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DOE OSTI2026

Solid-State Side-Chain Functionalization of Conjugated Polymers for Expanded Chemical and Functional Versatility

Conjugated polymers that integrate diverse chemical functionalities with high electronic performance are essential for advanced organic electronic, optoelectronic, and biointerfaced technologies. Achieving such multifunctionality typically requires grafting functional units onto polymer side chains. However, conventional solution-phase approaches remain constrained by solubility limitations, side-chain-induced packing disruptions, and challenges in preserving charge transport. Here, we introduce a solid-state side-chain functionalization strategy that exploits a swellable polar side-chain architecture and azide–alkyne click chemistry to enable efficient molecular diffusion and reaction throughout predeposited polymer thin films. This approach substantially broadens the chemical compatibility of graftable units and mitigates the adverse effects on the electrical property. Moreover, the method supports spatially selective functionalization within a continuous film, enabling the patterned incorporation of chemically distinct groups to produce spatially defined optical properties. Here, this solid-state strategy thus provides a versatile platform for constructing conjugated polymers with expanded chemical versatility, preserved electronic performance, and programmable spatial functionality.

Conjugated polymers↗

DOE OSTI2025

OzMALDI: A Gas-Phase, In-Source Ozonolysis Reaction for Efficient Double-Bond Assignment in Mass Spectrometry Imaging with Matrix-Assisted Laser Desorption/Ionization

Lipids make up an important class of biomolecules with diverse structures and varied chemical functions. This diversity is a major challenge in chemical analysis and limits our understanding of biological functions and regulation. A major way lipid isomers differ is by double-bond (db) position, and analyzing db-isomers is especially challenging for mass spectrometry imaging (MSI). Ozonolysis can be used to determine the dbposition and has been paired with MSI before. However, previous techniques require increased analysis time to allow for gas-phase reactions within an ion trap or ion mobility cell or additional sample preparation time to allow for offline ozonation. Here, we introduce a new ozonolysis method inside the matrix-assisted laser desorption-ionization (MALDI) source, termed OzMALDI, that simultaneously produces ozonides from all unsaturated lipids. This allows us to determine db-positions without adding additional reaction time while maintaining the high mass resolution provided by Orbitrap MS. This new technique is especially effective at determining multiple db-positions in lipids containing polyunsaturated fatty acids, which is a limitation of many previous techniques. OzMALDI-MSI was applied to the analysis of rat brain and genetically engineered Camelina and soybean seed samples, demonstrating the utility of this method and uncovering novel biological information.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

A genomic view of Earth’s biomes

Microorganisms are essential to all life on Earth through critical roles in key biological processes and diverse interactions with other organisms that shape ecosystems, drive biogeochemical cycles and influence both human health and environmental health. High-throughput sequencing from environmental samples has revolutionized the understanding of microbial diversity and functions. With vast amounts of genomes now available across Earth’s biomes, these data provide a blueprint of microbial life that can be harnessed for a more holistic understanding of microbiome structure and function across the various ecosystems on Earth. Here we review the application of genome-centric approaches, including recent advances in single-cell sequencing and functional profiling, to survey microbial and viral diversity. Furthermore, we highlight some of the most impactful evolutionary and functional discoveries, explore the spatial diversity and temporal dynamics of microorganisms across diverse environments, and discuss genome-enabled insights into host-associated microorganisms.

Ecology↗

DOE OSTI2026

Cellulose-MOFs hybrid materials: Chemistry and mechanism of applications in biomedical - A review

Rising costs and performance limits of modern biomedical materials motivate the search for advanced, biocompatible alternatives. Cellulose-based metal-organic frameworks (cellulose-MOFs) emerge as distinctive hybrids combining renewable polymer chemistry with tunable porous architectures, enabling uncommon structure–function relationships. Their large surface area, controllable pore size, adaptable functional groups, and efficient host–guest interactions underpin diverse biomedical functions. Till now, no comprehensive, application-focused review has systematically summarized cellulose-MOFs synthesis for biomedical applications. This review critically analyzes cellulose-MOFs, emphasizing mechanistic links between chemistry, synthesis routes, interfacial interactions, and biomedical performance, rather than cataloging applications alone. Antibacterial action, targeted drug delivery, and sensing/biosensing are discussed through comparative insights. The article identifies unresolved challenges and proposes future research pathways to rationally design next-generation cellulose-MOFs systems, guiding researchers and clinicians alike.

Biomedical↗

DOE OSTI2026

nf-core/proteinfamilies: a scalable pipeline for the generation of protein families

The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.

Nextflow↗

DOE OSTI2025

Rooting for function: community‐level fine‐root traits relate to many ecosystem functions

Humans are driving biodiversity change, which also alters community functional traits. However, how changes in the functional traits of the community alter ecosystem functions—especially belowground—remains an important gap in our understanding of the consequences of biodiversity change. We test hypotheses for how the root traits of the root economics space (composed of the collaboration and conservation gradients) are associated with proxies for ecosystem functioning across grassland and forest ecosystems in both observational and experimental datasets from 810 plant communities. First, we assessed whether community-weighted means of the root economics space traits adhered to the same trade-offs as species-level root traits. Then, we examined the relationships between community-weighted mean root traits and aboveground biomass production, root standing biomass, soil fauna biomass, soil microbial biomass, decomposition of standard and plot-specific material, ammonification, nitrification, phosphatase activity, and drought resistance. We found evidence for a community collaboration gradient but not for a community conservation gradient. Yet, links between community root traits and ecosystem functions were more common than we expected, especially for aboveground biomass, microbial biomass, and decomposition. These findings suggest that changes in species composition, which alter root trait means, will in turn affect critical ecosystem functions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Complementary effects of supplemental feeding and straw retention on winter biodiversity in rice agroecosystems

Rice paddies are both major food-production systems and critical winter habitats for wildlife. In the Civilian Control Zone (CCZ) adjoining the Korean Demilitarized Zone (DMZ), post-harvest interventions such as supplementary grain feeding and straw retention are promoted through agronomic and conservation incentives. These measures differ in ecological scope: feeding provides direct, concentrated energetic subsidies, whereas straw management alters habitat structure and resource bases. We clarified whether these pathways function in complementary or substitutive ways to support resilient, long-term conservation strategies in rice agroecosystems. Using camera traps, we evaluated the effects of three straw treatments (chopped-straw, whole-straw, straw-removed) and supplemental feeding on winter bird and mammal communities across 48 rice fields in the CCZ. Our results demonstrate that feeding produced strong, localized increases in bird abundance and richness, driven mainly by cranes (Grus japonensis and Antigone vipio) and geese (Anser spp.), with limited effects on Shannon diversity or functional structure. Among non-feeding fields, chopped-straw paddies consistently supported higher richness and Shannon diversity than whole-straw or straw-removed fields, while centroid shifts in taxonomic and functional space were modest. Mammal abundance and diversity were largely insensitive to feeding or straw regimes, varying instead with road and forest distance and regional context. Supplemental feeding and straw retention are therefore not interchangeable tools: feeding concentrates a few avian guilds, whereas chopped-straw retention enhances baseline diversity across farmland. Collectively, our findings suggest integrating low-input straw retention with targeted feeding offers a more robust pathway for sustaining winter biodiversity in rice agroecosystems.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Bacterial and fungal growth on fungal necromass and its diverse components: Shared profiles and divergent constraints revealed by high‐throughput phenotyping

1. While fungal necromass is increasingly recognized as a major source of persistent carbon (C) in soils, the relative functional roles of bacteria and fungi in decomposing necromass are not fully resolved, and the processes that select for necromass decomposer communities from the broader soil microbial community are an emerging area of interest. 2. In this study, we characterized the growth of 52 bacterial and 83 fungal strains isolated from necromass and soil on 22 C substrates, including different necromass phenotypes, fungal cell wall polymers, dimers and monomers. 3. We found that the isolation habitat of the strains used in this experiment (necromass vs. soil) had no effect on the substrates they were able to use. Isolates from both microbial domains were able to grow on different labile carbon substrates, polymers and necromass phenotypes. However, fungal growth was most limited by necromass melanin content, while bacterial growth was more limited by the abundance of cell wall polysaccharides. Additionally, overall differences in substrate use between bacteria and fungi were most pronounced on polymer substrates. 4. Collectively, our results suggest that there is substantial functional overlap in necromass substrate use across microbial domains, but some notable differences in bacterial and fungal utilization of cell wall polymers, which can function as a direct energy source or a means of accessing other compounds within necromass. Future studies assessing bacteria and fungi decomposing necromass together rather than in isolation will help to uncover potential physical and chemical interactions within and between these two domains during the decay of this important source of persistent soil C.

dead fungal biomass↗

DOE OSTI2026

Cross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screens.

Bacteriophages are being cataloged at an accelerating pace and are recognized as key players in nutrient and energy cycling across ecosystems. Yet the bacterial genetic determinants that govern phage-host specificity and infection success remain poorly understood, particularly in clinically and ecologically important genera such as Klebsiella where prior receptor characterization has been almost entirely limited to capsulated strains. Here we used a randomly barcoded, genome-wide, loss-of-function transposon mutant library (RB-TnSeq) of Klebsiella sp. M5al, a naturally acapsular, nitrogen-fixing rhizobacterium, to generate the first systematic, cross-family map of phage receptor gene dependencies in Klebsiella. Challenging the library against 25 double-stranded DNA phages spanning five families in 213 parallel assays, we identified 42 bacterial genes associated with phage infection, of which 15 had no prior association with phage infection in any bacterial system. Disruption of surface receptor biosynthesis genes conferred cross-resistance across multiple phage families, while intracellular gene disruptions had predominantly phage-specific effects. Clonal validation of eight genes confirmed LPS outer core biosynthesis genes as primary receptor determinants alongside additional host factors spanning outer membrane transport, cofactor biosynthesis, and two-component signaling. Comparative analysis across all 25 phages revealed that phage genus rather than family is the stronger predictor of host gene dependency profiles, a finding with direct implications for the functional annotation of uncharacterized phage isolates and rational phage cocktail design. Together, these findings provide a community resource for linking phage genomic diversity to functional host interaction space in this ecologically and clinically important genus.

Gittrich, Marissa R↗

DOE OSTI2024

Rooting for survival: how plants tackle a challenging environment through a diversity of root forms and functions

Abstract The current climate crisis has global impacts and will affect the physiology of plants across every continent. Ensuring resilience of our agricultural and natural ecosystems to the environmental stresses imposed by climate change will require molecular insight into the adaptations employed by a diverse array of plants. However, most current studies continue to focus on a limited set of model species or crops. Root systems are particularly understudied even though their functions in water and nutrient uptake are likely pivotal for plant stress resilience and sustainable agriculture. In this review, we highlight anatomical adaptations in roots that enable plant survival in different ecological niches. We then present the current state of knowledge for the molecular underpinnings of these adaptations. Finally, we identify areas where future research using a biodiversity approach can fill knowledge gaps necessary for the development of climate-resilient crops of the future.

Plant Sciences↗

DOE OSTI2025

Harnessing the Power of Machine Learning and Omics to Identify Environmental Regulation on Microbial Functional Composition for Soil C, N, and P Cycling

Microbial enzyme-mediated soil organic matter (SOM) decomposition regulates many key ecosystem functions, such as elemental cycling, soil carbon sequestration, and soil fertility. However, representing microbial processes in Earth system models (ESMs) remains challenging due to a limited understanding of the spatial patterns of diverse microbial functions responsible for soil carbon (C), nitrogen (N), and phosphorus (P) cycling as well as the underlying mechanisms regulating their relative abundances across various environments. We collected published metagenomics data across the continental US (CONUS) to identify hundreds of microbial genes involved in soil C, N, and P cycling and grouped them into eight enzyme functional classes (EFCs). Each EFC represented a group of gene-encoded potential enzymes that decompose similar soil compounds. By integrating the abundances of omics-informed EFCs with the corresponding environmental information, we trained a machine learning (ML) model to identify key edaphic, climate, and vegetation factors regulating the abundances of each EFC. Quantitative analysis of effects of these factors revealed that the spatial distribution of eight EFCs for soil C, N, and P cycling across CONUS reflected potential resource optimization strategies of microbial communities under nutrient limitation, preferential organic-mineral associations, and climatological stresses. This insight, together with the interpreted ML tool and the CONUS-level benchmark for EFCs abundances, paves the way for parameterizing environmental-regulated microbial functional dynamics in biogeochemical models.

machine learning↗

DOE OSTI2025

The microbiologist's guide to metaproteomics

Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.

bioinformatics↗

DOE OSTI2026

Transcriptomic and functional analyses uncover a conserved effector driving genotype-dependent virulence in the Sphaerulina musiva-Populus trichocarpa interaction

The introduction of invasive microbes compromises the structure, biodiversity, and function of naïve ecosystems. Sphaerulina musiva, a hemibiotrophic pathogen that causes leaf spot and stem cankers in Populus species, exemplifies an invasive fungal pathogen spread by human activities. However, the genetic mechanisms of pathogenicity and virulence are poorly understood, impeding mitigation strategies. We utilized RNA sequencing to identify fungal effectors linked to stem canker formation, informing the development of future strategies for effective disease management. Our analysis revealed 70 genes differentially expressed at 2 weeks and 110 genes at 3 weeks between inoculated trees and controls. Notably, the gene with the highest expression at 2 weeks and the second highest at 3 weeks was homologous to Extracellular protein 2 (Ecp2). Complementary genome-wide association studies linked sequence polymorphisms in this locus to phenotypic variation in disease severity. Infiltration of S. musiva Ecp2 into Populus trichocarpa leaves induced necrosis in susceptible genotypes. Gene disruption using a CRISPR-Cas9 RNP system resulted in a genotype-dependent reduction of stem canker and disease severity. Tracing the evolutionary history of this effector across the fungal kingdom, we uncovered clade-specific gene-family expansions and orthologs in new species. These findings raise questions about the function and adaptive significance of these gene families in fungal lifestyles. Our study provides the first tractable target for breeding resistant poplar genotypes, addressing the challenges of managing S. musiva and uncovering mechanisms that drive its virulence, and provides deeper insights into the evolutionary dynamics of a conserved small-secreted protein with a diversity of functions.

Sondreli, Kelsey L [Oregon State University]↗

DOE OSTI2025

Transcription factor binding divergence drives transcriptional and phenotypic variation in maize

Regulatory elements are essential components of plant genomes that have shaped the domestication and improvement of modern crops. However, their identity, function and diversity remain poorly characterized, limiting our ability to harness their full power for agricultural advances using induced or natural variation. Here, in this study, we mapped transcription factor (TF) binding for 200 TFs from 30 families in two distinct maize inbred lines historically used in maize breeding. TF binding comparison revealed widespread differences between inbreds, driven largely by structural variation, that correlated with gene expression changes and explained complex quantitative trait loci such as Vgt1, an important determinant of flowering time, and DICE, an herbivore resistance enhancer. CRISPR–Cas9 editing of TF binding regions validated the function and structure of regulatory regions at various loci controlling plant architecture and biotic resistance. Our maize TF binding catalogue identifies functional regulatory regions and enables collective and comparative analysis, highlighting its value for agricultural improvement.

Galli, Mary [Rutgers Univ., Piscataway, NJ (United↗

DOE OSTI2025

A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes

Plasmids play significant roles in microbial adaptation to ecosystems, yet their dynamics remain poorly understood due to identification challenges. We present the Global Soil Plasmidome Resource (GSPR), a comprehensive dataset of 98,728 plasmid sequences amassed from 6860 terrestrial microbial communities and isolates. We explore this resource through various computational approaches, including phylogenetic diversity analysis, host prediction, and extensive functional annotation, to understand the contribution of plasmids to the genetic and functional diversity in soil, correlating these findings with sample type, as well as the soil habitat they were retrieved from. Our analysis reveals insights into plasmid-encoded functions such as effector modules, quorum sensing, and stress resistance, which may contribute to their persistence and microbial adaptation in soil. Furthermore, CRISPR analysis suggests a prevalent role of these elements related to intra-plasmid competition. By contrasting plasmids from cultivated and uncultivated organisms, we identify important functions that expand existing knowledge of plasmid roles in these habitats. This study represents a notable step forward in elucidating plasmid diversity and function within soil microbiomes and establishes a foundational framework for exploring their roles in natural environments.

Fiamenghi, Mateus B↗

DOE OSTI2025

Produced Water DNA Database (PW-DNA): Utilizing KBase to generate an environmental specific curated molecular database

The deep subsurface is estimated to host the majority of Earth’s microbial biomass yet remains one of the most challenging environments to access and study. One common approach to investigate these microbial communities is through the analysis of produced water from subsurface reservoirs, where researchers can assess water and gas chemistry along with molecular (DNA/RNA) sequence data. Advances in high-throughput sequencing have greatly expanded our understanding of these environments and their biotechnological potential. However, further progress requires large-scale, integrative meta-analyses across diverse datasets. To address this need, we developed the Produced Water-DNA (PW-DNA) Database, a curated, publicly available resource that consolidates microbial DNA/RNA sequences, geochemical data, and relevant metadata from in situ hydrocarbon environments such as coal beds, oil reservoirs, and natural gas systems. The PW-DNA database delivers three core benefits to the research community: (1) it improves data sharing by linking environmental microbial datasets with corresponding geochemical parameters, enabling more robust filtering and analysis; (2) it connects with complementary research databases to promote broader dissemination and interoperability; and (3) it supports technological innovation by serving as a resource for identifying microbial trends and exploring genetic potential. While individual studies have highlighted basin-specific microbial communities and functional redundancy in biogeochemical cycling, a comprehensive, system-wide perspective is needed to better understand connectivity and novelty across subsurface ecosystems. By designing the PW-DNA in the KBase platform, we provide a reproducible, visual framework for integrating large-scale genomic and geochemical data, enabling researchers to perform more informed analyses and experimental design. Ultimately, this resource enhances the ability to identify, characterize, and interpret microbial functions across diverse subsurface environments, thereby accelerating discovery in subsurface microbiology and biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Henry’s Solubility and Diffusion Coefficients for 29 Volatile Organic Compounds in Polydimethylsiloxane Sylgard 184 at 293 K

Two-dimensional (2D) inverse gas chromatography (IGC) enables simultaneous determination of Henry’s solubility and Fickian diffusion coefficients for volatile organic compounds (VOCs) in polymer films. This technique offers a significant advantage over traditional cylindrical column IGC by providing precise control and measurement of the film thickness (here, 0.064 ± 0.002 mm), which is the critical length scale for accurate diffusivity determination. We apply this methodology to characterize VOC transport in Sylgard 184, a widely used polydimethylsiloxane (PDMS)-based polymer containing substantial silica filler content. At room temperature (20 °C), we measured solubility and diffusion coefficients for 29 common VOCs spanning diverse chemical functionalities, including alkanes, aromatics, chlorinated solvents, ketones, esters, and alcohols. Comparison with literature data for pure PDMS reveals that VOC solubility in Sylgard 184 is generally higher; for most non-hydrogen-bonding compounds it remains within a factor of 2 of pure PDMS, whereas alcohols are enhanced by roughly 1.8 to 3.7 times, which we attribute to favorable interactions with residual silanol groups on the silanized silica filler. Diffusion coefficients range from 1.0 × 10 –6 cm 2 /s (n-undecane) to 8.9 × 10–5 cm 2 /s (acetonitrile) and align well with extrapolated literature values for PDMS. This study provides essential thermodynamic and transport data for predicting VOC permeation in Sylgard 184 while demonstrating the utility of 2D IGC as a robust technique for characterizing rubbery polymer membranes across diverse industrial applications.

organic↗

DOE OSTI2024

Cultural Shifts in High Energy Physics Collaboration from the Cold War to the Present: A Historical and Philosophical Perspective

Here, this article employs empirical history and the philosophy of science to study cultural convergences and divergences in international collaborations in high energy physics. We examine two cases: (1) E-36, an experiment on small angle proton-proton scattering conducted during the Cold War at the National Accelerator Laboratory (NAL) in the USA by Soviet and US scientists and (2) an ongoing collaborative experiment, NICA, at the Joint Institute for Nuclear Research (JINR, Dubna), which is a project devoted to heavy-ion physics. The JINR, particularly its Laboratory of High Energy Physics (formerly the “Laboratory of High Energies”) is the main mediating actor between these two cases (i.e., E-36 and NICA), as the majority of Soviet participants in E-36 were representatives of the Institute. Using empirical data collected through archival searches, field observations conducted at JINR in 2018–2019, and in-depth interviews, we tell a story of cultural differences in high energy physics by applying the concepts of ‘trading zones’ (P. Galison) and the translation of interests in actor-networks (B. Latour, M. Callon and others). We analyze three types of cultural diversity (specialization, nationality, and generational) in light of the implications of temporal context and the dichotomy between East and West, showing the roles cultural diversity plays in scientific collaboration (which is an integral part of as well as obstacle to scientific research that can nevertheless provide learning opportunities). Our study aims to demonstrate how disunity and diversity may function in scientific research and how high energy physics collaborations can remain productive despite sometimes deep divergences, including those between East and West.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗