Studying population dynamics in diverse microbial communities

Ecological research focuses on understanding how population-level dynamics—such as the growth rate of a particular population of microbes—contribute to ecosystem-level processes. Ecosystem scientists researching climate change often study the role of microbes in the carbon cycle, for example, so knowing how quickly they grow is a fundamental metric to reaching that understanding. Until now, however, scientists have not had the ability to measure growth rates of individual microbial populations other than by studying them in pure cultures within a petri dish. Unlike larger organisms such as birds, fish, or mammals that can be tagged and monitored over time, individual microbial species are difficult to study effectively in their natural environment.

Scientists from Northern Arizona University, in collaboration with LLNL’s Steven Blazewicz and Jennifer Pett-Ridge (both NACS), have demonstrated a powerful new technique to simultaneously measure the growth rates of hundreds of individual bacterial taxa in any given soil sample. Measuring the rate at which each microbe grows within an environmental sample is fundamental to understanding which organisms play the most important roles in natural and engineered environments that matter most to people, such as natural and agricultural soils, lakes and streams, and the human microbiome. This new measurement technique is based on quantitative stable isotope probing. By adding rare stable isotopes to soil—tracers that contain heavy oxygen—and then sequencing the bacteria that incorporated that tracer, the scientists were able to estimate growth, mortality, and turnover rates for individual microbial populations within soil samples.

[B.J. Koch, T.A. McHugh, M. Hayer, E. Schwartz, S.J. Blazewicz, P. Dijkstra, N. van Gestel, J.C. Marks, R.L. Mau, E.M. Morrissey, J. Pett-Ridge, and B.A. Hungate, Estimating taxon-specific population dynamics in diverse microbial communities, Ecosphere 9(1), e02090 (2018), doi: 10.1002/ecs2.2090.]