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At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

No evidence of top–down effects by ants on litter decomposition in a temperate grassland

Ants play multiple roles in ecosystems, but their ability to affect decomposition processes in temperate grasslands is relatively unknown. We investigated whether the suppression of ant populations influenced litter decomposition in grasslands via predation of some decomposers (e.g., mites and springtails) and/or microbial activity and composition. We performed two successful ant suppression treatments (seven weeks, 37% suppression, year 1, 10 weeks, 70% suppression, year 2) over the course of a 59-week experiment. We then assayed the effects of ant suppression using coarse- and fine-mesh litterbags and evaluated litter chemistry, microbial and arthropod communities, and microbial enzyme activity. Ant suppression efforts reduced ant abundance and altered ant, arthropod decomposer, and non-ant predator community composition. However, ant suppression did not affect decomposer arthropod abundance, litter mass loss, microbial composition, or enzyme activity in litterbags. Litterbag mesh size did not alter microbial composition, perhaps due to a failure to exclude decomposers, as mites and springtails were more or equally abundant in fine-mesh bags. Nevertheless, mesh size did change litter chemistry, suggesting that mesh size-mediated microenvironments affect decomposition environment regardless of invertebrate exclusion. Coarse-mesh litterbags had higher concentrations of microbial sugars, lignin, and N and lower concentrations of litter C and crystalline cellulose than fine-mesh litterbags. Litterbag mesh size may alter decomposition processes irrespective of invertebrate abundance. We found no evidence that ant predation was an important driver of decomposer populations or decomposition in these systems, and we suspect redundancy at the top of the detrital food web dilutes the role of ants.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Dynamics of dark matter misalignment through the Higgs portal

A light singlet scalar field feebly coupled through the super-renormalizable Higgs portal provides a minimal and well-motivated realization of ultra-light bosonic dark matter. We study the cosmological production of dark matter in this model by elucidating the dynamics of two sources of scalar field misalignment generated during the radiation era. For large scalar masses (above $\mathcal{O}$ (10 −3 eV)), dark matter is produced through thermal misalignment, by which the scalar field is driven towards large field values as a result of the finite-temperature effective potential. The dominance of thermal misalignment in this mass range leads to a sharp relic abundance prediction which is, to a significant extent, insensitive to the initial conditions of the scalar field. On the other hand, for low mass scalars (below $\mathcal{O}$ (10 −5 eV)), dark matter is produced via VEV misalignment, which is caused by the induced scalar field vacuum expectation value triggered by the electroweak phase transition. We show that the relic abundance in this low mass range is sensitive to the scalar field initial conditions. In the intermediate mass range, the relic abundance is a consequence of a competition between thermal misalignment and VEV misalignment, which can potentially lead to novel forced resonance effects which cause a recurring enhancement and suppression in the late time oscillation amplitude as a function of the scalar mass. We compare our relic abundance predictions with constraints and projections from equivalence principle and inverse square law tests, stellar cooling, resonant molecular absorption, and observations of extra-galactic background light and diffuse X-ray backgrounds. New experimental ideas are needed to probe most of the cosmologically motivated regions of parameter space.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Electromagnetic signals of inelastic dark matter scattering

Light dark sectors in thermal contact with the Standard Model can naturally produce the observed relic dark matter abundance and are the targets of a broad experimental search program. A key light dark sector model is the pseudo-Dirac fermion with a dark photon mediator. The dynamics of the fermionic excited states are often neglected. We consider scenarios in which a nontrivial abundance of excited states is produced and their subsequent de-excitation yields interesting electromagnetic signals in direct detection experiments. We study three mechanisms of populating the excited state: a primordial excited fraction, a component up-scattered in the Sun, and a component up-scattered in the Earth. We find that the fractional abundance of primordial excited states is generically depleted to exponentially small fractions in the early universe. Nonetheless, this abundance can produce observable signals in current dark matter searches. MeV-scale dark matter with thermal cross sections and higher can be probed by down-scattering following excitation in the Sun. Up-scatters of GeV-scale dark matter in the Earth can give rise to signals in current and upcoming terrestrial experiments and X-ray observations. We comment on the possible relevance of these scenarios to the recent excess in XENON1T.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Rock weathering controls the potential for soil carbon storage at a continental scale

Abstract As rock-derived primary minerals weather to form soil, they create reactive, poorly crystalline minerals that bind and store organic carbon. By implication, the abundance of primary minerals in soil might influence the abundance of poorly crystalline minerals, and hence soil organic carbon storage. However, the link between primary mineral weathering, poorly crystalline minerals, and soil carbon has not been fully tested, particularly at large spatial scales. To close this knowledge gap, we designed a model that links primary mineral weathering rates to the geographic distribution of poorly crystalline minerals across the USA, and then used this model to evaluate the effect of rock weathering on soil organic carbon. We found that poorly crystalline minerals are most abundant and most strongly correlated with organic carbon in geographically limited zones that sustain enhanced weathering rates, where humid climate and abundant primary minerals co-occur. This finding confirms that rock weathering alters soil mineralogy to enhance soil organic carbon storage at continental scales, but also indicates that the influence of active weathering on soil carbon storage is limited by low weathering rates across vast areas.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

High fat intake sustains sorbitol intolerance after antibiotic-mediated Clostridia depletion from the gut microbiota

Carbohydrate intolerance, commonly linked to the consumption of lactose, fructose, or sorbitol, affects up to 30% of the population in high-income countries. Although sorbitol intolerance is attributed to malabsorption, the underlying mechanism remains unresolved. Here, we show that a history of antibiotic exposure combined with high fat intake triggered long-lasting sorbitol intolerance in mice by reducing Clostridia abundance, which impaired microbial sorbitol catabolism. The restoration of sorbitol catabolism by inoculation with probiotic Escherichia coli protected mice against sorbitol intolerance but did not restore Clostridia abundance. Inoculation with the butyrate producer Anaerostipes caccae restored a normal Clostridia abundance, which protected mice against sorbitol-induced diarrhea even when the probiotic was cleared. Butyrate restored Clostridia abundance by stimulating epithelial peroxisome proliferator-activated receptor-gamma (PPAR-γ) signaling to restore epithelial hypoxia in the colon. Collectively, these mechanistic insights identify microbial sorbitol catabolism as a potential target for approaches for the diagnosis, treatment, and prevention of sorbitol intolerance.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

High-dimensional isotomics, part 2: Observations of over 100 constraints on methionine's isotome

The abundances of different isotopic forms of a compound, or isotopologues, will vary based on its physical and chemical history. The number of isotopologues increases combinatorically with the size of a molecule, and even small molecules such as amino acids have thousands of potentially observable isotopic variants. However, due to the analytical challenges of separating and observing isotopologues, only a few dimensions of isotopic diversity are routinely measured. Overcoming these challenges requires both an experimental method to observe many isotopic properties and a theoretical framework for interpreting these experiments. In Part 1, we presented such a theoretical framework; here, we demonstrate an experimental method, which we apply to methionine. Our approach uses a Q Exactive HF Orbitrap to perform several “M + N experiments”, where a sample is ionized, a subset of its isotopologues with cardinal mass N daltons greater than the unsubstituted isotopologue is selected and fragmented, and the proportions of all detectable isotopic forms of those fragment ions are quantified. We perform M + 1, M + 2, M + 3, and M + 4 experiments of a methionine sample and standard where the sample has a 100 ‰ enrichment of 13C at the methyl carbon relative to the natural 13C abundance at that position in the standard, and is otherwise identical to the standard. We observe isotopic forms of 8 fragment ion species for each version of the M + N experiment. With the assistance of a forward model of expected mass spectra, we identify isotopic peaks for each fragment ion based on observed mass and abundance, screen these for data quality, and quantify abundances for 146 unique isotopic peaks at precisions of ≈ 0.3–3 ‰. We present our direct observations and use them to reconstruct the concentrations of 19 individual singly, doubly, and triply-substituted isotopologues; doing so gives fewer constraints and broader error bars than working with the direct observations, but may be more interpretable for some applications. We also examine possibilities for measuring additional peaks, which are primarily limited by the detection limit of the Orbitrap-IRMS method. We then suggest some possible uses of our direct measurements for chemical forensics and hypothesis testing. Furthermore, our results demonstrate the diversity of isotopic constraints currently observable and interpretable for organic molecules.

58 GEOSCIENCES↗
DOE OSTI2023

Dark matter is the new BBN

Measurements of the primordial element abundances provide us with an important probe of our universe’s early thermal history, allowing us to constrain the expansion rate and composition of our universe as early as ~ 1 s after the Big Bang. Prior to this time, we have essentially no empirical information on which to base any such claims. In this paper, we imagine a future time in which we have not only detected the particles that make up the dark matter, but have measured their mass and annihilation cross section with reasonable precision. In analogy to the light element abundances, the dark matter abundance in this scenario could be used to study and constrain the expansion rate and composition of our universe at the time of dark matter freeze out, which for a standard thermal relic occurs at T f ~ m χ /20, corresponding to t ~ 4 x 10 -10 s x (TeV/m χ ) 2 , many orders of magnitude prior to the onset of Big Bang nucleosynthesis. Here we consider how such measurements could be used to constrain scenarios which feature exotic forms of radiation or matter, a ultralight scalar, or modifications to gravity, each of which have the potential to be much more powerfully probed with dark matter than with the light element abundances.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Fungal diversity and function in metagenomes sequenced from extreme environments

Fungi are increasingly recognized as key players in various extreme environments. Here we present an analysis of publicly-sourced metagenomes from global extreme environments, focusing on fungal taxonomy and function. The majority of 855 selected metagenomes contained scaffolds assigned to fungi. Relative abundance of fungi was as high as 10% of protein-coding genes with taxonomic annotation, with up to 289 fungal genera per sample. Despite taxonomic clustering by environment, fungal communities were more dissimilar than archaeal and bacterial communities, both for within- and between-environment comparisons. Relatively abundant fungal classes in extreme environments included Dothideomycetes, Eurotiomycetes, Leotiomycetes, Pezizomycetes, Saccharomycetes, and Sordariomycetes. Broad generalists and prolific aerial spore formers were the most relatively abundant fungal genera detected in most of the extreme environments, bringing up the question of whether they are actively growing in those environments or just surviving as spores. More specialized fungi were common in some environments, such as zoosporic taxa in cryosphere water and hot springs. Relative abundances of genes involved in adaptation to general, thermal, oxidative, and osmotic stress were greatest in soda lake, acid mine drainage, and cryosphere water samples.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Nickel-rich, volatile depleted iron meteorites: Relationships and formation processes

Ungrouped iron meteorites Tishomingo, Willow Grove, and Chinga, and group IVB iron meteorites, are Ni-rich. Similarities include enrichments of 10–100 × CI for some refractory siderophile elements, and equivalent depletions in more volatile siderophile elements. Superimposed on the overall enrichment/depletion trend, certain siderophile elements (P, W, Fe, Mo) are depleted relative to elements of similar volatility. All three ungrouped irons derive from parent bodies formed in the early Solar System. Willow Grove and Chinga are characterized by cosmic ray exposure corrected 182 W/ 184 W consistent with metal-silicate segregation on their parent bodies within 1–3 Myr of Solar System formation, within the age range determined for segregation of magmatic iron meteorite parent bodies, including group IVB irons. Tishomingo is characterized by a younger model age 4–5 Myr subsequent to Solar System formation, reflecting either late stage melting resulting from 26 Al decay, or an impact resetting. The discovery of stishovite in Tishomingo, indicating exposure to a minimum shock pressure of 8–9 GPa, is consistent with the latter. Stishovite in Tishomingo and chromite included in troilite-daubréelite in IVB irons allows oxygen isotopic composition comparison between these meteorites. Different mass independent oxygen isotopic compositions of IVB irons and Tishomingo indicate genetically distinct parent bodies. By contrast, mass independent Mo isotopic compositions overlap within analytical uncertainties, indicating a similar, carbonaceous chondrite (CC) type genetic heritage. Molybdenum and 183 W isotopic data for Chinga and Willow Grove indicate derivation from CC type parent bodies. Willow Grove shares Mo and 183 W isotopic compositions with the Ni-rich South Byron Trio (SBT) grouplet and the Milton pallasite. These Ni-rich meteorites likely formed in the same general nebular environment as other CC planetesimals, likely the outer Solar System. Highly siderophile element (HSE) abundances of Willow Grove and Tishomingo are similar to some IVB meteorites, consistent with formation by moderate degrees of fractional crystallization from initial metallic melts with low S and P, and modestly fractionated HSE. The comparable HSE abundances of Tishomingo and Willow Grove to some IVB irons, yet substantially higher Ni concentrations, indicate formation on parent bodies with lower bulk HSE abundances or HSE concentration in proportionally smaller volumes of metal. HSE abundances in Chinga are considerably lower than in IVB irons, highly fractionated, and processes responsible for these remain elusive. For IVB irons and these ungrouped irons, high temperature condensation likely dominated the enrichment and depletion of the refractory and volatile siderophile elements, respectively. Parent body degassing may have also played a role. Relative depletion of volatile siderophile elements is not, however, a universal feature of high-Ni meteorites. The SBT and Milton pallasite are Ni-rich, but less depleted in the more volatile siderophile elements. Nickel enrichment was likely driven by oxidation of Fe metal during parent body accretion or core segregation. Oxidation of the Tishomingo and Willow Grove parent bodies may have occurred at ~ IW + 1, indicated by relative Mo and W depletions due to metal/water reaction during differentiation. Late-stage reduction, indicated by the presence of Cr-bearing sulfides in Tishomingo and IVB irons, may have resulted from exhaustion of the oxidant.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N 2 O production potential

The concentration of nitrous oxide (N 2 O), an ozone-depleting greenhouse gas, is rapidly increasing in the atmosphere. Most atmospheric N 2 O originates in terrestrial ecosystems, of which the majority can be attributed to microbial cycling of nitrogen in agricultural soils. Here, in this study, we demonstrate how the abundance of nitrogen cycling genes vary across intensively managed agricultural fields and adjacent restored wetlands in the Sacramento-San Joaquin Delta in California, USA. We found that the abundances of nirS and nirK genes were highest at the intensively managed organic-rich cornfield and significantly outnumber any other gene abundances, suggesting very high N 2 O production potential. The quantity of nitrogen transforming genes, particularly those responsible for denitrification, nitrification and DNRA, were highest in the agricultural sites, whereas nitrogen fixation and ANAMMOX was strongly associated with the wetland sites. Although the abundance of nosZ genes was also high at the agricultural sites, the ratio of nosZ genes to nir genes was significantly higher in wetland sites indicating that these sites could act as a sink of N 2 O. These findings suggest that wetland restoration could be a promising natural climate solution not only for carbon sequestration but also for reduced N 2 O emissions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Atomic masses with machine learning for the astrophysical r process

The astrophysical r process plays a vital role in the production of heavy elements. Modeling of the r process is sensitive to masses and further requires knowledge of masses beyond current experimental reach. Therefore, simulations of the r process offer a unique test bed for predicting mass extrapolations. We take a Machine-Learning (ML) approach to model the masses across the entire chart of nuclides. For the first time, we simulate r-process nucleosynthesis with a physics-based ML mass model. We compare simulated abundances to solar data in order to evaluate the model's performance far from stability. The resulting r-process abundances up to thorium and uranium qualitatively match those of the observed solar system abundance pattern, with the characteristic peaks well positioned. We propagate the mass uncertainties obtained from the ML model to r-process abundance yields to estimate an uncertainty band associated with our approach. The size of the uncertainty band is approximately one order of magnitude which aligns with the uncertainty reported using alternative techniques.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Uptake of individual and mixed per- and polyfluoroalkyl substances (PFAS) by soybean and their effects on functional genes related to nitrification, denitrification, and nitrogen fixation

Here in this study, we set up a soil-microbe-soybean system spiked with PFOA, PFOS, or a PFAS mixture of eight PFAS and investigated the distribution of PFAS in the system and impacts on the abundance and expression level of genes involved in the nitrogen (N) cycle. When soybean was exposed to the PFAS mixtures, synergistic uptake by shoots was detected. PFAS exhibited remarkable impacts on abundance of nitrification and denitrification genes in both bulk soil and rhizosphere as well as expression of N fixation gene in soybean nodules. The abundance of nitrification genes AOA and AOB amoA and denitrification gene nirK was significantly reduced (p < 0.05) in almost all treatments in bulk soil, except PFOA at 10 μg/kg. The abundance of other functional genes, such as nirS and norZ was affected differently depending on PFAS concentrations and sample location, either bulk soil or the rhizosphere. Interestingly, the N fixation gene nifH in soybean nodules was overexpressed by a PFAS mixture at 100 μg/kg. Hence, this work provided in-depth knowledge regarding the distribution of PFAS and their impacts on the N cycle for the studied system. Results from this study provide insights on assessing risks posed by individual or mixed PFAS to soybean.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Biomolecular budget of persistent, microbial-derived soil organic carbon: The importance of underexplored pools

The details of how soil microorganisms contribute to stable soil organic carbon pools are a pressing knowledge gap with direct implications for soil health and climate mitigation. It is now recognized that microbial necromass contributes substantially to the formation of stable soil carbon. However, the quantification of necromass in soils has largely been limited to model molecules such as aminosugar biomarkers. The abundance and chemical composition of other persistent microbial residues remain unresolved, particularly concerning how these pools may vary with microbial community structure, soil texture, and management practices. We use yearlong soil incubation experiments with an isotopic tracer to quantify the composition of persistent residues derived from microbial communities inhabiting sand or silt dominated soil with annual (corn) or perennial (switchgrass) monocultures. Persistent microbial residues were recovered in diverse soil biomolecular pools including metabolites, proteins, lipids, and mineral-associated organic matter (MAOM). The relative abundances of microbial contributions to necromass pools were consistent across cropping systems and soil textures. The greatest residue accumulation was not recovered in MAOM but in the light density fraction of soil debris that persisted after extraction by chemical fractionation using organic solvents. Necromass abundance was positively correlated with microbial biomass abundance and revealed a possible role of cell wall morphology in enhancing microbial carbon persistence; while gram-negative bacteria accounted for the greatest contribution to microbial-derived carbon by mass at one year, residues from gram-positive Actinobacteria and Firmicutes showed greater durability. Together these results offer a quantitative assessment of the relative importance of diverse molecular classes for generating durable soil carbon.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Prevalent root-derived phenolics drive shifts in microbial community composition and prime decomposition in forest soil

Phenolic compounds perform various functions in soil ranging from microbial substrate to toxin and form the basis of several plant-mediated processes. The aim of this study was to investigate how phenolics commonly exuded by tree roots influence soil organic matter (SOM) decomposition and interact with other labile forms of carbon (C) abundant in root exudates. Therefore, we performed a 38-day incubation experiment and assessed whether phenolic compounds (benzoic acid, caffeic acid and catechin) facilitated or inhibited SOM decomposition in a glucose-amended forest soil. Changes in decomposition, substrate use, fungal and bacterial community composition, and microbial abundance and activity were measured over time using 13 C-stable-isotope tracing, DNA-based molecular methods and enzyme assays. Our findings showed that phenolics inhibited microbial activity and abundance to varying degrees. Yet, benzoic acid was the only compound producing a substantial priming effect leading to a 21% increase in SOM decomposition, which was amplified in glucose-amended soils. This stimulation in microbial activity was associated with an increase in β-1,4-glucosidase activity and the bacterial genera Paraburkholderia and Caballeronia of the Burkholderiaceae family. Phenolics drove microbial community shifts in glucose-amended soils with negligible interactive effects. In conclusion, phenolic priming of SOM decomposition is associated with microbial community shifts and amplified in the presence of glucose. This evidence emphasizes the need for considering phenolics and interactions among root exudates as priming mechanisms in the rhizosphere and other soil environments where aromatics and phenolic compounds are abundant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Engineering Nanostructured Interfaces of Hexagonal Boron Nitride-Based Materials for Enhanced Catalysis

Hexagonal boron nitrides (h-BNs) are attractive two-dimensional (2D) nanomaterials that consist of alternating B and N atoms and layered honeycomb-like structures similar to graphene. They have exhibited unique properties and promising application potentials in the field of energy storage and transformation. Recent advances in utilizing h-BN as a metal-free catalyst in the oxidative dehydrogenation of propane have triggered broad interests in exploring h-BN in catalysis. However, h-BN-based materials as robust nanocatalysts in heterogeneous catalysis are still underexplored because of the limited methodologies capable of affording h-BN with controllable crystallinity, abundant porosity, high purity, and defect engineering, which played important roles in tuning their catalytic performance. Here, in this account, our recent progress in addressing the above issues will be highlighted, including the synthesis of high-quality h-BN-based nanomaterials via both bottom-up and top-down pathways and their catalytic utilization as metal-free catalysts or as supports to tune the interfacial electronic properties on the metal nanoparticles (NPs). First, we will focus on the large-scale fabrication of h-BN nanosheets (h-BNNSs) with high crystallinity, improved surface area, satisfactory purity, and tunable defects. h-BN derived from the traditional approaches using boron trioxide and urea as the starting materials generally contains carbon/oxygen impurities and has low crystallinity. Several new strategies were developed to address the issues. Using bulk h-BN as the precursor via gas exfoliation in liquid nitrogen, single- or few-layered h-BNNS with abundant defects could be generated. Amorphous h-BN precursors could be converted to h-BN nanosheets with high crystallinity assisted by a magnesium metallic flux via a successive dissolution/precipitation/crystallization procedure. The as-fabricated h-BNNS featured high crystallinity and purity as well as abundant porosity. An ionothermal metathesis procedure was developed using inorganic molten salts (NaNH 2 and NaBH 4 ) as the precursors. The h-BN scaffolds could be produced on a large scale with high yield, and the as-afforded materials possessed high purity and crystallinity. Second, utilization of the as-prepared h-BN library as metal-free catalysts in dehydrogenation and hydrogenation reactions will be summarized, in which they exhibited enhanced catalytic activity over the counterparts from the previous synthesis method. Third, the interface modulation between metal NPs with the as-prepared defects’ abundant h-BN support will be highlighted. The h-BN-based strong metal–support interaction (SMSI) nanocatalysts were constructed without involving reducible metal oxides via the ionothermal procedure we developed by deploying specific inorganic metal salts, acting as robust nanocatalysts in CO oxidation. Under conditions simulated for practical exhaust systems, promising catalytic efficiency together with high thermal stability and sintering resistance was achieved. Across all of these examples, unique insights into structures, defects, and interfaces that emerge from in-depth characterization through microscopy, spectroscopy, and diffraction will be highlighted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Mineral Protection and Resource Limitations Combine to Explain Profile-Scale Soil Carbon Persistence

The fate of soil carbon (C) is largely controlled by microbial oxidation of organic matter (OM), which is constrained by a variety of mechanisms. OM association with soil minerals provides pronounced protection against microbial decomposition. However, factors such as climate, occlusion, and resource limitations also contribute to OM preservation. Here, we explore the factors explaining C distribution and age within an upland rainforest soil in Hawai'i, a site with abundant preferential flow paths (PFPs) and high short-range order (SRO) mineral content. We characterized lateral and vertical changes in Δ 14 C, SRO mineral content, C-functional group chemistry, and microbial community composition to elucidate the contributions of multiple protection mechanisms to OM preservation. Consistent with our expectation, SRO mineral content and Δ 14 C were strongly correlated (R 2 = 0.95), indicating strong mineral protection of OM throughout the profile. Surprisingly, distance from PFP was also a significant predictor of Δ 14 C and improved model fit, particularly in the shallow horizons (R 2 = 0.97). Elevated C/N ratios, decreased microbial abundance, and greater SRO mineral content suggest nitrogen limitations and enhanced mineral protection constrain OM turnover with distance from PFPs in deep, subsurface mineral horizons. Steady microbial abundance, increasing putative anaerobe abundance, and changes in C-functional group chemistry indicate oxygen limitations constrain OM turnover in the matrix of shallow mineral horizons. Given that oxygen and nutrient limitations contribute to OM preservation in this high SRO system—an exemplar of mineral protection—resource limitations may play an even more important role in OM preservation in other well-structured soils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

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

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

machine learning↗
DOE OSTI2020

Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms

Massive releases of organic substrates during marine algal blooms trigger growth of many clades of heterotrophic bacteria. Algal polysaccharides represent the most diverse and structurally complex class of these substrates, yet their role in shaping the microbial community composition is poorly understood. We investigated, whether polysaccharide utilization capabilities contribute to niche differentiation of Polaribacter spp. (class Flavobacteriia; known to include relevant polysaccharidedegraders) that were abundant during 2009–2012 spring algal blooms in the southern North Sea. We identified six distinct Polaribacter clades using phylogenetic and phylogenomic analyses, quantified their abundances via fluorescence in situ hybridization, compared metagenome-assembled genomes, and assessed in situ gene expression using metaproteomics. Four clades with distinct polysaccharide niches were dominating. Polaribacter 2-a comprised typical first responders featuring small genomes with limited polysaccharide utilization capacities. Polaribacter 3-a were abundant only in 2010 and possessed a distinct sulfated α-glucoronomannan degradation potential. Polaribacter 3-b responded late in blooms and had the capacity to utilize sulfated xylan. Polaribacter 1-a featured high numbers of glycan degradation genes and were particularly abundant following Chattonella algae blooms. These results support the hypothesis that sympatric Polaribacter clades occupy distinct glycan niches during North Sea spring algal blooms.

59 BASIC BIOLOGICAL SCIENCES↗