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In situ single-cell activities of microbial populations revealed by spatial transcriptomics

Dar, Daniel and Dar, Nina and Cai, Long and Newman, Dianne K. (2021) In situ single-cell activities of microbial populations revealed by spatial transcriptomics. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20210226-074209469

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Abstract

Microbial populations and communities are heterogeneous, yet capturing their diverse activities has proven challenging at the relevant spatiotemporal scales. Here we present par-seqFISH, a targeted transcriptome-imaging approach that records both gene-expression and spatial context within microscale assemblies at a single-cell and molecule resolution. We apply this approach to the opportunistic bacterial pathogen, Pseudomonas aeruginosa, analyzing ~600,000 individuals across dozens of physiological conditions in planktonic and biofilm cultures. We explore the phenotypic landscape of this bacterium and identify metabolic and virulence related cell-states that emerge dynamically during growth. We chart the spatial context of biofilm-related processes including motility and kin-exclusion mechanisms and identify extensive and highly spatially-resolved metabolic heterogeneity. We find that distinct physiological states can co-exist within the same biofilm, just a few microns away, underscoring the importance of the microenvironment. Together, our results illustrate the complexity of microbial populations and present a new way of studying them at high-resolution.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2021.02.24.432792DOIDiscussion Paper
https://github.com/daniedar/seqFISHRelated ItemCode
ORCID:
AuthorORCID
Dar, Daniel0000-0002-6650-5488
Cai, Long0000-0002-7154-5361
Newman, Dianne K.0000-0003-1647-1918
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. This version posted February 25, 2021. We thank George A. O’Toole and Marvin Whiteley for help with designing the gene set. We also thank Megan Bergkessel and Rotem Sorek and members of the Newman lab for critically reading the manuscript. We thank the Newman lab for fruitful discussions and comments. Grants to DKN from the NIH (1R01AI127850-01A1 and 1R01HL152190-01) and ARO (W911NF-17-1-0024) supported this work. LC was funded by the Allen Frontier group. DD was supported by the Rothschild foundation, EMBO Long-Term, and the Helen Hay Whitney postdoctoral fellowships, as well as a Geobiology Postdoctoral Fellowship from the Division of Geological and Planetary Sciences, Caltech. Author contributions: DD ND, LC and DKN designed the study. DD led the study, designed the experiments, and performed the experiments with ND. Analyses were performed by DD. DKN and LC supervised the study, and all authors wrote the manuscript. The authors have declared no competing interest. Data and Code Availability: Custom MATLAB scripts and single-cell source data from this study were deposited in https://github.com/daniedar/seqFISH. Imaging data obtained during this study are available from the corresponding author upon reasonable request.
Funders:
Funding AgencyGrant Number
NIH1R01AI127850-01A1
NIH1R01HL152190-01
Army Research Office (ARO)W911NF-17-1-0024
Allen Frontier GroupUNSPECIFIED
Rothschild FoundationUNSPECIFIED
European Molecular Biology Organization (EMBO)UNSPECIFIED
Helen Hay Whitney FoundationUNSPECIFIED
Caltech Division of Geological and Planetary SciencesUNSPECIFIED
Record Number:CaltechAUTHORS:20210226-074209469
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210226-074209469
Official Citation:In situ single-cell activities of microbial populations revealed by spatial transcriptomics. Daniel Dar, Nina Dar, Long Cai, Dianne K. Newman. bioRxiv 2021.02.24.432792; doi: https://doi.org/10.1101/2021.02.24.432792
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:108227
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:26 Feb 2021 19:39
Last Modified:26 Feb 2021 19:39

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