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Exabiome: Advancing Microbial Science through Exascale Computing

The Exabiome project seeks to improve the understanding of microbiomes through the development of methods for accelerating metagenomic science using exascale computing. This article gives an overview of scientific impact of the three components of the project: metagenome assembly, protein family detection, and comparative analysis of metagenomes. Exabiome developed MetaHipMer, the only metagenome assembler capable of scaling to full exascale systems. MetaHipMer has enabled ground-breaking assemblies on the Frontier supercomputer, with many scientific benefits, such as the discovery of rare species and viral genomes. To investigate protein families, Exabiome developed two exascale tools, PASTIS and HipMCL. Together, these can utilize exascale resources to understand the functional diversity of billions of dark matter proteins and novel protein families. For comparative analysis, Exabiome developed kmerprof, a tool that can be used to compare huge metagenomes for many different scientific purposes, for example, grouping human microbiomes according to body location.

59 BASIC BIOLOGICAL SCIENCES↗

Synthesis, Isolation, and Study of Heterobimetallic Uranyl Crown Ether Complexes

Although crown ethers can selectively bind many metal cations, little is known regarding the solution properties of crown ether complexes of the uranyl dication, UO 2 2+ . Here, in this work, the synthesis and characterization of isolable complexes in which the uranyl dication is bound in an 18-crown-6-like moiety are reported. A tailored macrocyclic ligand, templated with a Pt(II) center, captures UO 2 2+ in the crown moiety, as demonstrated by results from single-crystal X-ray diffraction analysis. The U(V) oxidation state becomes accessible at a quite positive potential (E 1/2 ) of –0.18 V vs Fc +/0 upon complexation, representing the most positive U VI /U V potential yet reported for the UO 2 n+ core. Isolation and characterization of the U(V) form of the crown complex are also reported here; there are no prior reports of reduced uranyl crown ether complexes, but U(V) is clearly stabilized by crown chelation. Joint computational studies show that the electronic structure of the U(V) form results in significant weakening of U–O oxo bonding despite the quite positive reduction potential at which this species can be accessed, underscoring that crown-ligated uranyl species could demonstrate unique reactivity under only modestly reducing conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture

Trichoderma fungi support sustainable agriculture by suppressing plant diseases and improving crop performance. However, emerging pathogenicity of Trichoderma warrants further ecological and genetic characterization. Here we used machine learning to correlate genomic data from 37 Trichoderma strains with over 140 phenotypic traits, spanning metabolic versatility, biotic interactions, stress tolerance and reproductive strategies. We determined Trichoderma to be an ancient, genetically cohesive and physiologically diverse genus with spores capable of germination in water and dispersal via air and water droplets. Metabolic preferences indicate universal adaptation to mycoparasitism and to niches like arboreal microbial mats, alongside broader saprotrophic versatility. Our analyses are consistent with character displacement among close relatives and convergent evolution in distant lineages, with both processes shaping ecological plasticity and traits including dispersal modes, terrestrialization or endophytism. Our findings reveal that while some Trichoderma species show traits of biosafety concern, its vast ecophysiological diversity enables the development of safe, targeted bioeffectors.

Steindorff, Andrei S. [USDOE Joint Genome Institut↗

Evolutionary constraints and climate variability jointly shape starch–sugar balance in woody plants

Nonstructural carbohydrates (NSC) buffer plants against carbon imbalances, yet their partitioning between storage and soluble pools remains elusive at global scales. Here, we compiled a dataset of starch to soluble sugar ratio (St : Su) for 308 woody species across 220 sites world-wide and introduce a dimensionless index that integrates storage and demand while minimizing methodological artifacts. St : Su was strongly associated with growth, identifying it as a key axis of carbon allocation. Foliage consistently exhibited lower St : Su than lignified organs, reflecting a division between transient and conservative pools. Conifers accumulated more starch in foliage but less in stems relative to angiosperms, while leaf habits and mycorrhizal associations further modulated organ-specific strategies. Contrary to expectation, foliar and root St : Su varied little among biomes, but stems exhibited higher ratios in tropical rainforests than in boreal or arid regions, reflecting differences in species composition and adaptive storage under disturbance. Phylogeny constrained stem storage, whereas climatic variability, rather than mean conditions, dominated allocation in leaves and roots. These findings establish St : Su as a robust functional trait linking allocation strategies, growth, and resilience, which can be used to improve vegetation model prediction of forest productivity and mortality under climate variability.

Li, Weibin [Lanzhou Univ. (China)] (ORCID:00000001↗

Structural Evolution of Mixed-Addenda Keggin Polyoxometalate Anions with Atom-by-Atom Substitution

Polyoxometalates (POMs) are molecular metal oxides with distinctive electronic properties that make them promising materials for applications in energy, sensors, and memory devices. One of the most promising methods of tuning the stability, photochromic, redox, and electron-spin properties of POMs is through the substitution of the metal “addenda” atoms that, along with oxygen, constitute their cage-like structures. Because traditional synthesis methods typically produce a distribution of POMs, the isolation and characterization of multimetallic POMs with predetermined stoichiometry remains challenging. The presence of multiple energetically accessible isomers further complicates the experimental characterization and theoretical modeling of multimetallic POMs. Herein, we leverage the distinguishing mass-selection capabilities of ion soft landing to prepare stoichiometrically selected Keggin PMo x W 12-x O 40 3- (x = 0 – 6, 8, 10, and 12) POMs on self-assembled monolayer surfaces free of the solvent molecules and counterions that often confound characterization of complex species at interfaces. The structures of the supported POMs are characterized with atom-by-atom precision using in situ infrared (IR) reflection absorption spectroscopy complemented by detailed density functional theory calculations. Our joint experimental and theoretical results reveal an almost linear shift in the positions of the IR bands towards lower wavenumbers with an increase in the number of lighter molybdenum atoms compared to heavier W atoms in PMoxW 12-x O 40 3- . The theoretical calculations also indicate that numerous isomeric structures may be populated at the experimental conditions and, consequently, contribute to the overall IR spectra. In conclusion, our findings indicate that in addition to the number of substituted addenda atoms and the presence of multiple isomeric structures, interactions with the surface play an important role in determining the IR spectra and structure of supported bimetallic POMs.

Prabhakaran, Venkateshkumar [Pacific Northwest Nat↗

Hydrogen Evolution on Electrode‐Supported Pt n Clusters: Ensemble of Hydride States Governs the Size Dependent Reactivity

Abstract We report the size‐dependent activity and stability of supported Pt 1,4,7,8 for electrocatalytic hydrogen evolution reaction, and show that clusters outperform polycrystalline Pt in activity, with size‐dependent stability. To understand the size effects, we use DFT calculations to study the structural fluxionality under varying potentials. We show that the clusters can reshape under H coverage and populate an ensemble of states with diverse stoichiometry, structure, and thus reactivity. Both experiment and theory suggest that electrocatalytic species are hydridic states of the clusters (≈2 H/Pt). An ensemble‐based kinetic model reproduces the experimental activity trend and reveals the role of metastable states. The stability trend is rationalized by chemical bonding analysis. Our joint study demonstrates the potential‐ and adsorbate‐coverage‐dependent fluxionality of subnano clusters of different sizes and offers a systematic modeling strategy to tackle the complexities.

Zhang, Zisheng↗

Plant sulfate transporter protein sequences for phylogenetic analysis

Sulfur is an essential macronutrient that supports plant growth, development, and responses to environmental stress. Sulfate is the predominant inorganic form of sulfur in soils, and its uptake by roots and translocation to shoots are facilitated by the sulfate transporter (SULTR) family of proteins. Although the first plant SULTR gene was identified nearly three decades ago, several subfamily members, particularly those in the expansive and angiosperm-specific SULTR3 group, remain poorly characterized. To support comprehensive phylogenetic and sequence-based analyses, we compiled a curated dataset of 262 SULTR protein sequences from 22 plant species spanning the evolutionary breadth of land plants. This collection includes representatives from two basal lineages, two early-divergent angiosperms, six monocots, and ten dicots. All sequences were extracted from genome assemblies available in Phytozome v13 (Joint Genome Institute) and manually curated, with cross-referencing to additional databases such as NCBI when needed. This dataset provides a valuable resource for reconstructing the evolutionary history of the SULTR family, with particular emphasis on the diversification of SULTR3 transporters in flowering plants. This resource may also support functional annotation, comparative genomics, and structural modeling of sulfate transport proteins.

CBI↗

Hydrogen Evolution on Electrode–Supported Ptn Clusters: Ensemble of Hydride States Governs the Size Dependent Reactivity

We report the size-dependent activity and stability of supported Pt1,4,7,8 for electrocatalytic hydrogen evolution reaction, and show that clusters outperform polycrystalline Pt in activity, with sizedependent stability. To understand the size effects, we use DFT calculations to study the structural fluxionality under varying potentials. We show that the clusters can reshape under H coverage and populate an ensemble of states with diverse stoichiometry, structure, and thus reactivity. Both experiment and theory suggest that electrocatalytic species are hydridic states of the clusters (~2 H/Pt). An ensemble-based kinetic model reproduces the experimental activity trend and reveals the role of metastable states. Furthermore, the stability trend is rationalized by chemical bonding analysis. Our joint study demonstrates the potential- and adsorbate-coverage-dependent fluxionality of subnano clusters of different sizes and offers a systematic modeling strategy to tackle the complexities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probing physics beyond the standard model: limits from BBN and the CMB independently and combined

We present new Big Bang Nucleosynthesis (BBN) limits on the cosmic expansion rate or relativistic energy density, quantified via the number N ν of equivalent neutrino species. We use the latest light element observations, neutron mean lifetime, and update our evaluation for the nuclear rates d + d → 3 He + n and d + d → 3 H+p. Combining this result with the independent constraints from the cosmic microwave background (CMB) yields tight limits on new physics that perturbs N ν and η prior to cosmic nucleosynthesis: a joint BBN+CMB analysis gives N ν = 2.898 ± 0.141, resulting in N ν < 3.180 at 2σ. We apply these limits to a wide variety of new physics scenarios including right-handed neutrinos, dark radiation, and a stochastic gravitational wave background. The strength of the independent BBN and CMB constraints now opens a new window: we can search for limits on potential changes in N ν and/or the baryon-to-photon ratio η between the two epochs. The present data place strong constraints on the allowed changes in N ν between BBN and CMB decoupling; for example, we find -0.708 < N ν CMB - N ν BBN < 0.328 in the case where η and the primordial helium mass fraction Yp are unchanged between the two epochs; we also give limits on the allowed variations in η or in (η, N ν ) jointly. We discuss scenarios in which such changes could occur, and show that BBN+CMB results combine to place important constraints on some early dark energy models to explain the H 0 tension. Looking to the future, we forecast the tightened precision for N ν arising from both CMB Stage 4 measurements as well as improvements in astronomical 4 He measurements. Here, we find that CMB-S4 combined with present BBN and light element observation precision can give σ(N ν ) ≃ 0.03. Such future precision would reveal the expected effect of neutrino heating (N eff -3 = 0.044) of the CMB during BBN, and would be near the level to reveal any particle species ever in thermal equilibrium with the standard model. Improved Y p measurements can push this precision even further.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population

Bacterial species often undergo rampant recombination yet maintain cohesive genomic identity. Ecological differences can generate recombination barriers between species and sustain genomic clusters in the short term. But can these forces prevent genomic mixing during long-term coevolution? Cyanobacteria in Yellowstone hot springs comprise several diverse species that have coevolved for hundreds of thousands of years, providing a rare natural experiment. By analyzing more than 300 single-cell genomes, we show that despite each species forming a distinct genomic cluster, much of the diversity within species is the result of hybridization driven by selection, which has mixed their ancestral genotypes. This widespread mixing is contrary to the prevailing view that ecological barriers can maintain cohesive bacterial species and highlights the importance of hybridization as a source of genomic diversity.

Evolutionary Biology↗

TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii

Abstract Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt‐loving organism Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. However, the mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that the transcriptional regulator, TrmB, maintains the rod shape in the related species Halobacterium salinarum by activating the expression of enzyme‐coding genes in the gluconeogenesis metabolic pathway. In Hbt. salinarum , TrmB‐dependent production of glucose moieties is required for cell surface glycoprotein biogenesis. Here, we use a combination of genetics and quantitative phenotyping assays to demonstrate that TrmB is essential for growth under gluconeogenic conditions in Hfx. volcanii . The ∆ trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name t rm B s u p pressor, or TbsP (a.k.a. “tablespoon”). TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild‐type cell morphology and motility. We use functional genomics and promoter fusion assays to characterize the regulons controlled by each of TrmB and TbsP, including joint regulation of the glucose‐dependent transcription of gapII , which encodes an important gluconeogenic enzyme. We conclude that TrmB and TbsP coregulate gluconeogenesis, with downstream impacts on lifestyle transitions in response to nutrients in Hfx. volcanii .

Biochemistry & Molecular Biology↗

Cosmological parameter estimation with a joint-likelihood analysis of the cosmic microwave background and big bang nucleosynthesis

Here, we present a joint-likelihood analysis of big bang nucleosynthesis (BBN) and cosmic microwave background (CMB) data, consistently combining likelihoods and taking into account uncertainties in nuclear reaction rates for the first time. Bayesian inference is performed on the baryon abundance and the effective number of neutrino species, 𝑁 eff , using a CMB Boltzmann solver in combination with LINX , a new flexible and efficient BBN code. We marginalize over Planck nuisance parameters and nuclear rates to find 𝑁 eff =3.0⁢8$^{+0.15}_{−0.14}$, 2.9⁢4$^{+0.16}_{−0.15}$, or 2.96$^{+0.13}_{−0.14}$, for three separate reaction networks. This framework enables robust testing of the lambda cold dark matter paradigm and its variants with CMB and BBN data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Coccidioidomycosis Osteoarticular Dissemination

Valley fever or coccidioidomycosis is a pulmonary infection caused by species of Coccidioides fungi that are endemic to California and Arizona. Skeletal coccidioidomycosis accounts for about half of disseminated infections, with the vertebral spine being the preferred site of dissemination. Most cases of skeletal coccidioidomycosis progress to bone destruction or spread to adjacent structures such as joints, tendons, and other soft tissues, causing significant pain and restricting mobility. Manifestations of such cases are usually nonspecific, making diagnosis very challenging, especially in non-endemic areas. The lack of basic knowledge and research data on the mechanisms defining susceptibility to extrapulmonary infection, especially when it involves bones and joints, prompted us to survey available clinical and animal data to establish specific research questions that remain to be investigated. In this review, we explore published literature reviews, case reports, and case series on the dissemination of coccidioidomycosis to bones and/or joints. We highlight key differential features with other conditions and opportunities for mechanistic and basic research studies that can help develop novel diagnostic, prognostic, and treatment strategies.

59 BASIC BIOLOGICAL SCIENCES↗

Porous Interlayers that Getter Surface-Segregating Species for Improved Silver Wetting, Adhesion, and Electrical Contact on Stainless Steel SOFC Components

Here, porous nickel interlayers or porous platinum interlayers were shown to promote the wetting, spreading, and adhesion of silver on alumina-forming ferritic stainless steel (AFFSS) and chromia-forming ferritic stainless steel (CFFSS). These interlayers resulted in dense, crack-free AFFSS|Ag-Ni|CFFSS and AFFSS|Ag-Pt|CFFSS braze joints that, after 300 h in 650 °C air, displayed shear strengths up to 70 MPa similar to, or larger than, those of AFFSS|Ag-CuO|CFFSS or AFFSS|Ag|CFFSS joints subjected to identical treatment. Similarly, after exposure to 25 cycles of (50 switches between) 12 h of 650 °C air and 12 h of 650 °C 4%H 2 –96%N 2 , AFFSS|Ag-Ni|CFFSS and AFFSS|Ag-Pt|CFFSS braze joints displayed shear strengths significantly larger than those of AFFSS|Ag-CuO|CFFSS or AFFSS|Ag|CFFSS joints subjected to identical treatment. In addition, nickel and platinum were found to chemically getter surface-segregating steel constituents, particularly Al from the AFFSS. As a result, Ag-Ni and Ag-Pt electrical contact resistances on AFFSS and CFFSS substrates were several orders of magnitude lower than those of conventional Ag-CuO reactive air brazes or Heraeus C8710 Ag contact pastes. Together, these results suggest that Ag-Pt and especially Ag-Ni may be useful for the fabrication of durable joints, seals, and/or electrical contacts in electrical/electrochemical devices exposed to high temperatures and/or variable oxygen partial pressure environments.

36 MATERIALS SCIENCE↗

Joint Analysis of Small-scale Galaxy Clustering and Galaxy–Galaxy Lensing from BOSS Galaxies

We present a joint analysis of galaxy clustering and galaxy–galaxy lensing measurements from BOSS galaxies using a simulation-based emulation method combined with a halo occupation distribution model. Our emulators are constructed with the Aemulus ν simulations, a suite of wνCDM N-body simulations with massive neutrinos as independent particle species. We combine small-scale analysis of clustering from 0.1 to 60.2 h −1 Mpc and lensing from 1.7 to 60.2 h −1 Mpc to perform cosmological constraints. We split the BOSS galaxies into three redshift bins to measure their clustering and employ galaxies from Dark Energy Camera Legacy Survey and Hyper Suprime-Cam as source galaxies to measure lensing separately. We find that the addition of lensing significantly improves the constraining power on $S_8 = σ_8(Ω_m/0.3)^{0.5}$, with a weak improvement for fσ 8 . Our results of fσ 8 indicate tensions of around 1σ−4σ below the results of the cosmic microwave background observations of Planck. For S 8 , our results are also lower than Planck, and the tension can be mitigated when considering possible systematics in lensing measurement. As a by-product, our analysis prefers a nonzero neutrino mass but without strong significance, with the constraining power dominated by the clustering. Given the accuracy and precision of our model and the observational data, it is anticipated that larger and higher-quality spectroscopic data sets will improve the constraints on this fundamental property in the near future.

Gao, Wenhao [Shanghai Jiao Tong University (China)↗

Organic Iodide Sorption from Dilute Gas Streams

Reprocessing used nuclear fuel releases volatile radionuclides, including 129 iodine (I), into the off-gas of a processing plant. Volatile radioiodine could be present in several forms, depending on the chemistry of the process used and the off-gas stream. Inorganic I 2 is expected to be the predominant I species in the dissolver off-gas (DOG), with minor organic iodides present. The bulk of the I is expected to volatilize into the DOG in parts-per-million-level (ppm) concentrations. In contrast, in the vessel off-gas (VOG), most of the volatile I is expected to be found as organic iodides, such as CH 3 I, C 4 H 9 I, and C 12 H 25 I. These species are expected to be present in parts-per-billion-level (ppb) concentrations but require abatement, even at low expected concentrations, to meet regulatory emissions limits in the United States. Historically, studies of I abatement by Ag-functionalized sorbents have focused on inorganic I in the DOG, but in the last few years, more research attention has been given to organic iodides, especially longer chain species, such as C 4 H 9 I, and C 12 H 25 I. This report has three main goals: (1) to present new data generated at Oak Ridge National Laboratory (ORNL) in FY21 on the sorption behavior of organic iodides on AgZ, (2) to summarize and synthesize organic iodide data produced by ORNL and Idaho National Laboratory (INL) over the last 4 years to answer questions on organic iodides behavior outlined in the 2018 joint test plan (Jubin et al. 2018), and (3) to propose a VOG abatement system design that can provide the capture efficiencies required to meet I emission limits. The 2021 ORNL experimental campaign tested the effects of organic iodide speciation and concentration in the off-gas, superficial velocity of the off-gas, and effects of aging on AgZ sorbent capacity. These studies found that the sorption rate of organic iodides by AgZ depends on the hydrocarbon chain length and the concentration in the off-gas. Higher molecular weight organic iodides adsorb to AgZ more slowly than I. At a concentration of 50 ppm concentration in the off-gas, CH 3 I loads 8% slower, C 4 H 9 I loads 20% slower, and C 12 H 25 I loads 40% slower than I. The lowest concentration loading rates calculated were in 5 ppm organic iodide gas streams in which AgZ gained on average 0.14 mg I/g sorbent/hour in the bench scale test system. Thus, longer sorbent beds might be needed to accommodate slower loading rates onto AgZ in lower concentration gas streams. Although sorption rate varies as a function of hydrocarbon chain length, the saturation concentration of the sorbent for these I-bearing species does not vary. Aging AgZ in a humid air stream for 9 months drops the overall sorbent capacity by ~35% for CH 3 I, ~50% for C 4 H 9 I, and ~40% for C 12 H 25 I. This results in a saturation capacity between 35 and 70 mg I/g sorbent for the aged AgZ. In conjunction with recent data produced by INL, these data are used to estimate the mass transfer zone (MTZ) and decontamination factor (DF) for sorbent beds of AgZ. Sorption tests performed with iodide gas concentrations of about 1 ppm and higher at a superficial gas velocity of 10 m/min, indicate that MTZ depths for these conditions tend to range between about 8-20 cm. Tests performed at lower concentrations between 50-90 ppb and at gas superficial velocities of 1, 10, and 20 m/min indicate that the MTZ depth increases with increasing superficial gas velocity. The 20 m/min test indicates that the MTZ for those conditions was at least 22 cm, and doubling the superficial gas velocity from 10 to 20 m/min could roughly double or triple the MTZ depth. Doubling and tripling the bounding MTZ depth of 20 cm for the body of MTZ estimates made at with 10 m/min superficial velocity would extend the MTZ for a superficial velocity of 20 m/min to 40-60 cm. This bounding limit applies to all of the organic iodides that have been tested. These results also indicate that the sorption rate-limiting step is not sensitive to the superficial gas velocity; otherwise the MTZ depth would not have increased approximately in proportion to the increase in the gas superficial velocity. This further suggests that the rate limiting step is not associated with mass transfer of the sorbate to the sorbent surface, or mass transfer of the reaction byproducts from the sorbent surface, but is associated with sorption or chemical reactions on the sorbent surface or in sorbent pores. Deep bed testing at INL has established DFs of >2,000 for I, CH 3 I, and C 4 H 9 I under a range of conditions (Soelberg et al. 2021, Bruffey et al. 2019). DF does not seem to be affected by the concentration of the organic iodide in the gas stream over the range of 1 to 50 ppm. Thus, if the MTZ is accommodated in sorbent bed design for the DOG and VOG, then regulatory DFs will be met. To meet the third objective outlined in this report, these experimental data were used to update an engineering evaluation of the VOG first completed in 2016. The updated VOG design can be found in an accompanying document (Welty et al., 2021; INL- LTD-21-64587). This report finds that the VOG will decrease in both size and complexity, relative to previous designs, and will still meet regulatory requirements for all iodine forms.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

eDNAjoint: An R package for interpreting paired or semi‐paired environmental DNA and traditional survey data in a Bayesian framework

Abstract Environmental DNA (eDNA) sampling is increasingly used in surveys of species distribution as a potentially sensitive and efficient monitoring method. Yet access to modelling tools designed specifically for interpreting this new data type lags behind its ubiquity. While occupancy modelling software has dominated the analytical landscape for eDNA data analysis of single species, this type of model may not always be the most appropriate. The rate of eDNA detection often corresponds to species density, rather than just occupancy, and researchers often have access to observations from non‐genetic sampling methods at the same sites. To provide users access to a modelling framework designed to maximize the use of all available data, we developed an R package, eDNAjoint . The package provides an easy‐to‐use interface for fitting a ‘joint’ model that integrates data from paired or semi‐paired eDNA and traditional surveys in a Bayesian framework. The model can be used to estimate parameters like the probability of a false positive eDNA detection and mean catch rate at a site, and the package allows access to multiple model variations and Bayesian prior customization. Additional functionality can be used for model selection, summarising posteriors and comparing the relative sensitivities of the two survey methods. We demonstrate the use of eDNAjoint by fitting a variation of the model with site‐level covariates that scale the sensitivity of eDNA sampling relative to traditional sampling. The example workflow uses binary eDNA and seine count data for the endangered tidewater goby ( Eucyclogobius newberryi ) from a study by Schmelzle and Kinziger (2016). This use case includes a prior sensitivity analysis and an evaluation of the relationship between detection rates and environmental variables. eDNAjoint has the potential to greatly increase the range of users who will be able to rigorously analyse eDNA and traditional survey data in a Bayesian framework, understand if and how eDNA can improve monitoring practices, and gain confidence in the interpretability of eDNA data.

Keller, Abigail G. [Department of Environment Scie↗

Identification of Adaptive Fungal Pathogen Resistance Loci in Switchgrass (Final Report)

Switchgrass (Panicum virgatum) has great potential as a sustainable bioenergy and bioproducts feedstock. However, there are a number of challenges that must be overcome to achieve this goal. One of the most significant challenges to switchgrass productivity are fungal pathogens, especially rusts and smuts. The primary goals of our project were to characterize the distribution of fungal pathogens on switchgrass across central North America and to identify genetic loci that control resistance to those pathogens. The research was primarily conducted with large common garden plantings of a switchgrass, distributed along a latitudinal gradient from South Texas to South Dakota. By conducting this research simultaneously at 10 field locations, we were able establish the relative contributions of genes and the environment to pathogen resistance. Through this research, we identified multiple genomic regions (loci) that contribute to rust resistance and found that the effects of these loci on resistance were highly influenced by field site location. Our research revealed that most of the rust damage to switchgrass from Texas to the northern United States is caused by a single fungal species, Puccinia novopanici. Therefore, genetic variation within this species and/or local environmental conditions are responsible for the inconsistent efficacy of pathogen resistance loci. We are currently investigating these two non-mutually exclusive hypotheses. In addition to our studies of rust pathogens, we were able to identify resistance loci for the head smut fungal pathogen Tilletia maclaganii. The funding from this grant facilitated a collaboration with the DOE Joint Genome Institute to develop a reference genome for T. maclaganii. A reference genome will make population genetic studies of this smut fungus possible, which in turn will facilitate the development of strategies to mitigate its impact. Overall, the funded research has greatly advanced our understanding of the genetic basis of fungal pathogen resistance switchgrass. This knowledge will help facilitate the breeding of more resistant cultivars and thus, increase the productivity of swichgrass generally.

09 BIOMASS FUELS↗