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At least 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Kaluza-Klein graviton freeze-in and big bang nucleosynthesis

In models featuring extra spatial dimensions, particle collisions in the early Universe can produce Kaluza-Klein gravitons. Such particles will later decay, potentially impacting the process of big bang nucleosynthesis. In this paper, we consider scenarios in which gravity is free to propagate throughout n flat, compactified extra dimensions, while the fields of the Standard Model are confined to a ( 3 + 1 )-dimensional brane. We calculate the production and decay rates of the states that make up the Kaluza-Klein graviton tower and determine the evolution of their abundances in the early Universe. We then go on to evaluate the impact of these decays on the resulting light element abundances. We identify significant regions of previously unexplored parameter space that are inconsistent with measurements of the primordial helium and deuterium abundances. In particular, we find that for the case of one extra dimension (two extra dimensions), the fundamental scale of gravity must be M ⋆ ≳ 2 × 10 13 GeV ( M ⋆ ≳ 1 0 10 GeV ) unless the temperature of the early Universe was never greater than T ∼ 2 TeV ( T ∼ 1 GeV ). For larger values of n , these constraints are less stringent. For the case of n = 6 , for example, our analysis excludes all values of M ⋆ less than ∼ 10 6 GeV , unless the temperature of the Universe was never greater than T ∼ 3 TeV . The results presented here severely limit the possibility that black holes were efficiently produced through particle collisions in the early Universe’s thermal bath. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Direct Measurement of the Nickel Spectrum in Cosmic Rays in the Energy Range from 8.8 GeV/$\mathcal{n}$ to 240 GeV/$\mathcal{n}$ with CALET on the International Space Station

The relative abundance of cosmic ray nickel nuclei with respect to iron is by far larger than for all other transiron elements; therefore it provides a favorable opportunity for a low background measurement of its spectrum. Since nickel, as well as iron, is one of the most stable nuclei, the nickel energy spectrum and its relative abundance with respect to iron provide important information to estimate the abundances at the cosmic ray source and to model the Galactic propagation of heavy nuclei. However, only a few direct measurements of cosmic-ray nickel at energy larger than ~ 3 GeV/n are available at present in the literature, and they are affected by strong limitations in both energy reach and statistics. In this Letter, we present a measurement of the differential energy spectrum of nickel in the energy range from 8.8 to 240 GeV/n , carried out with unprecedented precision by the Calorimetric Electron Telescope (CALET) in operation on the International Space Station since 2015. The CALET instrument can identify individual nuclear species via a measurement of their electric charge with a dynamic range extending far beyond iron (up to atomic number Z = 40 ). The particle’s energy is measured by a homogeneous calorimeter (1.2 proton interaction lengths, 27 radiation lengths) preceded by a thin imaging section (3 radiation lengths) providing tracking and energy sampling. This Letter follows our previous measurement of the iron spectrum [O. Adriani et al. (CALET Collaboration), Phys. Rev. Lett. 126, 241101 (2021).], and it extends our investigation on the energy dependence of the spectral index of heavy elements. It reports the analysis of nickel data collected from November 2015 to May 2021 and a detailed assessment of the systematic uncertainties. In the region from 20 to 240 GeV/n our present data are compatible within the errors with a single power law with spectral index -2.51 ± 0.07 .

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Constraints on the normal branch of DGP gravity from SPT galaxy clusters with DES and HST weak-lensing mass calibration and from P l a n c k PR4 CMB anisotropies

We present constraints on the normal branch of the Dvali-Gabadadze-Porrati (nDGP) braneworld gravity model from the abundance of massive galaxy clusters. On scales below the nDGP crossover scale r c , the nDGP model features an effective gravitylike fifth force that alters the growth of structure, leading to an enhancement of the halo mass function (HMF) on cluster scales. The enhanced cluster abundance allows for constraints on the nDGP model using cluster samples. We employ the South Pole Telescope (SPT) cluster sample, selected through the thermal Sunyaev-Zel’dovich effect with the SPT and with mass calibration using weak-lensing data from the Dark Energy Survey (DES) and the Hubble Space Telescope (HST). The cluster sample contains 1,005 clusters with redshifts 0.25 < z < 1.78 , which are confirmed with the multicomponent matched filter algorithm using optical and near-infrared data. Weak-lensing data from DES and HST enable a robust mass measurement of the cluster sample. We use DES Year 3 data for 688 clusters with redshifts z < 0.95 , and HST data for 39 clusters with redshifts 0.6 < z < 1.7 . We account for the enhancement in the HMF through a semi-analytic correction factor to the standard cosmology HMF derived from the spherical collapse model in the nDGP model. We then further calibrate this model using N -body simulations. In addition, for the first time, we analyze the primary CMB temperature and polarization anisotropy measurements from Planck PR4 within the nDGP model. We obtain a competitive constraint from the joint analysis of the SPT cluster abundance with the Planck PR4 data, and report an upper bound of 1 / H 0 r c < 1.41 at 95% when assuming a cosmology with massive neutrinos.

Vogt, S. M.L. [Munich U. Observ.; LMU Munich (main↗
DOE OSTI2025

Parametric coincidence in the baryon to dark matter ratio from Affleck-Dine baryogenesis and UV freeze-in dark matter

We highlight that the observed concurrence between the baryon and dark matter relic densities can be explained via a parametric coincidence between two distinct production mechanisms: Affleck-Dine baryogenesis and dark matter UV freeze-in. In the Affleck-Dine mechanism, the baryon asymmetry is naturally proportional to the inflationary reheating temperature 𝑇 rh , which also plays a critical role in setting the relic abundance of UV freeze-in dark matter. Since Affleck-Dine baryogenesis requires flat directions in the potential, the framework is inherently supersymmetric, offering compelling UV freeze-in dark matter candidates such as the gravitino. We outline scenarios in which 𝑇 rh simultaneously determines both relic abundances, resulting in a baryon-to-dark matter ratio of order unity that is largely insensitive to 𝑇 rh . We also discuss the conditions required to avoid Q-ball formation or dark matter production by other mechanisms, such as next-to-lightest supersymmetric particle decays, to preserve the parametric coincidence between baryon and dark matter abundances.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Plant diversity and functional identity drive grassland rhizobacterial community responses after 15 years of CO 2 and nitrogen enrichment

Abstract Improved understanding of bacterial community responses to multiple environmental filters over long time periods is a fundamental step to develop mechanistic explanations of plant–bacterial interactions as environmental change progresses. This is the first study to examine responses of grassland root‐associated bacterial communities to 15 years of experimental manipulations of plant species richness, functional group and factorial enrichment of atmospheric CO 2 (eCO 2 ) and soil nitrogen (+N). Across the experiment, plant species richness was the strongest predictor of rhizobacterial community composition, followed by +N, with no observed effect of eCO 2 . Monocultures of C 3 and C 4 grasses and legumes all exhibited dissimilar rhizobacterial communities within and among those groups. Functional responses were also dependent on plant functional group, where N 2 ‐fixation genes, NO 3− ‐reducing genes and P‐solubilizing predicted gene abundances increased under resource‐enriched conditions for grasses, but generally declined for legumes. In diverse plots with 16 plant species, the interaction of eCO 2 +N altered rhizobacterial composition, while +N increased the predicted abundance of nitrogenase‐encoding genes, and eCO 2 +N increased the predicted abundance of bacterial P‐solubilizing genes. Synthesis : Our findings suggest that rhizobacterial community structure and function will be affected by important global environmental change factors such as eCO 2 , but these responses are primarily contingent on plant species richness and the selective influence of different plant functional groups.

Revillini, Daniel↗
DOE OSTI2020

Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil

Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 108 cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Prescribed fire selects for a pyrophilous soil sub‐community in a northern California mixed conifer forest

Abstract Prescribed fire is a critical strategy for mitigating the effects of catastrophic wildfires. While the above‐ground response to fire has been well‐documented, fewer studies have addressed the effect of prescribed fire on soil microorganisms. To understand how soil microbial communities respond to prescribed fire, we sampled four plots at a high temporal resolution (two burned, two controls), for 17 months, in a mixed conifer forest in northern California, USA. Using amplicon sequencing, we found that prescribed fire significantly altered both fungal and bacterial community structure. We found that most differentially abundant fungal taxa had a positive fold‐change, while differentially abundant bacterial taxa generally had a negative fold‐change. We tested the null hypothesis that these communities assembled due to neutral processes (i.e., drift and/or dispersal), finding that >90% of taxa fit this neutral prediction. However, a dynamic sub‐community composed of burn‐associated indicator taxa that were positively differentially abundant was enriched for non‐neutral amplicon sequence variants, suggesting assembly via deterministic processes. In synthesizing these results, we identified 15 pyrophilous taxa with a significant and positive response to prescribed burns. Together, these results lay the foundation for building a process‐driven understanding of microbial community assembly in the context of the classical disturbance regime of fire.

Microbiology↗
DOE OSTI2025

Composition, Growth, Succession, and Function in the Cladophora Microbiome: Insights From Quantitative Stable Isotope Probing and NanoSIMS Imaging

The branching green macroalga Cladophora glomerata and its epiphytic microbiome dominate summer biomass in the Eel River, a Northern California river under Mediterranean (summer drought, winter rain) seasonality. Green Cladophora streamers proliferate in early summer, then change to yellow and then red-brown as epiphyte loads increase. Here, we characterised successional changes in epiphytic bacteria on Cladophora, examining both community composition and growth rates, using quantitative Stable Isotope Probing (qSIP) and 16S rRNA gene amplicon sequencing. The number of bacterial taxa increased with succession while growth rates peaked in the middle stage. NanoSIMS imaging confirmed high sulphur (S) concentrations in Cladophora cell walls relative to surrounding biomass, coinciding with a bloom of sulphur bacteria (bacteria that reduce or oxidise sulphur/sulphates). In general, relative abundances and growth rates were independent, indicating that either metric alone is insufficient for understanding how taxonomy and functional groups affect ecosystem processes. For instance, the relative abundance of nitrogen fixers peaked in the late summer when their relative growth rates were slowest. Such patterns may be driven by space competition limiting growth. Together, changes in abundance and relative growth rates suggest different limiting factors for different functional groups in the Cladophora microbiome at multiple successional stages.

Biological and medical sciences↗
DOE OSTI2023

Bootstrapping outperforms community‐weighted approaches for estimating the shapes of phenotypic distributions

Abstract Estimating phenotypic distributions of populations and communities is central to many questions in ecology and evolution. These distributions can be characterized by their moments (mean, variance, skewness and kurtosis) or diversity metrics (e.g. functional richness). Typically, such moments and metrics are calculated using community‐weighted approaches (e.g. abundance‐weighted mean). We propose an alternative bootstrapping approach that allows flexibility in trait sampling and explicit incorporation of intraspecific variation, and show that this approach significantly improves estimation while allowing us to quantify uncertainty. We assess the performance of different approaches for estimating the moments of trait distributions across various sampling scenarios, taxa and datasets by comparing estimates derived from simulated samples with the true values calculated from full datasets. Simulations differ in sampling intensity (individuals per species), sampling biases (abundance, size), trait data source (local vs. global) and estimation method (two types of community‐weighting, two types of bootstrapping). We introduce the traitstrap R package, which contains a modular and extensible set of bootstrapping and weighted‐averaging functions that use community composition and trait data to estimate the moments of community trait distributions with their uncertainty. Importantly, the first function in the workflow, trait_fill , allows the user to specify hierarchical structures (e.g. plot within site, experiment vs. control, species within genus) to assign trait values to each taxon in each community sample. Across all taxa, simulations and metrics, bootstrapping approaches were more accurate and less biased than community‐weighted approaches. With bootstrapping, a sample size of 9 or more measurements per species per trait generally included the true mean within the 95% CI. It reduced average percent errors by 26%–74% relative to community‐weighting. Random sampling across all species outperformed both size‐ and abundance‐biased sampling. Our results suggest randomly sampling ~9 individuals per sampling unit and species, covering all species in the community and analysing the data using nonparametric bootstrapping generally enable reliable inference on trait distributions, including the central moments, of communities. By providing better estimates of community trait distributions, bootstrapping approaches can improve our ability to link traits to both the processes that generate them and their effects on ecosystems.

Maitner, Brian S.↗
DOE OSTI2025

Opposite Response of DNA and RNA Viruses to Soil Warming and Implications for Microbial Functions

Soil viruses control the dynamics and metabolism of their hosts, strongly modifying carbon and nutrient cycling as well as soil biochemistry. Warming specifically affects viruses and their hosts, but the consequences of climate warming on the virus–host interactions, and for soil functions, remain unknown. Here, we investigated the viral communities and the virus–host interactions under warming in situ based on a forest soil column translocation experiment. The abundance of the Petitvirales (DNA viruses) decreased by 25%, but that of the Durnavirales and Martellivirales (RNA viruses) strongly increased. The DNA viral lysogenic signals and RNA viral lytic proteins increased in soil, indicating the opposite lifestyles of DNA and RNA viruses. Correspondingly, the DNA abundance of viral hosts increased, whereas RNA viral hosts remained stable. The high DNA viruses/host ratios reflect very intensive interactions between the virus and host, leading to the drop in the host functions (such as carbon metabolism processes and nitrogen and phosphorus cycles) up to 43%. In contrast, the functions of the hosts for RNA viruses increased by up to 48%. The fundamental difference in behaviour of DNA and RNA viruses is that the former use mainly lysogenic, whereas the latter lytic, lifestyles and thus control the responses of host communities to warming. Conclusively, the opposite response of DNA and RNA viruses to warming in abundance, lifestyle, and interactions with hosts leads to divergent changes in nutrient fluxes in soil. These new perspectives on viral regulations of microbial communities and their function under soil warming reveal the undeniable role of viruses in microbial ecology.

forest soil↗
DOE OSTI2021

Soil enzymes as indicators of soil function: A step toward greater realism in microbial ecological modeling

Soil carbon (C) and nitrogen (N) cycles and their complex responses to environmental changes have received increasing attention. However, large uncertainties in model predictions remain, partially due to the lack of explicit representation and parameterization of microbial processes. One great challenge is to effectively integrate rich microbial functional traits into ecosystem modeling for better predictions. Here, using soil enzymes as indicators of soil function, we developed a competitive dynamic enzyme allocation scheme and detailed enzyme-mediated soil inorganic N processes in the Microbial-ENzyme Decomposition (MEND) model. We conducted a rigorous calibration and validation of MEND with diverse soil C-N fluxes, microbial C:N ratios, and functional gene abundances from a 12-year CO 2 × N grassland experiment (BioCON) in Minnesota, USA. In addition to accurately simulating soil CO 2 fluxes and multiple N variables, the model correctly predicted microbial C:N ratios and their negative response to enriched N supply. Model validation further showed that, compared to the changes in simulated enzyme concentrations and decomposition rates, the changes in simulated activities of eight C-N-associated enzymes were better explained by the measured gene abundances in responses to elevated atmospheric CO 2 concentration. In conclusion, our results demonstrated that using enzymes as indicators of soil function and validating model predictions with functional gene abundances in ecosystem modeling can provide a basis for testing hypotheses about microbially mediated biogeochemical processes in response to environmental changes. Further development and applications of the modeling framework presented here will enable microbial ecologists to address ecosystem-level questions beyond empirical observations, toward more predictive understanding, an ultimate goal of microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Impacts of Legacy and Contemporary Nitrogen Inputs on N 2 O and CO 2 Emissions in Miscanthus and Maize Cultivated Soils

ABSTRACT Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteus (M×g) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N 2 O) and carbon dioxide (CO 2 ) emissions, as well as key N cycling genes in soils where M×g and maize were grown. A 150‐day soil incubation experiment was conducted using soils from a long‐term M×g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha −1 year −1 ) and a contemporary amendment (60 mg N kg −1 ) with negative control (0 mg N kg −1 ). We observed significant increases in cumulative N 2 O emissions in Mxg soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amo A gene abundance, which plays a significant role in nitrification in nutrient‐rich soils, also increased with higher legacy fertilization rates in M×g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N 2 O emissions, but cumulative CO 2 emissions and amo A gene abundance significantly increased. The abundances of nor B genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N 2 O emissions, particularly for perennial bioenergy crops.

09 BIOMASS FUELS↗
DOE OSTI2020

Understanding relative metal prices and availability: Combining physical and economic perspectives

Abstract Scientists typically use physical indicators, such as average crustal abundance, and energy requirements in production, as measures of the availability of mineral resources. Economists, on the other hand, typically rely on measures such as prices, and extraction costs. This study investigates the role of crustal abundance, energy requirements, and other physical indicators in determining relative metal prices. The relationship between prices, and physical indicators is estimated statistically for a sample of 22 chemical elements over the period 1970–2013 using an economic market model. The results suggest that energy requirements in production explain 43% of observed variation in metal prices, crustal abundance 21%, and other physical indicators (toxicity, native metal status, and melting point) combine to explain 12% of the observed differences in metal prices.

Watson, Brett J.↗
DOE OSTI2021

Trace element geochemistry of coarse-grained angrites from Northwest Africa: Implications for their petrogenesis on the angrite parent body

The angrites are a class of achondrites that encompass a wide range of igneous textures from quenched, volcanic, and subvolcanic stones to slowly cooled, plutonic rocks. The compositions of the various geochemical reservoirs generating this variety of rocks have not been investigated fully because historically the numbers and masses of angrites available for study have been quite small. However, the rapid increase in meteorites from Northwest Africa (NWA) has enabled a renewed opportunity for such an investigation. In particular, three samples, NWA 2999, 4590, and 4801, have provided a new window into our understanding of the origin and petrogenesis of the coarse-grained (plutonic) angrites. We report here the trace element abundances in individual mineral grains of pyroxene, plagioclase, olivine/kirschsteinite, and phosphate and in the whole-rock samples. We utilize these data to constrain the petrogenetic history of each of these samples on the angrite parent body (e.g., parental melt compositions and oxygen fugacity conditions) and assess genetic relationships to previously investigated angrites. The trace element abundances in each of the three coarse-grained angrites studied here indicate a unique history for each. The observed trace element abundances and patterns in NWA 2999 show similarities with previously studied fine-grained, volcanic angrites and potentially indicate a common geochemical source reservoir, even though NWA 2999 is temporally distinct from the volcanic angrites. In contrast, NWA 4590 has trace element characteristics analogous to other coarse-grained angrites (e.g., Lewis Cliff [LEW] 86010), suggesting that these samples originated from geochemically similar source reservoirs. The third angrite, NWA 4801, exhibits geochemical characteristics most similar to the plutonic, coarse-grained angrites, but also appears to have some affinities in its trace element characteristics to the volcanic, fine-grained angrites. This suggests that NWA 4801 may represent a petrogenetic link between two distinct geochemical reservoirs on the angrite parent body. In aggregate, the trace element distributions in these three plutonic angrites suggest that while they may have originated up to several million years after the fine-grained angrites, they sampled a range of source reservoirs on the angrite parent body. Here, some of these source reservoirs were likely similar to those of the fine-grained angrites, but others had distinct geochemical characteristics.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Lack of xyloglucan in the cell walls of the Arabidopsis xxt1/xxt2 mutant results in specific increases in homogalacturonan and glucomannan

Mutations in both ArabidopsisXyloglucan Xylosyltransferase1 (XXT1) and Xyloglucan Xylosyltransferase2 (XXT2) result in the absence of the major hemicellulose, xyloglucan (XyG). The growth physiology, tensile strength, and cell wall compositions of etiolated hypocotyls of xxt1/xxt2 double and xxt1/xxt2/xxt5 triple mutants were characterized and compared with those of mur2 and mur3 mutations that alter the side group composition of XyG. Wild type and mur2 demonstrated normal elongation growth, whereas the xxt double and triple mutants and mur3 showed reduced elongation and cell swelling at the base of the hypocotyl at the later stages of elongation. Whereas mur3 hypocotyls had reduced tensile strength, the xxt double and triple mutants had similar tensile strengths as wild type, but reached breaking points at lower strains. Loss of XyG in hypocotyls and rosette leaf cell walls was associated with specific increases in the relative abundance of homogalacturonan and the hemicellulose glucomannan, but not arabinoxylan. The increased homogalacturonan and glucomannan abundance did not result from enhanced expression of their polymer synthases. An analysis of published transcriptomic data indicated that genes encoding some members of the expansin, xyloglucan endotransglucosylase/hydrolase, arabinogalactan-protein, and structural protein families were upregulated in the xxt mutants. We hypothesize that an as yet unknown mechanism exists by which pectin and hemicellulose abundance can be altered other than by increased rates of biosynthesis to maintain a structurally sound cell wall.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Multiplexed CRISPR-Cas9 mutagenesis of rice PSBS1 noncoding sequences for transgene-free overexpression

Understanding CRISPR-Cas9’s capacity to produce native overexpression (OX) alleles would accelerate agronomic gains achievable by gene editing. To generate OX alleles with increased RNA and protein abundance, we leveraged multiplexed CRISPR-Cas9 mutagenesis of noncoding sequences upstream of the rice PSBS1 gene. We isolated 120 gene-edited alleles with varying non-photochemical quenching (NPQ) capacity in vivo—from knockout to overexpression—using a high-throughput screening pipeline. Overexpression increased OsPsbS1 protein abundance two- to threefold, matching fold changes obtained by transgenesis. Increased PsbS protein abundance enhanced NPQ capacity and water-use efficiency. Across our resolved genetic variation, we identify the role of 5'UTR indels and inversions in driving knockout/knockdown and overexpression phenotypes, respectively. Complex structural variants, such as the 252-kb duplication/inversion generated here, evidence the potential of CRISPR-Cas9 to facilitate significant genomic changes with negligible off-target transcriptomic perturbations. Our results may inform future gene-editing strategies for hypermorphic alleles and have advanced the pursuit of gene-edited, non-transgenic rice plants with accelerated relaxation of photoprotection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling

The phylogenetic and functional diversities of microbial communities in tropical rainforests and how these differ from those of temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N 2 O) from the tropics. Toward closing these knowledge gaps, in this study we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity compared to those of temperate grasslands or agricultural soils. In contrast to the overall distinct community composition, the relative abundances and nucleotide sequences of N 2 O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N 2 O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest than in temperate soils, i.e., 20% versus 0.1 to 0.3% of bacterial genomes in each soil type harbored the gene, respectively. Finally, unlike temperate soils, LEF soils showed little stratification with depth in the first 0 to 30 cm, with ~45% of community composition differences explained solely by location. Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities and should facilitate future ecological studies of these ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Quantitative Proteome Profiling Reveals Cellobiose-Dependent Protein Processing and Export Pathways for the Lignocellulolytic Response in Neurospora crassa

Filamentous fungi are intensively used for producing industrial enzymes, including lignocellulases. Employing insoluble cellulose to induce the production of lignocellulases causes some drawbacks, e.g., a complex fermentation operation, which can be overcome by using soluble inducers such as cellobiose. Here, a triple β-glucosidase mutant of Neurospora crassa, which prevents rapid turnover of cellobiose and thus allows the disaccharide to induce lignocellulases, was applied to profile the proteome responses to cellobiose and cellulose (Avicel). Our results revealed a shared proteomic response to cellobiose and Avicel, whose elements included lignocellulases and cellulolytic product transporters. While the cellulolytic proteins showed a correlated increase in protein and mRNA levels, only a moderate correlation was observed on a proteomic scale between protein and mRNA levels (R 2 = 0.31). Ribosome biogenesis and rRNA processing were significantly overrepresented in the protein set with increased protein but unchanged mRNA abundances in response to Avicel. Ribosome biogenesis, as well as protein processing and protein export, was also enriched in the protein set that showed increased abundance in response to cellobiose. NCU05895, a homolog of yeast CWH43, is potentially involved in transferring a glycosylphosphatidylinositol (GPI) anchor to nascent proteins. This protein showed increased abundance but no significant change in mRNA levels. Disruption of CWH43 resulted in a significant decrease in cellulase activities and secreted protein levels in cultures grown on Avicel, suggesting a positive regulatory role for CWH43 in cellulase production. The findings should have an impact on a systems engineering approach for strain improvement for the production of lignocellulases.

59 BASIC BIOLOGICAL SCIENCES↗