Estimating taxon‐specific population dynamics in diverse microbial communities

Abstract

Abstract. Understanding how population-level dynamics contribute to ecosystem-level processes is a primary focus of ecological research and has led to important breakthroughs in the ecology of macroscopic organisms. However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists' understanding of how microbial populations interact to regulate ecosystem processes. Here, we use isotope incorporation within DNA molecules to model taxonspecific population growth in the presence of 18 O-labeled water. By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortality, and turnover for individual microbial populations within soil assemblages. When summed across the entire bacterial community, our taxon-specific estimates are within the range of other whole-assemblage measurements of bacterial turnover. Because it can be applied to environmental samples, the approach we present is broadly applicable to measuring population growth, mortality, and associated biogeochemical process rates of microbial taxa for a wide range of ecosystems and can help reveal how individual microbial populations drive biogeochemical fluxes.

Soil microbial moisture dependences and responses to drying–rewetting: The legacy of 18 years drought

“…Although we do not explicitly resolve between these possibilities, the high functional and taxonomic diversity of microbial communities (Delmont et al, ; Raes & Bork, ), along with recent experimental work (Fiegna, Moreno‐Letelier, Bell, & Barraclough, ; Gravel et al, ), suggest that functional shifts due to species sorting swamp those due to physiological or evolutionary changes in soil systems. Consistent with this interpretation, in one of the few studies with the power to resolve between growth responses of different microbial taxa to rewetting of dry soil, pronounced community changes were induced by a D/RW cycle (Koch et al, ). Hence, the observed change in functional response to D/RW most likely results from a microbial community shift, rather than evolutionary or physiological change.…”

Measurement error and resolution in quantitative stable isotope probing: implications for experimental design

“…Quantitative SIP (qSIP) is a recently developed adaptation of SIP that makes substrate uptake measurements possible at the individual or population genome scale (Hungate et al 2015; Koch et al 2018). In qSIP, isopycnic separation of nucleic acids in cesium chloride is combined with a mathematical model to quantify isotope enrichment.…”

“…The current practice is to examine many density fractions and perform statistical analyses comparing isotope-labeled versus unlabeled controls, to indicate the extent to which organisms have “shifted” within a density gradient in response to the isotope treatment (Hungate et al 2015; Youngblut, Barnett, and Buckley 2018). Density shifts can be used to calculate substrate assimilation rate per taxon (atom % excess), and when using the universal substrate H 2 18 O, they can be used to infer specific growth rates (Blazewicz and Schwartz 2011; Blazewicz, Schwartz, and Firestone 2014; Papp et al 2018; Koch et al 2018). However, even the most basic experiment (e.g one type of substrate, 2 timepoints, 3 replicates, 10 density fractions per sample) can easily generate over 100 samples for processing and sequencing.…”

Soil biodiversity and soil erosion: It is time to get married

“…Supposing the existence of rare, probably still unknown, species of soil organisms, soil erosion might be one of the main disturbance events in extinction processes (Veresoglou, Halley, & Rillig, ). New isotope‐based techniques allow us to mimic rain events and monitor the effects on soil organisms (Koch et al, ). The application of these methodologies to analysing the mortality rates associated with intensive water load would facilitate the comprehension of extinction phenomena occurring in soil. “Defence effect”: erosion being a stressor, it is likely that soil organisms have evolved mechanisms for reducing/eliminating potential related damage.…”

“…New isotope-based techniques allow us to mimic rain events and monitor the effects on soil organisms (Koch et al, 2018). The application of these methodologies to analysing the mortality rates associated with intensive water load would facilitate the comprehension of extinction phenomena occurring in soil.…”