Label-Free Raman Microspectroscopy for Identifying Prokaryotic Virocells

Monsees, Indra; Turzynski, Victoria; Esser, Sarah P.; Soares, André; Timmermann, Lara I; Weidenbach, Katrin; Banas, Jarno; Kloster, Michael; Beszteri, Bánk; Schmitz, Ruth A.; Probst, Alexander J.

doi:10.1128/msystems.01505-21

Cited by 3 publications

(2 citation statements)

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“…Another promising approach could be Raman microspectroscopy for identification of infected Ca. A. hamiconexum cells [57] and its coupling to embedding and transmission electron microscopy (TEM). While these approaches are based on correlative microscopy, traditional immunogold labeling of viral proteins in MSI biofilms will eventually lead to the discovery of the actual virion structure visualized by TEM.…”

Section: Discussionmentioning

confidence: 99%

Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition

Turzynski

Griesdorn

Moraru

et al. 2023

Viruses

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Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a period of four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections from 2019 to 2022. Based on fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by sulfate-reducing members affiliated with Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the uncultivated virus-host system described herein represents a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.

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Section: Discussionmentioning

confidence: 99%

Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition

Turzynski

Griesdorn

Moraru

et al. 2023

Viruses

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“…Monsees et al identified the Raman peak intensity ratio between nucleic acids and proteins useful for classification of virally infected cells from that of uninfected. They used Raman micro-spectroscopy for collecting the Raman signal from the phi6 (bacteriophage) infected Pseudomonas syringae and phi29 infected Bacillus subtilis as well as corresponding controls (Monsees et al 2022 ). They observed an increase in the ratio for the former case and a decrease in the latter.…”

Section: Raman Spectroscopy In Viral Diagnosticsmentioning

confidence: 99%

Raman spectroscopy for viral diagnostics

et al. 2023

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Raman spectroscopy offers the potential for fingerprinting biological molecules at ultra-low concentration and therefore has potential for the detection of viruses. Here we review various Raman techniques employed for the investigation of viruses. Different Raman techniques are discussed including conventional Raman spectroscopy, surface-enhanced Raman spectroscopy, Raman tweezer, tip-enhanced Raman Spectroscopy, and coherent anti-Stokes Raman scattering. Surface-enhanced Raman scattering can play an essential role in viral detection by multiplexing nanotechnology, microfluidics, and machine learning for ensuring spectral reproducibility and efficient workflow in sample processing and detection. The application of these techniques to diagnose the SARS-CoV-2 virus is also reviewed. Graphical abstract

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Virus-host dynamics in archaeal groundwater biofilms and the associated bacterial community composition

Turzynski

Griesdorn

Moraru

et al. 2023

Preprint

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Lytic viruses can be prevalent in deep groundwater, yet their spatial and temporal distribution in such an ecosystem remains unexplored. Here, we tackle this gap of knowledge by studying viral infections in individual, archaea-dominated biofilm flocks sampled from deep anoxic groundwater over a period of three years. Using virusFISH whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections between the years 2019 and 2022. Based on various fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the virus-host dynamics of Ca. Altiarchaeum hamiconexum and its abundant virus Altivir_1_MSI described herein represent a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.

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Label-Free Raman Microspectroscopy for Identifying Prokaryotic Virocells

Abstract: Viruses are highly diverse biological entities shaping many ecosystems across Earth. However, understanding the infection of individual microbial cells and the related biochemical changes remains limited.

Cited by 3 publications

References 36 publications

Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition

Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition

Raman spectroscopy for viral diagnostics

Virus-host dynamics in archaeal groundwater biofilms and the associated bacterial community composition

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