Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to stable isotope probing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in 18

Rising temperatures are expected to reduce global soil carbon (C) stocks, driving a positive feedback to climate change 1-3. However, the mechanisms underlying this prediction are not well understood, including how temperature affects microbial enzyme kinetics, growth efficiency (MGE), and turnover 4,5. Here, in a laboratory study, we show that microbial turnover accelerates with warming and, along with enzyme kinetics, determines the response of microbial respiration to temperature change. In contrast, MGE, which is generally thought to decline with warming 6-8 , showed no temperature sensitivity. Using a microbial-enzyme model, we show that temperature-sensitive microbial turnover promotes soil C accumulation with warming, in contrast to reduced soil C predicted by traditional biogeochemical models. Furthermore, the effect of increased microbial turnover differs from the effects of reduced MGE, causing larger increases in soil C stocks. Our results demonstrate that the response of soil C to warming is affected by changes in microbial turnover. This control should be included in the next generation of models to improve prediction of soil C feedbacks to warming.

No abstract

The rapid increase in microbial activity that occurs when a dry soil is rewetted has been well documented and is of great interest due to implications of changing precipitation patterns on soil C dynamics. Several studies have shown minor net changes in microbial population diversity or abundance following wet-up, but the gross population dynamics of bacteria and fungi resulting from soil wet-up are virtually unknown. Here we applied DNA stable isotope probing with H218O coupled with quantitative PCR to characterize new growth, survival, and mortality of bacteria and fungi following the rewetting of a seasonally dried California annual grassland soil. Microbial activity, as determined by CO2 production, increased significantly within three hours of wet-up, yet new growth was not detected until after three hours, suggesting a pulse of nongrowth activity immediately following wet-up, likely due to osmo-regulation and resuscitation from dormancy in response to the rapid change in water potential. Total microbial abundance revealed little change throughout the seven-day post-wet incubation, but there was substantial turnover of both bacterial and fungal populations (49% and 52%, respectively). New growth was linear between 24 and 168 hours for both bacteria and fungi, with average growth rates of 2.3 x 10(8) bacterial 16S rRNA gene copies x [g dry mass](-1) x h(-1) and 4.3 x 10(7) fungal ITS copies x [g dry mass](-1) x h(-1). While bacteria and fungi differed in their mortality and survival characteristics during the seven-day incubation, mortality that occurred within the first three hours was similar, with 25% and 27% of bacterial and fungal gene copies disappearing from the pre-wet community, respectively. The rapid disappearance of gene copies indicates that cell death, occurring either during the extreme dry down period (preceding five months) or during the rapid change in water potential due to wet-up, generates a significant pool of available C that likely contributes to the large pulse in CO2 associated with wet-up. A dynamic assemblage of growing and dying organisms controlled the CO2 pulse, but the balance between death and growth resulted in relatively stable total population abundances, even after a profound and sudden change in environment.

24Bacteria grow and transform elements at different rates, yet quantifying this variation in the 25 environment is difficult. Determining isotope enrichment with fine taxonomic resolution after 26 exposure to isotope tracers could help, but there are few suitable techniques. We propose a 27 modification to Stable Isotope Probing (SIP) that enables determining the isotopic composition 28 of DNA from individual bacterial taxa after exposure to isotope tracers. In our modification, after 29 isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is 30 sequenced separately. Taxon specific density curves are produced for labeled and non-labeled 31 treatments, from which the shift in density for each individual taxon in response to isotope 32 labeling is calculated. Expressing each taxon's density shift relative to that taxon's density 33 measured without isotope enrichment accounts for the influence of nucleic acid composition on 34 density and isolates the influence of isotope tracer assimilation.

No 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.

Organic carbon (C) and nitrogen (N) are essential for heterotrophic soil microorganisms, and their bioavailability strongly influences ecosystem C and N cycling. We show here that the natural (15)N abundance of the soil microbial biomass is affected by both the availability of C and N and ecosystem N processing. Microbial (15)N enrichment correlated negatively with the C : N ratio of the soil soluble fraction and positively with net N mineralization for ecosystems spanning semiarid, temperate and tropical climates, grassland and forests, and over four million years of ecosystem development. In addition, during soil incubation, large increases in microbial (15)N enrichment corresponded to high net N mineralization rates. These results support the idea that the N isotope composition of an organism is determined by the balance between N assimilation and dissimilation. Thus, (15)N enrichment of the soil microbial biomass integrates the effects of C and N availability on microbial metabolism and ecosystem processes.