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DOE OSTI2026

Spatiotemporal Dynamics of the Relative Abundance of Soil Nutrient‐Degrading Enzyme‐Encoding Genes Across Continental US Ecoregions

Understanding the spatiotemporal patterns in the relative abundance of soil extracellular enzyme‐encoding genes is critical for predicting microbial responses to environmental change and their potential role in nutrient cycling. Yet, integrating novel metagenomic observations with spatiotemporal environmental gradients to infer regional patterns and future trajectories has remained unclear. To address this gap, we applied a machine learning (ML) approach, integrating soil metagenomic data with environmental variables—soil properties, topography, vegetation, and climate—to predict the relative abundance of enzyme‐encoding genes for soil carbon (C), nitrogen (N), and phosphorus (P) across surface soils of the continental United States. We assessed potential responses under future emission scenarios (SSP2‐4.5 and SSP5‐8.5) by comparing a baseline (1985–2014) to a future period (2071–2100). The ML model explained 57%–63% of baseline variation. Precipitation was identified as the most influential factor for the relative abundance of C‐ and N‐degrading enzyme‐encoding genes, while slope length, representing horizontal distance that water can travel downslope, was the primary driver for P‐degrading enzyme‐encoding genes abundance. Projections revealed spatially heterogeneous shifts across continental US ecoregions: the relative abundance of C‐ and N‐degrading enzyme‐encoding genes decreased in wetter ecoregions and increased in drier ecoregions under future climate, while P‐degrading enzyme‐encoding genes abundance decreased significantly in semiarid and Mediterranean ecoregions. This study demonstrates the utility of metagenomic data for mapping soil genetic potential and predicting its regional response to environmental change, to inform ecosystem management strategies.

extracellular enzyme-encoding genes↗

DOE OSTI2022

Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity

Background: Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean type grassland administrated with 14 years of 7 g m –2 year –1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century. Results: Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition. Conclusions: We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. Here, we showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Exploring Trait Trade-Offs for Fungal Decomposers in a Southern California Grassland

Fungi are important decomposers in terrestrial ecosystems, so their responses to climate change might influence carbon (C) and nitrogen (N) dynamics. We investigated whether growth and activity of fungi under drought conditions were structured by trade-offs among traits in 15 fungal isolates from a Mediterranean Southern California grassland. We inoculated fungi onto sterilized litter that was incubated at three moisture levels (4, 27, and 50% water holding capacity, WHC). For each isolate, we characterized traits that described three potential lifestyles within the newly proposed “YAS” framework: growth yield, resource acquisition, and stress tolerance. Specifically, we measured fungal hyphal length per unit litter decomposition for growth yield; the potential activities of the extracellular enzymes cellobiohydrolase (CBH), β -glucosidase (BG), β -xylosidase (BX), and N-acetyl- β - D -glucosaminidase (NAG) for resource acquisition; and ability to grow in drought vs. higher moisture levels for drought stress tolerance. Although, we had hypothesized that evolutionary and physiological trade-offs would elicit negative relationships among traits, we found no supporting evidence for this hypothesis. Across isolates, growth yield, drought stress tolerance, and extracellular enzyme activities were not significantly related to each other. Thus, it is possible that drought-induced shifts in fungal community composition may not necessarily lead to changes in fungal biomass or decomposer ability in this arid grassland.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Diversity and Distribution of Hydrocarbon-Degrading Genes in the Cold Seeps from the Mediterranean and Caspian Seas

Marine cold seeps are unique ecological niches characterized by the emergence of hydrocarbons, including methane, which fosters diverse microbial communities. This study investigates the diversity and distribution of hydrocarbon-degrading genes and organisms in sediments from the Caspian and Mediterranean Seas, utilizing 16S rRNA and metagenomic sequencing to elucidate microbial community structure and functional potential. Our findings reveal distinct differences in hydrocarbon degrading gene profiles between the two seas, with pathways for aerobic and anaerobic hydrocarbon degradation co-existing in sediments from both basins. Aerobic pathways predominate in the surface sediments of the Mediterranean Sea, while anaerobic pathways are favored in the surface sediments of the anoxic Caspian Sea. Additionally, sediment depths significantly influence microbial diversity, with variations in gene abundance and community composition observed at different depths. Aerobic hydrocarbon-degrading genes decrease in diversity with depth in the Mediterranean Sea, whereas the diversity of aerobic hydrocarbon-degrading genes increases with depth in the Caspian Sea. These results enhance our understanding of microbial ecology in cold seep environments and have implications for bioremediation practices targeting hydrocarbon pollutants in marine ecosystems.

Microbiology↗

DOE OSTI2026

CMIP7 data request: Earth system priorities and opportunities

This paper presents a comprehensive overview of the Coupled Model Intercomparison Project Phase 7 (CMIP7) request for data pertaining to Earth systems science, and provides justification for the resources needed to produce this data. Topics within the CMIP7 Earth System (CMIP7-ES) theme centre around tracking of flows of energy, carbon, water and other fluxes across domains, and constraining feedbacks between these cycles and the climate system. These topics are summarized in this paper as scientific “opportunities” describing specific model intercomparison experiments and use cases for next-generation Earth System Model (ESM) output. These opportunities were submitted by modelling groups and scientific consortia following an extended public consultation process. Contained within each opportunity are requests for groups of Climate & Forecasting (CF) variables, which are bundled into variable groups representing all data required to address the opportunities' needs. Novel opportunities in CMIP7 compared with previous phases will include running `emissions-driven' simulations that integrate carbon emissions and removal scenarios with updated representations of the global carbon cycle, expanded variable groups needed to model marine trophic interactions and biogeochemistry, and data needed to understand the risk of global tipping points, among others. The production of these variables will close key gaps and uncertainties identified during previous rounds of CMIP, and support the 7th Intergovernmental Panel on Climate Change Assessment Report (AR7). We argue that CMIP7-ES data will be broadly used by scientific, policy, governmental, industry, and other communities that rely on climate model projections for research and decision making. As an author group we also reflect on the evolution of the CMIP7-ES data request as a part of a deliberative process in support of the global CMIP program.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands

Viruses shape microbial communities, food web dynamics, and carbon and nutrient cycling in diverse ecosystems. However, little is known about the patterns and drivers of viral community composition, particularly in soil, precluding a predictive understanding of viral impacts on terrestrial habitats. To investigate soil viral community assembly processes, here we analyzed 43 soil viromes from a rainfall manipulation experiment in a Mediterranean grassland in California. We identified 5,315 viral populations (viral operational taxonomic units [vOTUs] with a representative sequence ≥10 kbp) and found that viral community composition exhibited a highly significant distance–decay relationship within the 200-m 2 field site. This pattern was recapitulated by the intrapopulation microheterogeneity trends of prevalent vOTUs (detected in ≥90% of the viromes), which tended to exhibit negative correlations between spatial distance and the genomic similarity of their predominant allelic variants. Although significant spatial structuring was also observed in the bacterial and archaeal communities, the signal was dampened relative to the viromes, suggesting differences in local assembly drivers for viruses and prokaryotes and/or differences in the temporal scales captured by viromes and total DNA. Despite the overwhelming spatial signal, evidence for environmental filtering was revealed in a protein-sharing network analysis, wherein a group of related vOTUs predicted to infect actinobacteria was shown to be significantly enriched in low-moisture samples distributed throughout the field. Overall, our results indicate a highly diverse, dynamic, active, and spatially structured soil virosphere capable of rapid responses to changing environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

What lies beneath: Vertical temperature heterogeneity in a Mediterranean woodland savanna

As the availability of satellite and airborne thermal infrared remote sensing (TIR-RS) data increases and their spatial, temporal, and spectral resolutions improve, researchers are finding diverse applications for TIR-RS measurements. TIR-RS is now commonly applied in regional- and continental-scale analyses, such as those focused on fire and surface energy balance. However, its application lags in plant physiology and ecology, for which a finer-scale understanding of plant canopy temperatures would be useful to elucidate plant water dynamics, for example. In particular, while methods to disaggregate TIR-RS pixels in horizontal space have advanced, possible vertical stratification of plant canopy temperature and its implications for understanding the correspondence between TIR-RS and finer-scale, field-based thermal measurements (e.g. made with a thermal camera) remain unexplored. Here, we use data from a thermal camera deployed concurrently with the recent ECOSTRESS mission to quantify vertical temperature gradients within tree canopies and temperatures of over- vs. under-story plants in a Mediterranean woodland savanna. We then leverage diverse ancillary data to maximize the geometric comparability of ECOSTRESS and thermal camera measurements, in order to assess the extent to which the two forms of thermal measurements correspond. Specifically, we ask: (1) What are the patterns of intra-canopy and over- vs. under-story vertical temperature in a Mediterranean woodland savanna?, and (2) How can vertically-resolved, but spatially-limited field-based temperature measurements be reconciled with spatially-extensive, but surface-only, temperature measurements of a space-borne remote sensor? Further, we found consistent patterns of vertical thermal heterogeneity both within tree canopies and between ecosystem over- and under-stories. The daytime difference between the top and bottom thirds of blue oak canopies was, on average, 0.48 ° C – and sometimes several times larger. Notably, canopy tops are cooler, likely associated with the under-story grass reaching daytime temperatures often exceeding over-story temperatures by 10° C. Given the consistency of the intra-canopy temperature gradients, we expected the ECOSTRESS sensor would be in better agreement with camera measurements of canopy tops than bulk canopies or canopy bottoms. However, within-canopy gradients were overwhelmed by other sources of disagreement between the measurements, in part associated with upscaling camera measurements across space. Overall, thermal camera and ECOSTRESS measurements were largely in agreement at night (pixel RMSE = 1.1°C), but they were more divergent during times of low (but >0 W/m2) and high incoming solar radiation (daytime pixel RMSE = 3.5°C).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Seabird distribution is better predicted by abundance of prey than oceanography. A case study in the Gulf of Cadiz (SW, Iberian Peninsula)

Abstract Quantifying factors that influence marine predator distributions is essential to understanding the current and future change in marine biodiversity. Here, we test whether marine predator distribution relates to prey, or is better predicted by other specific habitat features. We examine the correlation between spatial distribution of three seabird species and their prey, as well as environmental proxies (oceanographic characteristics) in the Gulf of Cadiz, NE Atlantic. We modeled the at-sea distribution of Cory's shearwater, Balearic shearwater and Northern gannet, based on: (i) pelagic fish abundance according to acoustic surveys, and (ii) a forecast-model of remotely sensed environmental variables (productivity, sea surface temperature, and salinity). In general, seabird distributions were better predicted by abundance of fish than by environmental variables at the habitat scale. We obtained consistent correlations between seabird presence and the abundance of medium-sized (10–20 cm) sardines, anchovies and Mediterranean horse mackerel, providing information on their preferred prey. Additionally, oceanographic productivity variables moderately contributed to seabird distribution models, with better predictive value for the critically endangered Balearic shearwater and Northern gannet in the summer, whilst the model for Cory's shearwater's produced poorer predictions. Predator–prey combined studies may represent essential tools for an efficient ecosystem-based management of marine environments.

de la Cruz, Andrés (ORCID:0000000203632498)↗

DOE OSTI2025

Composition, Growth, Succession, and Function in the Cladophora Microbiome: Insights From Quantitative Stable Isotope Probing and NanoSIMS Imaging

The branching green macroalga Cladophora glomerata and its epiphytic microbiome dominate summer biomass in the Eel River, a Northern California river under Mediterranean (summer drought, winter rain) seasonality. Green Cladophora streamers proliferate in early summer, then change to yellow and then red-brown as epiphyte loads increase. Here, we characterised successional changes in epiphytic bacteria on Cladophora, examining both community composition and growth rates, using quantitative Stable Isotope Probing (qSIP) and 16S rRNA gene amplicon sequencing. The number of bacterial taxa increased with succession while growth rates peaked in the middle stage. NanoSIMS imaging confirmed high sulphur (S) concentrations in Cladophora cell walls relative to surrounding biomass, coinciding with a bloom of sulphur bacteria (bacteria that reduce or oxidise sulphur/sulphates). In general, relative abundances and growth rates were independent, indicating that either metric alone is insufficient for understanding how taxonomy and functional groups affect ecosystem processes. For instance, the relative abundance of nitrogen fixers peaked in the late summer when their relative growth rates were slowest. Such patterns may be driven by space competition limiting growth. Together, changes in abundance and relative growth rates suggest different limiting factors for different functional groups in the Cladophora microbiome at multiple successional stages.

Biological and medical sciences↗

DOE OSTI2021

Evaluation of Atmospheric Boundary Layer Height From Wind Profiling Radar and Slab Models and Its Responses to Seasonality of Land Cover, Subsidence, and Advection

In this study, we evaluated the effect of land cover, atmospheric subsidence, and advection on the annual dynamics of atmospheric boundary layer (ABL) height from two contrasting sites. The first site is the Walker Branch forest, a deciduous forest of temperate climate, complex topography, and cloudy summers. The second site is the Sacramento-San Joaquin River Delta, a site of Mediterranean climate, flat terrain on a local scale, and clear summers. After testing a new algorithm to calculate ABL heights from 915 MHz radar wind profilers, we evaluated a hierarchy of three slab models to recreate the diurnal and annual patterns of ABL growth. We found that the lower ABL heights in the Delta, particularly during late summer, are driven by the combined effects of increased atmospheric subsidence and marine air advection. In both sites, the annual pattern of ABL height was strongly correlated to total daily incoming radiation, and in the Delta, the annual pattern of ABL height closely followed the seasonal patterns of sensible heat flux from a mosaic of different land covers. A land composite of latent and sensible heat fluxes obtained through a meso-network of eddy covariance measurements and the ECOsystem Spaceborne Thermal Radiometer Experiment on Space Station (ECOSTRESS) mission resulted in higher model skill, thus showing that land cover heterogeneity is an important driver of ABL growth. To conclude, model simulations show that in the Delta, restoring agricultural land to wetlands with large open water areas could result in a reduction of ABL height during those months with low subsidence and advection.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Dissolved Organic Carbon in Coastal Waters: Global Patterns, Stocks and Environmental Physical Controls

Abstract Dissolved organic carbon (DOC) in coastal waters is integral to biogeochemical cycling, but global and regional drivers of DOC are still uncertain. In this study we explored spatial and temporal differences in DOC concentrations and stocks across the global coastal ocean, and how these relate to temperature and salinity. We estimated a global median coastal DOC stock of 3.15 Pg C (interquartile range (IQR) = 0.85 Pg C), with median DOC concentrations being 2.2 times higher than in open ocean surface waters. Globally and seasonally, salinity was the main driver of DOC with concentrations correlated negatively with salinity, without a clear relationship to temperature. DOC concentrations and stocks varied with region and season and this pattern is likely driven by riverine inputs of DOC and nutrients that stimulate coastal phytoplankton production. Temporally, high DOC concentrations occurred mainly in months with high freshwater input, with some exceptions such as in Eastern Boundary Current margins where peaks are related to primary production stimulated by nutrients upwelled from the adjacent ocean. No spatial trend between DOC and temperature was apparent, but many regions (19 out of 25) had aligned peaks of seasonal temperature and DOC, related to increased phytoplankton production and vertical stratification at high temperatures. Links of coastal DOC with salinity and temperature highlight the potential for anthropogenic impacts to alter coastal DOC concentration and composition, and thereby ecosystem status.

Lønborg, Christian [Section for Marine Diversity a↗

DOE OSTI2026

CMIP7 data request: land and land ice priorities and opportunities

The Land and Land Ice Theme in the Coupled Model Intercomparison Project Phase 7 (CMIP7) represents the current understanding of physical processes in land surface ecosystems, hydrology, cryosphere, and their physical interactions with other Earth system components. Simulations from Earth system models (ESMs) could provide crucial information for assessing planetary safety, such as critical tipping elements, and be used to inform climate risks for improving climate impact assessments and policy decisions. This paper presents a collaborative effort to identify scientific opportunities in the Land and Land Ice Theme of the CMIP7 Data Request. The proposed opportunities build upon advances in ESMs, including new freshwater system and land ice processes being included in CMIP7, as well as the scientific community's demand for high-frequency and sub-grid-scale land surface outputs. In total, 25 variable groups that contain 716 variables have been identified to be potentially available to the broad scientific audience for performing analysis in land–atmosphere coupling, hydrological processes and freshwater systems, glacier and ice sheet mass balance and their influence on the sea levels, land use, and plant phenology. Key reflections from this data request effort include advocacy for closer engagement between the user community and modeling groups, reduction in the technical barriers to tracking existing parameters and defining new variables, and more streamlined variable management. These will be essential to enhance the usability and reliability of CMIP7 outputs for climate and Earth system research and applications to a broad audience that relies on the CMIP7 endeavor.

Li, Yue [Univ. of California, Los Angeles, CA (Uni↗