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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Uncertain Spatial Pattern of Future Land Use and Land Cover Change and Its Impacts on Terrestrial Carbon Cycle Over the Arctic–Boreal Region of North America

Land use and land cover change (LULCC) represents a key process of human-Earth system interaction and has profound impacts on terrestrial ecosystem carbon cycling. As a key input for ecosystem models, future gridded LULCC data is typically spatially downscaled from regional LULCC projections by integrated assessment models, such as the Global Change Analysis Model (GCAM). The uncertainty associated with the different spatial downscaling methods and its impacts on the subsequent model projections have been historically ignored and rarely examined. This study investigated this problem using two representative spatial downscaling methods and focused on their impacts on the carbon cycle over the Arctic-Boreal Vulnerability Experiment (ABoVE) domain, where extensive LULCC is expected. Specifically, we used the Future Land Use Simulation model (FLUS) and the Demeter model to generate 0.25° gridded LULCC data (i.e., LULCC FLUS and LULCC Demeter , respectively) with the same input of regional LULCC projections from GCAM, under both the low (i.e., SSP126) and high (i.e., SSP585) greenhouse gas emission scenarios. The two sets of downscaled LULCC were used to drive the Community Land Model version 5 and prognostically simulate the terrestrial carbon cycle dynamics over the 21st century. The results suggest large spatial-temporal differences between LULCC FLUS and LULCC Demeter , and the spatial distributions of the needleleaf evergreen boreal tree, broadleaf deciduous boreal tree, broadleaf deciduous boreal shrub, and C3 arctic grass are particularly different under both SSP126 and SSP585. Additionally, the spatiotemporal differences are larger under SSP126 than SSP585, due to more intensive LULCC under SSP126 than SSP585 from GCAM projection. The differences in LULCC further lead to large discrepancies in the spatial patterns of projected gross primary productivity, ecosystem respiration, and net ecosystem exchange, which represent more than 79% of the contributions of future LULCC in 2100. Additionally, the difference in carbon flux under SSP126 is generally larger than those under SSP585. This study highlights the importance of considering the uncertainties induced by the spatial downscaling process in future LULCC projections and carbon cycle simulations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

The Importance of Accounting for Landscape Position When Investigating Grasslands: A Multidisciplinary Characterisation of a California Coastal Grassland

Abstract Grasslands are one of the most common land‐cover types, providing important ecosystem services globally, yet few studies have examined grassland critical‐zone functioning throughout hillslopes. This study characterised a coastal grassland over a small hillslope at Point Reyes National Seashore, California, using multidisciplinary techniques, combining remotely‐sensed, geophysical, plant, and soil measurements. Clustering techniques delineated the study area into four landscape zones, up‐, mid‐, and down‐slope, and a bordering riparian ecotone, which had distinct environmental properties that varied spatially across the site, with depth, and time. Soil moisture increased with depth and down slope towards a bordering riparian zone, and co‐varied with soil CO 2 flux rates both spatially and temporally. This highlighted three distinct controls of soil moisture on soil respiration: CO 2 fluxes were inhibited by high moisture content in the down‐slope during the wet winter months, and converged across landscape positions in the dry summer months, while also displaying post‐rain pulses. The normalised difference vegetation index (NDVI) ranged from 0.32 (September)–0.80 (April) and correlated positively with soil moisture and aboveground biomass, moving down slope. Yet, NDVI, aboveground biomass, and soil moisture were not correlated to soil organic carbon (SOC) content (0.4%–4.5%), which was highest in the mid‐slope. The SOC content may instead be linked to shifts in dominant grassland species and their rhizosphere properties with landscape position. This multidisciplinary characterisation highlighted significant heterogeneity in grassland properties with landscape position, and demonstrated an approach that could be used to characterise other critical‐zone environments on hillslopes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

The Influence of Air‐Sea CO 2 Disequilibrium on Carbon Sequestration by the Ocean's Biological Pump

Abstract The ocean's biological carbon pump (BCP) affects the Earth's climate by sequestering CO 2 away from the atmosphere for decades to millennia. One primary control on the amount of carbon sequestered by the biological pump is air‐sea CO 2 disequilibrium, which is controlled by the rate of air‐sea CO 2 exchange and the residence time of CO 2 in surface waters. Here, we use a data‐assimilated model of the soft tissue BCP to quantify carbon sequestration inventories and time scales from remineralization in the water column to equilibration with the atmosphere. We find that air‐sea CO 2 disequilibrium enhances the global biogenic carbon inventory by ∼35% and its sequestration time by ∼70 years compared to identical calculations made assuming instantaneous air‐sea CO 2 exchange. Locally, the greatest enhancement occurs in the subpolar Southern Ocean, where air‐sea disequilibrium increases sequestration times by up to 600 years and the biogenic dissolved inorganic carbon inventory by >100% in the upper ocean. Contrastingly, in deep‐water formation regions of the North Atlantic and Antarctic margins, where biological production creates undersaturated surface waters which are subducted before fully equilibrating with the atmosphere, air‐sea CO 2 disequilibrium decreases the depth‐integrated sequestration inventory by up to ∼150%. The global enhancement of carbon sequestration by air‐sea disequilibrium is particularly important for carbon respired in deep waters that upwell in the Southern Ocean. These results highlight the importance of accounting for air‐sea CO 2 disequilibrium when evaluating carbon sequestration by the biological pump and for assessing the efficacy of ocean‐based CO 2 removal methods.

Environmental Sciences & Ecology↗
DOE OSTI2024

Characterizing the Atmospheric Mn Cycle and Its Impact on Terrestrial Biogeochemistry

Abstract The role of manganese (Mn) in ecosystem carbon (C) biogeochemical cycling is gaining increasing attention. While soil Mn is mainly derived from bedrock, atmospheric deposition could be a major source of Mn to surface soils, with implications for soil C cycling. However, quantification of the atmospheric Mn cycle, which comprises emissions from natural (desert dust, sea salts, volcanoes, primary biogenic particles, and wildfires) and anthropogenic sources (e.g., industrialization and land‐use change due to agriculture), transport, and deposition, remains uncertain. Here, we use compiled emission data sets for each identified source to model and quantify the atmospheric Mn cycle by combining an atmospheric model and in situ atmospheric concentration measurements. We estimated global emissions of atmospheric Mn in aerosols (<10 μm in aerodynamic diameter) to be 1,400 Gg Mn year −1 . Approximately 31% of the emissions come from anthropogenic sources. Deposition of the anthropogenic Mn shortened Mn “pseudo” turnover times in 1‐m‐thick surface soils (ranging from 1,000 to over 10,000,000 years) by 1–2 orders of magnitude in industrialized regions. Such anthropogenic Mn inputs boosted the Mn‐to‐N ratio of the atmospheric deposition in non‐desert dominated regions (between 5 × 10 −5 and 0.02) across industrialized areas, but that was still lower than soil Mn‐to‐N ratio by 1–3 orders of magnitude. Correlation analysis revealed a negative relationship between Mn deposition and topsoil C density across temperate and (sub)tropical forests, consisting with atmospheric Mn deposition enhancing carbon respiration as seen in in situ biogeochemical studies.

Environmental Sciences & Ecology↗
DOE OSTI2023

Sea–Level Rise Impacts on Tidal Marshes and Estuarine Biogeochemical Processes

We used a numerical model to investigate the effects of sea-level rise (SLR) on the biogeochemical processes in the York River Estuary with extensive tidal marshes. The fully-coupled hydrodynamic-water quality-marsh model accounts for the spatial and temporal variations of physical-biogeochemical interactions between the tidal marshes and surrounding waters. This study focuses on an SLR scenario where the vertical accretion of tidal marshes keeps pace with the rising sea levels. Results show that SLR amplifies the tidal range and prolongs flooding duration, which results in enhanced porewater exchanges of materials between the tidal marshes and the surrounding waters. The increased availability of shallow-water habitats and enhanced light utilization in the shallow areas under SLR promote phytoplankton production (PP) in the shallow-water regions of the York River. Consequently, the organic carbon in the open water is fueled by the contributions from shallow waters and the enhanced export of organic carbon from the marshes. The change in the dissolved oxygen (DO) budget in the York River Estuary is attributed to changes in water column respiration, net metabolism of the benthic layer, reaeration, PP, and increased stratification under SLR. The net DO flux out of the York River increases at the York River mouth. Diel DO variation, especially in the marshes in the upper estuary, promotes phosphorus release from the sediment. The changes in dissolved nitrogen under SLR are relatively minimal.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Generalizing Microbial Parameters in Soil Biogeochemical Models: Insights From a Multi‐Site Incubation Experiment

Abstract Incorporating microbial processes into soil biogeochemical models has received growing interest. However, determining the parameters that govern microbially driven biogeochemical processes typically requires case‐specific model calibration in various soil and ecosystem types. Here each case refers to an independent and individual experimental unit subjected to repeated measurements. Using the Microbial‐ENzyme Decomposition model, this study aimed to test whether a common set of microbially‐relevant parameters (i.e., generalized parameters) could be obtained across multiple cases based on a two‐year incubation experiment in which soil samples of four distinct soil series (i.e., Coland, Kesswick, Westmoreland, and Etowah) collected from forest and grassland were subjected to cellulose or no cellulose amendment. Results showed that a common set of parameters controlling microbial growth and maintenance as well as extracellular enzyme production and turnover could be generalized at the soil series level but not land cover type. This indicates that microbial model developments need to prioritize soil series type over plant functional types when implemented across various sites. This study also suggests that, in addition to heterotrophic respiration and microbial biomass data, extracellular enzyme data sets are needed to achieve reliable microbial‐relevant parameters for large‐scale soil model projections.

58 GEOSCIENCES↗
DOE OSTI2024

A New Coupled Biogeochemical Modeling Approach Provides Accurate Predictions of Methane and Carbon Dioxide Fluxes Across Diverse Tidal Wetlands

Abstract Tidal wetlands provide valuable ecosystem services, including storing large amounts of carbon. However, the net exchanges of carbon dioxide (CO 2 ) and methane (CH 4 ) in tidal wetlands are highly uncertain. While several biogeochemical models can operate in tidal wetlands, they have yet to be parameterized and validated against high‐frequency, ecosystem‐scale CO 2 and CH 4 flux measurements across diverse sites. We paired the Cohort Marsh Equilibrium Model (CMEM) with a version of the PEPRMT model called PEPRMT‐Tidal, which considers the effects of water table height, sulfate, and nitrate availability on CO 2 and CH 4 emissions. Using a model‐data fusion approach, we parameterized the model with three sites and validated it with two independent sites, with representation from the three marine coasts of North America. Gross primary productivity (GPP) and ecosystem respiration (R eco ) modules explained, on average, 73% of the variation in CO 2 exchange with low model error (normalized root mean square error (nRMSE) <1). The CH 4 module also explained the majority of variance in CH 4 emissions in validation sites ( R 2 = 0.54; nRMSE = 1.15). The PEPRMT‐Tidal‐CMEM model coupling is a key advance toward constraining estimates of greenhouse gas emissions across diverse North American tidal wetlands. Further analyses of model error and case studies during changing salinity conditions guide future modeling efforts regarding four main processes: (a) the influence of salinity and nitrate on GPP, (b) the influence of laterally transported dissolved inorganic C on R eco , (c) heterogeneous sulfate availability and methylotrophic methanogenesis impacts on surface CH 4 emissions, and (d) CH 4 responses to non‐periodic changes in salinity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Integrated Effects of Site Hydrology and Vegetation on Exchange Fluxes and Nutrient Cycling at a Coastal Terrestrial‐Aquatic Interface

Abstract The complex interactions among soil, vegetation, and site hydrologic conditions driven by precipitation and tidal cycles control the biogeochemical transformations and bi‐directional exchange of carbon and nutrients across the terrestrial–aquatic interfaces (TAIs) in coastal regions. This study uses a highly mechanistic model, Advanced Terrestrial Simulator (ATS)‐PFLOTRAN, to explore how these interactions affect exchanges of materials and carbon and nitrogen cycling. We used a transect in the Chesapeake Bay region that spans zones of open water, coastal wetland, transition, and upland forest. We designed several simulation scenarios to parse the effects of the individual controlling factors and the sensitivity of carbon cycling to reaction rate parameters derived from laboratory experiments. Our simulations reveal an active zone for carbon cycling under the transition zones between the wetland and the upland. Evapotranspiration is found to enhance the exchange fluxes between the surface and subsurface domains, resulting in a higher dissolved oxygen concentration in the TAIs. The transport of organic carbon derived from plant leaves and roots provide an additional source of organic carbon needed for the aerobic respiration and denitrification processes in the TAIs. The variability in reaction rate parameters associated with microbial activities is also found to play a dominant role in controlling the heterogeneity and dynamics of the simulated redox conditions. This modeling‐focused exploratory study enabled us to better understand the complex interactions among soil, water and microbes that govern the hydro‐biogeochemical processes at the TAIs, which is an important step toward representing coastal ecosystems in larger‐scale Earth system models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Numerical Investigation of Observational Flux Partitioning Methods for Water Vapor and Carbon Dioxide

Abstract While yearly budgets of CO 2 flux (F c ) and evapotranspiration (ET) above vegetation can be readily obtained from eddy‐covariance measurements, the separate quantification of their soil (respiration and evaporation) and canopy (photosynthesis and transpiration) components remains an elusive yet critical research objective. In this work, we investigate four methods to partition observed total fluxes into soil and plant sources: two new and two existing approaches that are based solely on analysis of conventional high frequency eddy‐covariance (EC) data. The physical validity of the assumptions of all four methods, as well as their performance under different scenarios, are tested with the aid of large‐eddy simulations, which are used to replicate eddy‐covariance field experiments. Our results indicate that canopies with large, exposed soil patches increase the mixing and correlation of scalars; this negatively impacts the performance of the partitioning methods, all of which require some degree of uncorrelatedness between CO 2 and water vapor. In addition, best performances for all partitioning methods were found when all four flux components are non‐negligible, and measurements are collected close to the canopy top. Methods relying on the water‐use efficiency (W) perform better whenWis known a priori, but are shown to be very sensitive to uncertainties in this input variable especially when canopy fluxes dominate. We conclude by showing how the correlation coefficient between CO 2 and water vapor can be used to infer the reliability of differentWparameterizations.

Environmental Sciences & Ecology↗
DOE OSTI2024

Comparison of Global Aboveground Biomass Estimates From Satellite Observations and Dynamic Global Vegetation Models

The global forest carbon stocks represent the amount of carbon stored in woody vegetation and are important for quantifying the ability of the global forests to sequester atmospheric CO 2 and to provide ecosystem services (e.g., timber) under climate change. The forest ecosystem carbon pool estimates are highly variable and poorly quantified in areas lacking forest inventory estimates. Here, we compare and analyze aboveground biomass (AGB) estimates from five satellite-based global data sets and nine dynamic global vegetation models (DVGMs). We find that across the data sets, mean AGB exhibits the largest variability around the tropical area. In addition, AGB shows a similar latitudinal trend but large variability among the data sets. Satellite-based AGB estimates are lower than those simulated by DVGMs. The divergence among the satellite-based AGB estimates can be driven by the methodology, input satellite products, and the forested areas used to estimate AGB. The modeled NPP, autotrophic respiration, and carbon allocation mostly drive the variability of AGB simulated by DGVMs. The future availability of a high-quality global forest area map is anticipated to improve AGB estimate accuracy and to reduce the discrepancies among different satellite- and model-based AGB estimates. Furthermore, we suggest the carbon-modeling community reexamine the methodology used to estimate AGB and forested areas for a more robust global forest carbon stock estimation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

BioRT‐HBV 1.0: A Biogeochemical Reactive Transport Model at the Watershed Scale

Abstract Reactive Transport Models (RTMs) are essential tools for understanding and predicting intertwined ecohydrological and biogeochemical processes on land and in rivers. While traditional RTMs have focused primarily on subsurface processes, recent watershed‐scale RTMs have integrated ecohydrological and biogeochemical interactions between surface and subsurface. These emergent, watershed‐scale RTMs are often spatially explicit and require extensive data, computational power, and computational expertise. There is however a pressing need to create parsimonious models that require minimal data and are accessible to scientists with limited computational background. To that end, we have developed BioRT‐HBV 1.0, a watershed‐scale, hydro‐biogeochemical RTM that builds upon the widely used, bucket‐type HBV model known for its simplicity and minimal data requirements. BioRT‐HBV uses the conceptual structure and hydrology output of HBV to simulate processes including advective solute transport and biogeochemical reactions that depend on reaction thermodynamics and kinetics. These reactions include, for example, chemical weathering, soil respiration, and nutrient transformation. The model uses time series of weather (air temperature, precipitation, and potential evapotranspiration) and initial biogeochemical conditions of subsurface water, soils, and rocks as input, and output times series of reaction rates and solute concentrations in subsurface waters and rivers. This paper presents the model structure and governing equations and demonstrates its utility with examples simulating carbon and nitrogen processes in a headwater catchment. As shown in the examples, BioRT‐HBV can be used to illuminate the dynamics of biogeochemical reactions in the invisible, arduous‐to‐measure subsurface, and their influence on the observed stream or river chemistry and solute export. With its parsimonious structure and easy‐to‐use graphical user interface, BioRT‐HBV can be a useful research tool for users without in‐depth computational training. It can additionally serve as an educational tool that promotes pollination of ideas across disciplines and foster a diverse, equal, and inclusive user community.

Sadayappan, Kayalvizhi↗
DOE OSTI2025

Representing Soil Microbial Dynamics and Organo‐Mineral Interactions in the E3SM Land Model (ELM‐ReSOM)

Explicit representation of soil microbial processes and interactions with biotic and abiotic processes in Earth System Models (ESMs) remains limited, despite their importance in biogeochemical cycles. To address this gap, which hinders prediction of global biogeochemial cycling and responses to atmospheric conditions, we integrated a microbe- and mineral-surface-explicit model, the Reaction-network-based model of soil organic matter and Microbes (ReSOM), into the Energy Exascale ESM (E3SM) land model (ELM). Here, we describe ELM-ReSOM and show a case study at a conifer forest in California. ELM-ReSOM accurately simulated surface CO 2 fluxes and SOM stocks, demonstrating improved representations of microbial and mineral interactions compared to the default ELM. We examined ELM-ReSOM sensitivity to microbial traits, enzyme properties, and organo-mineral interactions. Microbial traits such as the maximum mortality rate, transporter-density scaling factor, and maximum monomer assimilation rate were strong controllers of heterotrophic respiration, while these microbial traits and enzyme-related properties collectively influenced SOM stocks. Mineral surfaces primarily affected SOM stocks by adsorbing enzymes, thereby limiting depolymerization. Synergies among processes led to stronger impacts of parameters when evaluated together versus separately (i.e., most parameters had greater indirect than direct effects). For example, due to interactions of microbial necromass with mineral surface adsorption, the indirect effect of the maximum microbial mortality rate was 33% larger than its direct effect on SOM stock. Thus, microbial and enzyme dynamics and their interactions with mineral surfaces play critical roles in SOM cycling. Tackling the challenges of microbe-explicit models will advance understanding and modeling of SOM dynamics.

Tao, Jing [Lawrence Berkeley National Laboratory (↗
DOE OSTI2025

Reduce Revenue Versus Increase Expenditure: Fires and Plant Invasion Drive Soil Carbon Loss With Different Mechanisms in a Mediterranean Shrubland

Fires and plant invasions threaten Mediterranean ecosystems substantially, particularly in the context of changing climate. Our study utilized a data-model integration approach to assess the response of soil organic carbon (SOC) to fires and plant invasion under three Shared Socio-Economic Pathway (SSP) scenarios (SSP1-26, SSP2-45, and SSP5-85). We parameterized the CLM-Microbe model and then investigated the individual and interactive impacts of fires and plant invasion on soil C by comparing factorial simulations of initialization (fire/no wildfire in 2021), fire module on/off, and with and without plant invasion during 2023–2100 in a Mediterranean ecosystem. The simulations indicated a marked C loss due to the 2021 wildfire, projected fires, and plant invasion across all future climate scenarios. Specifically, the 2021 wildfire, projected fires, and plant invasion reduced the SOC (0–30 cm) by 0.12, 0.26, and 0.15 kg C m −2 under SSP1-26, 0.12, 0.30, and 0.12 kg C m −2 under SSP2-45, and 0.12, 0.24, and 0.13 kg C m −2 under SSP5-85, respectively. However, fires and plant invasion decreased SOC through distinct mechanisms. The effects of the 2021 wildfire occurred due to its negative legacy on soil microbial community and, thus, litter accumulation, suppressing the formation of soil carbon via decomposition. Influences of projected fires happen via consuming fuel and suppressing carbon input to soils. In contrast, the impacts of plant invasions were due to enhanced microbial respiration, leading to C loss. In conclusion, these findings emphasize the need for tailored C sequestration strategies considering the disparate effects of fires and plant invasions in the Mediterranean climate.

microbe↗
DOE OSTI2026

Model‐Based Interpretation of Solute Exports and Carbon Partitioning During Shale Weathering in a Mountainous Hillslope

The weathering of sedimentary rocks in high-elevation catchments influences freshwater quality and the global carbon cycle. While individual biogeochemical mechanisms involved in this process are relatively well understood, quantifying their contributions to solute export and carbon fluxes under natural, transient conditions remains challenging. Here, we implement a numerical multidimensional and multiphase model to simulate coupled hydrological and biogeochemical processes in a shale-underlain, snow-dominated hillslope in the Rocky Mountains, Colorado. The model captures the dynamic interplay between soil respiration, mineral weathering, and climate-driven hydrological forcing, reproducing observed soil CO 2 dynamics, groundwater chemistry, and subsurface flow. Our results reveal that seasonal snowmelt enhances carbonate weathering by promoting the infiltration of CO 2 -rich water to depth, while pyrite oxidation is primarily sensitive to low water saturation that facilitates O 2 diffusion through the regolith. Topography modulates the spatial distribution of shale weathering, as steeper slopes enhance lateral drainage, favoring the delivery of reactants to greater depths. While shale weathering at our site acts as a transient carbon sink, with silicates and carbonates buffering acidity and promoting atmospheric CO 2 consumption (1% of soil-derived CO 2 ), the exported dissolved inorganic carbon is predominantly geogenic (∼73%). Consequently, when accounting for long-term marine carbonate precipitation. The current weathering regime represents a net source of carbon to the atmosphere. The oxidation of pyrite and petrogenic organic carbon together release approximately 0.9 mol·m −2 ·yr −1 of CO 2 . Our findings highlight the role of topography, hydroclimate, and the coupling between acid-base reactions in shaping the carbon balance and the solute exports in mountainous critical zones.

carbon cycling↗
DOE OSTI2020

Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris

Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO 3 for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. In this work, we observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Additionally, mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles

Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO 2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO 2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO 2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions

Abstract Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization of interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early mutations improve cooperativity by manifesting in synergistic epistasis between genomes of the mutually interacting species. Specifically, we have characterized evolutionary trajectories of syntrophic interactions of Desulfovibrio vulgaris (Dv) with Methanococcus maripaludis (Mm) by longitudinally monitoring mutations accumulated over 1000 generations of nine independently evolved communities with analysis of the genotypic structure of one community down to the single-cell level. We discovered extensive parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance within many evolution lines of a rare lineage of Dv that retained sulfate-respiration (SR+) capability, which is not required for metabolic cross-feeding. An in-depth investigation revealed that synergistic epistasis across pairings of Dv and Mm genotypes had enhanced cooperativity within SR− and SR+ assemblages, enabling their coexistence within the same community. Thus, our findings demonstrate that cooperativity of a mutualism can improve through synergistic epistasis between genomes of the interacting species, enabling the coexistence of mutualistic assemblages of generalists and their specialized variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics

Abstract The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.

59 BASIC BIOLOGICAL SCIENCES↗