Conversion to bioenergy crops alters the amount and age of microbially-respired soil carbon
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Szymanski, Laura M. (ORCID:0000000292823076)↗
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Model Inputs, Outputs, and Scripts associated with: “Spatial microbial respiration variations in the hyporheic zones within the Columbia River Basin”
This data package is associated with the publication “Spatial microbial respiration variations in the hyporheic zones within the Columbia River Basin” published in the Journal of Geophysical Research: Biogeosciences (Son et al. 2022) available at doi: 10.1029/2021JG006654. This data package includes the key model inputs/outputs of the river corridor model for the Columbia River Basin (CRB) and the model source codes, which were used in the manuscript. The model is a carbon-nitrogen-coupled river corridor model (RCM), and the model is used to quantify hyporheic zone (HZ) aerobic and anaerobic respiration at the NHDPLUS stream reach scales. The RCM used in this study combines empirical substrate models derived from observations and three microbially driven reactions to compute respiration of the HZ for each National Hydrography Dataset (NHD) reach within the CRB. The reactions in HZs of each NHD reach include anaerobic respiration and two-step anaerobic respiration via denitrification. Our HZ respiration estimates are limited to the lotic (or flowing) stream/river systems, and do not account for the respiration process in water column. Note that the RCM only simulates the HZ’s contribution to the dissolved carbon dioxide (CO2) concentrations in the streams, and the CO2 emissions to the atmosphere are not modelled. The model computes at hourly timesteps because of the fast reaction rates. The key input data of the model are exchange flux, residence time, and stream solute (dissolved organic carbon (DOC), dissolved oxygen (DO), and nitrate concentrations). These inputs are constant over time and represent long-term averaged values.This modeling framework successfully quantified HZ respiration components over multiple scales. It revealed key mechanisms driving the spatial variation of HZ aerobic and anaerobic respiration in reaches with varying hydrologic and substrate conditions. Thus, this modeling study offers a testing hypothesis in different river system (e.g., climate and biomes) for the HZ respiration processes, and can be used as a sampling design tool for large-scale HZ experimental studies.This dataset contains five folders: (1) model_inputs, (2) model_outputs, (3) Rscripts, (4) figures, and (5) model_codes. It also contains a readme, file level metadata (FLMD), and data dictionary (dd). Please see the FLMD for a list of all the files contained in this data package and descriptions for each. The model_inputs folder contains the model inputs used to drive the model simulations. The model_outputs folder contains key model output files from the river corridor model. The Rscripts folder contains the Rscripts for pre- and post- processing model results. The figures folder contains the raw figures associated with the manuscript. The model_codes folder includes key model source codes/input files. All files are .jpg, .jpeg, .out, .e, .od, .dat, .sub, .F90, .0, .R, .sbx, .cpg, .sbn, .shx, .shp, .dbf, .prj, .tfw, .tif, .xml, .pdf, or .csv.
54 ENVIRONMENTAL SCIENCES↗
On the role of soil water retention characteristic on aerobic microbial respiration
Soil water status is one of the most important environmental factors that control microbial activity and rate of soil organic matter (SOM) decomposition. Its effect can be partitioned into effect of water energy status (water potential) on cellular activity, effect of water volume on cellular motility, and aqueous diffusion of substrate and nutrients, as well as the effect of air content and gas-diffusion pathways on concentration of dissolved oxygen. Nonetheless,moisture functions widely used in SOM decomposition models are often based on empirical functions rather than robust physical foundations that account for these disparate impacts of soil water. The contributions of soil water content and water potential varyfrom soil to soil according to the soil water characteristic (SWC), which in turn is strongly dependent on soil texture and structure. The overall goal of this study is to introduce a physically based modeling framework of aerobic microbial respiration that incorporates the role of SWC under arbitrary soil moisture status. The model was tested by contrasting it with published data sets of SOM decomposition under laboratory conditions.
54 ENVIRONMENTAL SCIENCES↗
Ecohydrological controls on root and microbial respiration in the East River watershed of Colorado
The main objective of this project was to conduct exploratory work to quantify how snow and rain water inputs influence the CO2 coming from the soil surface (soil CO2 flux), and its plant and microbial sources, in the East River watershed, near Crested Butte, Colorado. Knowledge gained from this effort laid the groundwork for a more comprehensive (ongoing) follow-on grant that is using a combination of experiments, field observations, machine learning and simulation modeling to fully disentangle these relationships. New field measurements were made at four locations along an elevational transect on Snodgrass Mountain at Rocky Mountain Biological Laboratory. These sites were chosen to differ in total snowpack and water table depth, and included both deciduous (aspen) and evergreen (spruce/fir) forest types. We used automated measurements of soil CO2 concentrations to quantify the total soil CO2 flux, and the vertical CO2 production within the soil profile at each site. Isotope (radiocarbon, 14C) measurements determined how much of the CO2 emitted from the soil surface came from plant respiration (root metabolism) versus microbial respiration (decomposition of soil organic matter) sources. Supporting data on plant phenology and microbial dynamics provided context for the observed variation in respiration sources. This work was motivated by our overarching hypothesis that quantifying belowground plant and microbial processes separately, and how they are influenced by snow and rain inputs, is necessary for understanding and predicting how the East River watershed ecosystems will respond to future environmental change.
54 ENVIRONMENTAL SCIENCES↗
Velocity-amplified microbial respiration rates in the lower Amazon River: Amazon River respiration
Most measurements of respiration rates in large tropical rivers do not account for the influence of river flow conditions on microbial activity. We developed a ship-board spinning incubation system for measuring O2 drawdown under different rotation velocities and deployed the system along the lower Amazon River during four hydrologic periods. Average respiration rates in incubation chambers rotated at 0.22 and 0.66 m s-1 were 1.4 and 2.4 times higher than stationary chambers, respectively. On average, depth-integrated respiration rates in chambers spun at 0.22 and 0.66 m s-1 accounted for 64 ± 22% and 104 ± 36% of CO2 outgassing rates, respectively, in mainstem sites. Continuous measurements of in situ pCO2 were also made along with cross-channel profiles of river velocity. A positive correlation between river velocity and pCO2 was observed along the lower river (r2=0.67-0.96) and throughout a tidal cycle.
Amazon↗
In situ detection of microbial respiration in soils and salt flats
Increase in CO2 partial pressures over a desert soil treated with casamino-acids glucose solution correlated with bacterial growth. Few or no increases in numbers of bacteria or CO2 concentrations were noted in similar plots treated with water only or receiving no treatment. Growth in the soil appeared to be severely nutrient limited during the 10 day experiment. Especially rapid growth took place between the third and fifth day, when temperatures ranged from 0 deg. (night) to a maximum of 17.4 deg. (day). Under the conditions of the experiment, intermittent CO2 assay was an insensitive indicator of growth, possibly because of restiction of gas escape by the desert pavement or solution, exchange, or precipitation of carbonate, but more likely because of inefficient sealing of hoods to and below the soil surface. CO2 assay was unable to detect microbial successions. The unpredictable course of these successions, plus unpredictable relative retentions mitigates against assay of organic gases as reliable in situ detection of microbial activity, except perhaps in very alkaline environments such as Owens Lake salts.
Tew, R. W.↗
Spatial Microbial Respiration Variations in the Hyporheic Zones Within the Columbia River Basin
Abstract While the hyporheic zone (HZ) accounts for a significant portion of whole stream CO 2 concentrations, HZ respiration modeling studies are lacking in quantifying their contributions to the total CO 2 at large watershed/basin scales. Quantifying the contribution of anaerobic respiration is also underappreciated. This study used a carbon‐nitrogen‐coupled river corridor model to quantify HZ aerobic and anaerobic respiration and determined the key factors controlling their spatial variability within the Columbia River Basin (CRB). The modeled respiration patterns showed high spatial variability. Among the nine sub‐basins composing the CRB, the Lower Columbia and the Willamette, which receive higher precipitation, had higher respiration. Medium‐sized rivers (fourth to sixth orders) produced the highest aerobic and anaerobic respiration among reaches of different sizes. At the basin scale, aerobic respiration is dominant, representing approximately 98.7% of the total respiration across the CRB. While most of the reaches were dominant with aerobic respiration, reaches in agricultural land showed a relatively higher anaerobic respiration (18%) ratio. A variable importance analysis showed that hyporheic exchange flux controlled most of the spatial variability of HZ respiration, dominating over other physical variables such as residence time, stream dissolved organic carbon (DOC), nitrate, and dissolved oxygen (DO). The influence of substrate concentration (DOC and DO) is larger in modeling anaerobic respiration than aerobic respiration. Future efforts will focus on improving the estimation of the HZ exchange flux and the implementation of spatially explicit parameterizations for the reactions of interest to reduce model uncertainty.
54 ENVIRONMENTAL SCIENCES↗
Partitioning sources of CO 2 emission after soil wetting using high-resolution observations and minimal models
Wetting dry soil triggers a pulse of microbial respiration. Respiration pulses after wetting can be complex, evolving through several stages before subsiding—possibly reflecting contributions from multiple carbon (C) sources. In this work we hypothesized that respiration after wetting combines C from cellular sources (notably trehalose, a cellular osmo-protectant) and soluble extracellular C made available by the physical effects of wetting, with cellular sources contributing early during the pulse and extracellular C dominating later. We tested this hypothesis by making measurements of soil respiration, microbial biomass, trehalose, and water extractable organic C after wetting dry soil in the laboratory. We then devised several alternative minimal models to evaluate the potential contributions of trehalose and extracellular C to the respiration pulse. We found that the chloroform-labile fraction of the microbial biomass was comprised of 50% trehalose in dry soil. Both trehalose and water extractable organic C pools declined rapidly after wetting; trehalose disappeared within 3 h of water addition. Chloroform-labile glucose increased 3 h after water addition and then declined, suggesting rapid hydrolysis of trehalose and consumption of the resulting glucose. Respiration dynamics after wetting could be best explained by models that included two C sources, combining rapid metabolism of trehalose with slower consumption of extracellular soluble C. These results suggest that pulses of respiration after wetting reflect both osmolyte consumption within the microbial biomass and enhanced extracellular C availability; hence, models of microbial drought response must account for both processes to fully resolve soil C dynamics.
54 ENVIRONMENTAL SCIENCES↗
The Q 10 of in situ microbial soil respiration varies with mean annual temperature, precipitation, pH, and plant cover: a meta-analysis and spatial prediction of Q 10
The temperature sensitivity of soil microbial respiration, commonly quantified using the Q 10 coefficient, is a key parameter in carbon cycle models. Uncovering how environmental factors affect in situ Q 10 values can therefore provide critical insight into potential shifts in global carbon stocks under climate change. We collected data from previously published field experiments that measured soil microbial respiration across a range of temperatures. We hypothesized that the Q 10 coefficient of in situ soil microbial respiration would vary based on environmental factors including mean annual temperature (MAT), mean annual precipitation (MAP), plant cover type, pH, soil C:N, and latitude. Linear regression revealed that Q 10 correlates negatively with MAT and MAP and positively with pH and absolute latitude. Additionally, average Q 10 varied significantly across different plant cover types; it was highest in mountain grasslands and lowest in tropical moist forests. Variation in microbial Q 10 across environmental factors may arise from underlying mechanisms such as enzyme kinetics, substrate availability and complexity, and microbial adaptation. To capture patterns in Q 10 more comprehensively, we developed a multiple linear regression model of Q 10 based on the most individually significant environmental drivers and applied it to public datasets to generate a global map of predicted Q 10 . Q 10 was higher in high-latitude and high-altitude regions, where large permafrost carbon stores are vulnerable to thawing and decomposition. We also compared fits between the Q 10 equation and a model produced from macromolecular rate theory (MMRT). We found that the MMRT model had the superior fit and may be better suited to model temperature sensitivity of complex biological reactions. Overall, our results emphasize that relationships between microbial Q 10 and environmental variables should be accounted for in climate models. Incorporating these variations in the Q 10 parameter, rather than using a fixed value, will help predict whether CO 2 emissions will be buffered or exacerbated by soil microbial respiration under climate change.
54 ENVIRONMENTAL SCIENCES↗
Soil Respiration and Microbial Biomass from Soil Incubations with 13C Labeled Additions
This data set provides the respiration and soil microbial biomass data from a series of short and long-term laboratory incubation experiments with 13C labeled substrates to examine how plant communities (forest vs. grassland), edaphic properties, and microbial communities influence C cycling and the long-term fate of C in soil systems. Paired forest and grassland soils from four locations were incubated with 13C labeled glucose in a short-term (144 hours) study while 13C labeled cellulose was added to soils used in the long-term (729 days) study. Soil respiration, microbial biomass, and soil 13C values were monitored throughout the study. Soils were collected from paired forest and grassland locations in the following states in the United States of America: Tennessee (TN), Ohio (OH), Iowa (IA), and Missouri (MO). This dataset contains one data file in comma-separate (*.csv) format.
54 ENVIRONMENTAL SCIENCES↗
Microbial seasonality promotes soil respiratory carbon emission in natural ecosystems: A modeling study
Seasonality is a key feature of the biosphere and the seasonal dynamics of soil carbon (C) emissions represent a fundamental mechanism regulating the terrestrial–climate interaction. We applied a microbial explicit model—CLM-Microbe—to evaluate the impacts of microbial seasonality on soil C cycling in terrestrial ecosystems. Additionally, the CLM-Microbe model was validated in simulating belowground respiratory fluxes, that is, microbial respiration, root respiration, and soil respiration at the site level. On average, the CLM-Microbe model explained 72% (n = 19, p < 0.0001), 65% (n = 19, p < 0.0001), and 71% (n = 18, p < 0.0001) of the variation in microbial respiration, root respiration, and soil respiration, respectively. We then compared the model simulations of soil respiratory fluxes and soil organic C content in top 1 m between the CLM-Microbe model with (CLM-Microbe) and without (CLM-Microbe_wos) seasonal dynamics of soil microbial biomass in natural biomes. Removing soil microbial seasonality reduced model performance in simulating microbial respiration and soil respiration, but led to slight differences in simulating root respiration. Compared with the CLM-Microbe, the CLM-Microbe_wos underestimated the annual flux of microbial respiration by 0.6%–32% and annual flux of soil respiration by 0.4%–29% in natural biomes. Correspondingly, the CLM-Microbe_wos estimated higher soil organic C content in top 1 m (0.2%–7%) except for the sites in Arctic and boreal regions. Our findings suggest that soil microbial seasonality enhances soil respiratory C emissions, leading to a decline in SOC storage. An explicit representation of soil microbial seasonality represents a critical improvement for projecting soil C decomposition and reducing the uncertainties in global C cycle projection under the changing climate.
59 BASIC BIOLOGICAL SCIENCES↗
Interaction of Soil pH and Mineralogy Controls Soil Organic Matter Persistence through Changes in the Composition and Amount of Microbial Necromass
Microbial necromass–mineral associations are key to long-term soil organic matter (SOM) persistence. However, how soil pH and mineralogy interact to regulate SOM stability remains poorly understood. Here, we used artificial soils to test how three clay minerals (bentonite, kaolinite, and goethite), adjusted to four pH levels (5–8), affect microbial activity (respiration), microbial physiology (carbon use efficiency, CUE), microbial-derived residue material (necromass), and the formation and stability of mineral-associated organic matter (MAOM). Artificial soils were inoculated with a rhizosphere-derived microbial community cultured under the same pH conditions and on two representative simulated exudate types (organic acids and carbohydrates) and incubated for 6 weeks. In two complementary experiments, we added necromass from known microbial taxa to the same minerals across pH levels to isolate the role of necromass chemistry and loading. We found that soil pH shaped MAOM chemistry by altering microbial activity and necromass composition. In interaction with mineral type, pH also controlled MAOM thermal stability. Higher necromass loading weakened mineral-organic bonding, reducing MAOM stability, consistent with zonal mineral–organic interaction models. Our results demonstrate that microbial activity, rather than carbon use efficiency, better predicts MAOM formation and that pH-dependent necromass composition and loading govern MAOM persistence. These findings advance mechanistic understanding of SOM stabilization and have implications for predicting soil carbon dynamics under shifting environmental conditions.
carbon use efficiency↗
Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming
Abstract Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration ( Q 10 ) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5–19%, and reduces model parametric uncertainty by 55–71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.
54 ENVIRONMENTAL SCIENCES↗
Hyporheic Zone Microbiome Assembly Is Linked to Dynamic Water Mixing Patterns in Snowmelt-Dominated Headwater Catchments
We report that terrestrial and aquatic elemental cycles are tightly linked in upland fluvial networks. Biotic and abiotic mineral weathering, microbially mediated degradation of organic matter, and anthropogenic influences all result in the movement of solutes (e.g., carbon, metals, and nutrients) through these catchments, with implications for downstream water quality. Within the river channel, the region of hyporheic mixing represents a hot spot of microbial activity, exerting significant control over solute cycling. To investigate how snowmelt-driven seasonal changes in river discharge affect microbial community assembly and carbon biogeochemistry, depth-resolved pore water samples were recovered from multiple locations around a representative meander on the East River near Crested Butte, CO, USA. Vertical temperature sensor arrays were also installed in the streambed to enable seepage flux estimates. Snowmelt-driven high river discharge led to an expanding zone of vertical hyporheic mixing and introduced dissolved oxygen into the streambed that stimulated aerobic microbial respiration. These physicochemical processes contributed to microbial communities undergoing homogenizing selection, in contrast to other ecosystems where lower permeability may limit the extent of mixing. Conversely, lower river discharge conditions led to a greater influence of upwelling groundwater within the streambed and a decrease in microbial respiration rates. Finally, associated with these processes, microbial communities throughout the streambed exhibited increasing dissimilarity between each other, suggesting that the earlier onset of snowmelt and longer periods of base flow may lead to changes in the composition (and associated function) of streambed microbiomes, with consequent implications for the processing and export of solutes from upland catchments.
58 GEOSCIENCES↗
Physical protection regulates microbial thermal responses to chronic soil warming
Climate warming can affect the temperature sensitivity of microbial activity and growth efficiency, possibly explained by changes to microbially unavailable carbon (C) protected within in soil aggregates. Here, we assessed physical protection by crushing macroaggregates (250–2000 μm) and microaggregates (<250 μm) isolated from mineral soils exposed to 27 years of experimental warming (+5 °C). We hypothesized that removal of physical protection would increase microbial activity and reduce C use efficiency (CUE). We found that crushing increased microbial respiration and biomass turnover rate, but did not affect CUE. We also hypothesized that long-term warming would reduce the effect of physical protection on microbial activity, and that physical protection would attenuate microbial temperature sensitivity in heated compared to control soils. We found that long-term warming was associated with a smaller effect of physical protection for microbial respiration but with a larger effect for biomass turnover rate in macroaggregates. Physical protection reduced the temperature sensitivity of respiration but enhanced the temperature sensitivity of microbial biomass turnover rate in heated compared to control soils. Our work shows that long-term warming has contrasting effects on how microbial respiration, biomass turnover rate, and their thermal responses are mediated by physical protection within soil aggregates.
59 BASIC BIOLOGICAL SCIENCES↗
Differential effects of warming and nitrogen fertilization on soil respiration and microbial dynamics in switchgrass croplands
Not Available
54 ENVIRONMENTAL SCIENCES↗