Evaluation of Genomic Sequence-Based Growth Rate Methods for Synchronized Synechococcus Cultures

Julia Carroll, Nicolas Van Oostende, Bess B. Ward

Research output: Contribution to journalArticlepeer-review

Abstract

Standard methods for calculating microbial growth rates (m) through the use of proxies, such as in situ fluorescence, cell cycle, or cell counts, are critical for determining the magnitude of the role bacteria play in marine carbon (C) and nitrogen (N) cycles. Taxon-specific growth rates in mixed assemblages would be useful for attributing biogeochemical processes to individual species and understanding niche differentiation among related clades, such as found in Synechococcus and Prochlorococcus. We tested three novel DNA sequencing-based methods (iRep, bPTR, and GRiD) for evaluating the growth of light-synchronized Synechococcus cultures under different light intensities and temperatures. In vivo fluorescence and cell cycle analysis were used to obtain standard estimates of growth rate for comparison with those of the sequence-based methods (SBM). None of the SBM values were correlated with growth rates calculated by standard techniques despite the fact that all three SBM were correlated with the percentage of cells in S phase (DNA replication) over the diel cycle. Inaccuracy in determining the time of maximum DNA replication is unlikely to account entirely for the absence of a relationship between SBM and growth rate, but the fact that most microbes in the surface ocean exhibit some degree of diel cyclicity is a caution for application of these methods. SBM correlate with DNA replication but cannot be interpreted quantitatively in terms of growth rate.

Original languageEnglish (US)
Article numbere01743-21
JournalApplied and Environmental Microbiology
Volume88
Issue number1
DOIs
StatePublished - Jan 2022

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Food Science
  • Ecology
  • Applied Microbiology and Biotechnology

Keywords

  • BPTR
  • Cell cycle
  • GRiD
  • Growth rate
  • IRep
  • Metagenomic growth rate estimator
  • Sequence-based method
  • Synechococcus

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