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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Microbial macroecology: In search of mechanisms governing microbial biogeographic patterns

Abstract Introduction Rapidly advancing technologies and accumulating information about microbial communities across the globe allow the quantification of microbial properties and functions at a macro‐scale. These emerging microbial biogeographic patterns call for a practical macroecological approach to investigate their underlying mechanisms. Aims The primary aims of this paper are to review the advancements of microbial macroecology in seeking mechanisms governing microbial biogeographic patterns, and to further lay out a roadmap for microbial macroecology in 10 years. Methods We reviewed the progress of microbial macroecology and demonstrated the application of the microbial macroecological approach to microbial biogeographic patterns with three case studies. Results Microbial macroecology provides a platform for understanding microbial abundance, community structure, and functioning across space, time, and taxonomic hierarchy. It emphasizes the integral effects of environmental filtering, microbial responses, diversification, dispersal, and local extinction that drive the microbial biogeographic patterns. The microbial macroecological approach emphasizes the last two stages of the four‐stage scientific method applied to microbial ecology: (a) describing microbial traits across scales to reveal patterns, (b) mathematically representing these patterns, (c) developing and testing conceptual models to build a mechanistic understanding of these patterns from a macroecological perspective, (d) plugging the new knowledge into the theoretical advancements. Three case studies were used to demonstrate the microbial macroecological approach for understanding the global patterns of microbial biomass carbon, microbial composition (fungi : bacteria ratio), and microbial carbon use efficiency. Conclusions Microbial macroecology offers a platform for understanding the mechanisms that drive biogeographic patterns of microbial abundance, diversity and functions. It is likely that these patterns and mechanisms will be increasingly incorporated into predictive models that link climate, carbon dynamics, and biogeochemical processes. A roadmap is outlined for the growing microbial macroecology field; we expect significant progress will be made in five research directions over the next 10 years.

Xu, Xiaofeng↗
DOE OSTI2024

Simulated nitrogen deposition and precipitation events alter microbial carbon cycling during early stages of litter decomposition

Plant litter decomposition is a major nutrient input to terrestrial ecosystems that is primarily driven by microorganisms. Litter quality is considered a key drive of decomposition; however, human-induced global disturbance like nitrogen deposition and increasing extreme precipitation events will shift nutrient availability during litter decomposition. Little is known about how shifting nutrient availability will impact dissolved organic matter concentrations and microbially driven carbon cycling that are critical to soil organic matter formation. This study investigated the effect of simulated nitrogen deposition and repeated precipitation events on microbially driven carbon flow during short-term litter decomposition using a ‘common garden’ experiment with microcosms containing sand and blue grama grass litter inoculated with different microbial communities. Overall, nitrogen deposition decoupled respiration and dissolved organic carbon (DOC) by increasing respiration and not affecting DOC concentrations. Moreover, nitrogen deposition had no effect on microbial carbon use efficiency (CUE). Repeated simulated precipitation events significantly increased DOC concentrations, decreased microbial CUE, increased the microbial metabolic quotient (qCO2), and altered microbial composition and diversity. These findings highlight the complex interactions and responses of surface litter decomposers to shifting nutrient availability and contradicts previous findings that nitrogen deposition will increase soil carbon sequestration from a larger supply of DOC and reduced respiration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Stem respiration and growth in a central Amazon rainforest

Tropical forests cycle a large amount of CO 2 between the land and atmosphere, with a substantial portion of the return flux due tree respiratory processes. However, in situ estimates of woody tissue respiratory fluxes and carbon use efficiencies (CUEW) and their dependencies on physiological processes including stem wood production (Pw) and transpiration in tropical forests remain scarce. In this work, we synthesize monthly Pw and daytime stem CO 2 efflux (ES) measurements over one year from 80 trees with variable biomass accumulation rates in the central Amazon. On average, carbon flux to woody tissues, expressed in the same stem area normalized units as ES, averaged 0.90 ± 1.2 µmol m -2 s -1 for Pw, and 0.55 ± 0.33 µmol m -2 s -1 for daytime ES. A positive linear correlation was found between stem growth rates and stem CO 2 efflux, with respiratory carbon loss equivalent to 15 ± 3% of stem carbon accrual. CUEW of stems was non-linearly correlated with growth and was as high as 77-87% for a fast-growing tree. Diurnal measurements of stem CO 2 efflux for three individuals showed a daytime reduction of ES by 15-50% during periods of high sap flow and transpiration. The results demonstrate that high daytime ES fluxes are associated with high CUE W during fast tree growth, reaching higher values than previously observed in the Amazon Basin (e.g. maximum CUEW up to 77-87%, versus 30-56%). The observations are consistent with the emerging view that diurnal dynamics of stem water status influences growth processes and associated respiratory metabolism.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Techno-economic and life-cycle assessment of fuel production from mixotrophic Galdieria sulphuraria microalgae on hydrolysate

Outdoor photoautotrophic algal growth is limited by light attenuation and attendant respiratory CO 2 losses during dark periods, limiting its productivity potential and carbon use efficiency. Developing a system that leverages mixotrophic growth (combining the benefits of both heterotrophic and photoautotrophic growth) has the potential to dramatically improve the total productivity and economics of the system. However, it is unknown if the productivity gains offset the added costs of outdoor mixotrophic cultivation using cellulosic hydrolysate as the feedstock. In this study, corn stover-derived cellulosic sugars were evaluated as the mixotrophic organic carbon source for the cultivation of Galdieria sulphuraria, which can metabolize both glucose and xylose from corn stover hydrolysate. A techno-economic analysis (TEA) and a life-cycle assessment (LCA) were conducted based on a detailed engineering process model for both glass helical photobioreactor and covered pond cultivation platforms, coupled with downstream conversion and upgrading to renewable diesel through hydrothermal liquefaction. Results show the minimum biomass selling price for cultivation in the photobioreactor design assuming a productivity of 1.575 kg m -3 day -1 and a substrate yield of 0.57 g g -1 is $2869 per dry metric ton. The costs are dramatically reduced in the covered pond design which assumes a productivity of 0.8 kg m -3 day -1 and a substrate yield of 0.7 g g -1 , 921 dollars per dry metric ton. Expanding the system boundary to include downstream processing results in a minimum fuel selling price of 8.24 dollars and 3.32 dollars dm 3 GE -1 for the photobioreactor and covered pond systems, respectively. Finally, life-cycle results demonstrate a global warming potential of 339 and 9.1 gCO 2 -eq. MJ -1 on a well-to-wheels basis and a net energy ratio of 2.21 and 0.25 MJ MJ -1 for the photobioreactor and covered pond systems, respectively. Discussion focuses on a required co-product selling price as a function of biomass diversion to meet economic parity with conventional fuels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The three major axes of terrestrial ecosystem function

The leaf economics spectrum and the global spectrum of plant forms and functions revealed fundamental axes of variation in plant traits, which represent different ecological strategies that are shaped by the evolutionary development of plant species. Ecosystem functions depend on environmental conditions and the traits of species that comprise the ecological communities. However, the axes of variation of ecosystem functions are largely unknown, which limits our understanding of how ecosystems respond as a whole to anthropogenic drivers, climate and environmental variability. Here we derive a set of ecosystem functions from a dataset of surface gas exchange measurements across major terrestrial biomes. We find that most of the variability within ecosystem functions (71.8%) is captured by three key axes. The first axis reflects maximum ecosystem productivity and is mostly explained by vegetation structure. The second axis reflects ecosystem water-use strategies and is jointly explained by variation in vegetation height and climate. The third axis, which represents ecosystem carbon-use efficiency, features a gradient related to aridity, and is explained primarily by variation in vegetation structure. We show that two state-of-the-art land surface models reproduce the first and most important axis of ecosystem functions. However, the models tend to simulate more strongly correlated functions than those observed, which limits their ability to accurately predict the full range of responses to environmental changes in carbon, water and energy cycling in terrestrial ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile

Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile—but to a greater extent in the subsoil—physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Calcium promotes persistent soil organic matter by altering microbial transformation of plant litter

Abstract Calcium (Ca) can contribute to soil organic carbon (SOC) persistence by mediating physico-chemical interactions between organic compounds and minerals. Yet, Ca is also crucial for microbial adhesion, potentially affecting colonization of plant and mineral surfaces. The importance of Ca as a mediator of microbe-mineral-organic matter interactions and resulting SOC transformation has been largely overlooked. We incubated 44 Ca labeled soils with 13 C 15 N labeled leaf litter to study how Ca affects microbial transformation of litter and formation of mineral associated organic matter. Here we show that Ca additions promote hyphae-forming bacteria, which often specialize in colonizing surfaces, and increase incorporation of litter into microbial biomass and carbon use efficiency by approximately 45% each. Ca additions reduce cumulative CO 2 production by 4%, while promoting associations between minerals and microbial byproducts of plant litter. These findings expand the role of Ca in SOC persistence from solely a driver of physico-chemical reactions to a mediator of coupled abiotic-biotic cycling of SOC.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Leveraging High-resolution Molecular Composition of Soil Organic Matter to Enhance Carbon Cycling Modeling

Soils store more carbon than the atmosphere and vegetation combined, yet Earth system models still struggle to predict how this vast reservoir will respond to environmental change. A central limitation is that most soil biogeochemical models represent organic matter using bulk conceptual pools or chemically homogeneous fractions, preventing direct use of rapidly expanding molecular-scale datasets. Here we develop and test a new soil decomposition framework that explicitly integrates high-resolution information on organic matter composition. First, we construct a molecularly informed litter decomposition module in which plant inputs are partitioned into five functional compound classes—carbohydrates, proteins, lignin-like aromatics, lipids, and carbonyls—using a molecular mixing model calibrated to solid-state 13 C Nuclear Magnetic Resonance (NMR) spectra. Class-specific kinetics, lignin-dependent physical protection, and substrate-driven microbial carbon use efficiency allow the module to capture metabolic tradeoffs associated with enzyme production and nutrient limitation. We then embed this litter module within a microbially explicit whole-soil model that tracks the transformation of these compound classes through particulate organic matter, dissolved organic matter, mineral-associated organic matter, and microbial biomass. High-resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FTICR-MS) data are used to link internal pools to measurable soil organic matter fractions and to constrain key process parameters. Applications at soil-core and ecosystem scales demonstrate that the new model reproduces observed soil respiration dynamics while providing mechanistic attribution of CO 2 fluxes to specific chemical classes and pools. Compared to existing frameworks such as the Community Land Model soil biogeochemistry module and the Millennial model, our approach maintains competitive predictive skill while substantially improving interpretability and opportunities for data–model integration. This work illustrates a viable pathway for leveraging molecular-scale observations to reduce structural uncertainty in soil carbon–climate feedback projections.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Fast-decaying plant litter enhances soil carbon in temperate forests but not through microbial physiological traits

Abstract Conceptual and empirical advances in soil biogeochemistry have challenged long-held assumptions about the role of soil micro-organisms in soil organic carbon (SOC) dynamics; yet, rigorous tests of emerging concepts remain sparse. Recent hypotheses suggest that microbial necromass production links plant inputs to SOC accumulation, with high-quality (i.e., rapidly decomposing) plant litter promoting microbial carbon use efficiency, growth, and turnover leading to more mineral stabilization of necromass. We test this hypothesis experimentally and with observations across six eastern US forests, using stable isotopes to measure microbial traits and SOC dynamics. Here we show, in both studies, that microbial growth, efficiency, and turnover are negatively (not positively) related to mineral-associated SOC. In the experiment, stimulation of microbial growth by high-quality litter enhances SOC decomposition, offsetting the positive effect of litter quality on SOC stabilization. We suggest that microbial necromass production is not the primary driver of SOC persistence in temperate forests. Factors such as microbial necromass origin, alternative SOC formation pathways, priming effects, and soil abiotic properties can strongly decouple microbial growth, efficiency, and turnover from mineral-associated SOC.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Disturbance-accelerated succession increases the production of a temperate forest

Many secondary deciduous forests of eastern North America are approaching a transition in which maturing early successional tree species are declining, resulting in an uncertain future for these forests’ century-long carbon (C) sink. We initiated the Forest Accelerated Succession Experiment (FASET) at the University of Michigan Biological Station to examine the patterns and mechanisms underlying forest C cycling following the stem-girdling induced mortality of >6,700 early successional Populus spp. (aspen) and Betula papyrifera (paper birch). Since 2008, meteorological flux tower-based C cycling observations from the 33-ha treatment forest have been paired with those from a nearby unmanipulated forest. Following over a decade of observations, herein we revisit our core hypothesis: that net ecosystem production (NEP) would increase following the transition to mid-late successional species dominance due to increased canopy structural complexity. Supporting our hypothesis, NEP was stable, briefly declined, and then increased relative to the control in the decade following disturbance; however, increasing NEP was not associated with rising structural complexity but rather the rapid 1-year recovery of total LAI as mid-late successional Acer, Quercus, and Pinus assumed canopy dominance. The transition to mid-late successional species dominance improved carbon-use efficiency (CUE = NEP/gross primary production) as ecosystem respiration declined. Similar soil respiration rates in control and treatment forests, along with species differences in leaf physiology and the rising relative growth rates of mid-late successional species in the treatment forest, suggest changes in aboveground plant respiration and growth, respectively, were primarily responsible for increases in NEP. We conclude that deciduous forests transitioning from early to middle succession are capable of sustained or increased NEP, even when experiencing extensive tree mortality. This adds to mounting evidence that aging deciduous forests in the region will function as C sinks for decades to come.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Thermodynamic control on the decomposition of organic matter across different electron acceptors

The increasing availability of high-resolution characterization of natural organic matter (OM) data has shifted the paradigm of lumped descriptions of OM components and potential microbial activities. Our recent development of a substrate-explicit thermodynamic model uniquely enables incorporating complex OM pools to formulate biogeochemical reaction models based on their elemental compositions. While this previous work facilitates prediction of aerobic respiration of complex OM, it is equally imperative to consider the role of non-oxygenic electron acceptors in regulating OM turnover and the fate of carbon. In this study, we significantly expand our previous model by flexibly incorporating both detailed OM chemistry and electron acceptors other than oxygen. Here, our modeling analysis has revealed substantial variations in the energy status of OM molecules across different soils, which drive the co-occurrence of different electron-accepting processes. We demonstrated the effectiveness of the proposed model using a consistency check with experimental data. Through systematic evaluation of the impact of diverse chemical inputs (both electron donors and acceptors) on OM decomposition, the new model also revealed how key microbial growth parameters such as carbon use efficiency (CUE) and reaction rates vary across different electron-accepting processes. Our model provides a unified framework integrating thermodynamic and kinetic constraints on microbial metabolic activities. It complements traditional kinetic models, which are often designed solely to capture mass fluxes. We conclude that thermodynamic modeling emerges as a powerful tool for describing the mechanisms underlying the interplay between microbial growth and OM chemistry and cycling across different electron acceptors, enhancing our ability to project complex ecosystem behaviors in dynamic environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Warming effects on grassland soil microbial communities are amplified in cool months

Abstract Global warming modulates soil respiration (RS) via microbial decomposition, which is seasonally dependent. Yet, the magnitude and direction of this modulation remain unclear, partly owing to the lack of knowledge on how microorganisms respond to seasonal changes. Here, we investigated the temporal dynamics of soil microbial communities over 12 consecutive months under experimental warming in a tallgrass prairie ecosystem. The interplay between warming and time altered (P < 0.05) the taxonomic and functional compositions of microbial communities. During the cool months (January to February and October to December), warming induced a soil microbiome with a higher genomic potential for carbon decomposition, community-level ribosomal RNA operon (rrn) copy numbers, and microbial metabolic quotients, suggesting that warming stimulated fast-growing microorganisms that enhanced carbon decomposition. Modeling analyses further showed that warming reduced the temperature sensitivity of microbial carbon use efficiency (CUE) by 28.7% when monthly average temperature was low, resulting in lower microbial CUE and higher heterotrophic respiration (Rh) potentials. Structural equation modeling showed that warming modulated both Rh and RS directly by altering soil temperature and indirectly by influencing microbial community traits, soil moisture, nitrate content, soil pH, and gross primary productivity. The modulation of Rh by warming was more pronounced in cooler months compared to warmer ones. Together, our findings reveal distinct warming-induced effects on microbial functional traits in cool months, challenging the norm of soil sampling only in the peak growing season, and advancing our mechanistic understanding of the seasonal pattern of RS and Rh sensitivity to warming.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

The metabolic origins of non-photorespiratory CO 2 release during photosynthesis: a metabolic flux analysis

Respiration in the light (R L ) releases CO 2 in photosynthesizing leaves and is a phenomenon that occurs independently from photorespiration. Since R L lowers net carbon fixation, understanding R L could help improve plant carbon-use efficiency and models of crop photosynthesis. Although R L was identified more than 75 years ago, its biochemical mechanisms remain unclear. To identify reactions contributing to R L , we mapped metabolic fluxes in photosynthesizing source leaves of the oilseed crop and model plant camelina (Camelina sativa). We performed a flux analysis using isotopic labeling patterns of central metabolites during 13 CO 2 labeling time course, gas exchange, and carbohydrate production rate experiments. To quantify the contributions of multiple potential CO 2 sources with statistical and biological confidence, we increased the number of metabolites measured and reduced biological and technical heterogeneity by using single mature source leaves and quickly quenching metabolism by directly injecting liquid N 2 ; we then compared the goodness-of-fit between these data and data from models with alternative metabolic network structures and constraints. Our analysis predicted that R L releases 5.2 μmol CO2 g –1 FW h –1 of CO 2 , which is relatively consistent with a value of 9.3 μmol CO 2 g –1 FW h –1 measured by CO 2 gas exchange. The results indicated that ≤10% of R L results from TCA cycle reactions, which are widely considered to dominate R L . Further analysis of the results indicated that oxidation of glucose-6-phosphate to pentose phosphate via 6-phosphogluconate (the G6P/OPP shunt) can account for >% of CO 2 released by R L .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Modeling Plant Nutrient Acquisition Strategies Alters Projections of Carbon and Nitrogen Dynamics in Bioenergy Agroecosystems

Plant strategies to acquire nutrients from limited environments help shape ecosystem carbon (C) and nitrogen (N) cycling and response to environmental change. The effects of plant strategies on ecosystem dynamics are largely uncharacterized in bioenergy agroecosystems, where the impacts could determine bioenergy's ability to meet its sustainability goals of storing C and reducing N loss. We used FUN-BioCROP (Fixation and Uptake of Nitrogen-Bioenergy Carbon, Rhizosphere, Organisms and Protection), a plant–microbe interaction model of coupled plant nutrient uptake and soil organic matter decomposition, to simulate the effects of nutrient acquisition strategies on soil microbial activity and ecosystem nutrient cycling in bioenergy feedstocks miscanthus (Miscanthus × giganteus) and sorghum (Sorghum bicolor (L.) Moench). We examined the model's ability to reproduce the relative effects of belowground nutrient uptake on microbial activity using a reanalysis of empirical data showing that miscanthus root exudation provoked a larger soil microbial response than sorghum. From baseline model simulations, we found that the ability of miscanthus to retranslocate N resulted in higher N uptake at a lower C cost than the sorghum/soybean rotation and that soil C and N pools increased under perennial (miscanthus) and decreased under annual (sorghum/soybean) cultivation. The model also predicted that greater root exudation increased soil C accumulation, highlighting the role of roots in forming stable soil C. Overall, the baseline model was unable to reproduce field observations of miscanthus root exudation stimulating microbial activity more than sorghum. To improve the model, we updated the soil microbial parameters in miscanthus to have faster decomposition, a higher C/N ratio, and greater carbon use efficiency. These changes improved the simulated soil microbial response to miscanthus root exudation, supporting the hypothesis that miscanthus soils foster a microbial community that is more responsive to root exudation than that of sorghum.

09 BIOMASS FUELS↗
DOE OSTI2026

Soil fertility controls on tropical forest productivity and mortality: synthesis and roadmap

Tropical forests are highly diverse and productive ecosystems and store nearly 60% of vegetation biomass. Across the tropics, forests span large gradients of soil fertility, from vast regions situated on highly weathered, ancient geological formations to others on young, nutrient-rich landscapes. Tropical forest productivity, mortality, and biomass all vary systematically across these gradients in soil fertility. Aboveground forest productivity tends to increase with higher soil fertility, while counterintuitively, aboveground biomass does not increase proportionally. This disconnect is likely due to coinciding increases in mortality with higher soil fertility. However, we know relatively little about the mechanisms underlying how soil fertility regulates productivity or mortality – two critical determinants of forest biomass – and even less about how these relationships will shape tropical forest responses to global change. Here, we present a mechanistic framework for understanding how soil fertility affects productivity through photosynthesis, carbon allocation, and carbon-use efficiency; how it modulates mortality via direct and indirect interactions with various drivers of mortality; and how global change may alter these relationships. Based on this synthesis, we outline a roadmap to advance our understanding of tropical forests and improve predictions of their responses to global change.

Wong, Michelle Y [Yale University] (ORCID:00000002↗
DOE OSTI2022

BrzostekEcologyLab/CORPSE-soil-jars

Efforts to manage soils for carbon (C) sequestration remain limited by our understanding of how differences in plant traits and microbial traits mechanistically drive soil organic C (SOC) storage. Addressing this uncertainty is particularly critical in bioenergy agriculture, due to its potential to enhance soil C and provide a C neutral fuel. As such, we examined differences between two contrasting feedstocks, Zea mays (corn) and Miscanthus x giganteus (miscanthus), in the ability of their litter to form new chemically resistant particulate SOC vs. physically protected mineral associated SOC and used this data to improve the parameterization of a microbial SOC model. We tested a hypothesized conceptual model whereby easy to decompose corn litters drive greater microbial carbon use efficiency (CUE) and the formation of more mineral associated SOC over particulate SOC than more complex miscanthus litters. To do this, we performed a soil microcosm experiment where we added 13C enriched aboveground and belowground litters to soils and traced the fate of the 13C into microbial respiration and SOC pools. We found that corn litters promoted higher microbial CUE (0.37) than miscanthus litters (0.24). In turn, corn litter formed approximately 50% more mineral associated SOC than miscanthus litters. Similarly, structurally complex root litters promoted a lower CUE and formed less mineral associated SOC than leaf and shoot litters for both crops. When we used our data to parameterize the SOC model, we found that modeling microbial trait differences uniquely allowed the model to capture the fate of litter C in SOC. Collectively, we found a robust link between litter quality, microbial efficiency, and the formation of SOC. This link bridges the empirical uncertainty in how different crops can form new soil C and provides an empirical basis for modeling SOC transformations.

Ridgeway, Joanna↗
DOE OSTI2026

Data for Zheng et al. (2025), "AquaMEND: Reconciling multiple impacts of salinization on soil carbon biogeochemistry"

Soil salinization, exacerbated by climate change, poses a global threat to coastal ecosystems and soil function. Salinity affects soil carbon cycling by directly impacting microbial activity and indirectly altering soil physicochemical properties, but current models inadequately represent these complexities. This dataset contains the observational and modeling data from Zheng et al. (2025), which described a process-based modeling framework that couples soil solution chemistry with microbial carbon cycling reactions to study the impacts of soil salinization. This conceptual model is implemented numerically into the open-source geochemical program PHREEQC 3.0 (Parkhurst and Appelo, 2013). This dataset consists of: - Figure2_AquaMEND_salinity_buffer: Contains model simulation outputs to assess the impact of three different cation exchange and surface complexation processes on salinity buffering (Fig. 2 from Zheng et al. 2025). - Figure3_Salinity_function: Contains salinity function fitting for literature data (Fig. 3 from Zheng et al. 2025). - Figure4_AquaMEND_microbial_mechanisms: Contains model simulation outputs for testing various microbial process-based hypotheses related to soil salinization, including microbial mortality, carbon use efficiency (CUE), extracellular enzyme activity, and other microbial mechanisms (Fig. 4 from Zheng et al. 2025). - Figure5_AquaMEND_Redox: Contains on model simulation outputs to evaluate shifts among key redox processes, such as aerobic respiration, sulfate reduction, and methanogenesis (Fig.5 from Zheng et al. 2025). - Figure6_AquaMEND_sorption: Contains on model simulation outputs for investigating the effects of salinity on dissolved organic matter (DOM) sorption and desorption processes (Fig. 6 from Zheng et al. 2025). - Figure7_AquaMEND_process_couple: Contains on model simulation outputs for exploring coupled biotic-abiotic processes and their interactions (Fig. 7 from Zheng et al. 2025). - data: Includes datasets used to develop salinity response functions and evaluate salinity buffering capacity. Datasets for MEND model calibration. - database: Contains the `.dat` file required by PHREEQC for model execution. - README.md: A Markdown plain text file describing the computational tools and directories. Files are a mixture of plain text CSV (comma-separated value) and plain text *.dat files written by the model; no special software is required to read them.

EARTH SCIENCE > AGRICULTURE > SOILS > SOIL SALINIT↗
DOE OSTI2021

Diurnal observations of basal stem CO2 efflux in three canopy dominant trees in the central Amazon

We explored mechanisms responsible for disturbance-induced shifts in carbon metabolism in forests north of Manaus, Brazil (S2º 38' 17", W60º 09' 25"), using data from a selective logging experiment (BIONTE). BIONTE (the BIOmass and NuTrient Experiment) selective logging treatments were initiated in the mid-1980s and comprised variable removal of commercial tree (not total) species basal area (T1 =32%, T2 = 42%, T3 = 69%), and control plots with no logging (T0). Raw data including tree base diameter (Db), CO2 concentration versus time inside a static stem chamber, and wood density were used to derive stem respiration rates (Rw), wood production rates (Pw), and wood carbon use efficiency (CUE). Changes in tree base diameter (Db; measured at 1.3 m height, or above the buttresses) was used to calculate wood production for individual trees (Pw). Wood density enabled calculation of stem growth rate in the same units as stem respiration (mmol C m-2 s-1). Four trees were randomly selected from five tree growth rate classes for each treatment block, for a total of 20 trees per treatment block, or 80 trees total from the BIONTE plots. Each of the 80 trees selected for the Rw study were outfitted with dendrometer bands (da Silva et al. 2002). Stem respiration was measured using the method described in Chambers et al. (2004). Briefly, an infra-red gas analyzer (LiCor 820) was operated as a closed dynamic chamber with a flow rate of 1.0 L min-1. Polyvinyl chloride (PVC) semi-cylindrical chambers (250–400 mL) were secured to the tree stem near the dendrometer bands using nylon straps. The measurement interval spanned 1–2 min, and the CO2 flux from the stem of each tree was quantified using the enclosed stem area and slope of the stem CO2 concentration versus time.

54 ENVIRONMENTAL SCIENCES↗