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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Community stability is related to animal diversity change

Abstract Understanding the drivers of community stability in times of increasing anthropogenic pressure is an urgent issue. Biodiversity is known to promote community stability, but studies of the biodiversity–stability relationship rarely consider the full complexity of biodiversity change. Furthermore, finding generalities that hold across taxonomic groups and spatial and temporal scales remains challenging because most investigations have narrow taxonomic, spatial, and temporal scopes. We used organismal data collected through the National Ecological Observatory Network (NEON) at sites across the contiguous United States to evaluate linkages between community stability and biodiversity change for four taxonomic groups: small mammals, ground beetles, fish, and freshwater macroinvertebrates. We defined community stability as constancy of aggregate species' abundance. We quantified change in biodiversity as (1) dissimilarity in community taxonomic and functional composition and species replacement and richness change components of that dissimilarity and (2) change in species' abundance distributions as captured by change in species rank, richness, and evenness. We found that community stability increased with species replacement and with contribution of species replacement to overall dissimilarity for all taxonomic groups, but declined with increasing change in species richness and evenness. This is consistent with the notion that temporal fluctuations in species abundance can help stabilize community properties. We also found that community stability was highest when change in community functional composition was either lower or higher than expected given reshuffling of each community's taxonomic composition. This suggests that long‐term community stability can result from fluctuations of functionally similar species in assemblages with high taxonomic reshuffling. On the contrary, the functional uniqueness of fluctuating species compensates for lower taxonomic reshuffling to drive stabilization of community properties. Our study provides an initial assessment of the relationship between community stability and biodiversity change and illustrates the utility of fine temporal resolution data collected across ecosystems and biomes to understand the general mechanisms underlying biodiversity–stability relationships.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Embolism resistance explains mortality and recovery of five subtropical evergreen broadleaf trees to persistent drought

Subtropical evergreen broadleaf forest (SEBF) is experiencing and expected to suffer more frequent and severe drought events. However, how the hydraulic traits directly link to the mortality and recovery of SEBF trees remains unclear. In this study, we conducted a drought-rewatering experiment on tree seedlings of five dominant species to investigate how the hydraulic traits were related to tree mortality and the resistance and recovery of photosynthesis (A) and transpiration (E) under different drought severities. Species with greater embolism resistance (P 50 ) survived longer than those with the weaker P 50 . However, there was no general hydraulic threshold associated with tree mortality, with the lethal hydraulic failure varying from 64% to 93% loss of conductance. Further, the photosynthesis and transpiration of tree species with greater P 50 were more resistant to and recovered faster from drought than those with lower P 50 . Other plant traits could not explain the interspecific variation in tree mortality and drought resistance and recovery. These results highlight the unique importance of embolism resistance in driving carbon and water process under persistent drought across different trees in SEBF. The absence of multiple efficient drought strategies in SEBF seedlings implies the difficulty of natural seedling regeneration under future droughts, which often occurs after destructive disturbances (e.g., extreme drought events and typhoon), suggesting that this biome may be highly vulnerable to co-occurring climate extremes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Differences in soil organic matter between EcM- and AM-dominated forests depend on tree and fungal identity

As global change shifts the species composition of forests, we need to understand which species characteristics affect soil organic matter (SOM) cycling to predict future soil carbon (C) storage. Recently, whether a tree species forms a symbiosis with arbuscular (AM) versus ectomycorrhizal (EcM) fungi has been suggested as a strong predictor of soil C storage, but there is wide variability within EcM systems. In this study, we investigated how mycorrhizal associations and the species composition of canopy trees and mycorrhizal fungi related to the proportion of soil C and nitrogen (N) in mineral associations and soil C:N across four sites representing distinct climates and tree communities in the eastern US broadleaf forest biome. In two of our sites, we found the expected relationship of declining mineral-associated C and N and increasing soil C:N ratios as the basal area of EcM-associating trees increased. However, across all sites these soil properties strongly correlated with canopy tree and fungal species composition. Sites where the expected pattern with EcM basal area was observed were (1) dominated by trees with lower quality litter in the Pinaceae and Fagaceae families and (2) dominated by EcM fungi with medium-distance exploration type hyphae, melanized tissues, and the potential to produce peroxidases. Here, this observational study demonstrates that differences in SOM between AM and EcM systems are dependent on the taxa of trees and EcM fungi involved. Important information is lost when the rich mycorrhizal symbiosis is reduced to two categories.

mineral-associated organic matter↗
DOE OSTI2025

TropiRoot 1.0: Database of tropical root characteristics across environments

Tropical ecosystems contain the world's largest biodiversity of vascular plants. Yet, our understanding of tropical functional diversity and its contribution to global diversity patterns is constrained by data availability. This discrepancy underscores an urgent need to bridge data gaps by incorporating comprehensive tropical root data into global datasets. Here, we provide a database of tropical root characteristics. This new database, TropiRoot 1.0, will be instrumental in evaluating an array of hypotheses pertaining to root functional ecology and plant biogeography, both within the tropics and relative to other global biomes. The data compilation was conducted by the TropiRoot Initiative, in partnership with the Fine-Root Ecology Database (FRED) and the Global Root Trait (GRooT) database, Colorado State University (CSU) and the Smithsonian Tropical Research Institute (STRI). Literature search and data extraction were conducted between 2020 and 2024. Literature was identified using Web of Science, Scopus, and complemented using the expert knowledge of members of TropiRoot. To provide broad environmental and geographical distributions, literature searches included root characteristics (traits) across global change drivers, natural gradients, and from different continents. We adopted FRED standardized data columns and streamlined the format to enhance accessibility for data extraction across various user groups. This optimized framework resulted in a smaller, yet comprehensive datasheet. To make the database compatible with other global root trait initiatives, column identification was standardized following the codes provided by FRED. These efforts culminated in data extracted from 104 new sources, resulting in more than 8000 rows of data (either species or community data). Most of the data in TropiRoot 1.0 include root characteristics such as root biomass, morphology, root dynamics, mass fraction, architecture, anatomy, physiology, and root chemistry. This initiative represents a 30% increase in the currently available data for tropical roots in FRED. TropiRoot 1.0 contains root characteristics from 25 different countries, where seven are located in Asia, six in South America, five in Central America and the Caribbean, four in Africa, two in North America, and 1 in Oceania. Due to the volume of data, when ancillary data were available, including soil data, these data were either extracted and included in the database or its availability was recorded in an additional column. Multiple contributors checked the entries for outliers during the collation process to ensure data quality. For text-based observations, we examined all cells to ensure that their content relates to their specific categories. For numerical observations, we ordered each numerical value from least to greatest and plotted the values, checking apparent outliers against the data in their respective sources and correcting or removing incorrect or impossible values. Some data (soil and aboveground) have different columns for the same variable presented in different units, including originally published units, but root characteristics data had units converted to match those reported in FRED. By filling a gap from global databases, TropiRoot 1.0 expands our knowledge of otherwise so far underrepresented regions and our ability to assess global trends. This advancement can be used to improve tropical forest representation in vegetation models. The data are freely available and should be cited when used.

FRED↗
DOE OSTI2023

Spatial and temporal variation in forest transpiration across a forested boreal peatland complex

Transpiration is a globally important component of evapotranspiration. Careful upscaling of transpiration from point measurements is thus crucial for quantifying water and energy fluxes. In spatially heterogeneous landscapes common across the boreal biome, upscaled transpiration estimates are difficult to determine due to variation in local environmental conditions (e.g., basal area, soil moisture, permafrost). Here, we sought to determine stand-level attributes that influence transpiration scalars for a forested boreal peatland complex consisting of sparsely treed wetlands and densely treed permafrost plateaus as land cover types. The objectives were to quantify spatial and temporal variability in stand-level transpiration, and to identify sources of uncertainty when scaling point measurements to the stand-level. Using heat ratio method sap flow sensors, we determined sap velocity for black spruce and tamarack for 2-week periods during peak growing season in 2013, 2017 and 2018. We found greater basal area, drier soils, and the presence of permafrost increased daily sap velocity in individual trees, suggesting that local environmental conditions are important in dictating sap velocity. When sap velocity was scaled to stand-level transpiration using gridded 20 × 20 m resolution data across the ~10 ha Scotty Creek ForestGEO plot, we observed significant differences in daily plot transpiration among years (0.17–0.30 mm), and across land cover types. Daily transpiration was lowest in grid-cells with sparsely treed wetlands compared to grid-cells with well-drained and densely treed permafrost plateaus, where daily transpiration reached 0.80 mm, or 30% of the daily evapotranspiration. When transpiration scalars (i.e., sap velocity) were not specific to the different land cover types (i.e., permafrost plateaus and wetlands), scaled stand-level transpiration was overestimated by 42%. To quantify the relative contribution of tree transpiration to ecosystem evapotranspiration, we recommend that sampling designs stratify across local environmental conditions to accurately represent variation associated with land cover types, especially with different hydrological functioning as encountered in rapidly thawing boreal peatland complexes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Anthromes and forest carbon responses to global change

Human effects on ecosystems date back thousands of years, and anthropogenic biomes—anthromes—broadly incorporate the effects of human population density and land use on ecosystems. Forests are integral to the global carbon cycle, containing large biomass carbon stocks, yet their responses to land use and climate change are uncertain but critical to informing climate change mitigation strategies, ecosystem management, and Earth system modeling. Using an anthromes perspective and the site locations from the Global Forest Carbon (ForC) Database, we compare intensively used, cultured, and wildland forest lands in tropical and extratropical regions. We summarize recent past (1900-present) patterns of land use intensification, and we use a feedback analysis of Earth system models from the Coupled Model Intercomparison Project Phase 6 to estimate the sensitivity of forest carbon stocks to CO 2 and temperature change for different anthromes among regions. Modeled global forest carbon stock responses are positive for CO 2 increase but neutral to negative for temperature increase. Across anthromes (intensively used, cultured, and wildland forest areas), modeled forest carbon stock responses of temperate and boreal forests are less variable than those of tropical forests. Tropical wildland forest areas appear especially sensitive to CO 2 and temperature change, with the negative temperature response highlighting the potential vulnerability of the globally significant carbon stock in tropical forests. The net effect of anthropogenic activities—including land-use intensification and environmental change and their interactions with natural forest dynamics—will shape future forest carbon stock changes. These interactive effects will likely be strongest in tropical wildlands.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Harmonizing direct and indirect anthropogenic land carbon fluxes indicates a substantial missing sink in the global carbon budget since the early 20th century

Inconsistencies in the calculation of the two anthropogenic land flux terms of the global carbon cycle are investigated. The two terms—the direct anthropogenic flux (caused by direct human disturbance in anthromes, currently a carbon source to the atmosphere) and the indirect anthropogenic flux (caused indirectly by human activities that lead to global change and affecting all biomes, currently an atmospheric carbon sink)—are typically calculated independently, resulting in inconsistent underlying assumptions. We harmonize the estimation of the two anthropogenic land flux terms by incorporating previous estimates of these inconsistencies. We recalculate the global carbon budget (GCB) and apply change-point analysis to the cumulative budget imbalance. Cumulative over 1850–2018 (1959–2018), harmonization results in a 13% lesser (4% greater) land use source from anthromes and a 20% (23%) lesser land sink. This recalculation yields a greater non-closure of the GCB, indicating a missing carbon sink averaging 0.65 Pg C year -1 since the early 20th century. The imbalance likely results from a combination of method discontinuity and structural errors in the assessment of the direct anthropogenic land use flux, greater ocean carbon uptake, structural errors in land models, and in how these land terms are quantified for the budget. We caution against overconfidence in considering the GCB a solved problem and recommend further study of methodological discontinuities in budget terms. We strongly recommend studies that quantify the direct and indirect anthropogenic land fluxes simultaneously to ensure consistency, with a deeper understanding of human disturbance and legacy effects in anthromes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A minor respiratory process with major global implications: is atmospheric methane oxidation in tree stems driven by stem respiration rather than microbial methanotrophy?

Tree stem surfaces are widely recognized as sites of carbon dioxide (CO₂) efflux and oxygen (O₂) influx, reflecting the dynamics of aerobic respiration of photosynthate substrates, such as sugars, delivered via the phloem. Stems are also largely considered passive conduits for methane (CH₄) produced in anoxic soils via microbial methanogenesis, where CH₄ is thought to be transported upward through the transpiration stream and/or diffusion and emitted through stem surfaces and the canopy. However, recent observations from dynamic stem chambers suggest that stems may also act as active sinks for atmospheric CH₄. Despite these findings, the extent and drivers of stem CH₄ consumption remain poorly characterized across biomes, species, and environmental gradients, and its quantitative relationship to stem respiration has not been established. Moreover, previous studies captured only snapshot fluxes, leaving diurnal patterns of CH₄ exchange uncharacterized. Here, we address these limitations by combining real-time measurements of stem CH₄ and O₂ uptake under ambient conditions in a California cherry tree, using a dynamic stem gas exchange system with three chambers receiving a continuous flow of ambient air and automated chamber and reference air sampling every 10 min. Our results confirm that stems of upland trees can actively consume both atmospheric CH₄ and O₂, but with decreasing temperature sensitivity as daily temperatures increase. Early mornings were marked by rapid influxes of both gases, followed by declining uptake as temperatures rose further. Methane uptake was tightly coupled with O₂ influx and represented a minor (0.012% ± 0.002%) fraction of stem respiratory activity, as determined by concurrent O₂ uptake. These findings suggest that while atmospheric CH₄ oxidation is a minor respiratory process in stems, it is strongly linked with stem physiological activity. This challenges the current assumption that terrestrial CH₄ uptake is driven solely by microbial methanotrophy and raises the possibility that living stem tissues may contribute to CH₄ oxidation through an as-yet-unidentified plant-based mechanism.

Atmospheric greenhouse gases↗
DOE OSTI2021

Carbon content of soil fractions varies with season, rainfall, and soil fertility across a lowland tropical moist forest gradient

Tropical forests contain some of the largest soil carbon (C) stocks on Earth, making them broadly relevant to terrestrial-climate feedbacks, yet our understanding of how their soil organic C (SOC) fractions vary over space and time is limited. We studied effects of season, fertility, and mean annual precipitation (MAP) on the C contents of soil fractions across 14 lowland forests in Panama. We measured free-debris, occluded-debris, and mineral-associated SOC fractions, as well as soluble C associated with each fraction. We hypothesized that mineral-associated SOC would be greatest in infertile, strongly weathered soils with large reactive mineral contents. We also hypothesized that the debris SOC fractions would accumulate during the dry season, reflecting seasonal increases in litterfall. To address this, we compared soil fractions in wet and dry seasons from fertile and infertile soils across a range of 1809 – 2864 mm MAP. The C content (mg C / g soil) of all soil fractions varied with fertility and MAP: specifically, free-debris SOC was greatest in wet, high-fertility soils, and occluded-debris SOC was greater in high-fertility than low-fertility soils. The mineral-associated SOC fraction, which contained the majority of bulk soil C, showed increasing C content with greater MAP in infertile sites, presumably driving similar spatial patterns in the bulk soil. Only the free-debris SOC fraction showed strong seasonal variation, increasing in mass during the dry season. Nitrogen behaved similarly to C. In summary, soil C contents increased with MAP in infertile sites but not fertile sites, driven by the mineral-associated SOC fraction. The dry season had greater free-debris SOC, but this seasonal trend was not apparent in bulk soil C, likely because of the small size of the free-debris SOC fraction. Furthermore, changes in the quantity and seasonality of precipitation, which are projected for tropical forests, might shift spatial and temporal patterns of soil C storage, which would in turn influence forest-climate feedbacks for this C-rich biome.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

The Freundlich isotherm equation best represents phosphate sorption across soil orders and land use types in tropical soils of Puerto Rico

Biomass production in the lowland wet tropical forest is greater than in any other biome, and it is typically limited by soil phosphorus (P) availability. However, the mechanisms involved in the P cycle remain poorly represented in Earth System Models (ESMs). Soil P sorption processes are key in the P cycle and for understanding the extent of P limitation for plant productivity. Currently, a few ESMs include isotherm equations to model these processes. Although the Langmuir equation is widely cited, other isotherm equations may better describe sorption in tropical soils. Here, we use a diverse range of soil samples from Puerto Rico to test the validity of the Langmuir, Freundlich, and Temkin equation. We found that across four soil orders (Inceptisols, Mollisols, Oxisols, Ultisols), and forested and cultivated land use types, the Freundlich equation best represented soil P sorption. Furthermore, the Langmuir and the Temkin equations poorly represent soil P adsorption, especially at low P concentrations. Specifically, the Langmuir equation underestimated soil P adsorption by 40% and the Temkin equation overestimated adsorption by 76%. We also found, as expected, that soil clay content and pH were the most important parameters explaining the variability of the Freundlich (K f ) constant. Greater clay content and lower pH, common in highly weathered Ultisols and Oxisols which are abundant in the tropics, led to greater K f values. Overall, our results suggest that a diversity of soils can prompt underestimation of P sorption when using the Langmuir isotherm, which leads to an overestimation of available P that can have repercussions on ESM predictions of the P cycle and tropical forest productivity.

Earth system models↗
DOE OSTI2021

Atmospheric humidity deficits tell us how soil moisture deficits down-regulate ecosystem evaporation

Knowing how actual evaporation is down-regulated from potential evaporation during periods with soil moisture deficits is one of the greatest challenges towards computing evaporation everywhere on a regular basis. We propose the hypothesis that vegetated landscapes transmit information on soil moisture deficits through its down-regulation of evaporation, which in turn affects the humidification and growth of the planetary boundary layer. To test this hypothesis, here, we examined how the evaporative fraction, defined as the ratio between actual and potential evaporation, corresponds with the soil moisture stress index, defined as the relative humidity with a power law dependence on vapor pressure deficit times a parameter, β. We tested the parameterized soil moisture stress index with direct eddy covariance measurements of actual evaporation and computations of potential evaporation based on meteorological conditions, averaged on monthly time steps. The analysis was conducted on a dataset obtained from 144 FLUXNET sites. These sites spanned much of the world's climates and biomes and contained over 5900 months of observations. Observations of the evaporative fraction fit the model of the soil moisture stress index best for semi-arid and arid ecosystems, and least for the humid and wet ecosystems. Consequently, a significant relationship between measurements of the evaporative fraction and soil moisture stress index held for about one-half of the population of sites. Under this condition, the median value of the parameter, β, was 1.41. To investigate the mechanism of this empirical soil moisture stress index, we diagnosed it with a coupled evaporation-planetary boundary layer model. The soil moisture stress index is strongly related to surface resistance, as defined by inverting Penman-Monteith equation. Consequently, this index provides an independent estimate of surface resistance based on easy to measure mean monthly weather conditions like relative humidity and temperature. Thereby, this soil moisture stress index has potential to be applied to weather, climate and biogeochemical models and the interpretation of satellite derived evaporation products, like the one provided by the ECOSTRESS mission.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Environment-sensitivity functions for gross primary productivity in light use efficiency models

The sensitivity of photosynthesis to environmental changes is essential for understanding carbon cycle responses to global climate change and for the development of modeling approaches that explains its spatial and temporal variability. We collected a large variety of published sensitivity functions of gross primary productivity (GPP) to different forcing variables to assess the response of GPP to environmental factors. These include the responses of GPP to temperature; vapor pressure deficit, some of which include the response to atmospheric CO 2 concentrations; soil water availability (W); light intensity; and cloudiness. These functions were combined in a full factorial light use efficiency (LUE) model structure, leading to a collection of 5600 distinct LUE models. Each model was optimized against daily GPP and evapotranspiration fluxes from 196 FLUXNET sites and ranked across sites based on a bootstrap approach. The GPP sensitivity to each environmental factor, including CO 2 fertilization, was shown to be significant, and that none of the previously published model structures performed as well as the best model selected. From daily and weekly to monthly scales, the best model's median Nash-Sutcliffe model efficiency across sites was 0.73, 0.79 and 0.82, respectively, but poorer at annual scales (0.23), emphasizing the common limitation of current models in describing the interannual variability of GPP. Although the best global model did not match the local best model at each site, the selection was robust across ecosystem types. The contribution of light saturation and cloudiness to GPP was observed across all biomes (from 23% to 43%). Temperature and W dominates GPP and LUE but responses of GPP to temperature and W are lagged in cold and arid ecosystems, respectively. The findings of this study provide a foundation towards more robust LUE-based estimates of global GPP and may provide a benchmark for other empirical GPP products.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Quantifying the drivers of ecosystem fluxes and water potential across the soil-plant-atmosphere continuum in an arid woodland

Dryland ecosystems occupy a vast swath of the terrestrial land surface and exert a sizeable impact on the cycling of carbon and water globally. These biomes are characterized by tightly coupled carbon and water cycles that respond rapidly to transient pulses in water availability. However, there exist many mechanistic uncertainties regarding the environmental drivers of, and linkages between, plant and ecosystem processes. Thus, drylands are often poorly represented in many vegetation and land surface models. An enhanced understanding of dryland ecosystem function is limited by the lack of long-term, co-located, and frequent measurements of plant and ecosystem processes. At a piñon-juniper woodland in southeastern Utah, USA, we collected a continuous dataset of meteorological conditions, soil water potential from surface to bedrock, tree water potential, and ecosystem carbon and water fluxes from eddy covariance. We found that predawn and midday tree water potential and daily ecosystem fluxes were highly sensitive to fluctuations in soil water availability, particularly in shallower layers, and that daytime variability in atmospheric drivers only loosely controlled these processes. The strong connections between shallow soil water potential, tree water potential, and ecosystem fluxes occurred because of the dominant role of precipitation pulses in driving vegetation activity, as even small pulses of moisture stimulated shallow soil water potential, tree water potential, and evapotranspiration for between 1 and 2 weeks. Carbon fluxes (net ecosystem exchange and gross primary productivity) were sensitive to precipitation pulses for longer, up to 3 weeks. Our results highlight that improved monitoring and sensing of shallow soil moisture can greatly enhance our understanding of dryland ecosystem function. Here, a better mechanistic understanding of the impacts of precipitation pulses is also needed to improve vegetation modeling of dryland ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Snow-corrected vegetation indices for improved gross primary productivity assessment in North American evergreen forests

North American evergreen forests cover large areas and influence the global carbon cycle. Satellite remote sensing has been used to track the phenology of ecosystem photosynthesis of these forests by detecting variation in vegetation optical properties associated with physiological and structural features, and most of these methods have been closely tied to vegetation greenness. However, in evergreens, the application of satellite data to monitor photosynthetic phenology is often limited by the lack of sensitivity of greenness-based indices. In this study, we identified 47 evergreen forest flux sites in North America that had MODIS observation overlapping with the flux tower records. We then calculated four vegetation indices using MODIS MAIAC data (MCD19A1), including NDVI, CCI, NIRv, and kNDVI, for the 47 flux sites and evaluated relationships between gross primary productivity (GPP) and vegetation indices across the North American evergreen forests. Our results showed that snow had substantial effects on the performance of all vegetation indices in tracking GPP phenology, particularly in the early spring when rapid changes occurred to both GPP and snow cover. Furthermore, different vegetation indices were affected differently, indicating contradictory and confounding effects of snow on these indices. After correcting for the snow effects, both CCI and NIRv performed well in tracking GPP phenology, albeit for different reasons. CCI is sensitive to seasonal changes in the relative levels of chlorophyll and carotenoid pigments, which are closely tied to GPP phenology in evergreens. NIRv is sensitive to the absorbed photosynthetically active radiation and to the contribution of deciduous components to the overall optical properties. We also found that correlations between GPP and vegetation indices varied among ecoregions and climate classes. In general, regions with pronounced seasonal GPP patterns had stronger correlations between GPP and greenness-based indices than regions with weaker seasonal GPP patterns. These biome differences were less pronounced for CCI. The snow artifacts and complementary vegetation index effects reported here should be considered in any large-scale studies of GPP using reflectance-based indices from optical satellites.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Network of networks: Time series clustering of AmeriFlux sites

Environmental observation networks, such as AmeriFlux, are foundational for monitoring ecosystem response to climate change, management practices, and natural disturbances; however, their effectiveness depends on their representativeness for the regions or continents. We proposed an empirical, time series approach to quantify the similarity of ecosystem fluxes across AmeriFlux sites. We extracted the diel and seasonal characteristics (i.e., amplitudes, phases) from carbon dioxide, water vapor, energy, and momentum fluxes, which reflect the effects of climate, plant phenology, and ecophysiology on the observations, and explored the potential aggregations of AmeriFlux sites through hierarchical clustering. While net radiation and temperature showed latitudinal clustering as expected, flux variables revealed a more uneven clustering with many small (number of sites < 5), unique groups and a few large (> 100) to intermediate (15–70) groups, highlighting the significant ecological regulations of ecosystem fluxes. Many identified unique groups were from under-sampled ecoregions and biome types of the International Geosphere-Biosphere Programme (IGBP), with distinct flux dynamics compared to the rest of the network. At the finer spatial scale, local topography, disturbance, management, edaphic, and hydrological regimes further enlarge the difference in flux dynamics within the groups. Nonetheless, our clustering approach is a data-driven method to interpret the AmeriFlux network, informing future cross-site syntheses, upscaling, and model-data benchmarking research. Finally, we highlighted the unique and underrepresented sites in the AmeriFlux network, which were found mainly in Hawaii and Latin America, mountains, and at under-sampled IGBP types (e.g., urban, open water), motivating the incorporation of new/unregistered sites from these groups.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization

To understand how a bacterium ultimately succeeds or fails in adapting to a new host, it is essential to assess the temporal dynamics of its fitness over the course of colonization. Here, we introduce a human-derived commensal organism, Bacteroides thetaiotaomicron (Bt), into the guts of germ-free mice to determine whether and how the genetic requirements for colonization shift over time. Combining a high-throughput functional genetics assay and transcriptomics, we find that gene usage changes drastically during the first days of colonization, shifting from high expression of amino acid biosynthesis genes to broad upregulation of diverse polysaccharide utilization loci. Within the first week, metabolism becomes centered around utilization of a predominant dietary oligosaccharide, and these changes are largely sustained through 6 weeks of colonization. Spontaneous mutations in wild-type Bt also evolve around this locus. These findings highlight the importance of considering temporal colonization dynamics in developing more effective micro biome-based therapies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Global overview and major challenges of host prediction methods for uncultivated phages

Bacterial communities play critical roles across all of Earth’s biomes, affecting human health and global ecosystem functioning. They do so under strong constraints exerted by viruses, i.e., bacteriophages or “phages”. Phages can reshape bacterial communities’ structure, influence long-term evolution of bacterial populations, and alter host cell metabolism during infection. Metagenomics approaches, i.e., shotgun sequencing of environmental DNA or RNA, recently enabled large-scale exploration of phage genomic diversity, yielding several millions of phage genomes now to be further analyzed and characterized. One major challenge however is the lack of direct host information for these phages. Several methods and tools have been proposed to bioinformatically predict the potential host(s) of uncultivated phages based only on genome sequence information. Here we review these different approaches and highlight their distinct strengths and limitations. We also outline complementary experimental assays which are being proposed to validate and refine these bioinformatic predictions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Oxidation of soil organic carbon during an anoxic-oxic transition

Redox reactions of iron (Fe) can play an important role in controlling the stability and transformation of organic carbon (OC) in soils. However, there is limited knowledge about the dynamics of Fe and OC in soils during anoxic-oxic transitions, which are common in temperate and tropical biomes. In this study, we investigated the fate and transformation of Fe and OC during a 5-day oxic incubation of four pre-reduced (8 days anoxic) forest soils. Up to 3.7% of total OC in the pre-reduced soils was oxidized to CO 2 , in conjunction with the oxidation of 31 –84% of the extractable Fe(II). OC oxidation in pre-reduced soils was lower than non-reducedcontrol soils, indicating that recently anoxically-incubated soils support lower OC metabolism upon re-oxidation than consistently oxic soils. Oxic OC oxidation was negatively correlated with the fraction of Fe-bound OC and also the fraction of short-range-ordered (SRO) Fe oxides. These results suggest that association with Fe oxides—especially SRO Fe oxides—can inhibit the availability of OC for oxidation. However, the difference between the oxidation of OC in pre40 reduced soils and consistently oxic controls could not be linked to the moderate changes in the Fe mineral composition during the anoxic-oxic transition, indicating the importance of longer term OC association with Fe oxides, as well as other processes, in regulating the oxidation of OC during the redox fluctuations. OC association with Fe oxides should be considered during simulations of biogeochemical cycling of OC in soils during the redox fluctuations, for which other processes such as the anoxic transformation of OC and response of the microbial community also need to be incorporated.

58 GEOSCIENCES↗