. [PMID: 34685375 PMCID: PMC8539138 DOI: 10.3390/life11101003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 11/17/2022] Open
Abstract
Raman stable isotope probing (Raman-SIP) is an excellent technique that can be used to access the overall metabolism of microorganisms. Recent studies have mainly used an excitation wavelength in the visible range to characterize isotopically labeled bacteria. In this work, we used UV resonance Raman spectroscopy (UVRR) to evaluate the spectral red-shifts caused by the uptake of isotopes (13C, 15N, 2H(D) and 18O) in E. coli cells. Moreover, we present a new approach based on the extraction of labeled DNA in combination with UVRR to identify metabolically active cells. The proof-of-principle study on E. coli revealed heterogeneities in the Raman features of both the bacterial cells and the extracted DNA after labeling with 13C, 15N, and D. The wavelength of choice for studying 18O- and deuterium-labeled cells is 532 nm is, while 13C-labeled cells can be investigated with visible and deep UV wavelengths. However, 15N-labeled cells are best studied at the excitation wavelength of 244 nm since nucleic acids are in resonance at this wavelength. These results highlight the potential of the presented approach to identify active bacterial cells. This work can serve as a basis for the development of new techniques for the rapid and efficient detection of active bacteria cells without the need for a cultivation step.
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