1
|
Gupte AP, Pierantoni DC, Conti A, Donati L, Basaglia M, Casella S, Favaro L, Corte L, Cardinali G. Renewing Lost Genetic Variability with a Classical Yeast Genetics Approach. J Fungi (Basel) 2023; 9:jof9020264. [PMID: 36836378 PMCID: PMC9958831 DOI: 10.3390/jof9020264] [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: 12/28/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Due to their long domestication time course, many industrial Saccharomyces cerevisiae strains are adopted in numerous processes mostly for historical reasons instead of scientific and technological needs. As such, there is still significant room for improvement for industrial yeast strains relying on yeast biodiversity. This paper strives to regenerate biodiversity with the innovative application of classic genetic methods to already available yeast strains. Extensive sporulation was indeed applied to three different yeast strains, specifically selected for their different origins as well as backgrounds, with the aim of clarifying how new variability was generated. A novel and easy method to obtain mono-spore colonies was specifically developed, and, to reveal the extent of the generated variability, no selection after sporulation was introduced. The obtained progenies were then tested for their growth in defined mediums with high stressor levels. A considerable and strain-specific increase in both phenotypic and metabolomic variability was assessed, and a few mono-spore colonies were found to be of great interest for their future exploitation in selected industrial processes.
Collapse
Affiliation(s)
- Ameya Pankaj Gupte
- Department of Agronomy Food natural Resources Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | | | - Angela Conti
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy
| | - Leonardo Donati
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy
| | - Marina Basaglia
- Department of Agronomy Food natural Resources Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Sergio Casella
- Department of Agronomy Food natural Resources Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Lorenzo Favaro
- Department of Agronomy Food natural Resources Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
- Correspondence: (L.F.); (L.C.)
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy
- Correspondence: (L.F.); (L.C.)
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy
| |
Collapse
|
2
|
Cabugao KGM, Gushgari-Doyle S, Chacon SS, Wu X, Bhattacharyya A, Bouskill N, Chakraborty R. Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges. Front Microbiol 2022; 13:864895. [PMID: 35602028 PMCID: PMC9114703 DOI: 10.3389/fmicb.2022.864895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.
Collapse
Affiliation(s)
- Kristine Grace M Cabugao
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sara Gushgari-Doyle
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Stephany S Chacon
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Xiaoqin Wu
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Amrita Bhattacharyya
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicholas Bouskill
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Department of Ecology, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| |
Collapse
|
3
|
Infrared-spectroscopic, dynamic near-field microscopy of living cells and nanoparticles in water. Sci Rep 2021; 11:21860. [PMID: 34750511 PMCID: PMC8576021 DOI: 10.1038/s41598-021-01425-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/26/2021] [Indexed: 11/17/2022] Open
Abstract
Infrared fingerprint spectra can reveal the chemical nature of materials down to 20-nm detail, far below the diffraction limit, when probed by scattering-type scanning near-field optical microscopy (s-SNOM). But this was impossible with living cells or aqueous processes as in corrosion, due to water-related absorption and tip contamination. Here, we demonstrate infrared s-SNOM of water-suspended objects by probing them through a 10-nm thick SiN membrane. This separator stretches freely over up to 250 µm, providing an upper, stable surface to the scanning tip, while its lower surface is in contact with the liquid and localises adhering objects. We present its proof-of-principle applicability in biology by observing simply drop-casted, living E. coli in nutrient medium, as well as living A549 cancer cells, as they divide, move and develop rich sub-cellular morphology and adhesion patterns, at 150 nm resolution. Their infrared spectra reveal the local abundances of water, proteins, and lipids within a depth of ca. 100 nm below the SiN membrane, as we verify by analysing well-defined, suspended polymer spheres and through model calculations. SiN-membrane based s-SNOM thus establishes a novel tool of live cell nano-imaging that returns structure, dynamics and chemical composition. This method should benefit the nanoscale analysis of any aqueous system, from physics to medicine.
Collapse
|
4
|
Valdespino-Castillo PM, Hu P, Merino-Ibarra M, López-Gómez LM, Cerqueda-García D, González-De Zayas R, Pi-Puig T, Lestayo JA, Holman HY, Falcón LI. Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba. Front Microbiol 2018; 9:510. [PMID: 29666607 PMCID: PMC5891642 DOI: 10.3389/fmicb.2018.00510] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/06/2018] [Indexed: 01/23/2023] Open
Abstract
Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (Corg), nitrogen and Corg:Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations.
Collapse
Affiliation(s)
- Patricia M Valdespino-Castillo
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States
| | - Ping Hu
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States
| | - Martín Merino-Ibarra
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luz M López-Gómez
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Daniel Cerqueda-García
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Teresa Pi-Puig
- Instituto de Geología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Laboratorio Nacional de Geoquímica y Mineralogía, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Julio A Lestayo
- Centro de Investigaciones de Ecosistemas Costeros, Cayo Coco, Cuba
| | - Hoi-Ying Holman
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States
| | - Luisa I Falcón
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
5
|
|
6
|
Loutherback K, Birarda G, Chen L, Holman HYN. Microfluidic approaches to synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy of living biosystems. Protein Pept Lett 2016; 23:273-82. [PMID: 26732243 PMCID: PMC4997923 DOI: 10.2174/0929866523666160106154035] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/30/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023]
Abstract
A long-standing desire in biological and biomedical sciences is to be able to probe cellular chemistry as biological processes are happening inside living cells. Synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy is a label-free and nondestructive analytical technique that can provide spatiotemporal distributions and relative abundances of biomolecules of a specimen by their characteristic vibrational modes. Despite great progress in recent years, SR-FTIR imaging of living biological systems remains challenging because of the demanding requirements on environmental control and strong infrared absorption of water. To meet this challenge, microfluidic devices have emerged as a method to control the water thickness while providing a hospitable environment to measure cellular processes and responses over many hours or days. This paper will provide an overview of microfluidic device development for SR-FTIR imaging of living biological systems, provide contrast between the various techniques including closed and open-channel designs, and discuss future directions of development within this area. Even as the fundamental science and technological demonstrations develop, other ongoing issues must be addressed; for example, choosing applications whose experimental requirements closely match device capabilities, and developing strategies to efficiently complete the cycle of development. These will require imagination, ingenuity and collaboration.
Collapse
Affiliation(s)
| | | | | | - Hoi-Ying N Holman
- Berkeley Synchrotron Infrared Structural Biology Program, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| |
Collapse
|
7
|
Zucchiatti P, Mitri E, Kenig S, Billè F, Kourousias G, Bedolla DE, Vaccari L. Contribution of Ribonucleic Acid (RNA) to the Fourier Transform Infrared (FTIR) Spectrum of Eukaryotic Cells. Anal Chem 2016; 88:12090-12098. [PMID: 28193045 DOI: 10.1021/acs.analchem.6b02744] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We report on an optimized protocol for the digestion of cellular RNA, which minimally affects the cell membrane integrity, maintaining substantially unaltered the vibrational contributions of the other cellular macromolecules. The design of this protocol allowed us to collect the first Fourier transform infrared (FTIR) spectra of intact hydrated B16 mouse melanoma cells deprived of RNA and to highlight the in-cell diagnostic spectral features of it. Complementing the cellular results with the FTIR analysis of extracted RNA, ds-DNA, ss-cDNA and isolated nuclei, we verified that the spectral component centered at ∼1220 cm-1 is a good qualitative and semiquantitative marker of cellular DNA, since it is minimally affected by cellular RNA removal. Conversely, the band centered at ∼1240 cm-1, conventionally attributed to RNA, is only a qualitative marker of it, since its intensity is majorly influenced by other macromolecules containing diverse phosphate groups, such as phospholipids and phosphorylated proteins. On the other hand, we proved that the spectral contribution centered at ∼1120 cm-1 is the most reliable indicator of variations in cellular RNA levels, that better correlates with cellular metabolic activity. The achievement of these results have been made possible also by the implementation of new methods for baseline correction and automated peak fitting, presented in this paper.
Collapse
Affiliation(s)
- Paolo Zucchiatti
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, 34151, Trieste, Italy.,Dipartimento di Fisica, Università degli Studi di Trieste , via Valerio 2, 34127 Trieste, Italy
| | - Elisa Mitri
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, 34151, Trieste, Italy
| | - Saša Kenig
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, 34151, Trieste, Italy
| | - Fulvio Billè
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, 34151, Trieste, Italy
| | - George Kourousias
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, 34151, Trieste, Italy
| | - Diana Eva Bedolla
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, 34151, Trieste, Italy
| | - Lisa Vaccari
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, 34151, Trieste, Italy
| |
Collapse
|
8
|
Hong X, Edirisinghe M, Mahalingam S. Beads, beaded-fibres and fibres: Tailoring the morphology of poly(caprolactone) using pressurised gyration. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016; 69:1373-82. [PMID: 27612839 DOI: 10.1016/j.msec.2016.07.071] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/21/2016] [Accepted: 07/26/2016] [Indexed: 11/26/2022]
Abstract
This work focuses on forming bead on string poly(caprolactone) (PCL) by using gyration under pressure. The fibre morphology of bead on string is an interesting feature that falls between bead-free fibres and droplets, and it could be effectively controlled by the rheological properties of spinning dopes and the major processing parameters of the pressurised gyration system which are working pressure and rotating speed. Bead products were not always spherical in shape and tended to be more elliptical, therefore both their width and length were measured. The average bead width and length produced spanned a range 145-660μm and 140-1060μm, respectively. The average distance between two adjacent beads (i.e. inter-bead distance) and the bead size (width and length) are shown to be a function of processing parameters and polymer concentration. An interesting morphology i.e. beads with short fibre was observed when using a high polymer concentration. Bead on string structure agglomeration was promoted by a low polymer concentration. Formation of droplets or agglomerated bead on string is promoted below 5wt% polymer concentration, and beads with short fibre were present in the microstructure beyond a polymer concentration of 20wt%.
Collapse
Affiliation(s)
- Xianze Hong
- Department of Mechanical Engineering, University College London (UCL), London WC1E 7JE, UK
| | - Mohan Edirisinghe
- Department of Mechanical Engineering, University College London (UCL), London WC1E 7JE, UK
| | | |
Collapse
|
9
|
Loutherback K, Chen L, Holman HYN. Open-Channel Microfluidic Membrane Device for Long-Term FT-IR Spectromicroscopy of Live Adherent Cells. Anal Chem 2015; 87:4601-6. [DOI: 10.1021/acs.analchem.5b00524] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kevin Loutherback
- Berkeley Synchrotron Infrared
Structural Biology (BSISB) Program, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Liang Chen
- Berkeley Synchrotron Infrared
Structural Biology (BSISB) Program, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hoi-Ying N. Holman
- Berkeley Synchrotron Infrared
Structural Biology (BSISB) Program, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
10
|
O'Brien JT, Williams ER, Holman HYN. Ambient infrared laser ablation mass spectrometry (AIRLAB-MS) of live plant tissue with plume capture by continuous flow solvent probe. Anal Chem 2015; 87:2631-8. [PMID: 25622206 DOI: 10.1021/ac503383p] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A new experimental setup for spatially resolved ambient infrared laser ablation-mass spectrometry (AIRLAB-MS) that uses an infrared microscope with an infinity-corrected reflective objective and a continuous flow solvent probe coupled to a Fourier transform ion cyclotron resonance mass spectrometer is described. The efficiency of material transfer from the sample to the electrospray ionization emitter was determined using glycerol/methanol droplets containing 1 mM nicotine and is ∼50%. This transfer efficiency is significantly higher than values reported for similar techniques. Laser desorption does not induce fragmentation of biomolecules in droplets containing bradykinin, leucine enkephalin and myoglobin, but loss of the heme group from myoglobin occurs as a result of the denaturing solution used. An application of AIRLAB-MS to biological materials is demonstrated for tobacco leaves. Chemical components are identified from the spatially resolved mass spectra of the ablated plant material, including nicotine and uridine. The reproducibility of measurements made using AIRLAB-MS on plant material was demonstrated by the ablation of six closely spaced areas (within 2 × 2 mm) on a young tobacco leaf, and the results indicate a standard deviation of <10% in the uridine signal obtained for each area. The spatial distribution of nicotine was measured for selected leaf areas and variation in the relative nicotine levels (15-100%) was observed. Comparative analysis of the nicotine distribution was demonstrated for two tobacco plant varieties, a genetically modified plant and its corresponding wild-type, indicating generally higher nicotine levels in the mutant.
Collapse
Affiliation(s)
- Jeremy T O'Brien
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720-0001, United States
| | | | | |
Collapse
|
11
|
Benomar S, Ranava D, Cárdenas ML, Trably E, Rafrafi Y, Ducret A, Hamelin J, Lojou E, Steyer JP, Giudici-Orticoni MT. Nutritional stress induces exchange of cell material and energetic coupling between bacterial species. Nat Commun 2015; 6:6283. [PMID: 25704114 DOI: 10.1038/ncomms7283] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 01/12/2015] [Indexed: 12/24/2022] Open
Abstract
Knowledge of the behaviour of bacterial communities is crucial for understanding biogeochemical cycles and developing environmental biotechnology. Here we demonstrate the formation of an artificial consortium between two anaerobic bacteria, Clostridium acetobutylicum (Gram-positive) and Desulfovibrio vulgaris Hildenborough (Gram-negative, sulfate-reducing) in which physical interactions between the two partners induce emergent properties. Molecular and cellular approaches show that tight cell-cell interactions are associated with an exchange of molecules, including proteins, which allows the growth of one partner (D. vulgaris) in spite of the shortage of nutrients. This physical interaction induces changes in expression of two genes encoding enzymes at the pyruvate crossroads, with concomitant changes in the distribution of metabolic fluxes, and allows a substantial increase in hydrogen production without requiring genetic engineering. The stress induced by the shortage of nutrients of D. vulgaris appears to trigger the interaction.
Collapse
Affiliation(s)
- Saida Benomar
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - David Ranava
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - María Luz Cárdenas
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Eric Trably
- INRA, UR050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, F-11100 Narbonne, France
| | - Yan Rafrafi
- INRA, UR050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, F-11100 Narbonne, France
| | - Adrien Ducret
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 13009 Marseille, France
| | - Jérôme Hamelin
- INRA, UR050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, F-11100 Narbonne, France
| | - Elisabeth Lojou
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Jean-Philippe Steyer
- INRA, UR050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, F-11100 Narbonne, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| |
Collapse
|
12
|
Reuben S, Banas K, Banas A, Swarup S. Combination of synchrotron radiation-based Fourier transforms infrared microspectroscopy and confocal laser scanning microscopy to understand spatial heterogeneity in aquatic multispecies biofilms. WATER RESEARCH 2014; 64:123-133. [PMID: 25046376 DOI: 10.1016/j.watres.2014.06.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 06/18/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
Understanding the spatial heterogeneity within environmental biofilms can provide an insight into compartmentalization of different functions in biofilm communities. We used a non-destructive and label-free method by combining Synchrotron Radiation-based Fourier Transform Infrared Microspectroscopy (SR-FTIR) with Confocal Laser Scanning Microscopy (CLSM) to distinguish the spatial chemical changes within multispecies biofilms grown from natural storm waters in flow cells. Among the different surfaces tested for biofilm growth and optimal imaging, mylar membranes were most suited and it enabled successful spatial infrared imaging of natural biofilms for obtaining reliable and interpretable FTIR spectra. Time series analysis of biofilm growth showed that influx of water during biofilm growth, results in significant changes in biofilm formation. Early biofilms showed active nutrient acquisition and desiccation tolerance mechanisms corresponding with accumulation of secreted proteins. Statistical approach used for the evaluation of chemical spectra allowed for clustering and classification of various regions of the biofilm. Microheterogeneity was observed in the polymeric components of the biofilm matrix, including cellulose, glycocalyx and dextran-like molecules. Fructan and glycan-rich regions were distinguishable and glycocalyx was abundant in the strongly adhering peripheral regions of biofilms. Inner core showed coexistence of oxygen dimers and ferrihydrite that will likely support growth of Fe (II)-oxidising bacteria. The combined SR-FTIR microspectroscopy and CSLM approach for complex natural biofilms described here will be useful both in understanding heterogeneity of matrix components and in correlating functions of juxtaposed microbial species in complex natural biofilms with physicochemical microenvironment to which they are exposed.
Collapse
Affiliation(s)
- Sheela Reuben
- Singapore Delft Water Alliance (SDWA), National University of Singapore, 2 Engineering Drive 2, Engineering Workshop 1, #02-05 Singapore 117577, Singapore
| | - Krzysztof Banas
- Singapore Synchrotron Light Source (SSLS), National University of Singapore, 5 Research Link, Singapore 117603, Singapore
| | - Agnieszka Banas
- Singapore Synchrotron Light Source (SSLS), National University of Singapore, 5 Research Link, Singapore 117603, Singapore
| | - Sanjay Swarup
- Metabolites Biology Laboratory, Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore; NUS Environmental Research Institute (NERI), T-Lab Building, 5A Engineering Drive 1, Singapore 117411, Singapore; Singapore Center for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore 637551, Singapore.
| |
Collapse
|
13
|
Mattson EC, Unger M, Clède S, Lambert F, Policar C, Imtiaz A, D'Souza R, Hirschmugl CJ. Toward optimal spatial and spectral quality in widefield infrared spectromicroscopy of IR labelled single cells. Analyst 2014; 138:5610-8. [PMID: 23826609 DOI: 10.1039/c3an00383c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Advancements in widefield infrared spectromicroscopy have recently been demonstrated following the commissioning of IRENI (InfraRed ENvironmental Imaging), a Fourier Transform infrared (FTIR) chemical imaging beamline at the Synchrotron Radiation Center. The present study demonstrates the effects of magnification, spatial oversampling, spectral pre-processing and deconvolution, focusing on the intracellular detection and distribution of an exogenous metal tris-carbonyl derivative 1 in a single MDA-MB-231 breast cancer cell. We demonstrate here that spatial oversampling for synchrotron-based infrared imaging is critical to obtain accurate diffraction-limited images at all wavelengths simultaneously. Resolution criteria and results from raw and deconvoluted images for two Schwarzschild objectives (36×, NA 0.5 and 74×, NA 0.65) are compared to each other and to prior reports for raster-scanned, confocal microscopes. The resolution of the imaging data can be improved by deconvolving the instrumental broadening that is determined with the measured PSFs, which is implemented with GPU programming architecture for fast hyperspectral processing. High definition, rapidly acquired, FTIR chemical images of respective spectral signatures of the cell 1 and shows that 1 is localized next to the phosphate- and Amide-rich regions, in agreement with previous infrared and luminescence studies. The infrared image contrast, localization and definition are improved after applying proven spectral pre-processing (principal component analysis based noise reduction and RMie scattering correction algorithms) to individual pixel spectra in the hyperspectral cube.
Collapse
Affiliation(s)
- Eric C Mattson
- Physics Dept., University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Morris BEL, Henneberger R, Huber H, Moissl-Eichinger C. Microbial syntrophy: interaction for the common good. FEMS Microbiol Rev 2013; 37:384-406. [PMID: 23480449 DOI: 10.1111/1574-6976.12019] [Citation(s) in RCA: 457] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 11/30/2022] Open
Abstract
Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds.
Collapse
Affiliation(s)
- Brandon E L Morris
- Microbiology, Institute for Biology II, University of Freiburg, Freiburg, Germany
| | | | | | | |
Collapse
|
15
|
Probst AJ, Holman HYN, DeSantis TZ, Andersen GL, Birarda G, Bechtel HA, Piceno YM, Sonnleitner M, Venkateswaran K, Moissl-Eichinger C. Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm. THE ISME JOURNAL 2013; 7:635-51. [PMID: 23178669 PMCID: PMC3578563 DOI: 10.1038/ismej.2012.133] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 09/03/2012] [Accepted: 09/24/2012] [Indexed: 02/01/2023]
Abstract
Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging.
Collapse
Affiliation(s)
- Alexander J Probst
- Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hoi-Ying N Holman
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Todd Z DeSantis
- Department of Bioinformatics, Second Genome Inc., San Bruno, CA, USA
| | - Gary L Andersen
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Giovanni Birarda
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hans A Bechtel
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yvette M Piceno
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Maria Sonnleitner
- Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | | |
Collapse
|
16
|
Bargoma E, La Duc MT, Kwan K, Vaishampayan P, Venkateswaran K. Differential recovery of phylogenetically disparate microbes from spacecraft-qualified metal surfaces. ASTROBIOLOGY 2013; 13:189-202. [PMID: 23421553 DOI: 10.1089/ast.2012.0917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Universal and species-specific quantitative polymerase chain reaction-based methods were employed to compare the effectiveness of four distinct materials used to collect biological samples from metal surfaces. Known cell densities of a model microbial community (MMC) were deposited onto metal surfaces and subsequently collected with cotton and nylon-flocked swabs for small surface areas and biological sampling kits (BiSKits) and polyester wipes for large surface areas. Ribosomal RNA gene-based quantitative PCR (qPCR) analyses revealed that cotton swabs were superior to nylon-flocked swabs for recovering nucleic acids (i.e., DNA) from small surface areas. Similarly, BiSKits outperformed polyester wipes for sampling large surface areas. Species-specific qPCR results show a differential recovery of rRNA genes of the various MMC constituents, seemingly dependent on the type of sampling device employed. Both cotton swabs and BiSKits recovered the rDNA of all nine of the MMC constituent microbes assayed, whereas nylon-flocked swabs and polyester wipes recovered the rDNA of only six and four of these MMC strains, respectively. The findings of this study demonstrate the importance and proficiency of molecular techniques in gauging the effectiveness and efficiency of various modes of biological sample collection from metal surfaces.
Collapse
Affiliation(s)
- E Bargoma
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109, USA
| | | | | | | | | |
Collapse
|
17
|
Mattson EC, Nasse MJ, Rak M, Gough KM, Hirschmugl CJ. Restoration and Spectral Recovery of Mid-Infrared Chemical Images. Anal Chem 2012; 84:6173-80. [DOI: 10.1021/ac301080h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eric C. Mattson
- Department of Physics, University of Wisconsin, Milwaukee, Wisconsin 53211,
United States
| | - Michael J. Nasse
- Department of Physics, University of Wisconsin, Milwaukee, Wisconsin 53211,
United States
- Synchrotron
Radiation Center,
University of Wisconsin, Wisconsin 53589,
United States
| | - Margaret Rak
- Department
of Chemistry, University of Manitoba, Winnipeg,
Canada, R3T 2N2
| | - Kathleen M. Gough
- Department
of Chemistry, University of Manitoba, Winnipeg,
Canada, R3T 2N2
| | - Carol J. Hirschmugl
- Department of Physics, University of Wisconsin, Milwaukee, Wisconsin 53211,
United States
| |
Collapse
|
18
|
Chen L, Holman HYN, Hao Z, Bechtel HA, Martin MC, Wu C, Chu S. Synchrotron Infrared Measurements of Protein Phosphorylation in Living Single PC12 Cells during Neuronal Differentiation. Anal Chem 2012; 84:4118-25. [DOI: 10.1021/ac300308x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Liang Chen
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California
94720, United States
| | - Hoi-Ying N. Holman
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California
94720, United States
| | - Zhao Hao
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California
94720, United States
| | - Hans A. Bechtel
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California
94720, United States
| | - Michael C. Martin
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California
94720, United States
| | - Chengbiao Wu
- Department
of Neurosciences, University of California at San Diego School of Medicine, La Jolla, California 92093, United
States
| | - Steven Chu
- Departments of Physics
and Molecular
and Cell Biology, University of California at Berkeley, Berkeley, California 94720, United States
- California Institute for Quantitative
Biosciences (QB3), University of California at Berkeley, Berkeley, California 94720, United States
| |
Collapse
|
19
|
Quaroni L, Zlateva T. Infrared spectromicroscopy of biochemistry in functional single cells. Analyst 2011; 136:3219-32. [DOI: 10.1039/c1an15060j] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
20
|
Holman HYN, Hao Z, Martin MC, Bechtel HA. Infrared Spectromicroscopy: Probing Live Cellular Responses to Environmental Changes. ACTA ACUST UNITED AC 2010. [DOI: 10.1080/08940886.2010.516737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
21
|
Holman HYN, Bechtel HA, Hao Z, Martin MC. Synchrotron IR spectromicroscopy: chemistry of living cells. Anal Chem 2010; 82:8757-65. [PMID: 20839782 DOI: 10.1021/ac100991d] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Advanced analytical capabilities of synchrotron IR spectromicroscopy meet the demands of modern biological research for studying molecular reactions in individual living cells. (To listen to a podcast about this article, please go to the Analytical Chemistry multimedia page at pubs.acs.org/page/ancham/audio/index.html.).
Collapse
|
22
|
Miller LM, Dumas P. From structure to cellular mechanism with infrared microspectroscopy. Curr Opin Struct Biol 2010; 20:649-56. [PMID: 20739176 DOI: 10.1016/j.sbi.2010.07.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 07/23/2010] [Accepted: 07/23/2010] [Indexed: 10/19/2022]
Abstract
Current efforts in structural biology aim to integrate structural information within the context of cellular organization and function. X-rays and infrared radiation stand at opposite ends of the electromagnetic spectrum and act as complementary probes for achieving this goal. Intense and bright beams are produced by synchrotron radiation, and are efficiently used in the wavelength domain extending from hard X-rays to the far-infrared (or THz) regime. While X-ray crystallography provides exquisite details on atomic structure, Fourier transform infrared microspectroscopy (FTIRM) is emerging as a spectroscopic probe and imaging tool for correlating molecular structure to biochemical dynamics and function. In this manuscript, the role of synchrotron FTIRM in bridging the gap towards 'functional biology' is discussed based upon recent achievements, with a critical assessment of the contributions to biological and biomedical research.
Collapse
Affiliation(s)
- Lisa M Miller
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY, USA.
| | | |
Collapse
|
23
|
Senger RS. Biofuel production improvement with genome-scale models: The role of cell composition. Biotechnol J 2010; 5:671-85. [DOI: 10.1002/biot.201000007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
24
|
Martin MC, Schade U, Lerch P, Dumas P. Recent applications and current trends in analytical chemistry using synchrotron-based Fourier-transform infrared microspectroscopy. Trends Analyt Chem 2010. [DOI: 10.1016/j.trac.2010.03.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
25
|
Holman HYN, Miles R, Hao Z, Wozei E, Anderson LM, Yang H. Real-time chemical imaging of bacterial activity in biofilms using open-channel microfluidics and synchrotron FTIR spectromicroscopy. Anal Chem 2010; 81:8564-70. [PMID: 19775125 DOI: 10.1021/ac9015424] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Real-time chemical imaging of bacterial activities can facilitate a comprehensive understanding of the dynamics of biofilm structures and functions. Synchrotron-radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy can yield high spatial resolution and label-free vibrational signatures of chemical bonds in biomolecules, but the abundance of water in biofilms has hindered SR-FTIR's sensitivity in investigating bacterial activity. We developed a simple open-channel microfluidic system that can circumvent the water-absorption barrier for chemical imaging of the developmental dynamics of bacterial biofilms with a spatial resolution of several micrometers. This system maintains a 10 microm thick laminar-flow-through biofilm system that minimizes both the imaging volume in liquid and the signal interference from geometry-induced fringing. Here we demonstrate the ability of the open-channel microfluidic platform to maintain the functionality of living cells while enabling high-quality SR-FTIR measurements. We include several applications that show how microbes in biofilms adapt to their immediate environments. The ability to directly monitor and map bacterial changes in biofilms can yield significant insight into a wide range of microbial systems, especially when coupled to more sophisticated microfluidic platforms.
Collapse
Affiliation(s)
- Hoi-Ying N Holman
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.
| | | | | | | | | | | |
Collapse
|
26
|
Abstract
The complex physical and chemical conditions encountered in the gut present a range of physiological challenges to both the commensal microbiota and to pathogenic microorganisms attempting to colonise the gut. The innate immune system of the host, the host's diet and the microbial population present in the gut all contribute to the chemical complexity of the environment. The huge population of microorganisms in the gut also has a significant impact on the physicochemical properties of the gut environment. By focussing on some of the key physical and chemical stresses encountered by microorganisms in the gut, some of the molecular responses are described. Some promising new experimental approaches are outlined for studying the behaviour of microorganisms and their communities within the gut environment.
Collapse
Affiliation(s)
- Petra Louis
- Microbial Ecology Group, Gut Health Programme, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucks-burn, Aberdeen AB21 9SB, UK
| | - Conor P. O'Byrne
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| |
Collapse
|
27
|
Synchrotron Infrared Spectromicroscopy for Studying Chemistry of Microbial Activity in Geologic Materials. SYNCHROTRON-BASED TECHNIQUES IN SOILS AND SEDIMENTS 2010. [DOI: 10.1016/s0166-2481(10)34004-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|