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At least 1,261 records · Page 70
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Competition within low-density bacterial populations as an unexpected factor regulating carbon decomposition in bulk soil

Bacterial decomposition of organic matter in soils is generally believed to be mainly controlled by the access bacteria have to organic substrate. The influence of bacterial traits on this control has, however, received little attention. Using the substrate-dependent Monod growth model, we develop a bioreactive transport model to screen the interactive impacts of spatial dispersion and bacterial traits on mineralization. Bacterial traits primarily involved in the bacterial response to the substrate concentration, such as the maximum specific uptake rate and efficiency, the adaptation time of the uptake rate and the initial population density, are considered. We compare the model results with two sets of previously performed cm-scale soil-core experiments in which the mineralization of the pesticide 2,4-D was measured under well-controlled initial distributions and transport conditions. Bacterial dispersion away from the initial substrate location induced a significant increase in 2,4-D mineralization. Additionally, it reveals an increase of specific uptake rates at lower bacterial densities, more than compensating the decrease of specific uptake rates caused by substrate dilution. This regulation of bacterial activities by density, caused by the local depletion of substrate by competing bacteria, becomes dominant for bacteria with an efficient uptake of substrate at low substrate concentrations (a common feature of oligotrophs). Such oligotrophs, commonly found in soils, compete with each other for substrate even at remarkably low population densities. The ratio-dependent Contois growth model, which includes a density regulation in the expression of the uptake efficiency, is more accurate and convenient to calibrate than the substrate-dependent Monod model, at least under these conditions. In view of their strong interactions, bioreactive and transport processes cannot be handled independently but should be integrated, in particular when reactive processes of interest are carried out by oligotrophs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Resilience in soil bacterial communities of the boreal forest from one to five years after wildfire across a severity gradient

Wildfires can represent a major disturbance to ecosystems, including soil microbial communities belowground. Furthermore, fire regimes are changing in many parts of the world, altering and often increasing fire severity, frequency, and size. The boreal forest and taiga plains ecoregions of northern Canada are characterized by naturally-occurring stand-replacing wildfires on a 40–350 year basis. We previously studied the effects of wildfire on soil microbial communities one year post-fire across 40 sites, spanning a range of burn severity. Here, we return to the same sites five years post-fire to test a series of hypotheses about the effects of fire on bacterial community composition. We ask questions on two themes: which factors control bacterial community composition during post-fire recovery, and how does the importance of different fire-responsive traits change during post-fire recovery? We find the following: Five years post-fire, vegetation community, moisture regime, pH, total carbon, texture, and burned/unburned all remained significant predictors of bacterial community composition with similar predictive value (R 2 ). Bacterial communities became more similar to unburned sites five years post-fire, across the range of severity, suggesting resilience, while general structure of co-occurrence networks remained similar one and five years post-fire. Fast growth potential, as estimated using predicted 16S rRNA copy numbers, was no longer significantly correlated with burn severity five years post-fire, indicating the importance of this trait for structuring bacterial community composition may be limited to relatively short timescales. Many taxa that were enriched in burned sites one year post-fire remained enriched five years post-fire, although the degree to which they were enriched generally decreased. Specific taxa of interest from the genera Massilia, Blastococcus, and Arthrobacter all remained significantly enriched, suggesting that they may have traits that allow them to continue to flourish in the post-fire environment, such as tolerance to increased pH or ability to degrade pyrogenic organic matter. This hypothesis-based work expands our understanding of the post-fire recovery of soil bacterial communities and raises new hypotheses to test in future studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Effects of root litter traits on soil organic matter dynamics depend on decay stage and root branching order

Decaying roots contribute disproportionately to soil organic carbon (SOC) stocks in many ecosystems, yet few studies have examined the afterlife effects of root trait variability on the formation, stability and mineralization of SOC. In order to assess how root functional class (absorptive vs. transport) and mycorrhizal association (ectomycorrhizal vs. arbuscular mycorrhizal fungi) affect both formation and loss of SOC, we decayed lower-order absorptive (orders 1–2) and higher-order transport (orders 3–4) roots from six arbuscular mycorrhizal (AM) and six ectomycorrhizal (EcM) associated hardwood tree species in an isotopically distinct soil under laboratory conditions. We found that root litter effects on SOC differed significantly among root functional classes and mycorrhizal types. AM absorptive and transport roots (high in nitrogen and soluble compounds) contributed more to the formation of new mineral-associated organic carbon (MAOC), but also contributed to higher mineralization of native SOC (via priming effects). Moreover, absorptive AM roots formed MAOC gradually and rates saturated, whereas ECM roots formed MAOC more quickly, despite slower decay (via greater formation efficiency). Altogether, these findings demonstrate how different combinations of root traits might contribute to soil C balance, and that failure to account for the chemical and morphological heterogeneity of roots, as well their interactions with microbes over time, may lead to incorrect projections of SOC stocks and turnover.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Spatial Predictions and Associated Uncertainty of Annual Soil Respiration at the Global Scale

Abstract Soil respiration (Rs), the soil‐to‐atmosphere CO 2 flux produced by microbes and plant roots, is a critical but uncertain component of the global carbon cycle. Our current understanding of the variability and dynamics is limited by the coarse spatial resolution of existing estimates. We predicted annual Rs and associated uncertainty across the world at 1‐km resolution using a quantile regression forest algorithm trained with observations from the global Soil Respiration Database spanning from 1961 to 2011. This model yielded a global annual Rs estimate of 87.9 Pg C/year with an associated global uncertainty of 18.6 (mean absolute error) and 40.4 (root mean square error) Pg C/year. The estimated annual heterotrophic respiration (Rh), derived from empirical relationships with Rs, was 49.7 Pg C/year over the same period. Predicted Rs rates and associated uncertainty varied widely across vegetation types, with the greatest predicted rates of Rs in evergreen broadleaf forests (accounting for 20.9% of global Rs). The greatest prediction uncertainties were in northern latitudes and arid to semiarid ecosystems, suggesting that these areas should be targeted in future measurement campaigns. This study provides predictions of Rs (and associated prediction uncertainty) at unprecedentedly high spatial resolution across the globe that could help constrain local‐to‐global process‐based models. Furthermore, it provides insights into the large variability of Rs and Rh across vegetation classes and identifies regions and vegetation types with poor model performance that should be prioritized for future data collection.

Warner, D. L.↗
DOE OSTI2022

Relative Controls of Vapor Pressure Deficit and Soil Water Stress on Canopy Conductance in Global Simulations by an Earth System Model

Climate change impacts drought and vapor pressure deficit (VPD) that critically influence land-atmosphere water vapor and CO 2 exchange. There is a lack of model-based global evaluation of the relative roles of the two types of water stresses in limiting canopy conductance (G c ). Using the Energy Exascale Earth System Model (E3SM), we conducted four land-atmosphere coupled simulations for the historical period with and without a plant hydraulics scheme (PHS) and under present-day and quadrupling of CO 2 concentrations. By fitting an empirical model of G c to the E3SM simulations, we evaluated the sensitivity of G c to water stresses caused by VPD and soil water (SW) in the growing season. The empirical model is based on a multiplicative algorithm that adjusts G c according to VPD, soil water saturation, and their interaction. Our results show positive trends of VPD over land during the historical period, with large differences between simulations with and without PHS. Despite the differences, a majority of land pixels that experience both SW and VPD stresses are in semi-arid and tropical savanna ecosystems. G c is more sensitive to VPD than SW in less than 20% of land pixels where the empirical model provides a good fit for the simulated G c . Ignoring SW and VPD interaction may underestimate the relative role of VPD on G c by as much as 28%. Including PHS accentuates SW stress limitation on G c by simulating wetter soil and higher ET that lower VPD. Elevated CO 2 reduces G c by increasing water use efficiency and ameliorates SW stress on G c .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Evaluation of Extreme Soil Moisture Conditions During the 2020 Sahel Floods and Implications for Disease Outbreaks

The June-October 2020 growing season was characterized by sustained and extreme flooding across the African Sahel. One consequence of flooding events such as this is outbreaks of vector borne diseases (VBDs) which are often associated with climate anomalies. In this study, data from the soil moisture active passive (SMAP) mission is used with other soil moisture and precipitation data to show that the 2020 Sahelian growing season was the most extreme over the past four decades, ranking first in seasonally accumulated precipitation, which on average exceeded the climatology by around 300 mm. VBD outbreaks of Rift Valley fever and Chikungunya followed in Mauritania/Senegal and Chad, respectively. In some cases, soil moisture is a better indicator of VBD outbreak risk than precipitation, which has so far been more commonly used in studies of VBD outbreaks. It is expected that this finding will inform future monitoring and prediction efforts for VBD risk.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Microbial Models for Simulating Soil Carbon Dynamics: A Review

Abstract Soils store the largest amount of carbon (C) in the biosphere, and the C pool in soil is critical to the global C balance. Numerous microbial models have been developed over the last few decades to represent microbial processes that regulate the responses of soil organic carbon (SOC) to climate change. However, the representation of microbial processes varies, and how microbial processes are incorporated into SOC models has not been well explored. Here, we reviewed 71 microbial models to characterize the microbial processes incorporated into SOC models and analyzed variations in mechanistic complexity. We revealed that (a) four processes (microbial‐mediated decomposition, mineral interaction, microbial necromass recycling, and active and dormant microbial dynamics) are commonly incorporated in microbial models, (b) ∼48% of models simulate only one microbial process (i.e., microbial‐mediated decomposition) and 35% of models simulate two microbial processes: for example, microbial‐mediated decomposition and mineral interaction, (c) more than 80% microbial models use nonlinear equations, such as forward Michaelis‐Menten kinetics, to represent SOC decomposition, (d) the concept of persistence of SOC due to its intrinsic properties has been replaced by organo‐mineral interaction (∼39% of microbial models) that protects SOC from decomposition, and (e) various temperature and moisture modifiers and pH effects have been used to explain the environmental effect on microbial processes. In the future, to realistically incorporate microbial processes into Earth System Models, it is imperative to identify experimental evidence on rate limitation processes and firmly ground model structure on the field and laboratory data.

Environmental Sciences & Ecology↗
DOE OSTI2020

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 (H218O) 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 CO2 production. Together, these results illustrate how previously “invisible” population responses can translate quantitatively to emergent observations of ecosystem-scale biogeochemistry.

58 GEOSCIENCES↗
DOE OSTI2022

Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

Soil microbiomes harbour unparalleled functional and phylogenetic diversity. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. As methylation was proposed to be catalysed by sulfate-reducing bacteria. However, to date, there are no available anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harbouring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomics to identify the microorganisms actively methylating As in anoxic soil-derived microbial cultures. Based on the metagenome-assembled genomes of microorganisms expressing ArsM, we isolated Paraclostridium sp. strain EML, which was confirmed to actively methylate As anaerobically. This work is an example of the application of meta-omics to the isolation of elusive microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Life history strategies among soil bacteria—dichotomy for few, continuum for many

Abstract Study of life history strategies may help predict the performance of microorganisms in nature by organizing the complexity of microbial communities into groups of organisms with similar strategies. Here, we tested the extent that one common application of life history theory, the copiotroph-oligotroph framework, could predict the relative population growth rate of bacterial taxa in soils from four different ecosystems. We measured the change of in situ relative growth rate to added glucose and ammonium using both 18O–H2O and 13C quantitative stable isotope probing to test whether bacterial taxa sorted into copiotrophic and oligotrophic groups. We saw considerable overlap in nutrient responses across most bacteria regardless of phyla, with many taxa growing slowly and few taxa that grew quickly. To define plausible life history boundaries based on in situ relative growth rates, we applied Gaussian mixture models to organisms’ joint 18O–13C signatures and found that across experimental replicates, few taxa could consistently be assigned as copiotrophs, despite their potential for fast growth. When life history classifications were assigned based on average relative growth rate at varying taxonomic levels, finer resolutions (e.g., genus level) were significantly more effective in capturing changes in nutrient response than broad taxonomic resolution (e.g., phylum level). Our results demonstrate the difficulty in generalizing bacterial life history strategies to broad lineages, and even to single organisms across a range of soils and experimental conditions. We conclude that there is a continued need for the direct measurement of microbial communities in soil to advance ecologically realistic frameworks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Soil carbon storage capacity of drylands under altered fire regimes

The determinants of fire-driven changes in soil organic carbon (SOC) across broad environmental gradients remains unclear, especially in global drylands. Here we combined datasets and field sampling of fire-manipulation experiments to evaluate where and why fire changes SOC and compared our statistical model to simulations from ecosystem models. Drier ecosystems experienced larger relative changes in SOC than humid ecosystems—in some cases exceeding losses from plant biomass pools—primarily explained by high fire-driven declines in tree biomass inputs in dry ecosystems. Many ecosystem models underestimated the SOC changes in drier ecosystems. Upscaling our statistical model predicted that soils in savannah–grassland regions may have gained 0.64 PgC due to net-declines in burned area over the past approximately two decades. Consequently, ongoing declines in fire frequencies have probably created an extensive carbon sink in the soils of global drylands that may have been underestimated by ecosystem models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Growth rate as a link between microbial diversity and soil biogeochemistry

The growth rate of a microorganism is a simple yet profound way to quantify its impact on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production, and element transformation, some of the many ways that organisms affect Earth’s ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favorable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining ‘omics and stable isotope probing enable sensitive measurements of growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions, and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake, and ecosystem productivity. Finally, measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Rapid loss of complex polymers and pyrogenic carbon in subsoils under whole-soil warming

Subsoils contain more than half of soil organic carbon (SOC) and are expected to experience rapid warming in the coming decades. Yet our understanding of the stability of this vast carbon pool under global warming is uncertain. In particular, the fate of complex molecular structures (polymers) remains debated. Here we show that 4.5 years of whole-soil warming (+4 °C) resulted in less polymeric SOC (sum of specific polymers contributing to SOC) in the warmed subsoil (20–90 cm) relative to control, with no detectable change in topsoil. Warming stimulated the subsoil loss of lignin phenols (–17 ± 0%) derived from woody plant biomass, hydrolysable lipids cutin and suberin, derived from leaf and woody plant biomass (–28 ± 3%), and pyrogenic carbon (–37 ± 8%) produced during incomplete combustion. Given that these compounds have been proposed for long-term carbon sequestration, it is notable that they were rapidly lost in warmed soils. We conclude that complex polymeric carbon in subsoil is vulnerable to decomposition and propose that molecular structure alone may not protect compounds from degradation under future warming.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt

Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.

Sorensen, Patrick O↗
DOE OSTI2020

Intercropping kura clover with prairie cordgrass mitigates soil greenhouse gas fluxes

Prairie cordgrass (PCG) ( Spartina pectinata Link) has a high tolerance to soil salinity and waterlogging, therefore, it can thrive on marginal lands. Optimizing the nitrogen (N) input is crucial to achieving desirable biomass production of PCG without negatively impacting the environment. Thus, this study was based on the hypothesis that the use of legumes such as kura clover ( Trifolium ambiguum M. Bieb.) (KC) as an intercrop with PCG can provide extra N to the crop reducing the additional N fertilizer and mitigating soil surface greenhouse gas (GHG) emissions. Specific objective of the study was to assess the impact of PCG managed with different N rates [0 kg N ha -1 (PCG-0N), 75 kg N ha -1 (PCG-75N), 150 kg N ha -1 (PCG-150N), and 225 kg N ha -1 (PCG-255N)], and PCG intercropped with KC (PCG-KC) on GHG fluxes and biomass yield. The experimental site was established in 2010 in South Dakota under a marginally yielding cropland. The GHG fluxes were measured from 2014 through 2018 growing seasons using the static chamber. Net global warming potential (GWP) was calculated. Data showed that cumulative CH 4 and CO 2 fluxes were similar for all the treatments over the study period. However, the PCG-KC, PCG-0N, and PCG-75N recorded lower cumulative N 2 O fluxes (384, 402, and 499 g N ha -1 , respectively) than the PCG-150N (644 g N ha -1 ) and PCG-255N (697 g N ha -1 ). The PCG-KC produced 85% and 39% higher yield than the PCG-0N in 2016 and 2017, respectively, and similar yield to the other treatments (PCG-75N, PCG-150N, and PCG-255N) in these years. Net GWP was 52% lower for the PCG-KC (112.38 kg CO 2 -eq ha -1 ) compared to the PCG-225N (227.78 kg CO 2 -eq ha -1 ), but similar to other treatments. Soil total N was 15%% and 13% higher under PCG-KC (3.7 g kg -1 ) than that under PCG-0N (3.2 g kg -1 ) and PCG-75N (3.3 g kg -1 ), respectively. This study concludes that intercropping prairie cordgrass with kura clover can enhance biomass yield and reduce fertilizer-derived N 2 O emissions and net global warming potential.

09 BIOMASS FUELS↗
DOE OSTI2023

The environmental controls on efficiency of enhanced rock weathering in soils

Abstract Enhanced rock weathering (ERW) in soils is a promising carbon removal technology, but the realistically achievable efficiency, controlled primarily by in situ weathering rates of the applied rocks, is highly uncertain. Here we explored the impacts of coupled biogeochemical and transport processes and a set of primary environmental and operational controls, using forsterite as a proxy mineral in soils and a multiphase multi-component reactive transport model considering microbe-mediated reactions. For a onetime forsterite application of ~ 16 kg/m 2 , complete weathering within five years can be achieved, giving an equivalent carbon removal rate of ~ 2.3 kgCO 2 /m 2 /yr. However, the rate is highly variable based on site-specific conditions. We showed that the in situ weathering rate can be enhanced by conditions and operations that maintain high CO 2 availability via effective transport of atmospheric CO 2 (e.g. in well-drained soils) and/or sufficient biogenic CO 2 supply (e.g. stimulated plant–microbe processes). Our results further highlight that the effect of increasing surface area on weathering rate can be significant—so that the energy penalty of reducing the grain size may be justified—only when CO 2 supply is nonlimiting. Therefore, for ERW practices to be effective, siting and engineering design (e.g. optimal grain size) need to be co-optimized.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Fine root and soil carbon stocks are positively related in grasslands but not in forests

Increasing fine root carbon (FRC) inputs into soils has been proposed as a solution to increasing soil organic carbon (SOC). However, FRC inputs can also enhance SOC loss through priming. Here, we tested the broad-scale relationships between SOC and FRC at 43 sites across the US National Ecological Observatory Network. We found that SOC and FRC stocks were positively related with an across-ecosystem slope of 7 ± 3 kg SOC m −2 per kg FRC m −2 , but this relationship was driven by grasslands. Grasslands had double the across-ecosystem slope while forest FRC and SOC were unrelated. Furthermore, deep grassland soils primarily showed net SOC accrual relative to FRC input. Conversely, forests had high variability in whether FRC inputs were related to net SOC priming or accrual. We conclude that while FRC increases could lead to increased SOC in grasslands, especially at depth, the FRC-SOC relationship remains difficult to characterize in forests.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Methane-derived carbon flows into host–virus networks at different trophic levels in soil

Significance The impact of soil viruses on prokaryotic hosts and their functional processes is largely unknown. While metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts, this does not necessarily identify contemporary interactions. To enable a detailed analysis of active virus–host interactions between individual populations, we focused on the critical biogeochemical process of methane (CH 4 ) oxidation and followed the transfer of carbon from hosts to their associated viruses in situ. Analysis of 13 C-enriched metagenomic DNA demonstrated that CH 4 -derived carbon is transferred into viral biomass via both primary and secondary utilizers of CH 4 and suggests viral predation is an important mechanism for releasing CH 4 -derived organic carbon into the soil matrix.

Lee, Sungeun↗