Idea paper: Predicting culturability of microbes from population dynamics under field conditions

Abstract

Isolation and cultivation of microbes from environmental samples have been fundamental and important for species identification and investigating functions and ecology of target microbes. Although cultivation and isolation of microbes are not easy, the natural environment can “culture” any endemic microbes, and thus key information for culturing and isolating microbes may be encoded in the natural population dynamics of microbes. In this article, I present the idea that culturability of microbes may be inferred by quantifying the dynamic properties of microbes using nonlinear time series analysis and empirical dynamic modeling (EDM). To briefly demonstrate the idea, I analyzed high‐frequency, quantitative microbial time series obtained for experimental rice plots. I selected bacterial phyla that included sufficient numbers of microbial taxa and analyzed 398 microbial taxa using EDM. The nine phyla analyzed generally followed a similar pattern: many microbial taxa fell into the “Simple” dynamics category, and a small proportion of taxa were categorized in “Simple but nonlinear” or “Nearly random” dynamics categories. The present analysis suggested that many microbes in the study system might be cultivated by modifying a relatively small number of conditions. However, the present idea as well as the result is preliminary, and more precise taxonomic information (i.e., species‐level identification) and a culturability data set will help to validate the idea. If the present idea was found to be valid, a priori evaluation of the culturability of microbes would become possible, which would avoid unnecessary costs (labor, time and money) of attempts to cultivate microbes.