Carbon turnover and microbial activity in an artificial soil under imposed cyclic drainage and imbibition

Abstract

Water table fluctuations generate temporally and spatially dynamic physicochemical conditions that drive biogeochemical hot spots and hot moments in the vadose zone. However, their role in the cycling of soil C remains poorly known. Here, we present results from unvegetated column experiments filled with 45 cm of artificial soil containing 10% humus, and inoculated with a natural microbial extract. In one series of three replicate columns, five cycles, each consisting of a 4-wk drainage followed by a 4-wk imbibition period, were imposed, whereas in a second series, the water table remained static. Depth-resolved O 2 concentration profiles and headspace CO 2 effluxes were markedly different between the two regimes. In the fluctuating regime, drainage periods yielded 2.5 times greater CO 2 effluxes than imbibition periods. At the end of the experiment, the fluctuating water table columns exhibited a distinct zone of organic C (OC) depletion in the depth interval of 8-20 cm that was not observed under the static regime. Although this zone showed elevated levels of adenosine triphosphate (ATP), the microbial biomass was actually lower than at the corresponding depth interval of the static regime. A vertically stratified microbial community established in all columns that depended on oxygenation with depth. The 16S ribosomal RNA (rRNA) gene analyses showed a slightly higher diversity in the Abbreviations: ATP, adenosine triphosphate; bss, below the soil surface; DIC, dissolved inorganic carbon; DOC, dissolved organic carbon; MBC, microbial biomass carbon; OC, organic carbon; OTU, operational taxonomic unit; rRNA, ribosomal RNA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Denitrification‐Driven Transcription and Enzyme Production at the River‐Groundwater Interface: Insights From Reactive‐Transport Modeling

“…The general, qualitative conclusions from our analysis should be transferable to other microbial reaction systems in environmental settings. Soils, for instance, are a very dynamic environment where redox conditions can change abruptly through changes in hydrological conditions like drainage or flooding (Pronk et al., 2020; Zhang & Furman, 2021). Such short‐term fluctuations will lead to a disconnect of quickly reacting transcript concentrations from enzyme concentrations and, consequently, reaction rates.…”

Shared Microbial Taxa Respond Predictably to Cyclic Time-Varying Oxygen Limitation in Two Disparate Soils

“…A number of previous experiments have assessed impacts of fluctuating oxic/anoxic conditions on microbial community composition ( Pett-Ridge and Firestone, 2005 ; DeAngelis et al, 2010 ; Frindte et al, 2016 ; Mejia et al, 2016 ; Randle-Boggis et al, 2018 ; Winkler et al, 2019 ; Pronk et al, 2020 ) but it was often difficult to discern whether increasing the relative durations of anoxic vs. oxic periods caused systematic changes, and whether these differences were sustained over time. Here, our treatments corresponded to cumulative anoxic durations of 0, 33, 50, 66, and 75% of the experiment.…”

“…Bacterial communities incubated under 5-week anoxic/1-week oxic cycles for 1 y diverged from initial conditions in one rice paddy soil but not another ( Winkler et al, 2019 ). Bacteria exposed to 4-week drained and flooded cycles in a synthetic soil did not differ from a static control ( Pronk et al, 2020 ), but repeated 2-week flooding events altered pasture soil communities ( Randle-Boggis et al, 2018 ). Overall, responses of soil microbial communities to experimental manipulations of O 2 availability have been mixed, and it is not clear whether community responses to cyclic anoxic events of increasing duration are generally consistent within or among soils.…”

“…Indeed, field measurements demonstrated that proxies for O 2 may predict spatial or depth variation in microbial community composition within individual sites ( Peralta et al, 2014 ; Lipson et al, 2015 ). An increasing number of studies has explicitly investigated the impact of temporal O 2 variation over timescales of hours to weeks on microbial community composition, but responses of particular microbial groups or taxa are often difficult to generalize among studies ( Pett-Ridge and Firestone, 2005 ; DeAngelis et al, 2010 ; Frindte et al, 2016 ; Mejia et al, 2016 ; Randle-Boggis et al, 2018 ; Winkler et al, 2019 ; Pronk et al, 2020 ). These differences raise the question of whether microbial communities or individual microbial taxa from disparate soils might share consistent responses to time-varying anoxic conditions, or whether differences in other soil characteristics, such as pH, organic matter availability, mineralogy, or other site-specific factors might override the effects of anoxia.…”

Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models?

“…However, many environments in which nitrogen cycling plays a crucial role are very dynamic. For example, rapid watercontent driven changes in the redox state of soils (Pronk et al, 2020) or diurnal fluctuations in river biogeochemistry (Kunz et al, 2017) can control nitrogen turnover. The lack of obvious correlations between transcripts of functional genes and reaction rates observed in our modeling results are likely representative for such dynamic environments.…”