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

Area of Science:

• Marine microbiology and biogeochemistry
• Molecular ecology and microbial physiology

Background:

• Microbial growth rates are crucial for understanding marine carbon and nitrogen cycles.
• Taxon-specific growth rates are needed to attribute biogeochemical processes to individual species, especially in diverse assemblages like Synechococcus and Prochlorococcus.

Purpose of the Study:

• To evaluate three novel DNA sequencing-based methods (iRep, bPTR, GRiD) for assessing microbial growth rates.
• To compare sequencing-based method (SBM) results with standard techniques (in vivo fluorescence, cell cycle analysis) in Synechococcus cultures.

Main Methods:

• Cultured light-synchronized Synechococcus under varying light intensities and temperatures.
• Applied three DNA sequencing-based methods (iRep, bPTR, GRiD).
• Used in vivo fluorescence and cell cycle analysis as standard growth rate proxies.

Main Results:

• None of the DNA sequencing-based methods (SBM) correlated with growth rates determined by standard methods.
• All three SBM correlated with the percentage of cells in the S phase (DNA replication) over the diel cycle.
• Diel cyclicity in microbes complicates the application of SBM for growth rate determination in natural environments.

Conclusions:

• DNA sequencing-based methods can detect DNA replication and cell cycle phases but are not quantitatively accurate for determining absolute growth rates in Synechococcus.
• Caution is advised when applying these SBM to natural microbial communities exhibiting diel cycles, as they may not reflect true growth rates.