Single-cell measurement of microbial growth rate with Raman microspectroscopy

Author:

Caro Tristan A1ORCID,Kashyap Srishti1,Brown George2,Chen Claudia2,Kopf Sebastian H1,Templeton Alexis S1

Affiliation:

1. Department of Geological Sciences, University of Colorado Boulder , Boulder, CO 80309 , United States

2. Department of Applied Mathematics, University of Colorado Boulder , Boulder, CO 80309 , United States

Abstract

Abstract Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2H. Relative to Raman, we find that nanoSIMS measurements of 2H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman–SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, nondestructive technique, represents an important step toward application of single-cell analysis into complex sample matrices or cellular assemblages.

Funder

NASA

Army Research Office

University of Colorado Boulder

National Science Foundation

Publisher

Oxford University Press (OUP)

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