Using fluorescence lifetime imaging to disentangle microbes from the heterogeneous soil matrix

Publikation: Beitrag in FachzeitschriftArtikelForschungPeer-Review

Autoren

  • Sebastian Loeppmann
  • Jan Tegtmeier
  • Yijie Shi
  • Alberto Andrino de la Fuente
  • Jens Boy
  • Georg Guggenberger
  • Andreas Fulterer
  • Martin Fritsch
  • Sandra Spielvogel

Organisationseinheiten

Externe Organisationen

  • Christian-Albrechts-Universität zu Kiel (CAU)
  • Leica Microsystems CMS GmbH
Forschungs-netzwerk anzeigen

Details

OriginalspracheEnglisch
Seiten (von - bis)249-260
Seitenumfang12
FachzeitschriftBiology and fertility of soils
Jahrgang59
Ausgabenummer2
Frühes Online-Datum3 Feb. 2023
PublikationsstatusVeröffentlicht - Feb. 2023

Abstract

Soil microbial communities are involved in most biogeochemical processes creating hotspots for nutrient cycling. The spatial visualization of such soil hotspots via microscopic techniques is still challenging caused by the intrinsic fluorescence and opacity of the soil. One way to differentiate microbial cells from the heterogeneous soil matrix is a fluorescence lifetime-based technique (FLIM) with subsequent phasor plot separation; it separates and visualizes the distinctly different photon arrival times of all photons per pixel. FLIM delivers additional independent information behind intensity-based image processing and image analysis which is often hampered by, e.g., autofluorescence, resolution issues, and photobleaching artifacts caused by the prevailing minerals and organic substances. We determined characteristic fluorescence lifetime profiles of BacLight™ Green for Rhodotorula mucilaginosa and Bacillus subtilits in phosphate-buffered saline (PBS) solution and water as well as in natural, autoclaved, glucose-activated, and soil mineral particles by FLIM measurements via confocal laser scanning fluorescence microscopy. Rhodotorula mucilaginosa and Bacillus subtilits from pure cultures measured in water and PBS accounted for 1.20 (± 0.2) ns and 1.3 (± 0.1) ns respectively. The lifetime profile within the cells was rather homogeneous for both microbial species tested. This suggests stable photon arrival times for microbial strains with minor effects of matrix components as tested in PBS and water. We identified a clear difference in fluorescence lifetime profiles between microorganisms (around 1 ns) and the surrounding soil matrix (0.2 to 0.7 ns, > 3.6 ns) via phasor plot separation. The results presented raise the feasibility to extend the applicability of FLIM to other soils and their accompanying microbiota.

ASJC Scopus Sachgebiete

Zitieren

Using fluorescence lifetime imaging to disentangle microbes from the heterogeneous soil matrix. / Loeppmann, Sebastian; Tegtmeier, Jan; Shi, Yijie et al.
in: Biology and fertility of soils, Jahrgang 59, Nr. 2, 02.2023, S. 249-260.

Publikation: Beitrag in FachzeitschriftArtikelForschungPeer-Review

Loeppmann, S, Tegtmeier, J, Shi, Y, de la Fuente, AA, Boy, J, Guggenberger, G, Fulterer, A, Fritsch, M & Spielvogel, S 2023, 'Using fluorescence lifetime imaging to disentangle microbes from the heterogeneous soil matrix', Biology and fertility of soils, Jg. 59, Nr. 2, S. 249-260. https://doi.org/10.1007/s00374-023-01704-w
Loeppmann, S., Tegtmeier, J., Shi, Y., de la Fuente, A. A., Boy, J., Guggenberger, G., Fulterer, A., Fritsch, M., & Spielvogel, S. (2023). Using fluorescence lifetime imaging to disentangle microbes from the heterogeneous soil matrix. Biology and fertility of soils, 59(2), 249-260. https://doi.org/10.1007/s00374-023-01704-w
Loeppmann S, Tegtmeier J, Shi Y, de la Fuente AA, Boy J, Guggenberger G et al. Using fluorescence lifetime imaging to disentangle microbes from the heterogeneous soil matrix. Biology and fertility of soils. 2023 Feb;59(2):249-260. Epub 2023 Feb 3. doi: 10.1007/s00374-023-01704-w
Loeppmann, Sebastian ; Tegtmeier, Jan ; Shi, Yijie et al. / Using fluorescence lifetime imaging to disentangle microbes from the heterogeneous soil matrix. in: Biology and fertility of soils. 2023 ; Jahrgang 59, Nr. 2. S. 249-260.
Download
@article{d470659e9ac84beab82cbc6d83a7c54f,
title = "Using fluorescence lifetime imaging to disentangle microbes from the heterogeneous soil matrix",
abstract = "Soil microbial communities are involved in most biogeochemical processes creating hotspots for nutrient cycling. The spatial visualization of such soil hotspots via microscopic techniques is still challenging caused by the intrinsic fluorescence and opacity of the soil. One way to differentiate microbial cells from the heterogeneous soil matrix is a fluorescence lifetime-based technique (FLIM) with subsequent phasor plot separation; it separates and visualizes the distinctly different photon arrival times of all photons per pixel. FLIM delivers additional independent information behind intensity-based image processing and image analysis which is often hampered by, e.g., autofluorescence, resolution issues, and photobleaching artifacts caused by the prevailing minerals and organic substances. We determined characteristic fluorescence lifetime profiles of BacLight{\texttrademark} Green for Rhodotorula mucilaginosa and Bacillus subtilits in phosphate-buffered saline (PBS) solution and water as well as in natural, autoclaved, glucose-activated, and soil mineral particles by FLIM measurements via confocal laser scanning fluorescence microscopy. Rhodotorula mucilaginosa and Bacillus subtilits from pure cultures measured in water and PBS accounted for 1.20 (± 0.2) ns and 1.3 (± 0.1) ns respectively. The lifetime profile within the cells was rather homogeneous for both microbial species tested. This suggests stable photon arrival times for microbial strains with minor effects of matrix components as tested in PBS and water. We identified a clear difference in fluorescence lifetime profiles between microorganisms (around 1 ns) and the surrounding soil matrix (0.2 to 0.7 ns, > 3.6 ns) via phasor plot separation. The results presented raise the feasibility to extend the applicability of FLIM to other soils and their accompanying microbiota.",
keywords = "Confocal laser scanning microscopy, FLIM, Microbial separation, Phasor plot, Photon arrival times, Soil staining",
author = "Sebastian Loeppmann and Jan Tegtmeier and Yijie Shi and {de la Fuente}, {Alberto Andrino} and Jens Boy and Georg Guggenberger and Andreas Fulterer and Martin Fritsch and Sandra Spielvogel",
note = "Funding Information: We thank Karl-Heinz Koertje (Leica Microsystems, Mannheim) for his technical assistance. We thank Dr. Evgenia Blagodatskaya (UFZ, Halle) and Prof. Dr. Andrea Polle (Forest Botany and Tree Physiology, Georg-August University, G{\"o}ttingen) for hosting preliminary microscopic experiments. We thank the Central Microscopy Facility at the Department of Biology, Kiel University and Dr. Urksa Repnik (https://www.biologie.uni-kiel.de/zm/) for technical support in using Zeiss LSM 900. Funding Information: This project was carried out in the framework of the priority program 1685 “Ecosystem Nutrition” funded by a SNF-DFG grant to Sandra Spielvogel (SS 20021E-171173). ",
year = "2023",
month = feb,
doi = "10.1007/s00374-023-01704-w",
language = "English",
volume = "59",
pages = "249--260",
journal = "Biology and fertility of soils",
issn = "0178-2762",
publisher = "Springer Verlag",
number = "2",

}

Download

TY - JOUR

T1 - Using fluorescence lifetime imaging to disentangle microbes from the heterogeneous soil matrix

AU - Loeppmann, Sebastian

AU - Tegtmeier, Jan

AU - Shi, Yijie

AU - de la Fuente, Alberto Andrino

AU - Boy, Jens

AU - Guggenberger, Georg

AU - Fulterer, Andreas

AU - Fritsch, Martin

AU - Spielvogel, Sandra

N1 - Funding Information: We thank Karl-Heinz Koertje (Leica Microsystems, Mannheim) for his technical assistance. We thank Dr. Evgenia Blagodatskaya (UFZ, Halle) and Prof. Dr. Andrea Polle (Forest Botany and Tree Physiology, Georg-August University, Göttingen) for hosting preliminary microscopic experiments. We thank the Central Microscopy Facility at the Department of Biology, Kiel University and Dr. Urksa Repnik (https://www.biologie.uni-kiel.de/zm/) for technical support in using Zeiss LSM 900. Funding Information: This project was carried out in the framework of the priority program 1685 “Ecosystem Nutrition” funded by a SNF-DFG grant to Sandra Spielvogel (SS 20021E-171173).

PY - 2023/2

Y1 - 2023/2

N2 - Soil microbial communities are involved in most biogeochemical processes creating hotspots for nutrient cycling. The spatial visualization of such soil hotspots via microscopic techniques is still challenging caused by the intrinsic fluorescence and opacity of the soil. One way to differentiate microbial cells from the heterogeneous soil matrix is a fluorescence lifetime-based technique (FLIM) with subsequent phasor plot separation; it separates and visualizes the distinctly different photon arrival times of all photons per pixel. FLIM delivers additional independent information behind intensity-based image processing and image analysis which is often hampered by, e.g., autofluorescence, resolution issues, and photobleaching artifacts caused by the prevailing minerals and organic substances. We determined characteristic fluorescence lifetime profiles of BacLight™ Green for Rhodotorula mucilaginosa and Bacillus subtilits in phosphate-buffered saline (PBS) solution and water as well as in natural, autoclaved, glucose-activated, and soil mineral particles by FLIM measurements via confocal laser scanning fluorescence microscopy. Rhodotorula mucilaginosa and Bacillus subtilits from pure cultures measured in water and PBS accounted for 1.20 (± 0.2) ns and 1.3 (± 0.1) ns respectively. The lifetime profile within the cells was rather homogeneous for both microbial species tested. This suggests stable photon arrival times for microbial strains with minor effects of matrix components as tested in PBS and water. We identified a clear difference in fluorescence lifetime profiles between microorganisms (around 1 ns) and the surrounding soil matrix (0.2 to 0.7 ns, > 3.6 ns) via phasor plot separation. The results presented raise the feasibility to extend the applicability of FLIM to other soils and their accompanying microbiota.

AB - Soil microbial communities are involved in most biogeochemical processes creating hotspots for nutrient cycling. The spatial visualization of such soil hotspots via microscopic techniques is still challenging caused by the intrinsic fluorescence and opacity of the soil. One way to differentiate microbial cells from the heterogeneous soil matrix is a fluorescence lifetime-based technique (FLIM) with subsequent phasor plot separation; it separates and visualizes the distinctly different photon arrival times of all photons per pixel. FLIM delivers additional independent information behind intensity-based image processing and image analysis which is often hampered by, e.g., autofluorescence, resolution issues, and photobleaching artifacts caused by the prevailing minerals and organic substances. We determined characteristic fluorescence lifetime profiles of BacLight™ Green for Rhodotorula mucilaginosa and Bacillus subtilits in phosphate-buffered saline (PBS) solution and water as well as in natural, autoclaved, glucose-activated, and soil mineral particles by FLIM measurements via confocal laser scanning fluorescence microscopy. Rhodotorula mucilaginosa and Bacillus subtilits from pure cultures measured in water and PBS accounted for 1.20 (± 0.2) ns and 1.3 (± 0.1) ns respectively. The lifetime profile within the cells was rather homogeneous for both microbial species tested. This suggests stable photon arrival times for microbial strains with minor effects of matrix components as tested in PBS and water. We identified a clear difference in fluorescence lifetime profiles between microorganisms (around 1 ns) and the surrounding soil matrix (0.2 to 0.7 ns, > 3.6 ns) via phasor plot separation. The results presented raise the feasibility to extend the applicability of FLIM to other soils and their accompanying microbiota.

KW - Confocal laser scanning microscopy

KW - FLIM

KW - Microbial separation

KW - Phasor plot

KW - Photon arrival times

KW - Soil staining

UR - http://www.scopus.com/inward/record.url?scp=85147355842&partnerID=8YFLogxK

U2 - 10.1007/s00374-023-01704-w

DO - 10.1007/s00374-023-01704-w

M3 - Article

AN - SCOPUS:85147355842

VL - 59

SP - 249

EP - 260

JO - Biology and fertility of soils

JF - Biology and fertility of soils

SN - 0178-2762

IS - 2

ER -

Von denselben Autoren