1
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Razi S, Tarcea N, Henkel T, Ravikumar R, Pistiki A, Wagenhaus A, Girnus S, Taubert M, Küsel K, Rösch P, Popp J. Raman-Activated, Interactive Sorting of Isotope-Labeled Bacteria. SENSORS (BASEL, SWITZERLAND) 2024; 24:4503. [PMID: 39065901 PMCID: PMC11281290 DOI: 10.3390/s24144503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024]
Abstract
Due to its high spatial resolution, Raman microspectroscopy allows for the analysis of single microbial cells. Since Raman spectroscopy analyzes the whole cell content, this method is phenotypic and can therefore be used to evaluate cellular changes. In particular, labeling with stable isotopes (SIPs) enables the versatile use and observation of different metabolic states in microbes. Nevertheless, static measurements can only analyze the present situation and do not allow for further downstream evaluations. Therefore, a combination of Raman analysis and cell sorting is necessary to provide the possibility for further research on selected bacteria in a sample. Here, a new microfluidic approach for Raman-activated continuous-flow sorting of bacteria using an optical setup for image-based particle sorting with synchronous acquisition and analysis of Raman spectra for making the sorting decision is demonstrated, showing that active cells can be successfully sorted by means of this microfluidic chip.
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Affiliation(s)
- Sepehr Razi
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance—Leibniz Health Technologies, 07745 Jena, Germany; (S.R.); (N.T.); (T.H.); (A.P.)
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany; (M.T.); (K.K.)
| | - Nicolae Tarcea
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance—Leibniz Health Technologies, 07745 Jena, Germany; (S.R.); (N.T.); (T.H.); (A.P.)
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany; (R.R.); (P.R.)
| | - Thomas Henkel
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance—Leibniz Health Technologies, 07745 Jena, Germany; (S.R.); (N.T.); (T.H.); (A.P.)
| | - Ramya Ravikumar
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany; (R.R.); (P.R.)
| | - Aikaterini Pistiki
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance—Leibniz Health Technologies, 07745 Jena, Germany; (S.R.); (N.T.); (T.H.); (A.P.)
| | - Annette Wagenhaus
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany; (R.R.); (P.R.)
| | - Sophie Girnus
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany; (R.R.); (P.R.)
| | - Martin Taubert
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany; (M.T.); (K.K.)
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Kirsten Küsel
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany; (M.T.); (K.K.)
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany; (R.R.); (P.R.)
| | - Jürgen Popp
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance—Leibniz Health Technologies, 07745 Jena, Germany; (S.R.); (N.T.); (T.H.); (A.P.)
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany; (M.T.); (K.K.)
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany; (R.R.); (P.R.)
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2
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Karlo J, Gupta A, Singh SP. In situ monitoring of the shikimate pathway: a combinatorial approach of Raman reverse stable isotope probing and hyperspectral imaging. Analyst 2024; 149:2833-2841. [PMID: 38587502 DOI: 10.1039/d4an00203b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Sensing and visualization of metabolites and metabolic pathways in situ are significant requirements for tracking their spatiotemporal dynamics in a non-destructive manner. The shikimate pathway is an important cellular mechanism that leads to the de novo synthesis of many compounds containing aromatic rings of high importance such as phenylalanine, tyrosine, and tryptophan. In this work, we present a cost-effective and extraction-free method based on the principles of stable isotope-coupled Raman spectroscopy and hyperspectral Raman imaging to monitor and visualize the activity of the shikimate pathway. We also demonstrated the applicability of this approach for nascent aromatic amino acid localization and tracking turnover dynamics in both prokaryotic and eukaryotic model systems. This method can emerge as a promising tool for both qualitative and semi-quantitative in situ metabolomics, contributing to a better understanding of aromatic ring-containing metabolite dynamics across various organisms.
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Affiliation(s)
- Jiro Karlo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, 580011, India.
| | - Aryan Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, 580011, India.
| | - Surya Pratap Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, 580011, India.
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3
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Zhang Z, Zhang Q, Yang H, Cui L, Qian H. Mining strategies for isolating plastic-degrading microorganisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123572. [PMID: 38369095 DOI: 10.1016/j.envpol.2024.123572] [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: 12/27/2023] [Revised: 01/29/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Plastic waste is a growing global pollutant. Plastic degradation by microorganisms has captured attention as an earth-friendly tactic. Although the mechanisms of plastic degradation by bacteria, fungi, and algae have been explored over the past decade, a large knowledge gap still exists regarding the identification, sorting, and cultivation of efficient plastic degraders, primarily because of their uncultivability. Advances in sequencing techniques and bioinformatics have enabled the identification of microbial degraders and related enzymes and genes involved in plastic biodegradation. In this review, we provide an outline of the situation of plastic degradation and summarize the methods for effective microbial identification using multidisciplinary techniques such as multiomics, meta-analysis, and spectroscopy. This review introduces new strategies for controlling plastic pollution in an environmentally friendly manner. Using this information, highly efficient and colonizing plastic degraders can be mined via targeted sorting and cultivation. In addition, based on the recognized rules and plastic degraders, we can perform an in-depth analysis of the associated degradation mechanism, metabolic features, and interactions.
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Affiliation(s)
- Ziyao Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Huihui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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4
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Smets B, Boschker HTS, Wetherington MT, Lelong G, Hidalgo-Martinez S, Polerecky L, Nuyts G, De Wael K, Meysman FJR. Multi-wavelength Raman microscopy of nickel-based electron transport in cable bacteria. Front Microbiol 2024; 15:1208033. [PMID: 38525072 PMCID: PMC10959288 DOI: 10.3389/fmicb.2024.1208033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Cable bacteria embed a network of conductive protein fibers in their cell envelope that efficiently guides electron transport over distances spanning up to several centimeters. This form of long-distance electron transport is unique in biology and is mediated by a metalloprotein with a sulfur-coordinated nickel (Ni) cofactor. However, the molecular structure of this cofactor remains presently unknown. Here, we applied multi-wavelength Raman microscopy to identify cell compounds linked to the unique cable bacterium physiology, combined with stable isotope labeling, and orientation-dependent and ultralow-frequency Raman microscopy to gain insight into the structure and organization of this novel Ni-cofactor. Raman spectra of native cable bacterium filaments reveal vibrational modes originating from cytochromes, polyphosphate granules, proteins, as well as the Ni-cofactor. After selective extraction of the conductive fiber network from the cell envelope, the Raman spectrum becomes simpler, and primarily retains vibrational modes associated with the Ni-cofactor. These Ni-cofactor modes exhibit intense Raman scattering as well as a strong orientation-dependent response. The signal intensity is particularly elevated when the polarization of incident laser light is parallel to the direction of the conductive fibers. This orientation dependence allows to selectively identify the modes that are associated with the Ni-cofactor. We identified 13 such modes, some of which display strong Raman signals across the entire range of applied wavelengths (405-1,064 nm). Assignment of vibrational modes, supported by stable isotope labeling, suggest that the structure of the Ni-cofactor shares a resemblance with that of nickel bis(1,2-dithiolene) complexes. Overall, our results indicate that cable bacteria have evolved a unique cofactor structure that does not resemble any of the known Ni-cofactors in biology.
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Affiliation(s)
- Bent Smets
- Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Henricus T. S. Boschker
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Maxwell T. Wetherington
- Materials Characterization Laboratory, Pennsylvania State University, State College, PA, United States
| | - Gérald Lelong
- Institut de Minéralogie, de Physique des Matériaux et Cosmochimie (IMPMC), Sorbonne Universités, France—Muséum National d’Histoire Naturelle, Paris, France
| | | | - Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Gert Nuyts
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | - Karolien De Wael
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Filip J. R. Meysman
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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Suzuki-Minakuchi C, Yamamoto N, Takahira S, Yamaguchi M, Takeda Y, Okada K, Shigeto S, Nojiri H. Transcriptional heterogeneity of catabolic genes on the plasmid pCAR1 causes host-specific carbazole degradation. Appl Environ Microbiol 2024; 90:e0124723. [PMID: 38289097 PMCID: PMC10880608 DOI: 10.1128/aem.01247-23] [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: 07/20/2023] [Accepted: 12/21/2023] [Indexed: 02/22/2024] Open
Abstract
To elucidate why plasmid-borne catabolic ability differs among host bacteria, we assessed the expression dynamics of the Pant promoter on the carbazole-degradative conjugative plasmid pCAR1 in Pseudomonas putida KT2440(pCAR1) (hereafter, KTPC) and Pseudomonas resinovorans CA10. The Pant promoter regulates the transcription of both the car and ant operons, which are responsible for converting carbazole into anthranilate and anthranilate into catechol, respectively. In the presence of anthranilate, transcription of the Pant promoter is induced by the AraC/XylS family regulator AntR, encoded on pCAR1. A reporter cassette containing the Pant promoter followed by gfp was inserted into the chromosomes of KTPC and CA10. After adding anthranilate, GFP expression in the population of CA10 showed an unimodal distribution, whereas a small population with low GFP fluorescence intensity appeared for KTPC. CA10 has a gene, antRCA, that encodes an iso-functional homolog of AntR on its chromosome. When antRCA was disrupted, a small population with low GFP fluorescence intensity appeared. In contrast, overexpression of pCAR1-encoded AntR in KTPC resulted in unimodal expression under the Pant promoter. These results suggest that the expression of pCAR1-encoded AntR is insufficient to ameliorate the stochastic expression of the Pant promoter. Raman spectra of single cells collected using deuterium-labeled carbazole showed that the C-D Raman signal exhibited greater variability for KTPC than CA10. These results indicate that heterogeneity at the transcriptional level of the Pant promoter due to insufficient AntR availability causes fluctuations in the pCAR1-borne carbazole-degrading capacity of host bacterial cells.IMPORTANCEHorizontally acquired genes increase the competitiveness of host bacteria under selective conditions, although unregulated expression of foreign genes may impose fitness costs. The "appropriate" host for a plasmid is empirically known to maximize the expression of plasmid-borne traits. In the case of pCAR1-harboring Pseudomonas strains, P. resinovorans CA10 exhibits strong carbazole-degrading capacity, whereas P. putida KT2440 harboring pCAR1 exhibits low degradation capacity. Our results suggest that a chromosomally encoded transcription factor affects transcriptional and metabolic fluctuations in host cells, resulting in different carbazole-degrading capacities as a population. This study may provide a clue for determining appropriate hosts for a plasmid and for regulating the expression of plasmid-borne traits, such as the degradation of xenobiotics and antibiotic resistance.
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Affiliation(s)
- Chiho Suzuki-Minakuchi
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Natsumi Yamamoto
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Saki Takahira
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masataka Yamaguchi
- Department of Chemistry, Graduate School of Science and Technology, Kwansei Gakuin University, Hyogo, Japan
| | - Yutaro Takeda
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazunori Okada
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shinsuke Shigeto
- Department of Chemistry, Graduate School of Science and Technology, Kwansei Gakuin University, Hyogo, Japan
| | - Hideaki Nojiri
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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6
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Sun Y, Li S, Si Y, Niu Y, Yang J, Liu Y, Dong L, Zhu P, Dai J, Yang F. Dual-Stable-Isotope-Probed Raman microspectroscopy reveals the metabolic dynamic of Streptococcus mutans. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123318. [PMID: 37703791 DOI: 10.1016/j.saa.2023.123318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023]
Abstract
Streptococcus mutans (S. mutans) is regarded as a cariogenic pathogen with the ability to metabolize sugars and form organic acids. However, its actual timely level of glucose consumption and cellular vitality in a polymicrobial culture system remains largely unknown. To tackle this challenge, we employed the S. mutans UA159 as a model and developed a dual-stable-isotope-probed Raman microspectroscopy method (Dual SIP-Raman) to simultaneously profile the general metabolic activity and glucose assimilative activity in situ. (i) Mono-SIP substrate feeding revealed that 0.5% 13C-glucose and 30% D2O were proper doses in the medium to obtain prominent and quantitative band shifts along with the 13C or D2O incorporation. In addition, the intensity of the 13C peak of phenylalanine (Phe) is proposed as a Raman-based biomarker for glucose utilization in a cell. (ii) The state of dual SIP substrate incorporation of 13C-glucose and D2O could be visualized by the corresponding spectral "red shifts" of Raman-scattered emissions; moreover, we also demonstrated that 13C/12C analysis was closely correlated with the C-D ratio. (iii) The application of the dual 13C-glucose and D2O feeding approach on a mock microbiota of S. mutans UA159 and C. albicans ATCC14053 revealed a stimulatory effect of fungus on both the glucose intake rate and general metabolic vitality of S. mutans UA159 (p < 0.05). Therefore, the 13C-glucose and D2O dual-feeding Raman Microspectroscopy approach is a valuable new tool for evaluating the glucose intake rate and general metabolic levels in situ, tracing the changing trend of the above metabolic activities, which is helpful to clarify the changes in the cariogenicity of oral microorganisms caused by the external environment at the single-cell level.
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Affiliation(s)
- Yanfei Sun
- Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, Shandong, 26607, China; School of Stomatology of Qingdao University, Qingdao 266003, China
| | - Shanshan Li
- Changhai Hospital of Shanghai, Shanghai, 200433, China
| | - Yuan Si
- Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, Shandong, 26607, China; School of Stomatology of Qingdao University, Qingdao 266003, China
| | - Yufen Niu
- School of Stomatology of Qingdao University, Qingdao 266003, China; Wuxi Stomatology Hospital, Jiangsu, Wuxi, 214000, China
| | - Jiazhen Yang
- Stomatological Hospital of Qingdao, Qingdao, 266000, China
| | - Yuhan Liu
- Stomatological Hospital of Qingdao, Qingdao, 266000, China
| | - Lei Dong
- School of Stomatology of Qingdao University, Qingdao 266003, China
| | - Pengfei Zhu
- Stomatological Hospital of Qingdao, Qingdao, 266000, China
| | - Jing Dai
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266003, China
| | - Fang Yang
- Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, Shandong, 26607, China; School of Stomatology of Qingdao University, Qingdao 266003, China.
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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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8
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He W, Cai R, Xi S, Yin Z, Du Z, Luan Z, Sun C, Zhang X. Study of Microbial Sulfur Metabolism in a Near Real-Time Pathway through Confocal Raman Quantitative 3D Imaging. Microbiol Spectr 2023; 11:e0367822. [PMID: 36809047 PMCID: PMC10101092 DOI: 10.1128/spectrum.03678-22] [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: 09/11/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
As microbial sulfur metabolism significantly contributes to the formation and cycling of deep-sea sulfur, studying their sulfur metabolism is important for understanding the deep-sea sulfur cycle. However, conventional methods are limited in near real-time studies of bacterial metabolism. Recently, Raman spectroscopy has been widely used in studies on biological metabolism due to its low-cost, rapid, label-free, and nondestructive features, providing us with new approaches to solve the above limitation. Here, we used the confocal Raman quantitative 3D imaging method to nondestructively detect the growth and metabolism of Erythrobacter flavus 21-3 in the long term and near real time, which possessed a pathway mediating the formation of elemental sulfur in the deep sea, but the dynamic process was unknown. In this study, its dynamic sulfur metabolism was visualized and quantitatively assessed in near real time using 3D imaging and related calculations. Based on 3D imaging, the growth and metabolism of microbial colonies growing under both hyperoxic and hypoxic conditions were quantified by volume calculation and ratio analysis. Additionally, unprecedented details of growth and metabolism were uncovered by this method. Due to this successful application, this method is potentially significant for analyzing the in situ biological processes of microorganisms in the future. IMPORTANCE Microorganisms contribute significantly to the formation of deep-sea elemental sulfur, so studies on their growth and dynamic sulfur metabolism are important to understand the deep-sea sulfur cycle. However, near real-time in situ nondestructive metabolic studies of microorganisms remain a great challenge due to the limitations of existing methods. We thus used an imaging-related workflow by confocal Raman microscopy. More detailed descriptions of the sulfur metabolism of E. flavus 21-3 were disclosed, which perfectly complemented previous research results. Therefore, this method is potentially significant for analyzing the in-situ biological processes of microorganisms in the future. To our knowledge, this is the first label-free and nondestructive in situ technique that can provide temporally persistent 3D visualization and quantitative information about bacteria.
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Affiliation(s)
- Wanying He
- CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | - Ruining Cai
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shichuan Xi
- CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
| | - Ziyu Yin
- CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zengfeng Du
- CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhendong Luan
- CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | - Chaomin Sun
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xin Zhang
- CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
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9
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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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10
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Patil N, Howe O, Cahill P, Byrne HJ. Monitoring and modelling the dynamics of the cellular glycolysis pathway: A review and future perspectives. Mol Metab 2022; 66:101635. [PMID: 36379354 PMCID: PMC9703637 DOI: 10.1016/j.molmet.2022.101635] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/28/2022] [Accepted: 11/06/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The dynamics of the cellular glycolysis pathway underpin cellular function and dysfunction, and therefore ultimately health, disease, diagnostic and therapeutic strategies. Evolving our understanding of this fundamental process and its dynamics remains critical. SCOPE OF REVIEW This paper reviews the medical relevance of glycolytic pathway in depth and explores the current state of the art for monitoring and modelling the dynamics of the process. The future perspectives of label free, vibrational microspectroscopic techniques to overcome the limitations of the current approaches are considered. MAJOR CONCLUSIONS Vibrational microspectroscopic techniques can potentially operate in the niche area of limitations of other omics technologies for non-destructive, real-time, in vivo label-free monitoring of glycolysis dynamics at a cellular and subcellular level.
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Affiliation(s)
- Nitin Patil
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland; School of Physics and Optometric & Clinical Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland.
| | - Orla Howe
- School of Biological and Health Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland
| | - Paul Cahill
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Hugh J Byrne
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland
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11
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Hyperglycemia and cancer in human lung carcinoma by means of Raman spectroscopy and imaging. Sci Rep 2022; 12:18561. [PMID: 36329066 PMCID: PMC9633797 DOI: 10.1038/s41598-022-21483-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Raman spectroscopy and Raman imaging were used to identify the biochemical and structural features of human cancer lung cells (CCL-185) and the cancer cells supplemented with glucose and deuterated glucose at normal and hyperglycemia conditions. We found that isotope substitution of glucose by deuterated glucose allows to separate de novo lipid synthesis from exogenous uptake of lipids obtained from the diet. We demonstrated that glucose is largely utilized for de novo lipid synthesis. Our results provide a direct evidence that high level of glucose decreases the metabolism via oxidative phosphorylation in mitochondria in cancer cells and shifts the metabolism to glycolysis via Warburg effect. It suggests that hyperglycemia is a factor that may contribute to a more malignant phenotype of cancer cells by inhibition of oxidative phosphorylation and apoptosis.
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12
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Grujcic V, Taylor GT, Foster RA. One Cell at a Time: Advances in Single-Cell Methods and Instrumentation for Discovery in Aquatic Microbiology. Front Microbiol 2022; 13:881018. [PMID: 35677911 PMCID: PMC9169044 DOI: 10.3389/fmicb.2022.881018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Studying microbes from a single-cell perspective has become a major theme and interest within the field of aquatic microbiology. One emerging trend is the unfailing observation of heterogeneity in activity levels within microbial populations. Wherever researchers have looked, intra-population variability in biochemical composition, growth rates, and responses to varying environmental conditions has been evident and probably reflect coexisting genetically distinct strains of the same species. Such observations of heterogeneity require a shift away from bulk analytical approaches and development of new methods or adaptation of existing techniques, many of which were first pioneered in other, unrelated fields, e.g., material, physical, and biomedical sciences. Many co-opted approaches were initially optimized using model organisms. In a field with so few cultivable models, method development has been challenging but has also contributed tremendous insights, breakthroughs, and stimulated curiosity. In this perspective, we present a subset of methods that have been effectively applied to study aquatic microbes at the single-cell level. Opportunities and challenges for innovation are also discussed. We suggest future directions for aquatic microbiological research that will benefit from open access to sophisticated instruments and highly interdisciplinary collaborations.
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Affiliation(s)
- Vesna Grujcic
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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13
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Khoshravesh R, Hoffmann N, Hanson DT. Leaf microscopy applications in photosynthesis research: identifying the gaps. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1868-1893. [PMID: 34986250 DOI: 10.1093/jxb/erab548] [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: 08/23/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Leaf imaging via microscopy has provided critical insights into research on photosynthesis at multiple junctures, from the early understanding of the role of stomata, through elucidating C4 photosynthesis via Kranz anatomy and chloroplast arrangement in single cells, to detailed explorations of diffusion pathways and light utilization gradients within leaves. In recent decades, the original two-dimensional (2D) explorations have begun to be visualized in three-dimensional (3D) space, revising our understanding of structure-function relationships between internal leaf anatomy and photosynthesis. In particular, advancing new technologies and analyses are providing fresh insight into the relationship between leaf cellular components and improving the ability to model net carbon fixation, water use efficiency, and metabolite turnover rate in leaves. While ground-breaking developments in imaging tools and techniques have expanded our knowledge of leaf 3D structure via high-resolution 3D and time-series images, there is a growing need for more in vivo imaging as well as metabolite imaging. However, these advances necessitate further improvement in microscopy sciences to overcome the unique challenges a green leaf poses. In this review, we discuss the available tools, techniques, challenges, and gaps for efficient in vivo leaf 3D imaging, as well as innovations to overcome these difficulties.
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Affiliation(s)
| | - Natalie Hoffmann
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - David T Hanson
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
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14
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6577122. [DOI: 10.1093/femsec/fiac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/07/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
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15
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Yakubovskaya E, Zaliznyak T, Martínez JM, Taylor GT. Raman Microspectroscopy Goes Viral: Infection Dynamics in the Cosmopolitan Microalga, Emiliania huxleyi. Front Microbiol 2021; 12:686287. [PMID: 34795644 PMCID: PMC8593419 DOI: 10.3389/fmicb.2021.686287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 10/12/2021] [Indexed: 11/18/2022] Open
Abstract
Emiliania huxleyi is a cosmopolitan member of the marine phytoplankton. This species’ capacities for carbon sequestration and sulfur mobilization make it a key player in oceanic biogeochemical cycles that influence climate on a planetary scale. Seasonal E. huxleyi blooms are abruptly terminated by viral epidemics caused by a clade of large DNA viruses collectively known as coccolithoviruses (EhVs). EhVs thereby mediate a significant part of material and energy fluxes associated with E. huxleyi population dynamics. In this study, we use spontaneous Raman microspectroscopy to perform label-free and non-invasive measurements of the macromolecular composition of individual virions and E. huxleyi host cells. Our novel autofluorescence suppression protocol enabled spectroscopic visualization of evolving macromolecular redistributions in individual E. huxleyi cells at different stages of EhV infection. Material transfer from E. huxleyi hosts to single EhV-163 virions was confirmed by combining stable isotope probing (SIP) experiments with Raman microspectroscopy. Inheritance of the host cells’ 13C-enriched isotopic signature was quantified based on red shifts of Raman peaks characteristic of phenylalanine’s phenyl ring. Two-dimensional Raman mapping of EhV-infected E. huxleyi cells revealed that the compact region producing an intense Raman DNA signal (i.e., the nucleus) in healthy E. huxleyi cells becomes diffuse during the first hours of infection. Raman DNA emissions integrated throughout individual cells decreased during the infection cycle. Our observations are consistent with EhV-163 degrading the host’s nuclear DNA, scavenging released nucleotides for its own genome replication, and shedding newly-produced virions prior to host lysis via budding.
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Affiliation(s)
- Elena Yakubovskaya
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Tatiana Zaliznyak
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | | | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
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16
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Using Stable Isotope Probing and Raman Microspectroscopy To Measure Growth Rates of Heterotrophic Bacteria. Appl Environ Microbiol 2021; 87:e0146021. [PMID: 34495689 DOI: 10.1128/aem.01460-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The suitability of stable isotope probing (SIP) and Raman microspectroscopy to measure growth rates of heterotrophic bacteria at the single-cell level was evaluated. Label assimilation into Escherichia coli biomass during growth on a complex 13C-labeled carbon source was monitored in time course experiments. 13C incorporation into various biomolecules was measured by spectral "red shifts" of Raman-scattered emissions. The 13C- and 12C-isotopologues of the amino acid phenylalanine (Phe) proved to be quantitatively accurate reporter molecules of cellular isotopic fractional abundances (fcell). Values of fcell determined by Raman microspectroscopy and independently by isotope ratio mass spectrometry (IRMS) over a range of isotopic enrichments were statistically indistinguishable. Progressive labeling of Phe in E. coli cells among a range of 13C/12C organic substrate admixtures occurred predictably through time. The relative isotopologue abundances of Phe determined by Raman spectral analysis enabled the accurate calculation of bacterial growth rates as confirmed independently by optical density (OD) measurements. The results demonstrate that combining SIP and Raman microspectroscopy can be a powerful tool for studying bacterial growth at the single-cell level on defined or complex organic 13C carbon sources, even in mixed microbial assemblages. IMPORTANCE Population growth dynamics and individual cell growth rates are the ultimate expressions of a microorganism's fitness under its environmental conditions, whether natural or engineered. Natural habitats and many industrial settings harbor complex microbial assemblages. Their heterogeneity in growth responses to existing and changing conditions is often difficult to grasp by standard methodologies. In this proof-of-concept study, we tested whether Raman microspectroscopy can reliably quantify the assimilation of isotopically labeled nutrients into E. coli cells and enable the determination of individual growth rates among heterotrophic bacteria. Raman-derived growth rate estimates were statistically indistinguishable from those derived by standard optical density measurements of the same cultures. Raman microspectroscopy can also be combined with methods for phylogenetic identification. We report the development of Raman-based techniques that enable researchers to directly link genetic identity to functional traits and rate measurements of single cells within mixed microbial assemblages, currently a major technical challenge in microbiological research.
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17
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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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18
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Azemtsop Matanfack G, Pistiki A, Rösch P, Popp J. Raman 18 O-labeling of bacteria in visible and deep UV-ranges. JOURNAL OF BIOPHOTONICS 2021; 14:e202100013. [PMID: 33773041 DOI: 10.1002/jbio.202100013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
Raman stable isotope labeling with 2 H, 13 C or 15 N has been reported as an elegant approach to investigate cellular metabolic activity, which is of great importance to reveal the functions of microorganisms in native environments. A new strategy termed Raman 18 O-labeling was developed to probe the metabolic activity of bacteria. Raman 18 O-labeling refers to the combination of Raman microspectroscopy with 18 O-labeling using H218 O. At an excitation wavelength of 532 nm, the incorporation of 18 O into the amide I group of proteins and DNA/RNA bases was observed in Escherichia coli cells, while for an excitation wavelength electronically resonant with DNA or aromatic amino acid absorption at 244 nm 18 O assimilation was detected using chemometric tools rather than visual inspection. Raman 18 O-labeling at 532 nm combined with 2D correlation analysis confirmed the assimilation of 18 O in proteins and nucleic acids and revealed the growth strategy of E. coli cells; they underwent protein synthesis followed by nucleic acid synthesis. Independent cultural replicates at different incubation times corroborated the reproducibility of these results. The variations in spectral features of 18 O-labeled cells revealed changes in physiological information of cells. Hence, Raman 18 O-labeling could provide a powerful tool to identify metabolically active bacterial cells.
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Affiliation(s)
- Georgette Azemtsop Matanfack
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology a member of the Leibniz Research Alliance Leibniz Health Technology (Leibniz-IPHT), Jena, Germany
- Research Campus Infectognostics e.v. Jena, Jena, Germany
| | - Aikaterini Pistiki
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology a member of the Leibniz Research Alliance Leibniz Health Technology (Leibniz-IPHT), Jena, Germany
- Research Campus Infectognostics e.v. Jena, Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Jena, Germany
- Research Campus Infectognostics e.v. Jena, Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology a member of the Leibniz Research Alliance Leibniz Health Technology (Leibniz-IPHT), Jena, Germany
- Research Campus Infectognostics e.v. Jena, Jena, Germany
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19
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Chisanga M, Muhamadali H, McDougall D, Xu Y, Lockyer N, Goodacre R. Metabolism in action: stable isotope probing using vibrational spectroscopy and SIMS reveals kinetic and metabolic flux of key substrates. Analyst 2021; 146:1734-1746. [PMID: 33465215 DOI: 10.1039/d0an02319a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Microbial communities play essential functions which drive various ecosystems supporting animal and aquatic life. However, linking bacteria with specific metabolic functions is difficult, since microbial communities consist of numerous and phylogenetically diverse microbes. Stable isotope probing (SIP) combined with single-cell tools has emerged as a novel culture-independent strategy for unravelling microbial metabolic roles and intertwined interactions in complex communities. In this study, we applied Raman and Fourier-transform infrared (FT-IR) spectroscopies, secondary ion mass spectrometry (SIMS) with SIP to probe the rate of 13C incorporation in Escherichia coli at 37 and 25 °C. Our results indicate quantitative enrichment and flow of 13C into E. coli at various time points. Multivariate and univariate analyses of Raman and FT-IR data demonstrated distinctive 13C concentration-dependent trends that were due to vibrational bands shifting to lower frequencies and these shifts were a result of incubation time and metabolic rate. SIMS results were in complete agreement with the spectroscopy findings, and confirmed the detected levels of 13C incorporation into microbial biomass at the investigated conditions. Having established that FT-IR and Raman spectroscopy with SIP can measure metabolism kinetics in this simple system, we have applied the kinetics concept to study the metabolism of phenol by Pseudomonas putida and metabolic interactions within a two-species consortia with E. coli that could not degrade phenol. Raman spectroscopy combined with SIP identified quantitative shifts in P. putida due to temporal assimilation of phenol. Although E. coli was unable to grow on phenol, in co-culture with P. putida, general metabolic probing using deuterated water for SIP revealed that E. coli displayed increasing metabolic activity, presumably due to cross feeding from metabolites generated by P. putida. This study clearly demonstrates that Raman and FT-IR combined with SIP provide rapid and sensitive detection of carbon incorporation rates and microbial interactions. These novel findings may guide the identification of primary substrate consumers in complex microbial communities in situ, which is a key step towards the characterisation of novel genes, enzymes and metabolic flux analysis in microbial consortia.
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Affiliation(s)
- Malama Chisanga
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
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20
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Development overview of Raman-activated cell sorting devoted to bacterial detection at single-cell level. Appl Microbiol Biotechnol 2021; 105:1315-1331. [PMID: 33481066 DOI: 10.1007/s00253-020-11081-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/17/2020] [Accepted: 12/27/2020] [Indexed: 12/14/2022]
Abstract
Understanding the metabolic interactions between bacteria in natural habitat at the single-cell level and the contribution of individual cell to their functions is essential for exploring the dark matter of uncultured bacteria. The combination of Raman-activated cell sorting (RACS) and single-cell Raman spectra (SCRS) with unique fingerprint characteristics makes it possible for research in the field of microbiology to enter the single cell era. This review presents an overview of current knowledge about the research progress of recognition and assessment of single bacterium cell based on RACS and further research perspectives. We first systematically summarize the label-free and non-destructive RACS strategies based on microfluidics, microdroplets, optical tweezers, and specially made substrates. The importance of RACS platforms in linking target cell genotype and phenotype is highlighted and the approaches mentioned in this paper for distinguishing single-cell phenotype include surface-enhanced Raman scattering (SERS), biomarkers, stable isotope probing (SIP), and machine learning. Finally, the prospects and challenges of RACS in exploring the world of unknown microorganisms are discussed. KEY POINTS: • Analysis of single bacteria is essential for further understanding of the microbiological world. • Raman-activated cell sorting (RACS) systems are significant protocol for characterizing phenotypes and genotypes of individual bacteria.
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21
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Deuterium-labeled Raman tracking of glucose accumulation and protein metabolic dynamics in Aspergillus nidulans hyphal tips. Sci Rep 2021; 11:1279. [PMID: 33446770 PMCID: PMC7809412 DOI: 10.1038/s41598-020-80270-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
Filamentous fungi grow exclusively at their tips, where many growth-related fungal processes, such as enzyme secretion and invasion into host cells, take place. Hyphal tips are also a site of active metabolism. Understanding metabolic dynamics within the tip region is therefore important for biotechnology and medicine as well as for microbiology and ecology. However, methods that can track metabolic dynamics with sufficient spatial resolution and in a nondestructive manner are highly limited. Here we present time-lapse Raman imaging using a deuterium (D) tracer to study spatiotemporally varying metabolic activity within the hyphal tip of Aspergillus nidulans. By analyzing the carbon-deuterium (C-D) stretching Raman band with spectral deconvolution, we visualize glucose accumulation along the inner edge of the hyphal tip and synthesis of new proteins from the taken-up D-labeled glucose specifically at the central part of the apical region. Our results show that deuterium-labeled Raman imaging offers a broadly applicable platform for the study of metabolic dynamics in filamentous fungi and other relevant microorganisms in vivo.
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22
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Braissant O, Astasov-Frauenhoffer M, Waltimo T, Bonkat G. A Review of Methods to Determine Viability, Vitality, and Metabolic Rates in Microbiology. Front Microbiol 2020; 11:547458. [PMID: 33281753 PMCID: PMC7705206 DOI: 10.3389/fmicb.2020.547458] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022] Open
Abstract
Viability and metabolic assays are commonly used as proxies to assess the overall metabolism of microorganisms. The variety of these assays combined with little information provided by some assay kits or online protocols often leads to mistakes or poor interpretation of the results. In addition, the use of some of these assays is restricted to simple systems (mostly pure cultures), and care must be taken in their application to environmental samples. In this review, the necessary data are compiled to understand the reactions or measurements performed in many of the assays commonly used in various aspects of microbiology. Also, their relationships to each other, as metabolism links many of these assays, resulting in correlations between measured values and parameters, are discussed. Finally, the limitations of these assays are discussed.
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Affiliation(s)
- Olivier Braissant
- Department of Biomedical Engineering, Faculty of Medicine, University of Basel, Allschwil, Switzerland
| | | | - Tuomas Waltimo
- Department Research, University Center for Dental Medicine, University of Basel, Basel, Switzerland
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23
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Sharma K, Palatinszky M, Nikolov G, Berry D, Shank EA. Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms. eLife 2020; 9:e56275. [PMID: 33140722 PMCID: PMC7609051 DOI: 10.7554/elife.56275] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 10/16/2020] [Indexed: 01/02/2023] Open
Abstract
Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil's opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.
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Affiliation(s)
- Kriti Sharma
- Department of Biology, University of North CarolinaChapel HillUnited States
| | - Márton Palatinszky
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of ViennaViennaAustria
| | - Georgi Nikolov
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of ViennaViennaAustria
| | - David Berry
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of ViennaViennaAustria
| | - Elizabeth A Shank
- Department of Biology, University of North CarolinaChapel HillUnited States
- Department of Microbiology and Immunology, University of North CarolinaChapel HillUnited States
- Program in Systems Biology, University of Massachusetts Medical SchoolWorcesterUnited States
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24
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Azemtsop Matanfack G, Rüger J, Stiebing C, Schmitt M, Popp J. Imaging the invisible-Bioorthogonal Raman probes for imaging of cells and tissues. JOURNAL OF BIOPHOTONICS 2020; 13:e202000129. [PMID: 32475014 DOI: 10.1002/jbio.202000129] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 06/11/2023]
Abstract
A revolutionary avenue for vibrational imaging with super-multiplexing capability can be seen in the recent development of Raman-active bioortogonal tags or labels. These tags and isotopic labels represent groups of chemically inert and small modifications, which can be introduced to any biomolecule of interest and then supplied to single cells or entire organisms. Recent developments in the field of spontaneous Raman spectroscopy and stimulated Raman spectroscopy in combination with targeted imaging of biomolecules within living systems are the main focus of this review. After having introduced common strategies for bioorthogonal labeling, we present applications thereof for profiling of resistance patterns in bacterial cells, investigations of pharmaceutical drug-cell interactions in eukaryotic cells and cancer diagnosis in whole tissue samples. Ultimately, this approach proves to be a flexible and robust tool for in vivo imaging on several length scales and provides comparable information as fluorescence-based imaging without the need of bulky fluorescent tags.
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Affiliation(s)
- Georgette Azemtsop Matanfack
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology - a member of the Leibniz Research Alliance Leibniz Health Technology (Leibniz-IPHT), Jena, Germany
- Research Campus Infectognostics e.V., Jena, Germany
| | - Jan Rüger
- Leibniz Institute of Photonic Technology - a member of the Leibniz Research Alliance Leibniz Health Technology (Leibniz-IPHT), Jena, Germany
| | - Clara Stiebing
- Leibniz Institute of Photonic Technology - a member of the Leibniz Research Alliance Leibniz Health Technology (Leibniz-IPHT), Jena, Germany
| | - Michael Schmitt
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology - a member of the Leibniz Research Alliance Leibniz Health Technology (Leibniz-IPHT), Jena, Germany
- Research Campus Infectognostics e.V., Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology - a member of the Leibniz Research Alliance Leibniz Health Technology (Leibniz-IPHT), Jena, Germany
- Research Campus Infectognostics e.V., Jena, Germany
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25
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Yonamine Y, Hiramatsu K, Ideguchi T, Ito T, Fujiwara T, Miura Y, Goda K, Hoshino Y. Spatiotemporal monitoring of intracellular metabolic dynamics by resonance Raman microscopy with isotope labeling. RSC Adv 2020; 10:16679-16686. [PMID: 35498863 PMCID: PMC9053077 DOI: 10.1039/d0ra02803g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/20/2020] [Indexed: 01/18/2023] Open
Abstract
We probed production process of a cellular metabolite with a stable isotope-labeled substrate exposed to various conditions.
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Affiliation(s)
- Yusuke Yonamine
- Research Institute for Electronic Science
- Hokkaido University
- Sapporo 001-0021
- Japan
| | - Kotaro Hiramatsu
- Department of Chemistry
- The University of Tokyo
- Tokyo 113-0033
- Japan
- Research Centre for Spectrochemistry
| | - Takuro Ideguchi
- Research Centre for Spectrochemistry
- The University of Tokyo
- Tokyo 113-0033
- Japan
- PRESTO
| | - Takuro Ito
- Japan Science and Technology Agency
- Kawaguchi-shi
- Japan
| | - Tomomi Fujiwara
- Department of Chemical Engineering
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Yoshiko Miura
- Department of Chemical Engineering
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Keisuke Goda
- Department of Chemistry
- The University of Tokyo
- Tokyo 113-0033
- Japan
- Japan Science and Technology Agency
| | - Yu Hoshino
- Department of Chemical Engineering
- Kyushu University
- Fukuoka 819-0395
- Japan
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26
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Ramanome technology platform for label-free screening and sorting of microbial cell factories at single-cell resolution. Biotechnol Adv 2019; 37:107388. [DOI: 10.1016/j.biotechadv.2019.04.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/08/2019] [Accepted: 04/23/2019] [Indexed: 01/09/2023]
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27
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Arul P, John SA. Organic solvent free in situ growth of flower like Co-ZIF microstructures on nickel foam for glucose sensing and supercapacitor applications. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.03.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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28
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Spectral tracing of deuterium for imaging glucose metabolism. Nat Biomed Eng 2019; 3:402-413. [PMID: 31036888 PMCID: PMC6599680 DOI: 10.1038/s41551-019-0393-4] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 03/17/2019] [Indexed: 01/31/2023]
Abstract
Cells and tissues often display pronounced spatial and dynamical metabolic heterogeneity. Prevalent glucose-imaging techniques report glucose uptake or catabolism activity, yet do not trace the functional utilization of glucose-derived anabolic products. Here, we report a microscopy technique for the optical imaging, via the spectral tracing of deuterium (referred to as STRIDE), of diverse macromolecules derived from glucose. Based on stimulated-Raman-scattering imaging, STRIDE visualizes the metabolic dynamics of newly synthesized macromolecules, such as DNA, protein, lipids and glycogen, via the enrichment and distinct spectra of carbon–deuterium bonds transferred from the deuterated glucose precursor. STRIDE can also use spectral differences derived from different glucose isotopologues to visualize temporally separated glucose populations in a pulse–chase manner. We also show that STRIDE can be used to image glucose metabolism in many mouse tissues, including tumours, the brain, the intestine and the liver, at a detection limit of 10 mM of carbon–deuterium bonds. STRIDE provides a high-resolution and chemically informative assessment of glucose anabolic utilization.
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29
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Taylor GT. Windows into Microbial Seascapes: Advances in Nanoscale Imaging and Application to Marine Sciences. ANNUAL REVIEW OF MARINE SCIENCE 2019; 11:465-490. [PMID: 30134123 DOI: 10.1146/annurev-marine-121916-063612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Geochemical cycles of all nonconservative elements are mediated by microorganisms over nanometer spatial scales. The pelagic seascape is known to possess microstructure imposed by heterogeneous distributions of particles, polymeric gels, biologically important chemicals, and microbes. While indispensable, most traditional oceanographic observational approaches overlook this heterogeneity and ignore subtleties, such as activity hot spots, symbioses, niche partitioning, and intrapopulation phenotypic variations, that can provide a deeper mechanistic understanding of planktonic ecosystem function. As part of the movement toward cultivation-independent tools in microbial oceanography, techniques to examine the ecophysiology of individual populations and their role in chemical transformations at spatial scales relevant to microorganisms have been developed. This review presents technologies that enable geochemical and microbiological interrogations at spatial scales ranging from 0.02 to a few hundred micrometers, particularly focusing on atomic force microscopy, nanoscale secondary ion mass spectrometry, and confocal Raman microspectroscopy and introducing promising approaches for future applications in marine sciences.
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Affiliation(s)
- Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794, USA;
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30
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Kelly J, Patrick R, Patrick S, Bell SEJ. Surface-Enhanced Raman Spectroscopy for the Detection of a Metabolic Product in the Headspace Above Live Bacterial Cultures. Angew Chem Int Ed Engl 2018; 57:15686-15690. [DOI: 10.1002/anie.201808185] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/21/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Jessica Kelly
- School of Chemistry & Chemical Engineering; Queen's University; Belfast BT9 5AG UK
| | - Robin Patrick
- School of Chemistry & Chemical Engineering; Queen's University; Belfast BT9 5AG UK
| | - Sheila Patrick
- School of Medicine, Dentistry and Biomedical Sciences; Centre for Infection and Immunity; Queen's University; Belfast BT9 5AG UK
| | - Steven E. J. Bell
- School of Chemistry & Chemical Engineering; Queen's University; Belfast BT9 5AG UK
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31
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Kelly J, Patrick R, Patrick S, Bell SEJ. Surface-Enhanced Raman Spectroscopy for the Detection of a Metabolic Product in the Headspace Above Live Bacterial Cultures. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jessica Kelly
- School of Chemistry & Chemical Engineering; Queen's University; Belfast BT9 5AG UK
| | - Robin Patrick
- School of Chemistry & Chemical Engineering; Queen's University; Belfast BT9 5AG UK
| | - Sheila Patrick
- School of Medicine, Dentistry and Biomedical Sciences; Centre for Infection and Immunity; Queen's University; Belfast BT9 5AG UK
| | - Steven E. J. Bell
- School of Chemistry & Chemical Engineering; Queen's University; Belfast BT9 5AG UK
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32
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Wilhelm RC, Hanson BT, Chandra S, Madsen E. Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater. Environ Microbiol 2018; 20:3543-3559. [PMID: 30051558 DOI: 10.1111/1462-2920.14309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/07/2018] [Indexed: 12/19/2022]
Abstract
Earlier research on the biogeochemical factors affecting natural attenuation in coal-tar contaminated groundwater, at South Glens Falls, NY, revealed the importance of anaerobic metabolism and trophic interactions between degrader and bacterivore populations. Field-based characterizations of both phenomena have proven challenging, but advances in stable isotope probing (SIP), single-cell imaging and shotgun metagenomics now provide cultivation-independent tools for their study. We tracked carbon from 13 C-labelled naphthalene through microbial populations in contaminated surface sediments over 6 days using respiration assays, secondary ion mass spectrometry imaging and shotgun metagenomics to disentangle the contaminant-based trophic web. Contaminant-exposed communities in hypoxic/anoxic groundwater were contrasted with those from oxic surface sediments to identify putative features of anaerobic catabolism of naphthalene. In total, six bacteria were responsible for naphthalene degradation. Cupriavidus, Ralstonia and Sphingomonas predominated at the earliest stages of SIP incubations and were succeeded in later stages by Stenotrophomonas and Rhodococcus. Metagenome-assembled genomes provided evidence for the ecological and functional characteristics underlying these temporal shifts. Identical species of Stenotrophomonas and Rhodococcus were abundant in the most contaminated, anoxic groundwater. Apparent increases in bacterivorous protozoa were observed following exposure to naphthalene, though insignificant amounts of carbon were transferred between bacterial degraders and populations of secondary feeders.
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Affiliation(s)
- Roland C Wilhelm
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Buck T Hanson
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Subhash Chandra
- Cornell SIMS Laboratory, Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Eugene Madsen
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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33
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Weitere M, Erken M, Majdi N, Arndt H, Norf H, Reinshagen M, Traunspurger W, Walterscheid A, Wey JK. The food web perspective on aquatic biofilms. ECOL MONOGR 2018. [DOI: 10.1002/ecm.1315] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Markus Weitere
- Department River Ecology; Helmholtz Centre of Environmental Research - UFZ; Brückstrasse 3a 39114 Magdeburg Germany
| | - Martina Erken
- Department River Ecology; Helmholtz Centre of Environmental Research - UFZ; Brückstrasse 3a 39114 Magdeburg Germany
| | - Nabil Majdi
- Department of Animal Ecology; University of Bielefeld; Konsequenz 45 33615 Bielefeld Germany
| | - Hartmut Arndt
- General Ecology; Zoological Institute; Cologne Biocenter; University of Cologne; Zülpicher Strasse 47b 50674 Cologne Germany
| | - Helge Norf
- Department River Ecology; Helmholtz Centre of Environmental Research - UFZ; Brückstrasse 3a 39114 Magdeburg Germany
- Department Aquatic Ecosystem Analyses and Management; Helmholtz Centre of Environmental Research - UFZ; Brückstrasse 3a 39114 Magdeburg Germany
| | - Michael Reinshagen
- General Ecology; Zoological Institute; Cologne Biocenter; University of Cologne; Zülpicher Strasse 47b 50674 Cologne Germany
| | - Walter Traunspurger
- Department of Animal Ecology; University of Bielefeld; Konsequenz 45 33615 Bielefeld Germany
| | - Anja Walterscheid
- General Ecology; Zoological Institute; Cologne Biocenter; University of Cologne; Zülpicher Strasse 47b 50674 Cologne Germany
| | - Jennifer K. Wey
- Department River Ecology; Helmholtz Centre of Environmental Research - UFZ; Brückstrasse 3a 39114 Magdeburg Germany
- Department of Animal Ecology; Federal Institute of Hydrology; Am Mainzer Tor 1 56068 Koblenz Germany
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34
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Noothalapati H, Iwasaki K, Yamamoto T. Biological and Medical Applications of Multivariate Curve Resolution Assisted Raman Spectroscopy. ANAL SCI 2018; 33:15-22. [PMID: 28070069 DOI: 10.2116/analsci.33.15] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Biological specimens such as cells, tissues and biofluids (urine, blood) contain mixtures of many different biomolecules, all of which contribute to a Raman spectrum at any given point. The separation and identification of pure biochemical components remains one of the biggest challenges in Raman spectroscopy. Multivariate curve resolution, a matrix factorization method, is a powerful, yet flexible, method that can be used with constraints, such as non-negativity, to decompose a complex spectroscopic data matrix into a small number of physically meaningful pure spectral components along with their relative abundances. This paper reviews recent applications of multivariate curve resolution by alternating least squares analysis to Raman spectroscopic and imaging data obtained either in vivo or in vitro from biological and medical samples.
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35
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Xu J, Zhu D, Ibrahim AD, Allen CCR, Gibson CM, Fowler PW, Song Y, Huang WE. Raman Deuterium Isotope Probing Reveals Microbial Metabolism at the Single-Cell Level. Anal Chem 2017; 89:13305-13312. [DOI: 10.1021/acs.analchem.7b03461] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jiabao Xu
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | - Di Zhu
- Kroto
Research Institute, University of Sheffield, Sheffield S3 7HQ, United Kingdom
| | - Aliyu D. Ibrahim
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 7BL, United Kingdom
| | - Christopher C. R. Allen
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 7BL, United Kingdom
| | | | - Patrick W. Fowler
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Yizhi Song
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | - Wei E. Huang
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
- Kroto
Research Institute, University of Sheffield, Sheffield S3 7HQ, United Kingdom
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36
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Yonamine Y, Suzuki Y, Ito T, Miura Y, Goda K, Ozeki Y, Hoshino Y. Monitoring Photosynthetic Activity in Microalgal Cells by Raman Spectroscopy with Deuterium Oxide as a Tracking Probe. Chembiochem 2017; 18:2063-2068. [DOI: 10.1002/cbic.201700314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Yusuke Yonamine
- Department of Chemical Engineering; Kyushu University; 744 Motooka Fukuoka 819-0395 Japan
| | - Yuta Suzuki
- Department of Electrical Engineering and Information Systems; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Takuro Ito
- Japan Science and Technology Agency; 4-1-8 Honcho Kawaguchi-shi Saitama 332-0012 Japan
| | - Yoshiko Miura
- Department of Chemical Engineering; Kyushu University; 744 Motooka Fukuoka 819-0395 Japan
| | - Keisuke Goda
- Japan Science and Technology Agency; 4-1-8 Honcho Kawaguchi-shi Saitama 332-0012 Japan
- Department of Chemistry; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Department of Electrical Engineering; University of California; 420 Westwood Plaza Los Angeles CA 90095 USA
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Yu Hoshino
- Department of Chemical Engineering; Kyushu University; 744 Motooka Fukuoka 819-0395 Japan
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37
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Cui L, Yang K, Zhou G, Huang WE, Zhu YG. Surface-Enhanced Raman Spectroscopy Combined with Stable Isotope Probing to Monitor Nitrogen Assimilation at Both Bulk and Single-Cell Level. Anal Chem 2017; 89:5793-5800. [DOI: 10.1021/acs.analchem.6b04913] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Li Cui
- Key
Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Department
of Engineering Science, University of Oxford, Oxford, OX1 3PJ, U.K
| | - Kai Yang
- Key
Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guowei Zhou
- Key
Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Wei E. Huang
- Department
of Engineering Science, University of Oxford, Oxford, OX1 3PJ, U.K
| | - Yong-Guan Zhu
- Key
Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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38
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Cultivation-Free Raman Spectroscopic Investigations of Bacteria. Trends Microbiol 2017; 25:413-424. [DOI: 10.1016/j.tim.2017.01.002] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/06/2017] [Accepted: 01/11/2017] [Indexed: 01/22/2023]
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39
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He Y, Zhang P, Huang S, Wang T, Ji Y, Xu J. Label-free, simultaneous quantification of starch, protein and triacylglycerol in single microalgal cells. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:275. [PMID: 29177009 PMCID: PMC5693592 DOI: 10.1186/s13068-017-0967-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/10/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Current approaches for quantification of major energy-storage forms in microalgae, including starch, protein and lipids, generally require cell cultivation to collect biomass followed by tedious and time-consuming analytical procedures. Thus, label-free, non-destructive and simultaneous quantification of such macromolecules at single-cell resolution is highly desirable in microalgal feedstock development and bioprocess control. RESULTS Here, we established a method based on single-cell Raman spectra (SCRS) that simultaneously quantifies the contents of starch, protein, triacylglycerol (TAG) and lipid unsaturation degree in individual Chlamydomonas reinhardtii cells. Measurement accuracy for the contents based on full SCRS spectrum each reached 96.86-99.24%, all significantly higher than single peak-based models. However, accuracy and reliability of measurement are dependent on the number of cells sampled, thus a formal mathematical framework was proposed and validated to rationally define "minimal sampling depth" for a given state of cellular population. Furthermore, a barcode consisting of 13 marker Raman peaks was proposed to characterize the temporal dynamics of these energy-storage products, which revealed that the average contents of starch and TAG increased, while their heterogeneity indices decreased, with those of protein being exactly the opposite. Finally, our method is widely applicable, as measurements among cells from liquid suspension culture, wet paste and frozen dried powder all exhibited excellent consistency. CONCLUSIONS When sampled at proper depth, SCRS can serve as a quantitative and generally applicable tool for characterization and screening of strains and bioprocesses based on the profile of energy-storage macromolecules and their among-cell heterogeneity.
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Affiliation(s)
- Yuehui He
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shi Huang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong China
- University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong China
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40
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Wang Y, Song Y, Tao Y, Muhamadali H, Goodacre R, Zhou NY, Preston GM, Xu J, Huang WE. Reverse and Multiple Stable Isotope Probing to Study Bacterial Metabolism and Interactions at the Single Cell Level. Anal Chem 2016; 88:9443-9450. [DOI: 10.1021/acs.analchem.6b01602] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Yun Wang
- Single
Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory
of Energy Genetics, Chinese Academy of Sciences, Qingdao, 266101, P. R. China
| | - Yizhi Song
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Yifan Tao
- Department
of Operative Dentistry and Endodontics, Guanghua School and Hospital
of Stomatology, Sun Yat-sen University, Guangzhou, 510055, P. R. China
| | - Howbeer Muhamadali
- School
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Royston Goodacre
- School
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Gail M. Preston
- Department
of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
| | - Jian Xu
- Single
Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory
of Energy Genetics, Chinese Academy of Sciences, Qingdao, 266101, P. R. China
| | - Wei E. Huang
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
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41
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Kumar B. N. V, Guo S, Bocklitz T, Rösch P, Popp J. Demonstration of Carbon Catabolite Repression in Naphthalene Degrading Soil Bacteria via Raman Spectroscopy Based Stable Isotope Probing. Anal Chem 2016; 88:7574-82. [DOI: 10.1021/acs.analchem.6b01046] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Vinay Kumar B. N.
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- InfectoGnostics, Forschungscampus Jena, Philosophenweg
7, D-07743 Jena, Germany
| | - Shuxia Guo
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Thomas Bocklitz
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- InfectoGnostics, Forschungscampus Jena, Philosophenweg
7, D-07743 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Petra Rösch
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- InfectoGnostics, Forschungscampus Jena, Philosophenweg
7, D-07743 Jena, Germany
| | - Jürgen Popp
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- InfectoGnostics, Forschungscampus Jena, Philosophenweg
7, D-07743 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
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42
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Wang Y, Huang WE, Cui L, Wagner M. Single cell stable isotope probing in microbiology using Raman microspectroscopy. Curr Opin Biotechnol 2016; 41:34-42. [PMID: 27149160 DOI: 10.1016/j.copbio.2016.04.018] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/17/2016] [Accepted: 04/19/2016] [Indexed: 12/14/2022]
Abstract
Microbial communities are essential for most ecosystem processes and interact in highly complex ways with virtually all eukaryotes. Thus, a detailed understanding of the function of such communities is a fundamental prerequisite for microbial ecologists, applied microbiologists and microbiome researchers. Using single cell Raman microspectroscopy, biochemical fingerprints of individual microbial cells can be obtained in an externally label-free and non-destructive manner. If combined with stable isotope probing (SIP), Raman spectroscopy can directly reveal functions of single microorganisms in their natural habitat. This review provides an update on various SIP-approaches suitable for combination with different Raman scattering techniques and illustrates how single cell Raman SIP can be directly combined with the omics-centric analysis pipelines to investigate microbial communities.
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Affiliation(s)
- Yun Wang
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics and Single Cell Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry Meets Microbiology', University of Vienna, 1090 Vienna, Austria
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43
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Smith R, Wright KL, Ashton L. Raman spectroscopy: an evolving technique for live cell studies. Analyst 2016; 141:3590-600. [PMID: 27072718 DOI: 10.1039/c6an00152a] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
One of the most exciting developments in Raman spectroscopy in the last decade has been its application to cells and tissues for diagnostic and pharmaceutical applications, and in particular its use in the analysis of cellular dynamics. Raman spectroscopy is rapidly advancing as a cell imaging method that overcomes many of the limitations of current techniques and is earning its place as a routine tool in cell biology. In this review we focus on important developments in Raman spectroscopy that have evolved into the exciting technique of live-cell Raman microscopy and highlight some of the most recent and significant applications to cell biology.
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Affiliation(s)
- Rachael Smith
- Department of Chemistry, Lancaster University, LA1 4YG, UK.
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44
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Naemat A, Elsheikha HM, Boitor RA, Notingher I. Tracing amino acid exchange during host-pathogen interaction by combined stable-isotope time-resolved Raman spectral imaging. Sci Rep 2016; 6:20811. [PMID: 26857158 PMCID: PMC4746650 DOI: 10.1038/srep20811] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/13/2016] [Indexed: 11/09/2022] Open
Abstract
This study investigates the temporal and spatial interchange of the aromatic amino acid phenylalanine (Phe) between human retinal pigment epithelial cell line (ARPE-19) and tachyzoites of the apicomplexan protozoan parasite Toxoplasma gondii (T. gondii). Stable isotope labelling by amino acids in cell culture (SILAC) is combined with Raman micro-spectroscopy to selectively monitor the incorporation of deuterium-labelled Phe into proteins in individual live tachyzoites. Our results show a very rapid uptake of l-Phe(D8) by the intracellular growing parasite. T. gondii tachyzoites are capable of extracting l-Phe(D8) from host cells as soon as it invades the cell. l-Phe(D8) from the host cell completely replaces the l-Phe within T. gondii tachyzoites 7-9 hours after infection. A quantitative model based on Raman spectra allowed an estimation of the exchange rate of Phe as 0.5-1.6 × 10(4) molecules/s. On the other hand, extracellular tachyzoites were not able to consume l-Phe(D8) after 24 hours of infection. These findings further our understanding of the amino acid trafficking between host cells and this strictly intracellular parasite. In particular, this study highlights new aspects of the metabolism of amino acid Phe operative during the interaction between T. gondii and its host cell.
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Affiliation(s)
- Abida Naemat
- School of Physics and Astronomy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK
| | - Radu A Boitor
- School of Physics and Astronomy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Ioan Notingher
- School of Physics and Astronomy, University of Nottingham, Nottingham, NG7 2RD, UK
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45
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Kubryk P, Kölschbach JS, Marozava S, Lueders T, Meckenstock RU, Niessner R, Ivleva NP. Exploring the Potential of Stable Isotope (Resonance) Raman Microspectroscopy and Surface-Enhanced Raman Scattering for the Analysis of Microorganisms at Single Cell Level. Anal Chem 2015; 87:6622-30. [DOI: 10.1021/acs.analchem.5b00673] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Patrick Kubryk
- Technische Universität München, Institute
of Hydrochemistry, Chair for Analytical Chemistry, Marchioninistr. 17, 81377 Munich, Germany
| | - Janina S. Kölschbach
- Helmholtz Zentrum München, Institute of Groundwater
Ecology, Ingolstädter
Landstr. 1, 85764 Neuherberg, Germany
| | - Sviatlana Marozava
- Helmholtz Zentrum München, Institute of Groundwater
Ecology, Ingolstädter
Landstr. 1, 85764 Neuherberg, Germany
| | - Tillmann Lueders
- Helmholtz Zentrum München, Institute of Groundwater
Ecology, Ingolstädter
Landstr. 1, 85764 Neuherberg, Germany
| | - Rainer U. Meckenstock
- Helmholtz Zentrum München, Institute of Groundwater
Ecology, Ingolstädter
Landstr. 1, 85764 Neuherberg, Germany
| | - Reinhard Niessner
- Technische Universität München, Institute
of Hydrochemistry, Chair for Analytical Chemistry, Marchioninistr. 17, 81377 Munich, Germany
| | - Natalia P. Ivleva
- Technische Universität München, Institute
of Hydrochemistry, Chair for Analytical Chemistry, Marchioninistr. 17, 81377 Munich, Germany
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Muhamadali H, Chisanga M, Subaihi A, Goodacre R. Combining Raman and FT-IR spectroscopy with quantitative isotopic labeling for differentiation of E. coli cells at community and single cell levels. Anal Chem 2015; 87:4578-86. [PMID: 25831066 DOI: 10.1021/acs.analchem.5b00892] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is no doubt that the contribution of microbially mediated bioprocesses toward maintenance of life on earth is vital. However, understanding these microbes in situ is currently a bottleneck, as most methods require culturing these microorganisms to suitable biomass levels so that their phenotype can be measured. The development of new culture-independent strategies such as stable isotope probing (SIP) coupled with molecular biology has been a breakthrough toward linking gene to function, while circumventing in vitro culturing. In this study, for the first time we have combined Raman spectroscopy and Fourier transform infrared (FT-IR) spectroscopy, as metabolic fingerprinting approaches, with SIP to demonstrate the quantitative labeling and differentiation of Escherichia coli cells. E. coli cells were grown in minimal medium with fixed final concentrations of carbon and nitrogen supply, but with different ratios and combinations of (13)C/(12)C glucose and (15)N/(14)N ammonium chloride, as the sole carbon and nitrogen sources, respectively. The cells were collected at stationary phase and examined by Raman and FT-IR spectroscopies. The multivariate analysis investigation of FT-IR and Raman data illustrated unique clustering patterns resulting from specific spectral shifts upon the incorporation of different isotopes, which were directly correlated with the ratio of the isotopically labeled content of the medium. Multivariate analysis results of single-cell Raman spectra followed the same trend, exhibiting a separation between E. coli cells labeled with different isotopes and multiple isotope levels of C and N.
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Affiliation(s)
- Howbeer Muhamadali
- ‡School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Malama Chisanga
- ‡School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom.,§School of Mathematics and Natural Sciences, Department of Chemistry, Copperbelt University, Kitwe, Zambia
| | - Abdu Subaihi
- ‡School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Royston Goodacre
- ‡School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
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Wang C, Ruan L, Chang XL, Zhang X, Yang ST, Guo X, Yuan H, Guo C, Shi W, Sun B, Zhao Y. The isotopic effects of 13C-labeled large carbon cage (C70) fullerenes and their formation process. RSC Adv 2015. [DOI: 10.1039/c5ra06588g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
13C-enriched large carbon cage-based fullerenes were synthesized on a large scale by an arc discharge method.
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Altermatt F, Fronhofer EA, Garnier A, Giometto A, Hammes F, Klecka J, Legrand D, Mächler E, Massie TM, Pennekamp F, Plebani M, Pontarp M, Schtickzelle N, Thuillier V, Petchey OL. Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12312] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florian Altermatt
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
- Institute of Evolutionary Biology and Environmental Studies University of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
| | - Emanuel A. Fronhofer
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
| | - Aurélie Garnier
- Institute of Evolutionary Biology and Environmental Studies University of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
| | - Andrea Giometto
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
- Laboratory of Ecohydrology School of Architecture Civil and Environmental Engineering École Polytechnique Fédérale de Lausanne CH‐1015 Lausanne Switzerland
| | - Frederik Hammes
- Department of Environmental Microbiology Eawag: Swiss Federal Institute of Aquatic Science and Technology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
| | - Jan Klecka
- Laboratory of Theoretical Ecology Institute of Entomology Biology Centre ASCR Branišovská 31 České Budějovice 37005 Czech Republic
- Department of Fish Ecology and Evolution Eawag: Swiss Federal Institute of Aquatic Science and Technology Seestrasse 79 CH‐6047 Kastanienbaum Switzerland
| | - Delphine Legrand
- Earth and Life Institute Biodiversity Research Centre Université catholique de Louvain Croix du Sud 4 L7.07.04 B‐1348 Louvain‐la‐Neuve Belgium
| | - Elvira Mächler
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
| | - Thomas M. Massie
- Institute of Evolutionary Biology and Environmental Studies University of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
| | - Frank Pennekamp
- Institute of Evolutionary Biology and Environmental Studies University of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
| | - Marco Plebani
- Institute of Evolutionary Biology and Environmental Studies University of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
| | - Mikael Pontarp
- Institute of Evolutionary Biology and Environmental Studies University of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
| | - Nicolas Schtickzelle
- Earth and Life Institute Biodiversity Research Centre Université catholique de Louvain Croix du Sud 4 L7.07.04 B‐1348 Louvain‐la‐Neuve Belgium
| | - Virginie Thuillier
- Earth and Life Institute Biodiversity Research Centre Université catholique de Louvain Croix du Sud 4 L7.07.04 B‐1348 Louvain‐la‐Neuve Belgium
| | - Owen L. Petchey
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
- Institute of Evolutionary Biology and Environmental Studies University of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
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49
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Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community. ISME JOURNAL 2014; 9:603-14. [PMID: 25191996 DOI: 10.1038/ismej.2014.161] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 07/21/2014] [Accepted: 07/27/2014] [Indexed: 11/09/2022]
Abstract
Although uncultured microorganisms have important roles in ecosystems, their ecophysiology in situ remains elusive owing to the difficulty of obtaining live cells from their natural habitats. In this study, we employed a novel magnetic nanoparticle-mediated isolation (MMI) method to recover metabolically active cells of a group of previously uncultured phenol degraders, Burkholderiales spp., from coking plant wastewater biosludge; five other culturable phenol degraders-Rhodococcus sp., Chryseobacterium sp. and three different Pseudomonas spp.-were also isolated from the same biosludge using traditional methods. The kinetics of phenol degradation by MMI-recovered cells (MRCs) was similar to that of the original sludge. Stable isotope probing (SIP) and pyrosequencing of the 16S rRNA from the 'heavy' DNA ((13)C-DNA) fractions indicated that Burkholderiales spp. were the key phenol degraders in situ in the biosludge, consistent with the results of MRCs. Single-cell Raman micro-spectroscopy was applied to probe individual bacteria in the MRCs obtained from the SIP experiment and showed that 79% of them were fully (13)C-labelled. Biolog assays on the MRCs revealed the impact of various carbon and nitrogen substrates on the efficiency of phenol degradation in the wastewater treatment plant biosludge. Specifically, hydroxylamine, a metabolite of ammonia oxidisation, but not nitrite, nitrate or ammonia, inhibited phenol degradation in the biosludge. Our results provided a novel insight into the occasional abrupt failure events that occur in the wastewater treatment plant. This study demonstrated that MMI is a powerful tool to recover live and functional cells in situ from a complex microbial community to enable further characterisation of their physiology.
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Noothalapati H, Shigeto S. Exploring metabolic pathways in vivo by a combined approach of mixed stable isotope-labeled Raman microspectroscopy and multivariate curve resolution analysis. Anal Chem 2014; 86:7828-34. [PMID: 24975289 DOI: 10.1021/ac501735c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding cellular metabolism is a major challenge in current systems biology and has triggered extensive metabolomics research, which in most cases involves destructive analysis. However, the information obtainable only in a nondestructive manner will be required for accurately mapping the global structure of the organism's metabolic network at a given instant. Here we report that metabolic pathways can be explored in vivo by mixed stable isotope-labeled Raman microspectroscopy in conjunction with multivariate curve resolution analysis. As a model system, we studied ergosterol biosynthesis in single living fission yeast cells grown in mixtures of normal and (13)C-labeled glucose as the sole carbon source. The multivariate spectral data analysis of space-resolved Raman spectra revealed the intrinsic spectra and relative abundances of all isotopomers of ergosterol whose carbon atoms in the 5,7-diene moiety of the sterol skeleton are either partly or fully substituted with (13)C. Our approach is applicable to other metabolites and will earn a place in the toolbox of metabolomic analysis.
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Affiliation(s)
- Hemanth Noothalapati
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University , Hsinchu 30010, Taiwan
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