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DOE OSTI2023

Seasonality regulates the structure and biogeochemical impact of ectomycorrhizal fungal communities across environmentally divergent neotropical dry forests

Abstract Ectomycorrhizal (ECM) symbioses support forest functioning globally, yet both the structure and function of ECM fungal communities in seasonally dry neotropical forests (SDTFs), known for extreme heterogeneity in vegetation and edaphic properties, remain under characterized. Here, we evaluated the relative influences of seasonal versus spatial variation in ECM fungal community structure in soils from four environmentally divergent SDTFs. We also assessed the importance of biotic and abiotic drivers of SDTF ECM fungal community structure at regional scales, as well as ECM impacts on soil carbon (C) and nitrogen (N) cycling. ECM fungal frequency, relative abundance and richness all increased in the wet season, but spatial rather than seasonal effects explained more variation in community composition. Across the four SDTFs investigated, differences in tree communities drove ECM fungal community turnover more than geographic distances, site abiotic conditions or soil chemistry. Although soil moisture and ECM tree basal area were stronger predictors of soil biogeochemistry, incorporating ECM fungal community composition and relative abundance added explanatory power to models of soil C and N cycling in the wet season. Synthesis : Our results highlight the importance of seasonality and plant community composition in shaping different aspects of SDTF ECM fungal community structure and diversity as well as the potential for both the plant and fungal components of ECM symbioses to impact soil functioning across heterogenous SDTFs. Furthermore, our findings suggest that alterations in SDTF plant community composition due to climate or land‐use change will have important consequences for ECM fungal diversity and associated effects on soil biogeochemical cycling.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Using soil library hyperspectral reflectance and machine learning to predict soil organic carbon: Assessing potential of airborne and spaceborne optical soil sensing

Soil organic carbon (SOC) is a key variable to determine soil functioning, ecosystem services, and global carbon cycles. Spectroscopy, particularly optical hyperspectral reflectance coupled with machine learning, can provide rapid, efficient, and cost-effective quantification of SOC. However, how to exploit soil hyperspectral reflectance to predict SOC concentration, and the potential performance of airborne and satellite data for predicting surface SOC at large scales remain relatively underknown. Here, this study utilized a continental-scale soil laboratory spectral library (37,540 full-pedon 350–2500 nm reflectance spectra with SOC concentration of 0–780 g·kg –1 across the US) to thoroughly evaluate seven machine learning algorithms including Partial-Least Squares Regression (PLSR), Random Forest (RF), K-Nearest Neighbors (KNN), Ridge, Artificial Neural Networks (ANN), Convolutional Neural Networks (CNN), and Long Short-Term Memory (LSTM) along with four preprocessed spectra, i.e. original, vector normalization, continuum removal, and first-order derivative, to quantify SOC concentration. Furthermore, by using the coupled soil-vegetation-atmosphere radiative transfer model, we simulated twelve airborne and spaceborne hyper/multi-spectral remote sensing data from surface bare soil laboratory spectra to evaluate their potential for estimating SOC concentration of surface bare soils. Results show that LSTM achieved best predictive performance of quantifying SOC concentration for the whole data sets (R 2 = 0.96, RMSE = 30.81 g·kg –1 ), mineral soils (SOC ≤ 120 g·kg –1 , R 2 = 0.71, RMSE = 10.60 g·kg –1 ), and organic soils (SOC > 120 g·kg –1 , R 2 = 0.78, RMSE = 62.31 g·kg –1 ). Spectral data preprocessing, particularly the first-order derivative, improved the performance of PLSR, RF, Ridge, KNN, and ANN, but not LSTM or CNN. We found that the SOC models of mineral and organic soils should be distinguished given their distinct spectral signatures. Finally, we identified that the shortwave infrared is vital for airborne and spaceborne hyperspectral sensors to monitor surface SOC. This study highlights the high accuracy of LSTM with hyperspectral/multispectral data to mitigate a certain level of noise (soil moisture <0.4 m 3 ·m –3 , green leaf area < 0.3 m 2 ·m –2 , plant residue <0.4 m 2 ·m –2 ) for quantifying surface SOC concentration. Forthcoming satellite hyperspectral missions like Surface Biology and Geology (SBG) have a high potential for future global soil carbon monitoring, while high-resolution satellite multispectral fusion data can be an alternative.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Functional Redundancy in Soil Microbial Community Based on Metagenomics Across the Globe

Understanding the contribution of soil microbial communities to ecosystem processes is critical for predicting terrestrial ecosystem feedbacks under changing climate. Our current understanding lacks a consistent strategy to formulate the linkage between microbial systems and ecosystem processes due to the presumption of functional redundancy in soil microbes. Here we present a global soil microbial metagenomic analysis to generalize patterns of microbial taxonomic compositions and functional potentials across climate and geochemical gradient. Our analyses show that soil microbial taxonomic composition varies widely in response to climate and soil physicochemical gradients, while microbial functional attributes based on metagenomic gene abundances are redundant. Among 17 climate zones, microbial taxonomic compositions were more distinct than functional potentials, as climate and edaphic properties showed more significant influence on microbial taxonomic compositions than on functional potentials. Microbial taxonomies formed a larger and more complex co-occurrence network with more module structures than functional potentials. Functional network was strongly inter-connected among different categories, whereas taxonomic network was more positively interactive in the same taxonomic groups. This study provides strong evidence to support the hypothesis of functional redundancy in soil microbes, as microbial taxonomic compositions vary to a larger extent than functional potentials based on metagenomic gene abundances in terrestrial ecosystems across the globe.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions

Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO 2 levels). For this purpose, we combined 18 O-water vapor equilibration with quantitative stable isotope probing (termed ‘vapor-qSIP’) to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO 2 ) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Curable polysiloxane compositions and slippery materials and coatings and articles made therefrom

The present teachings generally provide curable polysiloxane compositions including a base resin including a surface active polymer. Articles of manufacture including the curable polysiloxane compositions and slippery coatings and materials also are provided. The compositions may be used to provide slippery, lubricious, or repellent materials and coatings and may provide anti-fouling function. The compositions can provide anti-fouling or foul-release function on open surfaces, internal surfaces, membranes; to provide pinning free or low contact angle hysteresis surfaces; to provide homogeneous interface to suppress nucleation; to provide a barrier layer such as anti-corrosion; to provide anti-stain, anti-smudge, anti-fingerprint, anti-soil function.

Kim, Philseok↗

DOE OSTI2023

Curable polysiloxane compositions and slippery materials and coatings and articles made therefrom

Kim, Philseok↗

DOE OSTI2024

Composition and metabolism of microbial communities in soil pores

Delineation of microbial habitats within the soil matrix and characterization of their environments and metabolic processes are crucial to understand soil functioning, yet their experimental identification remains persistently limited. We combined single- and triple-energy X-ray computed microtomography with pore specific allocation of 13 C labeled glucose and subsequent stable isotope probing to demonstrate how long-term disparities in vegetation history modify spatial distribution patterns of soil pore and particulate organic matter drivers of microbial habitats, and to probe bacterial communities populating such habitats. Here we show striking differences between large (30-150 µm Ø) and small (4-10 µm Ø) soil pores in (i) microbial diversity, composition, and life-strategies, (ii) responses to added substrate, (iii) metabolic pathways, and (iv) the processing and fate of labile C. We propose a microbial habitat classification concept based on biogeochemical mechanisms and localization of soil processes and also suggests interventions to mitigate the environmental consequences of agricultural management.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

1 × 1 km maps of abundances of eight enzyme functional classes for soil C, N, and P cycling across the CONUS

This dataset includes eight 1 × 1 km maps of the abundances of eight enzyme functional classes (EFC) for soil C, N, and P cycling across the CONUS. These mappings are predicted by the machine learning model trained using metagenomics and the corresponding environmental data. This item corresponds to our article: Fan, C., Song, Y., Mishra, U., Gautam, S., & Mayes, M. A. (2025). Harnessing the Power of Machine Learning and Omics to Identify Environmental Regulation on Microbial Functional Composition for Soil C, N, and P Cycling. Journal of Geophysical Research: Biogeosciences, 130(10).

1 × 1 km↗

DOE OSTI2022

The impact of freeze-thaw history on soil carbon response to experimental freeze-thaw cycles

This dataset contains data used for the paper "The impact of freeze-thaw history on soil carbon response to experimental freeze-thaw cycles". The Related References field will be updated with a full citation when available.Freeze-thaw is a disturbance process in cold regions where permafrost soils are becoming vulnerable to temperature fluctuations above 0˚C. Freeze-thaw alters soil physical and biogeochemical properties with implications for carbon persistence and emissions in Arctic landscapes. We examined whether different freeze-thaw histories in two soil systems led to contrasting biogeochemical responses under a laboratory-controlled freeze-thaw incubation. We investigated controls on soil organic matter (SOM) composition through Fourier-transform ion cyclotron resonance mass spectroscopy (FT-ICR-MS) to identify nominal carbon oxidation states and relative abundances of aliphatic-type carbon molecules in both surface and subsurface soils. Soil cores (~ 60 cm-depth) were sampled from two sites in Alaskan permafrost landscapes with different in situ freeze-thaw characteristics: Healy (>40 freeze-thaw cycles annually) and Toolik (<150 freeze-thaw cycles annually). FT-ICR-MS was coupled with in situ temperature data and soil properties (i.e., soil texture, mineralogy) to assess (1) differences in SOM composition associated with previous freeze-thaw history and (2) sensitivity to experimental freeze-thaw in the extracted cores. Control (freeze-only) samples showed greater carbon oxidation in Healy soils compared with Toolik, even in lower mineral horizons where freeze-thaw history was comparable across both sites. Healy showed the most loss of carbon compounds following experimental freeze-thaw in the lower mineral depths, including a decrease in aliphatics. Toolik soils responded more slowly to freeze-thaw as shown by intermediary carbon oxidation distributed across multiple carbon compound classes. Variations in the response of permafrost carbon chemistry to freeze-thaw is an important factor for predicting changes in soil function as permafrost thaws in high northern latitudes.This dataset contains a compressed (.zip) archive of the data and R scripts used for this manuscript. The dataset includes files in .csv format, which can be accessed and processed using MS Excel or R. This archive can also be accessed on GitHub at https://github.com/Erin-Rooney/FTC-FTICR (DOI 10.5281/zenodo.6533064).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Microbial Community Analysis & Functional Evaluation in Soils

The overall objective of this proposal was to develop technologies to alter the composition and function of important members of microbial communities. In particular, the overall objective of the microbial community editing portion of the proposal focuses on developing foundational tools and understanding required to predict, alter and design grass rhizosphere communities impacting DOE missions. Specifically, the project is centered on the Microbial Community Analysis & Functional Evaluation in Soils (m-CAFES) to manipulate microbial consortia associated with plants of interest for the bioenergy sector, under the presumption that bacterial communities can be manipulated to enhance plant health. For tasks of specific interest to us, we are focusing on developing novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based technologies (primarily focusing on Aim 1) and their delivery modalities (notably subaim 1.2) to edit specific bacterial genomes of interest to enhance their functionalities, and programmably ablate specific undesirable members of bacterial communities for plant health. We are focusing on engineering bacteriophages (bacterial viruses, for subaim 1.2) to carry programmable CRISPR-Cas systems (subaim 1.1) to target (ablate) or alter (edit) genomes of interest. This will enable us to carry out microbial perturbations that will impact community composition and function and ultimately plant growth and health, to enable the next phase of the project by deploying them in situ (subaims 1.3 and 1.4).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Evaluating genetic and environmental controls on silicon accumulation in Populus trichocarpa leaves

Background and aims: Silicon (Si) accumulation and formation of non-crystalline silica particles (phytoliths) inside plant cells contribute to plant function, soil carbon storage, and Si reservoirs in soils. A better understanding of how genetic and environmental factors control Si accumulation may improve understanding of Si cycling between plants and soil and its impacts on other ecosystem processes. Methods: This study examined how genetic potential for Si uptake and silicification translated to Si concentrations and phytolith formation in Populus trichocarpa leaves. Leaves were collected from four different genotypes of cultivated poplar trees that were grown in a common garden and possess established differences in leaf-level gene expression related to Si transport and silicification. Scanning electron microscopy and subsequent image analysis were used to quantify Si concentrations and phytolith abundance and features. Results: Phytoliths were identified in nearly all leaves but were often absent at very low (< 0.5 wt.%) Si concentrations at the leaf surface. The proportion of leaf area occupied by phytoliths increased as Si content increased. Silicon content and phytolith abundance at the leaf surface did not vary across genotypes, but surface Si was weakly correlated with plant available Si in soil. Conclusion: Phytoliths were prevalent in P. trichocarpa leaves; however, the genetic potential for Si uptake and silicification at the leaf-level poorly predicted foliar Si and phytolith abundance. Uniformly low expression of Si uptake genes in the roots may have reduced differences across genotypes. Consequently, Si accumulation in leaves was likely more strongly influenced by soil Si bioavailability, phenology, or additional environmental factors.

Image analysis↗

DOE OSTI2025

Postfire Biogeochemical Processes: Implications to Source Water Quality in Fire-Influenced Watersheds

Forested watersheds are instrumental in providing purified and reliable water to millions of people worldwide. The changing climate has increased the frequency and severity of global fire events. Forested watersheds and their ecosystem functions are greatly disrupted during fire activity. Postfire concerns in forested watersheds include unpredictable and potentially simultaneous alterations in source water quality and hydro-biogeochemical processes. Here, the degree of fire severity can complexly modify water quality through the production of fire-transformed constituents on the burned forest floor (i.e., nutrients, metal(loid)s, dissolved organic matter, and the formation of disinfection byproducts). Correspondingly, fire severity and postfire rainfall patterns can refine hydro-biogeochemical processes that influence the transport of the fire-transformed constituents (i.e., vegetation function, soil structure, hydrological pathways, and microbial communities). Postfire alterations to water quality and hydro-biogeochemical processes introduce further complexity with varying temporal influence, which ranges from months to decades. As postfire water quality and watershed response research progresses, it is essential to homogenize interdisciplinary expertise to bridge knowledge gaps between fields ranging from forest ecology, hydrology, microbiology, and geochemistry. A multidisciplinary approach in wildfire research will facilitate a comprehensive perception of the diverse water quality risks associated with fire activity and mitigate fire concerns on a global level.

Disinfection Byproducts↗

DOE OSTI2022

The Impact of Freeze‐Thaw History on Soil Carbon Response to Experimental Freeze‐Thaw Cycles

Abstract Freeze‐thaw is a disturbance process in cold regions where permafrost soils are becoming vulnerable to temperature fluctuations above 0°C. Freeze‐thaw alters soil physical and biogeochemical properties with implications for carbon persistence and emissions in Arctic landscapes. We examined whether different freeze‐thaw histories in two soil systems led to contrasting biogeochemical responses under a laboratory‐controlled freeze‐thaw incubation. We investigated controls on carbon composition through Fourier‐transform ion cyclotron resonance mass spectrometry (FT‐ICR‐MS) to identify nominal carbon oxidation states and relative abundances of aliphatic‐type carbon molecules in both surface and subsurface soils. Soil cores (∼60 cm‐depth) were sampled from two sites in Alaskan permafrost landscapes with different in situ freeze‐thaw characteristics: Healy (>40 freeze‐thaw cycles annually) and Toolik (<15 freeze‐thaw cycles annually). FT‐ICR‐MS was coupled with in situ temperature data and soil properties (i.e., soil texture, mineralogy) to assess (a) differences in soil organic matter composition associated with previous freeze‐thaw history and (b) sensitivity to experimental freeze‐thaw in the extracted cores. Control (freeze‐only) samples showed greater carbon oxidation in Healy soils compared with Toolik, even in lower mineral horizons where freeze‐thaw history was comparable across both sites. Healy showed the most loss of carbon compounds following experimental freeze‐thaw in the lower mineral depths, including a decrease in aliphatics. Toolik soils responded more slowly to freeze‐thaw as shown by intermediary carbon oxidation distributed across multiple carbon compound classes. Variations in the response of permafrost carbon chemistry to freeze‐thaw is an important factor for predicting changes in soil function as permafrost thaws in high northern latitudes.

Rooney, Erin C.↗

DOE OSTI2024

Integrating viruses into soil food web biogeochemistry

The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct or facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. Finally, we highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Abstract Soil microbiomes are sensitive to current and previous soil conditions, and bacterial ‘bioindicators’ of biological, physical, and chemical soil properties have considerable potential for soil health assessment. However, the lack of ecological or physiological information for most soil microorganisms limits our ability to interpret the associations of bioindicators and, thus, their utility for guiding management. We identified bioindicators of tillage intensity and twelve soil properties used to rate soil health using a 16S rRNA gene-based survey of farmland across North America. We then inferred the genomic traits of bioindicators and evaluated their environment-wide associations (EWAS) with respect to agricultural management practice, disturbance, and plant associations with 89 studies from agroecosystems. Most bioindicators were either positively correlated with biological properties (e.g., organic matter) or negatively correlated with physical and chemical properties. Higher soil health ratings corresponded with smaller genome size and higher coding density, while lower ratings corresponded with larger genomes and higher rrn copy number. Community-weighted genome size explained most variation in health ratings. EWAS linked prominent bioindicators with the impacts of environmental disturbances. Our findings provide ecological insights into bioindicators of soil properties relevant to soil health management, illustrating the tight coupling of microbiome and soil function.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Multiple elements of soil biodiversity drive ecosystem functions across biomes

The role of soil biodiversity in regulating multiple ecosystem functions is poorly understood, limiting our ability to predict how soil biodiversity loss might affect human wellbeing and ecosystem sustainability. Furthermore, combining a global observational study with an experimental microcosm study, we provide evidence that soil biodiversity (bacteria, fungi, protists and invertebrates) is significantly and positively associated with multiple ecosystem functions. These functions include nutrient cycling, decomposition, plant production, and reduced potential for pathogenicity and belowground biological warfare. Our findings also reveal the context dependency of such relationships and the importance of the connectedness, biodiversity and nature of the globally distributed dominant phylotypes within the soil network in maintaining multiple functions. Moreover, our results suggest that the positive association between plant diversity and multifunctionality across biomes is indirectly driven by soil biodiversity. Together, our results provide insights into the importance of soil biodiversity for maintaining soil functionality locally and across biomes, as well as providing strong support for the inclusion of soil biodiversity in conservation and management programmes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Persistence Control of Engineered Functions in Complex Soil Microbiomes (PerCon SFA), Secure Biosystems Design Project Data Catalog at PNNL DataHub

The Persistence Control of Engineered Functions in Complex Soil Microbiomes Project (PerCon SFA) at Pacific Northwest National Laboratory (PNNL) is a Genomic Sciences Program Biosystems Design, Science Focus Area research project consortium. Collaborating across highly integrated institutions, PerCon SFA scientists are exploring how environmental niches can be sculpted using the mechanisms of genome reduction and metabolic addiction to drive secure rhizosphere community design for robust biomass cropping in challenging environments. The PerCon SFA DataHub project repository contains publication-relevant digital dataset and metadata DOI packages, enabling exploration and download of integrated experimental dataset catalogs publicly available to a global scientific community. and metadata repository allow for exploring and downloading integrated experimental biodesign omics dataset catalogs, including experimental protocols and/or workflows, raw and/or processed data, as required by the repository, and other relevant supporting materials and/or metadata required for research reproducibility and reporting.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Macroecological distributions of gene variants highlight the functional organization of soil microbial systems

Abstract The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗