Single-cell growth rates
Microbes are collectively responsible for much of primary and secondary production, are key drivers of biogeochemical cycles, and modulate the physiology of other organisms. In recent years, genomic and metagenomic efforts have also highlighted the enormous genetic and functional diversity co-existing within different types of microbiomes. However, although it is relatively easy with modern sequence techniques to determine the relative abundance of microbes in samples, fundamental questions remain on how microbes grow under varying spatial and temporal conditions, hampering our understanding of globally and locally important processes. For example, it is largely unknown how fast individual microbes grow under in situ conditions, how growth rates differ among groups of microbes and how they are modulated by ecological conditions. We are currently addressing this problem by coupling single cell estimates of biomass and growth rate with genomics, hence providing the full spectrum of measurements necessary to determine the importance of specific microbes within complex communities. The central element of our novel approach is the suspended microchannel resonator (SMR), which is a well-developed microfluidics-based mass-sensor that has sufficient resolution for measuring the natural range in size, biomass and growth rate of microbes. Single cell growth measurements will be the foundation of coupling of diversity estimates with biogeochemical activity or correlation to host physiology, and it will lead to a more quantitative estimate of microbial activity in global carbon cycle models.
Selected references:
Cermak, N., Becker, J.W., Knudsen, S.M., Chisholm, S.W., Manalis, S.R., Polz, M.F. (2017) Direct single-cell biomass estimation for marine bacteria using Archimedes’ principle. ISME J. 11(3):825-828.