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At least 1,369 records · Page 76
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome

Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala), which provides increased plant performance and greater tolerance to environmental stress compared to endophyte-free tall fescue. Whether this enhanced performance of tall fescue exclusively results from the grass–fungus symbiosis, or this symbiosis additionally results in the recruitment of soil microbes in the rhizosphere that in turn promote plant growth, remain a question. We investigated the soil bacterial and fungal community composition in iron-rich soil in the southeastern USA, and possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Our data revealed that plant-available phosphorus (P) was significantly (p < 0.05) influenced by endophyte infection in tall fescue. While the prominent soil bacterial phyla were similar, a clear fungal community shift was observed between endophyte-infected (E+) and endophyte-free (E−) tall fescue soil at the phylum level. Moreover, compared to E− soil, E+ soil showed a greater fungal diversity at the genus level. Our results, thus, indicate a possible three-way interaction between tall fescue, fungal endophyte, and soil fungal communities resulting in improved tall fescue performance.

Mahmud, Kishan↗
DOE OSTI2024

Relationships between Habitual Polyphenol Consumption and Gut Microbiota in the INCLD Health Cohort

While polyphenol consumption is often associated with an increased abundance of beneficial microbes and decreased opportunistic pathogens, these relationships are not completely described for polyphenols consumed via habitual diet, including culinary herb and spice consumption. This analysis of the International Cohort on Lifestyle Determinants of Health (INCLD Health) cohort uses a dietary questionnaire and 16s microbiome data to examine relationships between habitual polyphenol consumption and gut microbiota in healthy adults (n = 96). In this exploratory analysis, microbial taxa, but not diversity measures, differed by levels of dietary polyphenol consumption. Taxa identified as exploratory biomarkers of daily polyphenol consumption (mg/day) included Lactobacillus, Bacteroides, Enterococcus, Eubacterium ventriosum group, Ruminococcus torques group, and Sutterella. Taxa identified as exploratory biomarkers of the frequency of polyphenol-weighted herb and spice use included Lachnospiraceae UCG-001, Lachnospiraceae UCG-004, Methanobrevibacter, Lachnoclostridium, and Lachnotalea. Several of the differentiating taxa carry out activities important for human health, although out of these taxa, those with previously described pro-inflammatory qualities in certain contexts displayed inverse relationships with polyphenol consumption. Our results suggest that higher quantities of habitual polyphenol consumption may support an intestinal environment where opportunistic and pro-inflammatory bacteria are represented in a lower relative abundance compared to those with less potentially virulent qualities.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Variation in Gene Expression between Two Sorghum bicolor Lines Differing in Innate Immunity Response

Microbe associated molecular pattern (MAMPs) triggered immunity (MTI) is a key component of the plant innate immunity response to microbial recognition. However, most of our current knowledge of MTI comes from model plants (i.e., Arabidopsis thaliana) with comparatively less work done using crop plants. In this work, we studied the MAMP triggered oxidative burst (ROS) and the transcriptional response in two Sorghum bicolor genotypes, BTx623 and SC155-14E. SC155-14E is a line that shows high anthracnose resistance and the line BTx623 is susceptible to anthracnose. Our results revealed a clear variation in gene expression and ROS in response to either flagellin (flg22) or chitin elicitation between the two lines. While the transcriptional response to each MAMP and in each line was unique there was a considerable degree of overlap, and we were able to define a core set of genes associated with the sorghum MAMP transcriptional response. The GO term and KEGG pathway enrichment analysis discovered more immunity and pathogen resistance related DEGs in MAMP treated SC155-14E samples than in BTx623 with the same treatment. The results provide a baseline for future studies to investigate innate immunity pathways in sorghum, including efforts to enhance disease resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Auxin-Producing Bacteria from Duckweeds Have Different Colonization Patterns and Effects on Plant Morphology

The role of auxin in plant–microbe interaction has primarily been studied using indole-3-acetic acid (IAA)-producing pathogenic or plant-growth-promoting bacteria. However, the IAA biosynthesis pathway in bacteria involves indole-related compounds (IRCs) and intermediates with less known functions. Here, we seek to understand changes in plant response to multiple plant-associated bacteria taxa and strains that differ in their ability to produce IRCs. We had previously studied 47 bacterial strains isolated from several duckweed species and determined that 79% of these strains produced IRCs in culture, such as IAA, indole lactic acid (ILA), and indole. Using Arabidopsis thaliana as our model plant with excellent genetic tools, we performed binary association assays on a subset of these strains to evaluate morphological responses in the plant host and the mode of bacterial colonization. Of the 21 tested strains, only four high-quantity IAA-producing Microbacterium strains caused an auxin root phenotype. Compared to the commonly used colorimetric Salkowski assay, auxin concentration determined by LC–MS was a superior indicator of a bacteria’s ability to cause an auxin root phenotype. Studies with the auxin response mutant axr1-3 provided further genetic support for the role of auxin signaling in mediating the root morphology response to IAA-producing bacteria strains. Interestingly, our microscopy results also revealed new evidence for the role of the conserved AXR1 gene in endophytic colonization of IAA-producing Azospirillum baldaniorum Sp245 via the guard cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Isolation of Methane Enriched Bacterial Communities and Application as Wheat Biofertilizer under Drought Conditions: An Environmental Contribution

The search for methanotrophs as plant-growth-promoting rhizobacteria (PGPR) presents an important contribution to mitigating the impact of global warming by restoring the natural soil potential for consuming methane while benefiting plants during droughts. Our in silico simulations suggest that water, produced as a byproduct of methane oxidation, can satisfy the cell growth requirement. In addition to water, methanotrophs can produce metabolites that stimulate plant growth. Considering this, we proposed that applying methanotrophs as PGPR can alleviate the effect of droughts on crops, while stimulating atmospheric methane consumption. In this work, we isolated a series of methanotrophic communities from the rhizospheres of different crops, including Italian sweet pepper and zucchini, using an atmosphere enriched with pure methane gas, to determine their potential for alleviating drought stress in wheat plants. Subsequently, 23 strains of nonmethanotrophic bacteria present in the methanotrophic communities were isolated and characterized. We then analyzed the contribution of the methane-consuming consortia to the improvement of plant growth under drought conditions, showing that some communities contributed to increases in the wheat plants’ lengths and weights, with statistically significant differences according to ANOVA models. Furthermore, we found that the presence of methane gas can further stimulate the plant–microbe interactions, resulting in larger plants and higher drought tolerance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Performance of Closed Loop Venturi Aspirated Aeration System: Experimental Study and Numerical Analysis with Discrete Bubble Model

In wastewater treatment plants, aeration plays a significant role as it encourages aerobic respiration of microbes, which are necessary to break down carbonaceous matter in the waste stream. This process can account for the majority of energy use in wastewater treatment plants. The aeration process is also necessary in odor control in lagoons and in the aquaculture industry. Generally, the aeration process is accomplished with compressors or blowers which can be of low efficiency due to ideal gas laws. This study introduces the idea of increasing aeration efficiency by looping water from a reservoir through a piping network which includes a venturi aspirator at its inlet. For this purpose, an experimental study has been conducted in a laboratory setup with a pump which pulls water from a tank, passes it through a Venturi aspirator and a helical piping network intended to increase bubble residence time, before depositing it back into the bulk fluid tank. This same process is modeled computationally, using a discrete bubble method (DBM), with good agreement with experiments. The overall purpose here is to determine the optimal configurations for standard aeration efficiency (SAE) and the standard oxygen transfer rate (SOTR). A parametric study has been implemented using the DBM based on different hydraulic and flow parameters. The model is also used to predict the SAE of a hypothetical aeration system. Results indicate that it is possible to achieve SAE values in the range of surface aerators or submersed jet aerators using the proposed aeration system with less complex components, thereby decreasing overall costs.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Comparison of Microbial Profiling and Tracer Testing for the Characterization of Injector-Producer Interwell Connectivities

Insufficient understanding of the microbial communities and associated microbial processes in geological reservoirs hinders the utilization of this rich data source for improved resource management. In this study, along with four interwell tracer tests at a 1478-m deep fractured crystalline-rock aquifer, we analyzed the microbial communities in the injected and produced water by high-throughput sequencing. The microbial community similarities across boreholes during an interwell flow scenario frequently encountered in reservoir development was explored. Despite the significant tracer recoveries (~30%) in all tracer tests and the cumulatively >100,000 L of exogenous water (carrying exogenous microbes) injected into the 10-m-scale reservoir, the overall structure of produced-fluid microbiome did not increasingly resemble that of the injectate. However, producers with better connectivity with the injector (based on tracer test results) did have more amplicon sequence variants (ASVs) that overlapped with those in the injectate. We identified possible drivers behind our observations and verified the practicality of repeated microbial sampling in the context of reservoir characterization and long-term monitoring. We highlight that injector-producer microbial profiling could provide insights on the relative connectivities across different producers with a given injector, and that the associated logistical needs may be comparable or even less than that of classic tracer tests.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Intensified Positive Arctic–Methane Feedback under IPCC Climate Scenarios in the 21st Century

The positive Arctic–methane (CH 4 ) feedback forms when more CH 4 is released from the Arctic tundra to warm the climate, further stimulating the Arctic to emit CH 4 . This study utilized the CLM-Microbe model to project CH 4 emissions across five distinct Arctic tundra ecosystems on the Alaska North Slope, considering three Shared Socioeconomic Pathway (SSP) scenarios using climate data from three climate models from 2016 to 2100. Employing a hyper-resolution of 5 m × 5 m within 40,000 m 2 domains accounted for the Arctic tundra’s high spatial heterogeneity; three sites were near $Utqia\dot{g}vik$ (US-Beo, US-Bes, and US-Brw), with one each in Atqasuk (US-Atq) and Ivotuk (US-Ivo). Simulated CH 4 emissions substantially increased by a factor of 5.3 to 7.5 under the SSP5–8.5 scenario compared to the SSP1–2.6 and SSP2–4.5 scenarios. The projected CH 4 emissions exhibited a stronger response to rising temperature under the SSP5–8.5 scenario than under the SSP1–2.6 and SSP2–4.5 scenarios, primarily due to strong temperature dependence and the enhanced precipitation-induced expansion of anoxic conditions that promoted methanogenesis. The CH 4 transport via ebullition and plant-mediated transport is projected to increase under all three SSP scenarios, and ebullition dominated CH 4 transport by 2100 across five sites. Projected CH 4 emissions varied in temperature sensitivity, with a Q 10 range of 2.7 to 60.9 under SSP1–2.6, 3.8 to 17.6 under SSP2–4.5, and 5.7 to 17.2 under SSP5–8.5. Compared with the other three sites, US-Atq and US-Ivo were estimated to have greater increases in CH 4 emissions due to warmer temperatures and higher precipitation. The fact that warmer sites and warmer climate scenarios had higher CH 4 emissions suggests an intensified positive Arctic–CH 4 feedback in the 21st century. Microbial physiology and substrate availability dominated the enhanced CH 4 production. The simulated intensified positive feedback underscores the urgent need for a more mechanistic understanding of CH 4 dynamics and the development of strategies to mitigate CH 4 across the Arctic.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Bioaerosols as indicators of central Arctic ice nucleating particle sources

The Arctic is warming at a rapid rate, with implications for microbial communities as the ecosystems change. Some microbes and biogenic materials can affect the persistence of long-lived mixed-phase clouds by serving as ice nucleating particles (INPs). The presence of INPs modulates the cloud phase, and long-term measurements are important to elucidate their seasonal sources and to predict future change. The Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition in 2019–2020 provided the first year-long measurements of bioaerosols and INPs in the central Arctic, with 3 d filters for amplicon sequencing and cumulative INP concentrations from −5 to −30 °C. Here, we investigated the INP seasonal cycle and its relation to the seasonal cycle of bacteria and eukaryotes. INPs were greatly elevated and compositionally similar in summer, aligning with a greater prevalence of local bioaerosol sources, but, despite this, a diverse mixture of sources (marine and terrestrial) was present all times. A common broader Arctic INP population is hypothesized for much of the year by comparable coincident data collected in Svalbard and a sensitivity of both the INPs and bioaerosols to large-scale events.

Barry, Kevin R. [Colorado State Univ., Fort Collin↗
DOE OSTI2019

Metabolic tradeoffs and heterogeneity in microbial responses to temperature determine the fate of litter carbon in simulations of a warmer world

Abstract. Climate change has the potential to destabilize the Earth's massive terrestrial carbon (C) stocks, but the degree to which models project this destabilization to occur depends on the kinds and complexities of microbial processes they simulate. Of particular note is carbon use efficiency (CUE), which determines the fraction of C processed by microbes that is anabolized into microbial biomass rather than lost to the atmosphere and soil as carbon dioxide and extracellular products. The temperature sensitivity of CUE is often modeled as an intrinsically fixed (homogeneous) property of the community, which contrasts with empirical data and has unknown impacts on projected changes to the soil C cycle under global warming. We used the Decomposition Model of Enzymatic Traits (DEMENT) – which simulates taxon-level litter decomposition dynamics – to explore the effects of introducing organism-level heterogeneity into the CUE response to temperature for decomposition of leaf litter under 5 ∘C of warming. We found that allowing the CUE temperature response to differ between taxa facilitated increased loss of litter C, unless fungal taxa were specifically restricted to decreasing CUE with temperature. Litter C loss was exacerbated by variable and elevated CUE at higher temperature, which effectively lowered costs for extracellular enzyme production. Together these results implicate a role for diversity of taxon-level CUE responses in driving the fate of litter C in a warmer world within DEMENT, which should be explored within the framework of additional model structures and validated with empirical studies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Localized basal area affects soil respiration temperature sensitivity in a coastal deciduous forest

Abstract. Soil respiration (Rs), the flow of CO2 from the soil surface to the atmosphere, is one of the largest carbon fluxes in the terrestrial biosphere. The spatial variability of Rs is both large and poorly understood, limiting our ability to robustly scale it in space. One factor in Rs spatial variability is the autotrophic contribution from plant roots, but it is uncertain how the presence of plants affects the magnitude and temperature sensitivity of Rs. This study used 1 year of Rs measurements to examine the effect of localized basal area on Rs in the growing and dormant seasons, as well as during moisture-limited times, in a temperate, coastal, deciduous forest in eastern Maryland, USA. In a linear mixed-effects model, tree basal area within a 5 m radius (BA5) exerted a significant positive effect on the temperature sensitivity of soil respiration. Soil moisture was the dominant control on Rs during the dry portions of the year, while soil moisture, temperature, and BA5 all exerted significant effects on Rs in wetter periods. Our results suggest that autotrophic respiration is more sensitive to temperature than heterotrophic respiration at these sites, although we did not measure these source fluxes directly, and that soil respiration is highly moisture sensitive, even in a record-rainfall year. The Rs flux magnitudes (0.46–15.0 µmol m-2 s-1) and variability (coefficient of variability 10 %–23 % across plots) observed in this study were comparable to values observed in similar forests. Six Rs observations would be required in order to estimate the mean across all study sites to within 50 %, and 518 would be required in order to estimate it to within 5 %, with 95 % confidence. A better understanding of the spatial interactions between plants and microbes, as well as the strength and speed of above- and belowground coupling, is necessary to link these processes with large-scale soil-to-atmosphere C fluxes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Diverse organic carbon dynamics captured by radiocarbon analysis of distinct compound classes in a grassland soil

Soil organic carbon (SOC) is a large, dynamic reservoir composed of a complex mixture of plant- and microbe-derived compounds with a wide distribution of cycling timescales and mechanisms. The distinct residence times of individual carbon components within this reservoir depend on a combination of factors, including compound reactivity, mineral association, and climate conditions. To better constrain SOC dynamics, bulk radiocarbon measurements are commonly used to trace biosphere inputs into soils and to estimate timescales of SOC cycling. However, understanding the mechanisms driving the persistence of organic compounds in bulk soil requires analyses of SOC pools that can be linked to plant sources and microbial transformation processes. Here, we adapt approaches, previously developed for marine sediments, to isolate organic compound classes from soils for radiocarbon ( 14 C) analysis. We apply these methods to a soil profile from an annual grassland in Hopland, California (USA), to assess changes in SOC persistence with depth (down to 1 m). We measured the radiocarbon values of water-extractable organic carbon (WEOC), total lipid extracts (TLEs), total hydrolyzable amino acids (AAs), and an acid-insoluble (AI) fraction from bulk and physically separated size fractions (< 2 mm, 2 mm–63 µm, and < 63 µm). Our results show that Δ 14 C values of bulk soil, size fractions, and extracted compound classes became more depleted with depth, and individual SOC components have distinct age–depth distributions that suggest distinguishable cycling rates. We found that AAs and TLEs cycle faster than the bulk soils and the AI fraction. The AI was the most 14 C-depleted fraction, indicating that it is the most chemically inert in this soil. Our approach enables the isolation and measurement of SOC fractions that separate functionally distinct SOC pools that can cycle relatively quickly (e.g., plant and microbial residues) from more passive or inert SOC pools (associated with minerals or petrogenic) from bulk soils and soil physical fractions. With the effort to move beyond SOC bulk analysis, we find that compound class 14 C analysis can improve our understanding of SOC cycling and disentangle the physical and chemical factors driving OC cycling rates and persistence.

58 GEOSCIENCES↗
DOE OSTI2024

Position-specific kinetic isotope effects for nitrous oxide: a new expansion of the Rayleigh model

Nitrous oxide (N 2 O) is a potent greenhouse gas and the most significant anthropogenic ozone-depleting substance currently being emitted. A major source of anthropogenic N 2 O emissions is the microbial conversion of fixed nitrogen species from fertilizers in agricultural soils. Thus, understanding the enzymatic mechanisms by which microbes produce N 2 O has environmental significance. Measurement of the 15 N/ 14 N isotope ratios of N 2 O produced by purified enzymes or axenic microbial cultures is a promising technique for studying N 2 O biosynthesis. Typically, N 2 O-producing enzymes combine nitrogen atoms from two identical substrate molecules (NO or NH 2 OH). Position-specific isotope analysis of the central (N α ) and outer (N β ) nitrogen atoms in N 2 O enables the determination of the individual kinetic isotope effects (KIEs) for N α and N β , providing mechanistic insight into the incorporation of each nitrogen atom. Previously, position-specific KIEs (and fractionation factors) were quantified using the Rayleigh distillation equation, i.e., via linear regression of δ 15 N α or δ 15 N β against [–f In f / (1 – f)], where f is the fraction of substrate remaining in a closed system. This approach, however, is inaccurate for N α and N β because it does not account for fractionation at N α affecting the isotopic composition of substrate available for incorporation into the β position (and vice versa). Therefore, we developed a new expansion of the Rayleigh model that includes specific terms for fractionation at the individual N 2 O nitrogen atoms. By applying this Expanded Rayleigh model to a variety of simulated N 2 O synthesis reactions with different combinations of normal, inverse, and/or no KIEs at N α and N β , we demonstrate that our new model is both accurate and robust. We also applied this new model to two previously published datasets describing N 2 O production from NH 2 OH oxidation in a methanotroph culture (Methylosinus trichosporium) and N 2 O production from NO by a purified Histoplasma capsulatum (fungal) P450 NOR, demonstrating that the Expanded Rayleigh model is a useful tool in calculating position-specific fractionation for N 2 O synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Stoichiometrically coupled carbon and nitrogen cycling in the MIcrobial-MIneral Carbon Stabilization model version 1.0 (MIMICS-CN v1.0)

Explicit consideration of microbial physiology in soil biogeochemical models that represent coupled carbon–nitrogen dynamics presents opportunities to deepen understanding of ecosystem responses to environmental change. The MIcrobial-MIneral Carbon Stabilization (MIMICS) model explicitly represents microbial physiology and physicochemical stabilization of soil carbon (C) on regional and global scales. Here we present a new version of MIMICS with coupled C and nitrogen (N) cycling through litter, microbial, and soil organic matter (SOM) pools. The model was parameterized and validated against C and N data from the Long-Term Inter-site Decomposition Experiment Team (LIDET; six litter types, 10 years of observations, and 13 sites across North America). The model simulates C and N losses from litterbags in the LIDET study with reasonable accuracy (C: R 2 =0.63; N: R 2 =0.29), which is comparable with simulations from the DAYCENT model that implicitly represents microbial activity (C: R 2 =0.67; N: R 2 =0.30). Subsequently, we evaluated equilibrium values of stocks (total soil C and N, microbial biomass C and N, inorganic N) and microbial process rates (soil heterotrophic respiration, N mineralization) simulated by MIMICS-CN across the 13 simulated LIDET sites against published observations from other continent-wide datasets. We found that MIMICS-CN produces equilibrium values in line with measured values, showing that the model generates plausible estimates of ecosystem soil biogeochemical dynamics across continental-scale gradients. MIMICS-CN provides a platform for coupling C and N projections in a microbially explicit model, but experiments still need to identify the physiological and stoichiometric characteristics of soil microbes, especially under environmental change scenarios.

58 GEOSCIENCES↗
DOE OSTI2023

CORPSE model with litter decomposition parameters derived from the LIDET dataset

This is a version of the CORPSE model (Carbon, Organisms, Rhizosphere and Protection in the Soil Environment, Sulman et al. 2014) that uses litter decomposition parameters derived from a modified Monte Carlo simulation using the LIDET litter decomposition dataset (Long-term Intersite Decomposition Experiment Team, Harmon 2013). The code also includes the Baseline parameters, and the eight other best parameter sets identified in a modified Monte Carlo simulation. Related publication:Juice, S.M., Ridgeway, J.R., Hartman, M.D., Parton, W.J., Berardi, D.M., Sulman, B.N., Allen, K.E., & Brzostek, E.R. Reparameterizing litter decomposition using a simplified Monte Carlo method improves litter decay simulated by a microbial model and alters bioenergy soil carbon estimates. Description of files:The folder "Input Files" contains one folder for each LIDET site with data necessary to run the model. Note that "(site)" in the filenames below indicates where the LIDET site code appears (see Table 1 for site codes). Data streams include: CORPSE_full_spinup_litter.csv, CORPSE_full_spinup_rhizo.csv, CORPSE_full_spinup_bulk.csv, litterbag_init_100g_6spp.csv: initial C and N (kg C or N/m2) pool values for each soil layer, the litterbag_init_100_6spp.csv file is for the litterbag layer and is the same file for all sites. All initial C and N files have the same columns (Column - Description - Units) uFastC - Unprotected fast decomposing carbon - kg carbon/m2 uSlowC - Unprotected slow decomposing carbon - kg carbon/m2 uNecroC - Unprotected necromass carbon - kg carbon/m2 pFastC - Protected fast decomposing carbon - kg carbon/m2 pSlowC - Protected slow decomposing carbon - kg carbon/m2 pNecroC - Protected necromass carbon - kg carbon/m2 livingMicrobeC - Carbon in living microbial biomass - kg carbon/m2 uFastN - Unprotected fast decomposing nitrogen - kg nitrogen/m2 uSlowN - Unprotected slow decomposing nitrogen - kg nitrogen/m2 uNecroN - Unprotected necromass nitrogen - kg nitrogen/m2 pFastN - Protected fast decomposing nitrogen - kg nitrogen/m2 pSlowN - Protected slow decomposing nitrogen - kg nitrogen/m2 pNecroN - Protected necromass nitrogen - kg nitrogen/m2 inorganicN - Inorganic nitrogen - kg nitrogen/m2 CO2 - Carbon in carbon dioxide - kg carbon/m2 livingMicrobeN - Nitrogen in living microbial biomass - kg nitrogen/m2 soilT (site) DOY274start.csv: Average daily soil temperature (oC) interpolated from previously calculated monthly values used in DayCent LIDET simulations (Bonan et al., 2013). soilT (site) DOY274start.csv: Average daily soil volumetric water content (VWC) scalar interpolated from previously calculated monthly values used in DayCent LIDET simulations (Bonan et al., 2013). litter production.csv: Average daily litter production values for each site, data sources listed in Table S3 of related publication. litter (site) CN.csv: C:N ratio for each species from LIDET dataset (Table 2, Harmon 2013). (site).csv: Table indicating number of observations for each species decomposed at each site. Instructions: Save the model code ("CORPSE_LIDET.R") and "Input Files" folder in the same folder. Also make a folder for the model output (e.g., "results_Baseline") in the same folder. Set the working directory (setwd) in the model code to the folder with the files saved in step #1. Select the parameter set to use for the litter and litterbag compartments, comment out all other parameter sets. Run code. Output will be saved in the folder made in step 1. Output destination can be changed as necessary in code section called "Running the model." Table 1 LIDET sites and site codes used in model files. Site Code - Site AND - H.J. Andrews Experimental Forest BNZ - Bonanza Creek Experimental Forest BSF - Blodgett Research Forest CDR - Cedar Creek Natural History Area CPR - Central Plains Experimental Range HBR - Hubbard Brook Experimental Forest HFR - Harvard Forest JUN - Juneau KBS - Kellogg Biological Station KNZ - Konza Prairie Research Natural Area NWT - Niwot Ridge/Green Lakes Valley OLY - Olympic National Park OLY Conifer forest SEV - Sevilleta National Wildlife Refuge SMR - Santa Margarita Ecological Reserve UFL - University of Florida VCR - Virginia Coast Reserve Table 2 LIDET species and species codes used in model files (6 common species). Species - Species Code Sugar maple (Acer saccharum) - ACSA Drypetes (Drypetes glauca) - DRGL Red pine (Pinus resinosa) - PIRE Chestnut oak (Quercus prinus) - QUPR Western redcedar (Thuja plicata) - THPL Wheat (Triticum aestivum) - TRAE References:Bonan, G. B., Hartman, M. D., Parton, W. J., & Wieder, W. R. (2013). Evaluating litter decomposition in earth system models with long-term litterbag experiments: an example using the Community Land Model version 4 (CLM4). Global Change Biology, 19(3), 957-974. https://doi.org/https://doi.org/10.1111/gcb.12031 Harmon, M. (2013). LTER Intersite Fine Litter Decomposition Experiment (LIDET), 1990 to 2002. Long-Term Ecological Research. Forest Science Data Bank, Corvallis, OR. [Data set]. Accessed http://andlter.forestry.oregonstate.edu/data/abstract.aspx?dbcode=TD023. https://doi.org/10.6073/pasta/f35f56bea52d78b6a1ecf1952b4889c5. Sulman, B. N., Phillips, R. P., Oishi, A. C., Shevliakova, E., & Pacala, S. W. (2014). Microbe-driven turnover offsets mineral-mediated storage of soil carbon under elevated CO2. Nature Climate Change, 4, 1099 - 1102. https://doi.org/10.1038/nclimate2436

Juice, Stephanie↗
DOE OSTI2020

Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms

Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil’s opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structure-guided microbial targeting of antistaphylococcal prodrugs

Carboxy ester prodrugs are widely employed to increase oral absorption and potency of phosphonate antibiotics. Prodrugging can mask problematic chemical features that prevent cellular uptake and may enable tissue-specific compound delivery. However, many carboxy ester promoieties are rapidly hydrolyzed by serum esterases, limiting their therapeutic potential. While carboxy ester-based prodrug targeting is feasible, it has seen limited use in microbes as microbial esterase-specific promoieties have not been described. Here we identify the bacterial esterases, GloB and FrmB, that activate carboxy ester prodrugs in Staphylococcus aureus. Additionally, we determine the substrate specificities for FrmB and GloB and demonstrate the structural basis of these preferences. Finally, we establish the carboxy ester substrate specificities of human and mouse sera, ultimately identifying several promoieties likely to be serum esterase-resistant and microbially labile. These studies will enable structure-guided design of antistaphylococcal promoieties and expand the range of molecules to target staphylococcal pathogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The fluoride permeation pathway and anion recognition in Fluc family fluoride channels

Fluc family fluoride channels protect microbes against ambient environmental fluoride by undermining the cytoplasmic accumulation of this toxic halide. These proteins are structurally idiosyncratic, and thus the permeation pathway and mechanism have no analogy in other known ion channels. Although fluoride-binding sites were identified in previous structural studies, it was not evident how these ions access aqueous solution, and the molecular determinants of anion recognition and selectivity have not been elucidated. Using x-ray crystallography, planar bilayer electrophysiology, and liposome-based assays, we identified additional binding sites along the permeation pathway. We used this information to develop an oriented system for planar lipid bilayer electrophysiology and observed anion block at one of these sites, revealing insights into the mechanism of anion recognition. We propose a permeation mechanism involving alternating occupancy of anion-binding sites that are fully assembled only as the substrate approaches.

59 BASIC BIOLOGICAL SCIENCES↗