Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil

Abstract

Microbial activity increases after rewetting dry soil, resulting in a pulse of carbon mineralization and nutrient availability. The biogeochemical responses to wet-up are reasonably well understood and known to be microbially mediated. Yet, the population level dynamics, and the resulting changes in microbial community patterns, are not well understood as ecological phenomena. Here, we used sequencing of 16S rRNA genes coupled with heavy water (H 2 18 O) DNA quantitative stable isotope probing to estimate population-specific rates of growth and mortality in response to a simulated wet-up event in a California annual grassland soil. Bacterial growth and mortality responded rapidly to wet-up, within 3 h, and continued throughout the 168 h incubation, with patterns of sequential growth observed at the phylum level. Of the 37 phyla detected in the prewet community, growth was found in 18 phyla while mortality was measured in 26 phyla. Rapid growth and mortality rates were measurable within 3 h of wet-up but had contrasting characteristics; growth at 3 h was dominated by select taxa within the Proteobacteria and Firmicutes, whereas mortality was taxonomically widespread. Furthermore, across the community, mortality exhibited density-independence, consistent with the indiscriminate shock resulting from dry-down and wet-up, whereas growth was density-dependent, consistent with control by competition or predation. Total aggregated growth across the community was highly correlated with total soil CO 2 production. Together, these results illustrate how previously "invisible" population responses can translate quantitatively to emergent observations of ecosystem-scale biogeochemistry.

Rewiring of peatland plant-microbe networks outpaces species turnover

“…Specifically, we show that species turnover, likely caused by enviro-climatological changes resulted in a reshuffling of plant and microbial communities, which then led to a significant rewiring of plant-microbial interactions. Our results suggest that increasing network specialization may have been driven by a shift in physiological and metabolic activity across one organisational level (Blazewicz et al 2020;Williams & de Vries 2020), which then cascaded to the other level. Our findings highlight that while spatial patterns of diversity across trophic levels are indeed key to understand network specialization as forwarded by Galiana et al (2019), and that the contribution of novel associations between species that are common and shared across the networks is most prevalent.…”

Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design

“…Reducing the number of fractions from ϳ40 (typical for many high-resolution SIP studies [16,17,21,38]) to only 10 will substantially impact the feasibility of a SIP study, particularly for MG-SIP. As an example, we compared the resources and yield of a simplified experiment.…”

“…The current practice is to examine many density fractions and perform statistical analyses comparing isotope-labeled versus unlabeled control to indicate the extent to which organisms have "shifted" within a density gradient in response to the isotope treatment (9,10). Density shifts can be used to calculate substrate assimilation rate per taxon (atom% excess), and with the universal substrate H 2 18 O, they can be used to infer specific growth rates (13,15,(19)(20)(21). However, even the most basic SIP experiment (e.g., one type of substrate with labeled and unlabeled versions, 2 treatments, 2 time points, 3 replicates, 10 density fractions per sample) can easily generate nearly 250 samples for processing and sequencing.…”

The Functional Significance of Bacterial Predators

“…Even in macroscopic assemblages, taxa are known to vary in their influences on ecosystem processes ( 27 ). Techniques that combine isotopes and genetic sequencing hold promise for parsing the contributions of individual microbial taxa to interactions within microbial assemblages and to biogeochemical processes ( 28, 29 ).…”