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DOE OSTI2026

Data for "Adsorptive Separation and Recovery of Triacetic Acid Lactone from Fermentation Broth"

Triacetic acid lactone (TAL) can be microbially produced and further chemically upgraded to several high-value chemicals. In this work, several acidic and basic ion-exchange resins and activated charcoal were evaluated for their ability to adsorb microbially produced TAL. Activated charcoal and a weak base resin, Dowex 66, showed similar TAL adsorption capacity of 0.18 ± 0.002 g/g. At 15% w/v activated charcoal, about 98% of TAL present in fermentation broth could be adsorbed. Further, ethanol washing allowed recovery of 72% of adsorbed TAL. A biorefinery producing TAL from sucrose was designed, simulated, and evaluated (through technoeconomic analysis) under uncertainty, for an estimated TAL minimum product selling price (MPSP) of $4.27/kg [$3.71−4.94/kg; 5th-95th percentiles] for the current state of technology and $2.83/kg [$2.46–3.29/kg] following potential near-term improvements to fermentation. Thus, this work provides an adsorptive process to recover microbially produced TAL that can be chemically upgraded to several industrial products.

Bioproducts↗
DOE OSTI2021

Fungal and bacterial growth variation due to drought and nitrogen addition experimental treatments. Loma Ridge Experimental Project. 2010-2012

Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we decoupled the legacies of abiotic parameters versus that of the microbial community itself. After one rainy season, more variation in fungal composition could be explained by the original microbial inoculum than the litterbag environment (18% versus 5.5% of total variation). This compositional legacy persisted for 3 years, when 6% of the variability in fungal composition was still explained by the microbial origin. In contrast, bacterial composition was generally more resilient than fungal composition. Microbial functioning (measured as decomposition rate) was not immediately resilient to the global change manipulations; decomposition depended on both the contemporary environment and rainfall the year prior. Finally, using metagenomic sequencing, we showed that changes in precipitation, but not nitrogen availability, altered the potential for bacterial carbohydrate degradation, suggesting why the functional consequences of the two experiments may have differed. Predictions of how terrestrial ecosystem processes respond to environmental change may thus be improved by considering the legacies of microbial communities. This data package includes ten csv files (five data files and their corresponding data dictionaries) and one file-level metadata excel file. Data files contains information about which plots were exposed to treatments related to drought and nitrogen, information about litter bags reciprocal transplants manipulation for water input and nitrogen, detail information about water addition, precipitation records, and litter variables collected. Data dictionary files include detail explanation for each column in the data files. The file-level metadata file describes each file mentioned above. All the analyses were done using the R software.

54 ENVIRONMENTAL SCIENCES↗
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 OSTI2026

Finding the missing pieces: filling gaps that impede the translation of omics data into models

High-throughput omics technologies such as DNA sequencing have made the sequencing and computational assembly of microbial genomes recovered from the environment relatively routine. Computational inference of the protein products encoded by these genomes, and the associated biochemical functions, should enable the accurate prediction and modeling of microbial metabolism, organismal interactions, and ecosystem processes. However, a lack of scalable, probabilistic protein annotation tools limits the full potential of modeling for understanding the metabolism and biogeochemical cycles of microbial communities. Our approach to improve inference of protein annotations and metabolic models relied on learning from and emulating expert manual curation, leveraging software engineering and data science best practices to scale up the throughput and accuracy of annotations and metabolic model construction, building software to objectively evaluate different annotation strategies, and more closely linking the protein annotation and metabolic model inference process. Outcomes of this research include several improved or new computational tools, including DRAM (Distilled and Refined Annotation of Metabolism) for annotating microbial genomes with protein function and metabolic traits, CAMPER (Curated Annotations for Microbial Polyphenol Enzymes and Reactions) for annotating key polyphenol metabolisms, EC-Bench for comprehensive and unbiased benchmarking of annotation tools, and several apps available via the DOE Systems Biology Knowledgebase (KBase) for building genome-scale metabolic models. We demonstrate that these tools allow us to scalably annotate and understand thousands of genomes for microbial communities from a variety of systems and test cases, including rivers, thawing permafrost, and gut microbiomes. All of these computational tools are available as open-source software, with most broadly and easily accessible to the scientific community via KBase apps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cytochrome Nanowire XRD

Microbial metabolism plays an important role in the global cycling of carbon, nutrients, and metals. Recent discovery of microorganisms sharing energy using direct electrical connections might represent a prominent strategy by which anaerobic microorganisms interact with the diversity of environments. The purpose of the proposed research is to apply these newly developed principles of electron exchange in microbial communities to the study of biogeochemical cycling in climate and subsurface systems. Previous studies revealed that soil bacteria Geobacter sulfurreducens produce conductive pili nanofilaments that facilitate long-range electron transport to extracellular electron acceptors and other cells. This discovery has already transformed our understanding of the function of microbial communities in diverse environments, making basic contributions to microbial ecology and helping to improve practical applications such as increasing current output of microbial fuel cells and enhancing the conversion of organic waste to methane. Microbial electron exchange via pili may also contribute to methane production in terrestrial environments that are major sources of atmospheric methane. However, the mechanism of electron transport through pili is not well understood. Initial studies have suggested that pili exhibit metallic-like conductivity similar to conducting polymer polyaniline. However, these studies were limited to electrical measurements. X-ray diffraction studies have suggested that aromatic amino acids tyrosine and phenylalanine are closely packed in pili. But these studies used homology modeling to predict the pilus assembly and information about the number of monomers in each pilus assembly unit and their organization are still lacking. The central hypothesis of this proposal is aromatics in pili enable intermolecular electron delocalization due to pi-stacking that can give rise to metallic-like conductivity. By analyzing pili structure using infrared scattering-scanning near field optical microscope (IR s-SNOM) and combining with solution NMR, Focused Ion Beam (FIB and computational capabilities, this work will provide comprehensive understanding of the conduction mechanism from a structure-function perspective. The specific aims are: 1) With infrared scattering scanning near field optical microscope (IR s-SNOM), image the organization and density of pilin monomers and pH-induced conformational changes in a pilus filament. 2) With solution NMR, resolve pH-induced structural changes in the pilin monomer. 3) Using Focused Ion Beam (FIB), draw electrodes on single pili to measure their conductivity. 4) With computational modeling using the NWChem, simulate the effect of environment on the electronic properties of pili as a function of pH. The proposed work will gain the nanoscale insight into the structure of the pili, as the basis for understanding interspecies electrical communications. The improved understanding will be harnessed to accelerate bioenergy production and bioremediation using pili as well as for predictive modeling of carbon cycling in diverse environments to reach the central goals of DOE-BER to develop sustainable energy sources, regulate the contaminants in the subsurface and understand the effects of greenhouse gas emissions on biosphere. The proposed studies will provide design principles for engineering of electrical interactions among these communities by manipulating the amino acid composition of pili. Moreover, these studies will identify the forces that maintain the function of these communities in the face of environmental perturbation. Therefore, these studies will help to address the need "to incorporate process understanding of biogeochemical cycling into a scalable hierarchy of predictive capabilities" specified in EMSL's Science Themes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Metabolic activity and community structure of prokaryotes associated with particles in the twilight zone of the South China Sea

The twilight zone is an important depth of the ocean where particulate organic matter (POM) remineralization takes place, and prokaryotes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity associated with different particles in the twilight zone. The composition and distribution of particle-attached prokaryotes in the twilight zone of the South China Sea (SCS) were investigated using high-throughput sequencing and quantitative PCR, together with the Biolog Ecoplate™ microplates culture to analyze the microbial metabolic activity. We found that α- and γ-Proteobacteria dominating at the lower and upper boundary of the twilight zone, respectively; Methanosarcinales and Halobacteriales of the Euyarchaeota occupied in the larger particles at the upper boundary. Similar microbial community existed between euphotic layer and the upper boundary. Higher amount of shared Operational Taxonomic Units (OTUs) in the larger particles along the water depths, might be due to the fast sinking and major contribution of carbon flux of the larger particles from the euphotic layer. In addition to polymers as the major carbon source, carbohydrates and amino acids were preferentially used by microbial community at the upper and lower boundary, respectively. This could potentially be attributed to the metabolic capabilities of attached microbial groups in different particles, and reflected the initial preference of the carbon source by the natural microbes in the twilight zone as well. The microbial structure and carbon metabolic profiles could be complemented with metatranscriptomic analysis in future studies to augment the understanding of the complex carbon cycling pathways in the twilight zone.

Liu, Hao↗
DOE OSTI2022

Life and death in the soil microbiome: how ecological processes influence biogeochemistry

We report soil microorganisms shape global element cycles in life and death. Living soil microorganisms are a major engine of terrestrial biogeochemistry, driving the turnover of soil organic matter — Earth’s largest terrestrial carbon pool and the primary source of plant nutrients. Their metabolic functions are influenced by ecological interactions with other soil microbial populations, soil fauna and plants, and the surrounding soil environment. Remnants of dead microbial cells serve as fuel for these biogeochemical engines because their chemical constituents persist as soil organic matter. This non-living microbial biomass accretes over time in soil, forming one of the largest pools of organic matter on the planet. In this Review, we discuss how the biogeochemical cycling of organic matter depends on both living and dead soil microorganisms, their functional traits, and their interactions with the soil matrix and other organisms. With recent omics advances, many of the traits that frame microbial population dynamics and their ecophysiological adaptations can be deciphered directly from assembled genomes or patterns of gene or protein expression. Thus, it is now possible to leverage a trait-based understanding of microbial life and death within improved biogeochemical models and to better predict ecosystem functioning under new climate regimes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Nitrogen Deposition Weakens Soil Carbon Control of Nitrogen Dynamics Across the Contiguous United States

ABSTRACT Anthropogenic nitrogen (N) deposition is unequally distributed across space and time, with inputs to terrestrial ecosystems impacted by industry regulations and variations in human activity. Soil carbon (C) content normally controls the fraction of mineralized N that is nitrified ( ƒ nitrified ), affecting N bioavailability for plants and microbes. However, it is unknown whether N deposition has modified the relationships among soil C, net N mineralization, and net nitrification. To test whether N deposition alters the relationship between soil C and net N transformations, we collected soils from coniferous and deciduous forests, grasslands, and residential yards in 14 regions across the contiguous United States that vary in N deposition rates. We quantified rates of net nitrification and N mineralization, soil chemistry (soil C, N, and pH), and microbial biomass and function (as beta‐glucosidase (BG) and N ‐acetylglucosaminidase (NAG) activity) across these regions. Following expectations, soil C was a driver of ƒ nitrified across regions, whereby increasing soil C resulted in a decline in net nitrification and ƒ nitrified . The ƒ nitrified value increased with lower microbial enzymatic investment in N acquisition (increasing BG:NAG ratio) and lower active microbial biomass, providing some evidence that heterotrophic microbial N demand controls the ammonium pool for nitrifiers. However, higher total N deposition increased ƒ nitrified , including for high soil C sites predicted to have low ƒ nitrified , which decreased the role of soil C as a predictor of ƒ nitrified . Notably, the drop in contemporary atmospheric N deposition rates during the 2020 COVID‐19 pandemic did not weaken the effect of N deposition on relationships between soil C and ƒ nitrified . Our results suggest that N deposition can disrupt the relationship between soil C and net N transformations, with this change potentially explained by weaker microbial competition for N. Therefore, past N inputs and soil C should be used together to predict N dynamics across terrestrial ecosystems.

Nieland, Matthew A. [Stockbridge School of Agricul↗
DOE OSTI2026

Extracellular DNA Alters Detection of Subtle Bacterial Responses to Soil Rewetting

Microbial communities are often characterized using DNA-based sequencing, but these approaches also capture extracellular DNA (exDNA) released from dead cells, potentially altering inference about microbial responses to environmental change. This may be especially important during pulse disturbances, such as soil drying–rewetting, which can increase microbial mortality and transient necromass pools. We assessed whether exDNA altered inference about bacterial responses to drying–rewetting (an 80 mm simulated rainfall event following a 28-day drought) in conventionally tilled corn and perennial switchgrass soils. We quantified bacterial abundance (16 S rRNA gene copies), alpha diversity, and community composition in paired soil samples with exDNA included (+ exDNA) and in samples treated with propidium monoazide (PMAxx) to reduce amplification of exDNA (− exDNA). At our level of replication (n = 4), PMAxx treatment did not significantly alter overall temporal response patterns (i.e., no significant main effect of DNA treatment or DNA × time interaction). However, PMAxx treatment increased sensitivity to detect some pairwise temporal changes in bacterial abundance and community composition in corn soils following rewetting. exDNA pools were proportionally highest immediately after rewetting in corn soils, suggesting transient extracellular DNA may contribute to masking during disturbance recovery. In contrast, PMAxx treatment had comparatively small effects in switchgrass soils, which exhibited weaker temporal responses overall. Inclusion of exDNA also changed which taxa appeared most responsive to rewetting. Together, our results suggest that exDNA does not uniformly bias soil microbial inference, but may reduce detectability of subtle disturbance-driven shifts in certain soils. Future studies should advance knowledge of microbial turnover and necromass dynamics, particularly using multiple complementary methods, to help predict when exDNA is most likely to influence ecological inference.

drying-rewetting↗
DOE OSTI2026

Enhancing climate-smart crop performance in arid agrivoltaics systems: effects of photovoltaic shading and soil amendments on tepary bean growth, yield, and associated soil microbiome

As climate change expands the world’s arid and semiarid regions, sustainable systems that integrate food and energy production are becoming increasingly critical. Agrivoltaics—co-locating crops with photovoltaic (PV) panels—offers a dual land-use strategy that mitigates environmental stress by shading crops, conserving soil moisture, and enhancing PV efficiency. While climate-smart crops like the tepary bean ( Phaseolus acutifolius ) are well adapted to heat and drought, little is known about how these crops and their associated soil microbiomes respond to the unique microclimates created by PV shading. This study evaluated tepary bean performance and plant–microbial interactions under PV-shade vs. no shade across three soil amendment treatments at two experimental sites. We assessed plant traits including germination, phenology, biomass, height, as well as yield and bean morphology, alongside shifts in soil microbial composition and functional potential. Plants grown under PV-shade were generally taller, with extended reproductive periods and higher yields: 42% of shaded plants produced beans compared to only 8% under full sun. Shaded plants also produced rounder, higher-quality beans, whereas non-shaded plants yielded flatter, less developed beans. Microbial community composition was more strongly influenced by amendment and site conditions than by shading alone. Key microbial taxa (e.g., Glomeromycetes, Desulfobacterota ) and predicted functions (e.g., denitrification, nitrogen-respiration, sulfate reduction) were associated with differences in plant performance. Finally, combining agrivoltaic systems with targeted soil amendments can enhance crop yield and soil microbial functionality—offering a promising strategy for sustainable agriculture in arid landscapes.

14 SOLAR ENERGY↗
DOE OSTI2021

Impact of organic acids and sulfate on the biogeochemical properties of soil from urban subsurface environments

Urban subsurface environments are often different from undisturbed subsurface environments due to the impacts of human activities. For example, deterioration of underground infrastructure can introduce elevated levels of Ca, Fe, and heavy metals into subsurface soils and groundwater. Likewise, leakage from sewer systems can lead to contamination by organic C, N, S, and P. However, the impact of these organic and inorganic compounds on biogeochemical processes including microbial redox reactions, mineral transformations, and microbial community transitions in urban subsurface environments is poorly understood. Here we conducted a microcosm experiment with soil samples from an urban construction site to investigate the possible biotic and abiotic processes impacted when sulfate and acetate or lactate were introduced into an urban subsurface environment. In the top-layer soil (0-0.3 m) microcosms, which were highly alkaline (pH > 10), the major impact was on abiotic processes such as secondary mineral precipitation. In the mid-layer (2-3 m) soil microcosms, the rate of Fe(III)-reduction and the amount of Fe(II) produced were greatly impacted by the specific organic acid added, and sulfate-reduction was not observed until after Fe(III)-reduction was complete. Near the end of the incubation, some genera related to syntrophic acetate oxidation and methanogenesis were observed in the lactateamended microcosms. In the bottom-layer (7-8 m) soil microcosms, the rate of Fe(III)-reduction and the amount of Fe(II) produced were affected by the concentration of amended sulfate. Sulfate-reduction was concurrent with Fe(III)-reduction, suggesting that Fe(II) production was likely due to abiotic reduction of Fe(III) by sulfide produced by microbial sulfate reduction. The slightly acidic initial pH (~5.8) of the mid-soil system was a major factor controlling sequential microbial Fe(III) and sulfate reduction versus parallel Fe(III) and sulfate reduction in the bottom soil system, which had a neutral initial pH (~7.2). Finally, 16S rRNA gene-based community analysis revealed a variety of indigenous microbial groups including alkaliphiles, dissimilatory iron and sulfate reducers, syntrophes, and methanogens tightly coupled with, and impacted by, these complex abiotic and biogeochemical processes occurring in urban subsurface environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Partitioning sources of CO 2 emission after soil wetting using high-resolution observations and minimal models

Wetting dry soil triggers a pulse of microbial respiration. Respiration pulses after wetting can be complex, evolving through several stages before subsiding—possibly reflecting contributions from multiple carbon (C) sources. In this work we hypothesized that respiration after wetting combines C from cellular sources (notably trehalose, a cellular osmo-protectant) and soluble extracellular C made available by the physical effects of wetting, with cellular sources contributing early during the pulse and extracellular C dominating later. We tested this hypothesis by making measurements of soil respiration, microbial biomass, trehalose, and water extractable organic C after wetting dry soil in the laboratory. We then devised several alternative minimal models to evaluate the potential contributions of trehalose and extracellular C to the respiration pulse. We found that the chloroform-labile fraction of the microbial biomass was comprised of 50% trehalose in dry soil. Both trehalose and water extractable organic C pools declined rapidly after wetting; trehalose disappeared within 3 h of water addition. Chloroform-labile glucose increased 3 h after water addition and then declined, suggesting rapid hydrolysis of trehalose and consumption of the resulting glucose. Respiration dynamics after wetting could be best explained by models that included two C sources, combining rapid metabolism of trehalose with slower consumption of extracellular soluble C. These results suggest that pulses of respiration after wetting reflect both osmolyte consumption within the microbial biomass and enhanced extracellular C availability; hence, models of microbial drought response must account for both processes to fully resolve soil C dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL

Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput Fluidigm TM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N 2 fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. As a result, this research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Molecular Determination of Organic Adsorption Sites on Smectite during Fe Redox Processes Using ToF-SIMS Analysis

Turnover of soil organic carbon (SOC) is strongly affected by a balance between mineral protection and microbial degradation. However, the mechanisms controlling the heterogeneous and preferential adsorption of different types of SOC remain elusive, especially for humic substrates (HSs) and microbial carbon (MC), two hotly-debated forms of SOC prevalent in soils. In this work, the heterogeneous adsorption of HSs and MC on a clay mineral (nontronite NAu-2) during microbial-mediated Fe redox cycling was determined with the use of time-of-flight secondary ion mass spectrometry (ToF-SIMS). The results revealed that HSs pre-adsorbed on NAu-2 would partially inhibit the microbial Fe(III) reduction and structural modification of NAu-2, thus retarding the subsequent adsorption of MC. In contrast, NAu-2 without pre-coated HSs was adsorbed by a significant amount of MC from microbial polysaccharides as a result of Fe(III) reduction. This was attributed to the deposition of a thin Al-rich layer on clay surface, which provided active sites for MC adsorption. This study provides direct and detailed molecular evidence for the first time to explain the preferential adsorption of MC over HSs on the surface of clay minerals in the iron redox processes, which could be critical for the preservation of MC in soil. The results also indicate that ToF-SIMS is a unique tool for understanding complex organic-mineral-microbe interactions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning

Agricultural practices affect soil microbes which are critical to soil health and sustainable agriculture. To understand prokaryotic and fungal assembly under agricultural practices, we use machine learning-based methods. We show that fertility source is the most pronounced factor for microbial assembly especially for fungi, and its effect decreases with soil depths. Fertility source also shapes microbial co-occurrence patterns revealed by machine learning, leading to fungi-dominated modules sensitive to fertility down to 30 cm depth. Tillage affects soil microbiomes at 0-20 cm depth, enhancing dispersal and stochastic processes but potentially jeopardizing microbial interactions. Cover crop effects are less pronounced and lack depth-dependent patterns. Machine learning reveals that the impact of agricultural practices on microbial communities is multifaceted and highlights the role of fertility source over the soil depth. Machine learning overcomes the linear limitations of traditional methods and offers enhanced insights into the mechanisms underlying microbial assembly and distributions in agriculture soils.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Sulfur cycling at natural hydrocarbon and sulfur seeps in Santa Paula Creek, CA

Biogeochemical cycling of sulfur is relatively understudied in terrestrial environments compared to marine environments. However, the comparative ease of access, observation, and sampling of terrestrial settings can expand our understanding of organisms and processes important in the modern sulfur cycle. Furthermore, these sites may allow for the discovery of useful process analogs for ancient sulfur-metabolizing microbial communities at times in Earth's past when atmospheric O 2 concentrations were lower and sulfide was more prevalent in Earth surface environments. Here, we identified a new site at Santa Paula Creek (SPC) in Ventura County, CA—a remarkable freshwater, gravel-bedded mountain stream charged with a range of oxidized and reduced sulfur species and heavy hydrocarbons from the emergence of subsurface fluids within the underlying sulfur- and organic-rich Miocene-age Monterey Formation. SPC hosts a suite of morphologically distinct microbial biofacies that form in association with the naturally occurring hydrocarbon seeps and sulfur springs. We characterized the geology, stream geochemistry, and microbial facies and diversity of the Santa Paula Creek ecosystem. Using geochemical analyses and 16S rRNA gene sequencing, we found that SPC supports a dynamic sulfur cycle that is largely driven by sulfide-oxidizing microbial taxa, with contributions from smaller populations of sulfate-reducing and sulfur-disproportionating taxa. This preliminary characterization of SPC revealed an intriguing site in which to study geological and geochemical controls on microbial community composition and to expand our understanding of sulfur cycling in terrestrial environments.

58 GEOSCIENCES↗
DOE OSTI2023

Environmental microbiome engineering for the mitigation of climate change

Abstract Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune activities that regulate the long‐term stabilization of carbon in ecosystems. In this review, we outline the process of environmental engineering and synthesize key considerations about ecosystem functions to target, means of sourcing microorganisms, strategies for designing microbial inocula, methods to deliver inocula, and the factors that enable inocula to establish within a resident community and modify an ecosystem function target. Recent work, enabled by high‐throughput technologies and modeling approaches, indicate that microbial inocula designed from the top‐down, particularly through directed evolution, may generally have a higher chance of establishing within existing microbial communities than other historical approaches to microbiome engineering. We address outstanding questions about the determinants of inocula establishment and provide suggestions for further research about the possibilities and challenges of environmental microbiome engineering as a tool to combat climate change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Metagenomic clustering links specific metabolic functions to globally relevant ecosystems

ABSTRACT Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic traits of a community are needed to broaden the utility of existing data. Gene abundance profiles are a relatively low-dimensional embedding of a metagenome’s functional potential and are, thus, tractable for comparison across many samples. Here, we compare the abundance of KEGG Ortholog Groups (KOs) from 6,539 metagenomes from the Joint Genome Institute’s Integrated Microbial Genomes and Metagenomes (JGI IMG/M) database. We find that samples cluster into terrestrial, aquatic, and anaerobic ecosystems with marker KOs reflecting adaptations to these environments. For instance, functional clusters were differentiated by the metabolism of antibiotics, photosynthesis, methanogenesis, and surprisingly GC content. Using this functional gene approach, we reveal the broad-scale patterns shaping microbial communities and demonstrate the utility of ortholog abundance profiles for representing a rapidly expanding body of metagenomic data. IMPORTANCE Metagenomics, or the sequencing of DNA from complex microbiomes, provides a view into the microbial composition of different environments. Metagenome databases were created to compile sequencing data across studies, but it remains challenging to compare and gain insight from these large data sets. Consequently, there is a need to develop accessible approaches to extract knowledge across metagenomes. The abundance of different orthologs (i.e., genes that perform a similar function across species) provides a simplified representation of a metagenome’s metabolic potential that can easily be compared with others. In this study, we cluster the ortholog abundance profiles of thousands of metagenomes from diverse environments and uncover the traits that distinguish them. This work provides a simple to use framework for functional comparison and advances our understanding of how the environment shapes microbial communities.

54 ENVIRONMENTAL SCIENCES↗