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At least 1,315 records · Page 73
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Compositional changes of dissolved organic molecules along water flow and their influencing factors in the Three Gorges Reservoir

Molecular composition of dissolved organic matter (DOM) and its influencing factors in river reservoirs remains elusive. Here, molecular compositions of DOM, bacterial community structures, and water physiochemistry were investigated in the field and microcosm samples of the Three Gorges Reservoir (TGR). The results showed that DOM molecular compositions were significantly (R 2 = 0.245, p < 0.001) correlated with bacterial community structures in the studied field samples, suggesting that bacteria may actively interact with DOM molecules. In this study, the molecular compositions of DOM in the studied field samples were significantly (p < 0.05) affected by the distance between the sample sites and the Three Gorges Dam and by bacterial groups of Actinobacteria and Alphaproteobacteria, suggesting that both hydrological and bacterial processes may contribute to the variation in DOM molecular composition in the TGR water. Furthermore, microcosm experiments demonstrated that both microbial and abiotic processes may transform and/or produce DOM in the TGR, thereby affecting DOM molecular composition. Microbial process increased the average aromaticity index and decreased the carbon number of DOM molecules with increasing incubation duration; whereas average oxygen number, double bond equivalent, and oxidation state of carbon of DOM molecules increased during the first 14 days of incubation and began to decrease thereafter. Taken together, this study expands our understanding of the impact of microbial process on the DOM molecular composition in reservoir ecosystems, and has great implications for carbon cycling in major rivers.

58 GEOSCIENCES↗
DOE OSTI2023

Mercury methylation potential and bioavailability in the sediments of two distinct aquatic systems

Here, this study explored mercury (Hg) methylation potential in two distinct aquatic systems. Fourmile Creek (FMC) was historically polluted with Hg effluents from groundwater as it is a typical gaining stream, where organic matter and microorganisms in streambed are continuously winnowed. The H02 constructed wetland only receives atmospheric Hg and is rich in organic matter and microorganisms. Both systems receive Hg from atmospheric deposition now. Surface sediments were collected from FMC and H02, spiked with inorganic Hg, and cultivated in an anaerobic chamber to stimulate microbial Hg methylation reactions. Total mercury (THg) and methylmercury (MeHg) concentrations were measured at each spiking stage. Mercury methylation potential (MMP, %MeHg in THg) and Hg bioavailability were assessed with the deployment of diffusive gradients in thin films (DGTs). During the methylation process and at the same incubation stage, FMC sediment showed faster increasing rates of %MeHg and higher MeHg concentrations than H02, demonstrating a stronger MMP in the FMC sediment. Similarly, higher Hg bioavailability was observed in FMC sediment compared to the H02 as indicated by DGT-Hg concentrations. In conclusion, the H02 wetland with high levels of organic matter and microorganisms presented low MMP. But the Fourmile Creek as a gaining stream and a historical site of Hg pollution showed strong MMP and high Hg bioavailability. A related study on microbial community activities characterized the microorganisms between FMC and H02, which is attributed to be the main reason for their different methylation capabilities. Our study further brought up the considerations on remediated sites from Hg contamination: Hg bioaccumulation and biomagnification can still be elevated and higher than the surrounding environment due to lagged changes in microbial community structures. This study supported the sustainable ecological modifications of legacy Hg contamination and raised the necessity of long-term monitoring actions even after executing a remediation plan.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Mixed nitrate and metal contamination influences operational speciation of toxic and essential elements

Environmental contamination constrains microbial communities impacting diversity and total metabolic activity. The former S-3 Ponds contamination site at Oak Ridge Reservation (ORR), TN, has elevated concentrations of nitric acid and multiple metals from decades of processing nuclear material. To determine the nature of the metal contamination in the sediment, a three-step sequential chemical extraction (BCR) was performed on sediment segments from a core located upgradient (EB271, non-contaminated) and one downgradient (EB106, contaminated) of the S-3 Ponds. The resulting exchangeable, reducing, and oxidizing fractions were analyzed for 18 different elements. Comparison of the two cores revealed changes in operational speciation for several elements caused by the contamination. Those present from the S-3 Ponds, including Al, U, Co, Cu, Ni, and Cd, were not only elevated in concentration in the EB106 core but were also operationally more available with increased mobility in the acidic environment. Other elements, including Mg, Ca, P, V, As, and Mo, were less operationally available in EB106 having decreased concentrations in the exchangeable fraction. Here, the bioavailability of essential macro nutrients Mg, Ca, and P from the two types of sediment was determined using three metal-tolerant bacteria previously isolated from ORR. Mg and Ca were available from both sediments for all three strains; however, P was not bioavailable from either sediment for any strain. The decreased operational speciation of P in contaminated ORR sediment may increase the dependence of the microbial community on other pools of P or select for microorganisms with increased P scavenging capabilities. Hence, the microbial community at the former S-3 Ponds contamination site may be constrained not only by increased toxic metal concentrations but also by the availability of essential elements, including P.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Effects of red imported fire ant ( Solenopsis invicta ) control on carrion use by vertebrate scavengers

Carrion is an important resource, and competition for carrion by microbial, invertebrate, and vertebrate scavenging communities is great. In particular, carrion is important to facultative and obligate vertebrate scavengers globally, and these species provide an irreplaceable ecological service by efficiently removing carcasses, which potentially harbor pathogens, from the environment. Although vertebrates efficiently acquire carcasses, they compete intensively with invertebrate and microbial communities, especially during warmer months when invertebrate and microbial activity peaks. The presence of invasive invertebrates may further exacerbate competition among scavenging groups; however, little is known about how invasive invertebrates can influence invertebrate scavenger dynamics and ultimately competition with vertebrate scavengers. The red imported fire ant (Solenopsis invicta; RIFA) is an invasive species of particular interest in North America, as it is a dominant predator and decomposer throughout much their range. We hypothesized that in areas where abundant, RIFA can outcompete vertebrates for carrion resources, altering nutrient cycling and food web dynamics. We tested this hypothesis by experimentally excluding RIFA from rabbit carcasses and found strong seasonal effects in our data; however, surprisingly, we found no effect of RIFA control on vertebrate scavenging efficiency, rates of carcass detection, carcass persistence, or the richness of local scavengers. Rather, we observed a highly efficient vertebrate scavenging community that assimilated 87.4% of carcasses during our study. Furthermore, this high rate of vertebrate scavenging efficiency was maintained in both control (93.0%) and RIFA treatment (81.8%) sites, suggesting presence of abundant RIFA populations did not limit vertebrate acquisition of carrion. Future research should focus on the interactions of RIFA with the remaining invertebrate scavenging community to further investigate whether RIFA impact the assimilation of carrion resources within invertebrate communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Repeated freeze-thaw cycles increase extractable, but not total, carbon and nitrogen in a Maine coniferous soil

Northeastern North America has been experiencing warmer winters with reduced snow accumulation, with more frequent winter freeze-thaw cycles. We conducted a laboratory experiment to investigate how increased frequency of freeze-thaw cycles (FTC) would alter soil C and N availability. Organic (O) and mineral (B) horizon soils were collected from a coniferous forest in Maine, processed to exclude roots, and then frozen in the laboratory (-10 °C) with one (FTC-1), two (FTC-2), or six (FTC-6) thaw periods. Soils were analyzed for extractable inorganic ammonium (NH4-N), water extractable organic carbon (WEOC), carbon dioxide flux (respiration), and total C and N. Extractable NH4-N increased following FTC, for both horizons. WEOC in O horizons had a lower SUVA254, indicating a stronger microbial influence (i.e., microbial cell lysis) in these soils after FTC. Respiration in O horizon soils decreased post-incubation and did not differ between FTC and Control soils. In the B horizon, however, FTC soils showed greater respiration than Control soils, suggesting that the newly available nutrients may have stimulated microbial activity. In contrast to these results, total C and N remained unaltered by FTC, presumably because the FTC disturbances represented mostly a translocation of C and N from one pool into another, and losses due to respiration were too small to significantly influence the large TC and TN pools. The effect of FTC on NH4-N did not change with FTC frequency, suggesting that a single FTC is sufficient to alter both C and N availability and quality, and that additional FTC may not have a significant further effect. This study provides fresh insights on how organic and mineral soils might respond to increased freeze-thaw frequency in winter.

Patel, Kaizad F.↗
DOE OSTI2021

Vertical movement of soluble carbon and nutrients from biocrusts to subsurface mineral soils

Dryland ecosystems can be constrained by low soil fertility. Within drylands, the soil nutrient and organic carbon (C) cycling that does occur is often mediated by soil surface communities known as biological soil crusts (biocrusts), which cycle C and nutrients in the top ca. 0–2 cm of soil. However, the degree to which biocrusts are influencing soil fertility and biogeochemical cycling in deeper, subsurface mineral soils is unclear. The movement of dissolved resources from biocrusts to deeper soil layers in leachate may be one of the main mechanisms through which biocrust fertility is transferred downward towards deeper microbial communities and plant roots occurring within mineral soil. Here, in this study, we examined the role of biocrust leachate in contributing to subsurface nutrient and soluble C pools and subsurface microbial cycling. We collected biocrusts from three biocrust successional stages and explored resource pools in situ at multiple soil depths, while collecting leachate and measuring nutrient and organic C concentrations and metabolite composition from each successional stage in the laboratory. After four leachate collections, we conducted an incubation of mineral soil collected from below each biocrust successional stage to measure heterotrophic microbial CO 2 flux and biomass. Overall, our findings observed that the degree of nutrient and C connectivity between biocrusts and the sub-crust mineral soil depended on the biocrust successional stage and the element being considered, and the influence of biocrust successional stage on mineral soil CO 2 flux is likely related to long-term resource build up. Together, our results suggest that the influence of biocrust leachate on subsurface mineral soil is complex and context dependent, but, over longer time periods and at later successional stages, can have measurable effects on dryland soil biogeochemical cycling with feedbacks to resource availability and CO 2 flux.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Effects of ingested nanocellulose on intestinal microbiota and homeostasis in Wistar Han rats

Micron scale crystalline and fibrillar cellulose materials are “generally regarded as safe” (GRAS) as binders and thickeners in food products. Yet, partly due to a lack of relevant toxicological data, nanocellulose (NC) materials, which have unique properties that can be exploited to improve food quality and safety, have yet to receive FDA approval as food ingredients. Results of in vitro and in vivo toxicological studies of ingested NC, detailed in a recent companion report, revealed minimal acute in vitro cytotoxicity, and no toxicity in a subacute rat gavage model, suggesting that NC materials are non-hazardous. However, ingested materials may also modulate gut microbial populations, or alter aspects of intestinal function not evaluated in standard totoxicity testing, which could have important health implications. Here, we report the results of studies of the effects of ingested cellulose nanofibrils (CNF) on the fecal microbiome and metabolome, intestinal (ileal) epithelial cell mRNA expression of cell junction genes, and ileal cytokine production. Feces, plasma, and ileum samples were collected from Wistar Han rats before and after five weeks of biweekly gavages of water or cream, with or without 1% w/w CNF. Analysis of fecal microbial populations revealed that CNF caused changes in both genus and species diversity, with specific effects on species that produce short chain fatty acids, and that have been associated with increased IgA production and elevation of insulin levels. Fecal metabolomic analysis revealed relatively few effects of CNF, with significant changes in the levels of only ten metabolites out of 366 measured. Exposure to CNF also caused differential regulation of mRNA expression of several genes involved in epithelial cell junctions, and increased production of cytokines that both promote and inhibit proliferation of CD8 T cells. These perturbations in intestinal homeostasis contrast somewhat with the absence of in vitro and in vivo toxicity observed previously but would appear to represent minor effects. Additionally, the gut microbiome is highly sensitive to ingested substances, and such disturbances of the intestinal microbial ecosystem do not necessarily represent or predict meaningful pathology. Further studies, including chronic feeding studies, are needed to assess the real health implications, if any, of these changes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Engineering Citrobacter freundii using CRISPR/Cas9 system

The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated proteins) system is a useful tool to edit genomes quickly and efficiently. However, the use of CRISPR/Cas9 to edit bacterial genomes has been limited to select microbial chassis primarily used for bioproduction of high value products. Thus, expansion of CRISPR/Cas9 tools to other microbial organisms is needed. Here, our aim was to assess the suitability of CRISPR/Cas9 for genome editing of the Citrobacter freundii type strain ATCC 8090. We evaluated the commonly used two plasmid pCas/pTargetF system to enable gene deletions and insertions in C. freundii and determined editing efficiency. The CRISPR/Cas9 based method enabled high editing efficiency (~91%) for deletion of galactokinase (galk) and enabled deletion with various single guide RNA (sgRNA) sequences. To assess the ability of CRISPR/Cas9 tools to insert genes, we used the fluorescent reporter mNeonGreen, an endopeptidase (yebA), and a transcriptional regulator (xylS) and found successful insertion with high efficiency (81-100%) of each gene individually. These results strengthen and expand the use of CRISPR/Cas9 genome editing to C. freundii as an additional microbial chassis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Root exudate composition from different plant species influences the growth of rhizosphere bacteria

Plant roots release exudates that fuel microbial activities and can structure rhizosphere microbial communities, but how different plant species use their root exudate to potentially select for different soil microbes in the rhizosphere is not well understood. Here, we investigated how root exudate from plants of three diverging lineages, Lactuca sativa (lettuce), Brassica juncea (mustard cabbage), and Zea mays (maize) influence the growth of their own rhizosphere bacteria (host) and those from other plant species (non-host) in growth bioassays. We found that on the community level, lettuce rhizosphere bacteria grew better in non-host exudate, but mustard cabbage and maize rhizosphere bacteria grew similarly well in both host and non-host exudate. However, individual bacteria taxa showed strong preferences for exudate from different plant species. The bacterial growth patterns were independent of C and N quantity, suggesting that certain exometabolic compounds may drive the growth patterns. Our results demonstrate that root exudate from a given plant species have the potential to stimulate or suppress soil bacteria and hint at a mechanism that different plant species use to select for their specific suite of rhizosphere bacteria. Furthermore, these findings contribute to our broader understanding of how root exudate quality could be a mechanism that plants use to select for distinct microbial communities in the rhizosphere.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Disruption of the endogenous indole glucosinolate pathway impacts the Arabidopsis thaliana root exudation profile and rhizobacterial community

Root exudates are composed of primary and secondary metabolites known to modulate the rhizosphere microbiota. Glucosinolates are defense compounds present in the Brassicaceae family capable of deterring pathogens, herbivores and biotic stressors in the phyllosphere. In addition, traces of glucosinolates and their hydrolyzed byproducts have been found in the soil, suggesting that these secondary metabolites could play a role in the modulation and establishment of the rhizosphere microbial community associated with this family. Here, we used Arabidopsis thaliana mutant lines, including the cyp79B2cyp79B3 double mutant line with a disruption in the indole glucosinolate pathway and atr1D, which overexpresses ATR1 and increases glucosinolate production. These lines were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and 16S rRNA amplicon sequencing to evaluate how genetic modifications to the indole glucosinolate pathway affects the root exudate profile of Arabidopsis thaliana, and, in turn, impacts the rhizosphere microbial community. Metabolic analysis of root exudates from the wild-type Columbia (Col-0), along with the mutant lines, confirmed that alterations to the indole glucosinolate biosynthetic pathway result in shifts in the root exudate profile of the plant. We observed changes in the relative abundance of exuded metabolites. Moreover, 16S rRNA amplicon sequencing results provided evidence that the rhizobacterial communities associated with the plant lines used were directly impacted in diversity and community composition. Here, this work provides further information on the involvement of secondary metabolites and their role in modulating the rhizobacterial community. Root metabolites dictate the presence of different bacterial species, including plant growth-promoting rhizobacteria (PGPR). Our results suggest that genetic alterations in the indole glucosinolate pathway cause disruptions beyond the endogenous levels of the plant, significantly changing the abundance and presence of different metabolites in the root exudates of the plants as well as the microbial rhizosphere community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants

Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific 13 C-pyruvate labeling to examine the effects of three different plant species (Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana) and their associated microbial communities on soil organic carbon turnover in the rhizosphere. Here, our findings indicate that in these tropical plants, the rhizosphere metabolome is primarily shaped by the response of roots to drought rather than direct shifts in the rhizosphere bacterial community composition. Specifically, the reduced exudation of plant roots had a notable effect on the metabolome of the rhizosphere of P. auritum, with less reliance on neighboring microbes. Contrary to P. auritum, H. rosa sinensis and C. fairchildiana experienced changes in their exudate composition during drought, causing alterations to the bacterial communities in the rhizosphere. This, in turn, had a collective impact on the rhizosphere's metabolome. Furthermore, the exclusion of phylogenetically distant microbes from the rhizosphere led to shifts in its metabolome. Additionally, C. fairchildiana appeared to be associated with only a subset of symbiotic bacteria under drought conditions. These results indicate that plant species-specific microbial interactions systematically change with the root metabolome. As roots respond to drought, their associated microbial communities adapt, potentially reinforcing the drought tolerance strategies of plant roots. These findings have significant implications for maintaining plant health and preference during drought stress and improving plant performance under climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Rewetting of soil: Revisiting the origin of soil CO 2 emissions

Rewetting dry soils is associated with a burst of microbial activity and mineralization, which manifests itself as a pulse in soil CO 2 emissions, long-known as the Birch effect. In arid and semi-arid systems, soil CO 2 losses upon rewetting at the end of extended dry periods can contribute a significant fraction to the overall carbon (C) budget. Microbial biomass is one of the sources of mineralized C, as was demonstrated over 30 years ago (Kieft et al., 1987). The present paper offers a perspective on how the field has progressed since the 1987 paper was published in Soil Biology & Biochemistry, what it means in terms of current concerns about global climate change, and the needs and potential emphases of future research. Many studies since 1987 have addressed the origin of this CO 2 pulse, finding multiple possible C sources involving both biotic and abiotic processes. We propose that the magnitude of the rewetting event (Δψ) determines the relative contribution from the array of substrates that contribute to the soil CO 2 pulse upon rewetting. The magnitude of the CO 2 pulse is likely related to soil physical characteristics and to the size of the available C pool, which is partly controlled by plants. Further, the relative contributions of the mechanisms generating soil CO 2 pulses upon rewetting are likely to be modified by climate change. To understand and predict the magnitude of soil CO 2 pulses upon rewetting, we advocate continued cross-disciplinary research involving soil microbial ecology, soil physics, soil chemistry, as well as increased integration and recognition of the importance of plant-soil interactions in controlling the soil C pools contributing to soil CO 2 pulses.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Global biogeography of fungal and bacterial biomass carbon in topsoil

Bacteria and fungi, representing two major soil microorganism groups, play an important role in global nutrient biogeochemistry. Biogeographic patterns of bacterial and fungal biomass are of fundamental importance for mechanistically understanding nutrient cycling. We synthesized 1323 data points of phospholipid fatty acid-derived fungal biomass C (FBC), bacterial biomass C (BBC), and fungi:bacteria (F:B) ratio in topsoil, spanning 11 major biomes. The FBC, BBC, and F:B ratio display clear biogeographic patterns along latitude and environmental gradients including mean annual temperature, mean annual precipitation, net primary productivity, root C density, soil temperature, soil moisture, and edaphic factors. At the biome level, tundra has the highest FBC and BBC densities at 3684 (95% confidence interval: 1678–8084) mg kg -1 and 428 (237–774) mg kg -1 , respectively; desert has the lowest FBC and BBC densities at 16.92 (14.4–19.89) mg kg -1 and 6.83 (6.1–7.65) mg kg -1 , respectively. The F:B ratio varies dramatically, ranging from 1.8 (1.6–2.1) in savanna to 8.6 (6.7–11.0) in tundra. An empirical model was developed for the F:B ratio and it is combined with a global dataset of soil microbial biomass C to produce global maps for FBC and BBC in 0–30 cm topsoil. Across the globe, the highest FBC is found in boreal forest and tundra while the highest BBC is in boreal forest and tropical/subtropical forest, the lowest FBC and BBC are in shrub and desert. Global stocks of living microbial biomass C were estimated to be 12.6 (6.6–16.4) Pg C for FBC and 4.3 (0.5–10.3) Pg C for BBC in topsoil. These findings advance our understanding of the global distribution of fungal and bacterial biomass, which facilitates the incorporation of fungi and bacteria into Earth system models. The global maps of bacterial and fungal biomass serve as a benchmark for validating microbial models in simulating the global C cycle under a changing climate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Plant root exudates and rhizosphere bacterial communities shift with neighbor context

A plant's neighborhood context can alter its interactions with other organisms, but little is known about how these dynamics occur belowground, especially with soil microbes. Microbial communities in rhizosphere soil are influenced by many factors, including abiotic conditions and root-derived signals. In particular, root exudates have strong effects on rhizosphere assembly, respond to changes in abiotic conditions, and help plants interact with neighbors. Therefore, we predicted that root exudates likely play a central role in neighbor-induced shifts in rhizosphere communities. We conducted a greenhouse experiment to test this and determine how the rhizosphere bacterial community of a focal plant, Panicum virgatum, changed when beside different neighbors, and whether these shifts were mediated by neighbor-induced changes in root exudation. We found that neighbor altered both focal plant exudates and rhizosphere community, and that changes were largest when the focal plant was beside the most competitive neighbor, Rudbeckia hirta, which reduced both focal plant growth and nitrogen uptake. Several factors contributed to neighbor impacts on rhizosphere assembly, including neighbor-induced changes in root exudates during nitrogen-limitation and microbial spillover from roots of larger neighbors. Using an additional soil incubation, we also found that these changes in exudates can have even greater effects on soil nutrients than on microbial assembly. Overall, we show that neighbors influence one another's microbiomes, and highlight neighbor-induced changes in root exudates as one mechanism through which this may occur. Furthermore, this work suggests that rhizosphere assembly may differ in mixed-species communities and thus emphasizes a need for microbiome studies that consider neighborhood context.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The nitrogen gap in soil health concepts and fertility measurements

Soil nitrogen (N) often limits productivity in agroecosystems, prompting fertilizer applications that increase crop yields but can degrade the environment. Nitrogen's dual role in both productivity and environmental quality should center it in soil health frameworks. We use recent evidence to argue that N availability is an emergent property of the integrated soil biogeochemical system and is strongly influenced by plant traits and their interactions with microbes and minerals. Building upon this, we theorize that the sources of plant and microbial N shift across soil health gradients, from inorganic N dependence in ecologically simple systems with poor soil health to a highly networked supply of organic N in healthy soils; ergo, investments in soil health should increase ecological complexity and the pathways by which plants can access N, leading to more resilient nutrient supplies and yields in a variable climate. However, current N assessment methods derive from a historical emphasis on inorganic N pool sizes and are unable to capture the shifting drivers of N availability across soil health gradients. We highlight the need to better understand the plant-microbial-mineral interactions that regulate bioavailable N as a first step to improving our ability to measure it. We conclude it will be necessary to harness agroecosystem complexity, account for plant and microbial drivers, and carefully integrate external N inputs into soils' internal N network to expand the routes by which N from organic pools can be made bioavailable. Finally, by emphasizing N in soil health concepts, we argue that researchers can accelerate advances in N use efficiency and resiliency.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Revising the dynamic energy budget theory with a new reserve mobilization rule and three example applications to bacterial growth

Dynamic energy budget (DEB) theory has been applied to model a wide range of organisms, including microbes. In the standard DEB model, biomass is partitioned into reserve and structural compartments, where reserve biomass is mobilized in a pseudolinear manner (while the reserve biomass density, defined as the ratio between reserve and structural biomass, decays linearly) to drive maintenance and the growth of structural biomass (and extracellular enzyme production if it is considered). However, the linear dynamics of the reserve biomass density makes the standard DEB model incapable of explaining the slowdown of microbial growth at high reserve density that is caused by macromolecular crowding effect which reduces biochemical reaction rates (a typical situation occurs when microbes are experiencing severe moisture stress) and is inconsistent with the observation that intracellular enzymatic reactions generally follow non-linear kinetics. By partitioning biomass into reserve, kinetic, and structural compartments, we show here that the Equilibrium Chemistry Approximation (ECA) kinetics can be used to represent enzymatically catalyzed reserve biomass mobilization that can then drive the kinetic and structural biomass synthesis. This revised DEB model better represents the tradeoff in ribosome allocation for structural growth and internal enzyme production, is structurally compatible with metabolic models of cell individuals, and includes the standard DEB model and the popular compromise model as special cases for representing population growth. We then applied the revised DEB model to interpret components of bacterial respiration, their dependence on substrate availability, and emergent microbial carbon use efficiency dynamics for an exponentially growing population. We found that the revised DEB model enables a better understanding of bacterial substrates use (carbon in our examples) than that can be derived from a few other models in the literature. In particular, the revised DEB model explains why carbon use efficiency may first increase, then plateau, and finally decrease with growth rate (and substrate uptake rate), as a function of proteomics. Additionally, the revised DEB model explains why the kinetic biomass compartment needs to be divided to reasonably incorporate proteomic control of microbial growth.

59 BASIC BIOLOGICAL SCIENCES↗