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Xiang Q, Stryhanyuk H, Schmidt M, Kümmel S, Richnow HH, Zhu YG, Cui L, Musat N. Stable isotopes and nanoSIMS single-cell imaging reveals soil plastisphere colonizers able to assimilate sulfamethoxazole. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 355:124197. [PMID: 38782163 DOI: 10.1016/j.envpol.2024.124197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
The presence and accumulation of both, plastics and antibiotics in soils may lead to the colonization, selection, and propagation of soil bacteria with certain metabolic traits, e.g., antibiotic resistance, in the plastisphere. However, the impact of plastic-antibiotic tandem on the soil ecosystem functioning, particularly on microbial function and metabolism remains currently unexplored. Herein, we investigated the competence of soil bacteria to colonize plastics and degrade 13C-labeled sulfamethoxazole (SMX). Using single-cell imaging, isotope tracers, soil respiration and SMX mineralization bulk measurements we show that microbial colonization of polyethylene (PE) and polystyrene (PS) surfaces takes place within the first 30 days of incubation. Morphologically diverse microorganisms were colonizing both plastic types, with a slight preference for PE substrate. CARD-FISH bacterial cell counts on PE and PS surfaces formed under SMX amendment ranged from 5.36 × 103 to 2.06 × 104, and 2.06 × 103 to 3.43 × 103 hybridized cells mm-2, respectively. Nano-scale Secondary Ion Mass Spectrometry measurements show that 13C enrichment was highest at 130 days with values up to 1.29 atom%, similar to those of the 13CO2 pool (up to 1.26 atom%, or 22.55 ‰). Independent Mann-Whitney U test showed a significant difference between the control plastisphere samples incubated without SMX and those in 13C-SMX incubations (P < 0.001). Our results provide direct evidence demonstrating, at single-cell level, the capacity of bacterial colonizers of plastics to assimilate 13C-SMX from contaminated soils. These findings expand our knowledge on the role of soil-seeded plastisphere microbiota in the ecological functioning of soils impacted by anthropogenic stressors.
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Affiliation(s)
- Qian Xiang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Matthias Schmidt
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Steffen Kümmel
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Niculina Musat
- Department of Isotope Biochemistry, Currently Merged As Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany; Department of Biology, Section for Microbiology, Aarhus University, 8000, Aarhus C, Denmark.
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Burr DJ, Drauschke J, Kanevche K, Kümmel S, Stryhanyuk H, Heberle J, Perfumo A, Elsaesser A. Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-Dependent Spectral Features. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2400289. [PMID: 38708804 DOI: 10.1002/smll.202400289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/16/2024] [Indexed: 05/07/2024]
Abstract
This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of 13C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP- nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of 13C-13C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes, and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science, and cancer research.
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Affiliation(s)
- David J Burr
- Department of Physics, Experimental Biophysics and Space Sciences, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Janina Drauschke
- Department of Physics, Experimental Biophysics and Space Sciences, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Katerina Kanevche
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Steffen Kümmel
- Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Joachim Heberle
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Amedea Perfumo
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Telegrafenberg, 14473, Potsdam, Germany
| | - Andreas Elsaesser
- Department of Physics, Experimental Biophysics and Space Sciences, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
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Lee KS, Landry Z, Athar A, Alcolombri U, Pramoj Na Ayutthaya P, Berry D, de Bettignies P, Cheng JX, Csucs G, Cui L, Deckert V, Dieing T, Dionne J, Doskocil O, D'Souza G, García-Timermans C, Gierlinger N, Goda K, Hatzenpichler R, Henshaw RJ, Huang WE, Iermak I, Ivleva NP, Kneipp J, Kubryk P, Küsel K, Lee TK, Lee SS, Ma B, Martínez-Pérez C, Matousek P, Meckenstock RU, Min W, Mojzeš P, Müller O, Kumar N, Nielsen PH, Notingher I, Palatinszky M, Pereira FC, Pezzotti G, Pilat Z, Plesinger F, Popp J, Probst AJ, Riva A, Saleh AAE, Samek O, Sapers HM, Schubert OT, Stubbusch AKM, Tadesse LF, Taylor GT, Wagner M, Wang J, Yin H, Yue Y, Zenobi R, Zini J, Sarkans U, Stocker R. MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data. Nat Microbiol 2024; 9:1152-1156. [PMID: 38714759 DOI: 10.1038/s41564-024-01656-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2024]
Affiliation(s)
- Kang Soo Lee
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland.
| | - Zachary Landry
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, USA
| | - Awais Athar
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK
| | - Uria Alcolombri
- Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Pratchaya Pramoj Na Ayutthaya
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - David Berry
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | | | - Ji-Xin Cheng
- Department of Electrical and Computer Engineering and Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Gabor Csucs
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zurich, Switzerland
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Volker Deckert
- Institute of Physical Chemistry (IPC) and Abbe Center of Photonics (ACP), Friedrich Schiller University Jena, member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany
- Leibniz Institute of Photonic Technology e.V. Jena, member of Leibniz Health Technology, member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany
| | | | - Jennifer Dionne
- Department of Materials Science and Engineering, and Department of Radiology, Stanford University, Stanford, CA, USA
| | - Ondrej Doskocil
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i, Brno, Czech Republic
| | - Glen D'Souza
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Cristina García-Timermans
- CMET, Center for Microbial Technology and Ecology, Department of Biotechnology, Ghent University, Gent, Belgium
| | - Notburga Gierlinger
- Institute of Biophysics, Department of Bionanosciences, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
- Institute of Technological Sciences, Wuhan University, Wuhan, China
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Department of Microbiology and Cell Biology, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Richard J Henshaw
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Oxford, UK
| | | | - Natalia P Ivleva
- Chair of Analytical Chemistry and Water Chemistry, Institute of Water Chemistry, TUM School of Natural Sciences (Dep. Chemistry), Technical University of Munich, Garching, Germany
| | - Janina Kneipp
- Department of Chemistry, Humboldt- Universität zu Berlin, Berlin, Germany
| | | | - Kirsten Küsel
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Tae Kwon Lee
- Department of Environmental and Energy Engineering, Yonsei University, Wonju, Republic of Korea
| | - Sung Sik Lee
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zurich, Switzerland
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioengineering and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Clara Martínez-Pérez
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Pavel Matousek
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, UKRI, Harwell, UK
| | - Rainer U Meckenstock
- Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Essen, Germany
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY, USA
| | - Peter Mojzeš
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Oliver Müller
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Naresh Kumar
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Ioan Notingher
- School of Physics and Astronomy, University of Nottingham, Nottingham, UK
| | - Márton Palatinszky
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Fátima C Pereira
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Zdenek Pilat
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i, Brno, Czech Republic
| | - Filip Plesinger
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i, Brno, Czech Republic
| | - Jürgen Popp
- Institute of Physical Chemistry (IPC) and Abbe Center of Photonics (ACP), Friedrich Schiller University Jena, member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany
- Leibniz Institute of Photonic Technology e.V. Jena, member of Leibniz Health Technology, member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Alessandra Riva
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Amr A E Saleh
- Department of Engineering Mathematics and Physics, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Ota Samek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i, Brno, Czech Republic
| | - Haley M Sapers
- Centre for Research in Earth and Space Sciences, York University, Toronto, Ontario, Canada
| | - Olga T Schubert
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Astrid K M Stubbusch
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Geological Institute, Department of Earth Sciences, ETH Zurich, Zurich, Switzerland
| | - Loza F Tadesse
- Department of Mechanical Engineering, MIT, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Jameel Clinic for AI & Healthcare, MIT, Cambridge, MA, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Michael Wagner
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Jing Wang
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
- Advanced Analytical Technologies, Empa, Dübendorf, Switzerland
| | - Huabing Yin
- Division of Biomedical Engineering, James Watt School of Engineering, University of Glasgow, Glasgow, UK
| | - Yang Yue
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
- Advanced Analytical Technologies, Empa, Dübendorf, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Jacopo Zini
- Timegate Instruments Oy, Oulu, Finland
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK.
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland.
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Garg D, Patel N, Rawat A, Rosado AS. Cutting edge tools in the field of soil microbiology. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100226. [PMID: 38425506 PMCID: PMC10904168 DOI: 10.1016/j.crmicr.2024.100226] [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] [Indexed: 03/02/2024] Open
Abstract
The study of the whole of the genetic material contained within the microbial populations found in a certain environment is made possible by metagenomics. This technique enables a thorough knowledge of the variety, function, and interactions of microbial communities that are notoriously difficult to research. Due to the limitations of conventional techniques such as culturing and PCR-based methodologies, soil microbiology is a particularly challenging field. Metagenomics has emerged as an effective technique for overcoming these obstacles and shedding light on the dynamic nature of the microbial communities in soil. This review focuses on the principle of metagenomics techniques, their potential applications and limitations in soil microbial diversity analysis. The effectiveness of target-based metagenomics in determining the function of individual genes and microorganisms in soil ecosystems is also highlighted. Targeted metagenomics, including high-throughput sequencing and stable-isotope probing, is essential for studying microbial taxa and genes in complex ecosystems. Shotgun metagenomics may reveal the diversity of soil bacteria, composition, and function impacted by land use and soil management. Sanger, Next Generation Sequencing, Illumina, and Ion Torrent sequencing revolutionise soil microbiome research. Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)'s third and fourth generation sequencing systems revolutionise long-read technology. GeoChip, clone libraries, metagenomics, and metabarcoding help comprehend soil microbial communities. The article indicates that metagenomics may improve environmental management and agriculture despite existing limitations.Metagenomics has revolutionised soil microbiology research by revealing the complete diversity, function, and interactions of microorganisms in soil. Metagenomics is anticipated to continue defining the future of soil microbiology research despite some limitations, such as the difficulty of locating the appropriate sequencing method for specific genes.
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Affiliation(s)
- Diksha Garg
- Department of Microbiology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Niketan Patel
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
| | - Anamika Rawat
- Center of Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
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