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Measuring the growth rate of a microorganism is a simple yet profound way to quantify its effect on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production and element transformation—some of the many ways in which organisms affect Earth’s ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favourable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining omics and stable isotope probing enable sensitive measurements of the growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake and ecosystem productivity. Measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry. 

The growth rate of a microorganism is a simple yet profound way to quantify its impact on the world. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favorable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their growth rate. At the population level, per capita growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production, and element transformation, some of the many ways that organisms affect Earth’s ecosystems and climate. For soil microorganisms, most of our understanding of growth is based on observations made in culture. This is a crucial limitation given that many soil microbes are not readily cultured and in vitro conditions are unlikely to reflect conditions in the wild. New approaches in ‘omics and stable isotope probing make it possible to sensitively measure growth rates of microbial assemblages and individual taxa in nature, and to couple these measurements to biogeochemical fluxes. Microbial ecologists can now explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions, and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms will allow scientists to test and refine ecological theory and advance processbased models of carbon flux, nutrient uptake, and ecosystem productivity. Measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry.  

Abstract Ice-free terrestrial environments of the western Antarctic Peninsula are expanding and subject to colonization by new microorganisms and plants, which control biogeochemical cycling. Measuring growth rates of microbial populations and ecosystem carbon flux is critical for understanding how terrestrial ecosystems in Antarctica will respond to future warming. We implemented a field warming experiment in early (bare soil; +2 °C) and late (peat moss-dominated; +1.2 °C) successional glacier forefield sites on the western Antarctica Peninsula. We used quantitative stable isotope probing with H218O using intact cores in situ to determine growth rate responses of bacterial taxa to short-term (1 month) warming. Warming increased the growth rates of bacterial communities at both sites, even doubling the number of taxa exhibiting significant growth at the early site. Growth responses varied among taxa. Despite that warming induced a similar response for bacterial relative growth rates overall, the warming effect on ecosystem carbon fluxes was stronger at the early successional site—likely driven by increased activity of autotrophs which switched the ecosystem from a carbon source to a carbon sink. At the late-successional site, warming caused a significant increase in growth rate of many Alphaproteobacteria, but a weaker and opposite gross ecosystem productivity response that decreased the carbon sink—indicating that the carbon flux rates were driven more strongly by the plant communities. Such changes to bacterial growth and ecosystem carbon cycling suggest that the terrestrial Antarctic Peninsula can respond fast to increases in temperature, which can have repercussions for long-term elemental cycling and carbon storage. 

Soil carbon stocks in the tundra and underlying permafrost have become increasingly vulnerable to microbial decomposition due to climate change. The microbial responses to Arctic warming must be understood in order to predict the effects of future microbial activity on carbon balance in a warming Arctic. 

Abstract Predicting ecosystem function is critical to assess and mitigate the impacts of climate change. Quantitative predictions of microbially mediated ecosystem processes are typically uninformed by microbial biodiversity. Yet new tools allow the measurement of taxon-specific traits within natural microbial communities. There is mounting evidence of a phylogenetic signal in these traits, which may support prediction and microbiome management frameworks. We investigated phylogeny-based trait prediction using bacterial growth rates from soil communities in Arctic, boreal, temperate, and tropical ecosystems. Here we show that phylogeny predicts growth rates of soil bacteria, explaining an average of 31%, and up to 58%, of the variation within ecosystems. Despite limited overlap in community composition across these ecosystems, shared nodes in the phylogeny enabled ancestral trait reconstruction and cross-ecosystem predictions. Phylogenetic relationships could explain up to 38% (averaging 14%) of the variation in growth rates across the highly disparate ecosystems studied. Our results suggest that shared evolutionary history contributes to similarity in the relative growth rates of related bacteria in the wild, allowing phylogeny-based predictions to explain a substantial amount of the variation in taxon-specific functional traits, within and across ecosystems. 

Abstract When leaves fall in rivers, microbial decomposition commences within hours. Microbial assemblages comprising hundreds of species of fungi and bacteria can vary with stream conditions, leaf litter species, and decomposition stage. In terrestrial ecosystems, fungi and bacteria that enter soils with dead leaves often play prominent roles in decomposition, but their role in aquatic decomposition is less known. Here, we test whether fungi and bacteria that enter streams on senesced leaves are growing during decomposition and compare their abundances and growth to bacteria and fungi that colonize leaves in the water. We employ quantitative stable isotope probing to identify growing microbes across four leaf litter species and two decomposition times. We find that most of the growing fungal species on decomposing leaves enter the water with the leaf, whereas most growing bacteria colonize from the water column. Results indicate that the majority of bacteria found on litter are growing, whereas the majority of fungi are dormant. Both bacterial and fungal assemblages differed with leaf type on the dried leaves and throughout decomposition. This research demonstrates the importance of fungal species that enter with the leaf on aquatic decomposition and the prominence of bacteria that colonize decomposing leaves in the water.