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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Comparing the Recovery of Arbuscular and Ectomycorrhizal Stands from Long-Term Nitrogen Fertilization at the Fernow Experimental Forest, WV (2021 and 2022)

This data was generated to answer the research question: After the end of a 30-year nitrogen (N) fertilization experiment in an Eastern temperate forest, to what extent do plant microbial interactions and carbon cycling in arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) dominated stands follow different recovery trajectories?The soil and the roots used in this dataset were sampled from two watersheds (N-fertilized watershed 3 and Reference watershed 7) with 6 AM and 6 ECM dominated stands each, over the course of three months (June, July, August) in 2021 and 2022. The "All_Roots.csv" data includes fine root biomass (in g) scaled to sampled soil (m2) (Scaled_Rt_Bm_gm2), and AM and ECM root colonization (%) in two soil fractions: the organic horizon (O) and the mineral horizon (B). The "All_Enzymes.csv" data includes extracellular soil enzyme activity (N-acetyl-glucosaminidase (NAG), acid phosphatase (AP), β-glucosidase (BG), phenol oxidase and peroxidase), and the ratios of BG to AP (BG:AP) and BG to NAG (BG:NAG) in three soil fractions: the organic horizon (O), the bulk soil (B), and the rhizosphere (R).The "All_Nmin" data includes inorganic N (NO3- and NH4+) pools (unit: μg of N per g of dry soil) measured pre- (I_Nitrate_ugNgsoil and I_Ammonia_ugNgsoil) and post-incubation (F_Nitrate_ugNgsoil and F_Ammonia_ugNgsoil), as well as calculated nitrification (Nitrification_day) and nitrogen mineralization (Mineralization_day) rates per day, in three soil fractions: the organic horizon (O), the bulk soil (B), and the rhizosphere (R).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Potential Activities and Long Lifetimes of Organic Carbon-Degrading Extracellular Enzymes in Deep Subsurface Sediments of the Baltic Sea

Heterotrophic microorganisms in marine sediments produce extracellular enzymes to hydrolyze organic macromolecules, so their products can be transported inside the cell and used for energy and growth. Therefore, extracellular enzymes may mediate the fate of organic carbon in sediments. The Baltic Sea Basin is a primarily depositional environment with high potential for organic matter preservation. The potential activities of multiple organic carbon-degrading enzymes were measured in samples obtained by the International Ocean Discovery Program Expedition 347 from the Little Belt Strait, Denmark, core M0059C. Potential maximum hydrolysis rates (V max ) were measured at depths down to 77.9mbsf for the following enzymes: alkaline phosphatase, β- d -xylosidase, β- d -cellobiohydrolase, N-acetyl-β- d -glucosaminidase, β-glucosidase, α-glucosidase, leucyl aminopeptidase, arginyl aminopeptidase, prolyl aminopeptidase, gingipain, and clostripain. Extracellular peptidase activities were detectable at depths shallower than 54.95mbsf, and alkaline phosphatase activity was detectable throughout the core, albeit against a relatively high activity in autoclaved sediments. β-glucosidase activities were detected above 30mbsf; however, activities of other glycosyl hydrolases (β-xylosidase, β-cellobiohydrolase, N-acetyl-β-glucosaminidase, and α-glucosidase) were generally indistinguishable from zero at all depths. These extracellular enzymes appear to be extremely stable: Among all enzymes, a median of 51.3% of enzyme activity was retained after autoclaving for an hour. We show that enzyme turnover times scale with the inverse of community metabolic rates, such that enzyme lifetimes in subsurface sediments, in which metabolic rates are very slow, are likely to be extraordinarily long. A back-of-the-envelope calculation suggests enzyme lifetimes are, at minimum, on the order of 230days, and may be substantially longer. These results lend empirical support to the hypothesis that a population of subsurface microbes persist by using extracellular enzymes to slowly metabolize old, highly degraded organic carbon.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Microbial community shifts correspond with suppression of decomposition 25 years after liming of acidic forest soils

Microbial community structure and function regularly covary with soil pH, yet effects of these interactions on soil carbon are rarely tested experimentally within natural ecosystems. We investigated the enduring (25 year) impacts of liming on microbial community structure and decomposition at an acidic northern hardwood forest, where experimental liming increased pH one unit and surprisingly doubled the organic carbon stocks of the forest floor. Here we show that this increase in carbon storage corresponded with restructuring of the bacterial and fungal communities that drive decomposition. In the Oe horizon, liming reduced the activities of five extracellular enzymes that mediate decomposition, while the Oa horizon showed an especially large (64%) reduction in the activity of a sixth, peroxidase, which is an oxidative enzyme central to lignocellulose degradation. Decreased enzyme activities corresponded with loss of microbial taxa important for lignocellulose decay, including large reductions in the dominant ectomycorrhizal genera Russula and Cenococcum, saprotrophic and wood decaying fungi, and Actinobacteria (Thermomonosporaceae). These results demonstrate the importance of pH as a dominant regulator of microbial community structure and illustrate how changes to this structure can produce large, otherwise unexpected increases in carbon storage in forest soils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Reactive iron, not fungal community, drives organic carbon oxidation potential in floodplain soils

Wetlands host ∼20% of terrestrial organic carbon and serve as a major sink for atmospheric carbon. Anoxic soils and sediments accrue soil organic carbon (SOC) partly by hampering the activity of extracellular oxidative enzymes that break down phenolic polymers. Upon aeration, fungal-driven oxidative enzymatic depolymerization and microbial respiration of released monomers ensue. Redox-active metals can simultaneously catalyze abiotic nonspecific oxidation of SOC, notable examples including Mn(III) or Fe(II) through Fenton-like, hydrogen peroxide-catalyzed oxidative radical production. However, the extent of reactive metal contributions to biotic and abiotic SOC degradation is not understood in the context of natural environments with diverse redox chemistry. We tested the relative contributions of fungi, Mn(III) and Fe(II) to phenolic substrate (L-DOPA) oxidation in floodplain soils representing a range of transient redox conditions driven by permanent vs. periodic flooding. Phenol oxidative potential was highest in permanently flooded soils with fewer fungal taxa known for observed (per)oxidase activity and instead correlated with HCl-extractable Fe(II), Fe(total) and Fe(II)/Fe(total), suggesting a specific role of Fe(II). Fe(II) additions enhanced phenol oxidative potential in sterilized and non-sterilized soils in the presence of hydrogen peroxide, indicating abiotic Fe-mediated radical chemistry could significantly enhance wetland SOC oxidative depolymerization throughout redox-active floodplain soils. Fungal community composition did not correlate to phenol oxidative potential overall and only more oxic soils adjacent to the river with diverse fungal communities showed declining oxidative potential after sterilization. Mn(III) addition did not significantly enhance phenol oxidative potential across all soils, although it appeared to drive fungal-mediated oxidative potential in the most aerated floodplain soils. Understanding how metals mediate SOC depolymerization as abiotic oxidants or microbially-harnessed enzyme cofactors and substrates in soils under variable hydrologic controls will improve our ability to represent depolymerization in terrestrial carbon models in wetland and other frequently saturated soils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Declining carbohydrate solubilization with increasing solids loading during fermentation of cellulosic feedstocks by Clostridium thermocellum: documentation and diagnostic tests

Abstract Background For economically viable 2nd generation biofuels, processing of high solid lignocellulosic substrate concentrations is a necessity. The cellulolytic thermophilic anaerobe Clostridium thermocellum is one of the most effective biocatalysts for solubilization of carbohydrate harbored in lignocellulose. This study aims to document the solubilization performance of Clostridium thermocellum at increasing solids concentrations for two lignocellulosic feedstocks, corn stover and switchgrass, and explore potential effectors of solubilization performance. Results Monocultures of Clostridium thermocellum demonstrated high levels of carbohydrate solubilization for both unpretreated corn stover and switchgrass. However, fractional carbohydrate solubilization decreases with increasing solid loadings. Fermentation of model insoluble substrate (cellulose) in the presence of high solids lignocellulosic spent broth is temporarily affected but not model soluble substrate (cellobiose) fermentations. Mid-fermentation addition of cells ( C. thermocellum ) or model substrates did not significantly enhance overall corn stover solubilization loaded at 80 g/L, however cultures utilized the model substrates in the presence of high concentrations of corn stover. An increase in corn stover solubilization was observed when water was added, effectively diluting the solids concentration mid-fermentation. Introduction of a hemicellulose-utilizing coculture partner, Thermoanaerobacterium thermosaccharolyticum, increased the fractional carbohydrate solubilization at both high and low solid loadings. Residual solubilized carbohydrates diminished significantly in the presence of T. thermosaccharolyticum compared to monocultures of C. thermocellum, yet a small fraction of solubilized oligosaccharides of both C 5 and C 6 sugars remained unutilized. Conclusion Diminishing fractional carbohydrate solubilization with increasing substrate loading was observed for C. thermocellum -mediated solubilization and fermentation of unpretreated lignocellulose feedstocks. Results of experiments involving spent broth addition do not support a major role for inhibitors present in the liquid phase. Mid-fermentation addition experiments confirm that C. thermocellum and its enzymes remain capable of converting model substrates during the middle of high solids lignocellulose fermentation. An increase in fractional carbohydrate solubilization was made possible by (1) mid-fermentation solid loading dilutions and (2) coculturing C. thermocellum with T. thermosaccharolyticum , which ferments solubilized hemicellulose. Incomplete utilization of solubilized carbohydrates suggests that a small fraction of the carbohydrates is unaffected by the extracellular carbohydrate-active enzymes present in the culture.

09 BIOMASS FUELS↗
DOE OSTI2021

Low-intensity frequent fires in coniferous forests transform soil organic matter in ways that may offset ecosystem carbon losses

The impact of shifting disturbance regimes on soil carbon (C) storage is a key uncertainty in global change research. Wildfires in coniferous forests are becoming more frequent in many regions, potentially causing large C emissions. Repeated low-intensity prescribed fires can mitigate wildfire severity, but repeated combustion may decrease soil C unless compensatory responses stabilize soil organic matter. Here, we tested how 30 years of decadal prescribed burning affected C and nitrogen (N) in plants, detritus, and soils in coniferous forests in the Sierra Nevada mountains, USA. Tree basal area and litter stocks were resilient to fire, but fire reduced forest floor C by 77% (-36.4 Mg C/ha). In mineral soils, fire reduced C that was free from minerals by 41% (-4.4 Mg C/ha) but not C associated with minerals, and only in depths ≤ 5 cm. Fire also transformed the properties of remaining mineral soil organic matter by increasing the proportion of C in a pyrogenic form (from 3.2% to 7.5%) and associated with minerals (from 46% to 58%), suggesting the remaining soil C is more resistant to decomposition. Laboratory assays illustrated that fire reduced microbial CO2 respiration rates by 55% and the activity of eight extracellular enzymes that degrade cellulosic and aromatic compounds by 40–66%. Lower decomposition was correlated with lower inorganic N (-49%), especially ammonium, suggesting N availability is coupled with decomposition. The relative increase in forms of soil organic matter that are resistant to decay or stabilized onto mineral surfaces, and the associated decline in decomposition suggest that low-intensity fires may promote mineral soil C storage in pools with long mean residence times in coniferous forests.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Moisture Effect on Chitin Decomposition Biogeochemistry

This dataset contains data files for multiple measurements of sample biogeochemistry and function collected for the Soils SFA Chitin Decomposition project in task 2.2. Samples were generated from soil incubated under different moisture levels, with and without chitin. Each sheet in the file refers to the preprocessed data collected. Sheet 1 "Respiration" measures CO2 production daily for the course of the incubation. Sheet 2 "Biomass" contains the microbial biomass and salt extractable measurements for carbon and nitrogen. Sheet 3 "Chitin" is for HPLC measured chitin from each sample. Sheet 4 "Extracellular Enzyme Assays" records the level of activity for several enzyme assays. Sheet 5 "Enzyme Kinetics" measures degradation of substrate over time for all samples.

Reichart, Nicholas J [Pacific Northwest National L↗
DOE OSTI2019

Bacterial Tradeoffs in Growth Rate and Extracellular Enzymes

Like larger organisms, bacteria possess traits, or phenotypic characteristics, that influence growth and impact ecosystem processes. Still, it remains unclear how these traits are organized across bacterial lineages. Using 49 bacterial strains isolated from leaf litter in Southern California, we tested the hypothesis that bacterial growth rates trade off against extracellular enzyme investment. We also tested for phylogenetic conservation of these traits under high and low resource conditions represented, respectively, by Luria broth (LB) and a monomer-dominated medium extracted from plant litter. In support of our hypotheses, we found a negative correlation between the maximum growth rate and the total activity of carbon-, nitrogen-, and phosphorus-degrading extracellular enzymes. However, this tradeoff was only observed under high resource conditions. We also found significant phylogenetic signal in maximum growth rate and extracellular enzyme investment under high and low resource conditions. Driven by our bacterial trait data, we proposed three potential life history strategies. Resource acquisition strategists invest heavily in extracellular enzyme production. Growth strategists invest in high growth rates. Bacteria in a third category showed lower potential for enzyme production and growth, so we tentatively classified them as maintenance strategists that may perform better under conditions we did not measure. These strategies were related to bacterial phylogeny, with most growth strategists belonging to the phylum Proteobacteria and most maintenance and resource acquisition strategists belonging to the phylum Actinobacteria. By accounting for extracellular enzyme investment, our proposed life history strategies complement existing frameworks, such as the copiotroph-oligotroph continuum and Grime’s competitorstress tolerator-ruderal triangle. Our results have biogeochemical implications because allocation to extracellular enzymes versus growth or stress tolerance can determine the fate and form of organic matter cycling through surface soil.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Low soil phosphorus availability triggers maize growth stage specific rhizosphere processes leading to mineralization of organic P

Phosphorus (P) is one of the essential nutrients for all living organisms. High-quality mineral P fertilizer is a finite resource with only an estimated 80-100 years of reserves remaining globally. Both plants and microbes have developed several mechanisms such as secretion of organic acids, acidification of the rhizosphere, and production of extracellular enzymes to enhance the acquisition of P from soils. Increased activity of phosphatase occurs in response to P deficiency as part of P starvation responses which catalyze the hydrolysis of P o from soil organic matter (SOM) and release inorganic P (P i ). However, the specific interactions between plants and microbial communities in the rhizosphere soil triggered by P deficiency are largely unknown. In a greenhouse study we grew maize plants in low and high P containing soils and examined the role of rhizosphere processes on mineralization of organic P (P o ) in soils with low and high P availability and different P speciation 23 (Po dominated versus P i dominated) and determine its effect on plant growth. Plant biomass was determined and rhizosphere soils, and soil samples from pots with and without plants were collected at key vegetative growth stages (VGS). A variety of biogeochemical parameters (e.g. microbial biomass C and P, potential phosphatase activities, plant biomass P, soil P species etc.) were determined using both conventional (sequential chemical extraction) and advanced (e.g. high resolution mass spectrometry (FTICR-MS) and 3129 P solution NMR) techniques. Here, we used phospholipid fatty acid (PLFA) and DNA based microbial community analysis to track changes in microbial community structure and diversity. Low P availability induced changes in biogeochemical processes and microbial community composition in the rhizosphere soils of plants grown in low P containing soil. At early VGS, the plants in low P soil were visually struggling which correlated with greater rhizosphere potential acid phosphatase activity and a reduction in P o fractions. At late VGS, the plants appeared to recover which correlated with a decrease in Meh (III) extractable P, an increase in microbial biomass C and P and greater total P in the plant biomass (roots, shoots and leaves). In high P containing soil, on the other hand, greater P availability masked these rhizosphere processes. Our results confirmed the degradation of SOM and Po mineralization in rhizosphere soils driven by microbe and plant need for P. P deficiency may have favored the abundance of fungi which utilized easily degradable root exudates for the production of extracellular enzymes responsible for the mineralize of SOM P o . This study highlights the intertwined mechanisms involved, and emphasizes the importance of, P o sources for plant nutrition and survival in marginal soils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Impact of moisture on microbial decomposition phenotypes and enzyme dynamics

Soil organic matter decomposition is a complex process reflecting microbial composition and environmental conditions. Moisture can modulate the connectivity and interactions of microbes. Due to heterogeneity, a deeper understanding of the influence of soil moisture on the dynamics of organic matter decomposition and resultant phenotypes remains a challenge. Soils from a long-term field experiment exposed to high and low moisture treatments were incubated in the laboratory to investigate organic matter decomposition using chitin as a model substrate. By combining enzymatic assays, biomass measurements, and microbial enrichment via activity-based probes, we determined the microbial functional response to chitin amendments and field moisture treatments at both the community and cell scales. Chitinolytic activities showed significant responses to the amendment of chitin, independent of differences in field moisture treatments. However, for other measurements of carbon metabolism and cellular functions, soils from high moisture field treatments had greater potential enzyme activity than soils from low moisture field treatments. A cell tagging approach was used to enrich and quantify bacterial taxa that are actively producing chitin-degrading enzymes. By integrating organism, community, and soil core measurements we show that (i) a small subset of taxa compose the majority (>50%) of chitinase production despite broad functional redundancy, (ii) the identity of key chitin degraders varies with moisture level, and (iii) extracellular enzymes that are not cell-associated account for most potential chitinase activity measured in field soil.

activity-based probes↗
DOE OSTI2025

Plant-microbial interplay for organic nitrogen mediated by functional specificity of root compartments

The organic form of nitrogen (N) is a critical intermediate in mutualistic and competitive root-microbial interactions, mediated by extracellular enzymes. Visualization of the hotspots of organic N and proteolytic activity might be valuable for revealing root functional specificity in N acquisition and transformation at the level of individual roots and compartments. For the first time, we used time-lapse amino-mapping and zymography to co-localize and map the spatial distribution of amino-N and leucine aminopeptidase (LAP) activity in the soil and different root parts of maize (Zea mays L.). Amino-N distribution was mainly associated with seminal roots and root tips, where it overlapped with LAP activity hotspots. In the lateral roots and bulk soil, however, LAP activity was decoupled from amino-N. Distinct functional traits revealed themselves as the highest amino-N content and LAP activity in seminal root tips and as the largest relative extent of the rhizosphere in lateral root tips. Co-localized amino-N and LAP activities highlighted different nutrient acquisition strategies mediated by root-microbe interactions, depending on the root compartment. Seminal roots and their tips appeared to adopt mutualistic strategies, potentially attracting root-associated microorganisms through releasing oligo- and polypeptides. In contrast, lateral roots, with amino-N detected only at their tips, demonstrated stronger N competition, relying on the enzyme activity of the rhizosphere microbial community for N acquisition. These insights emphasized the role of root functional specialization in shaping plant-microbe interactions, offering pathways to enhance nutrient use efficiency.

Maize (Zea mays L.)↗
DOE OSTI2024

Differential Organic Carbon Mineralization Responses to Soil Moisture in Three Different Soil Orders Under Mixed Forested System: Supporting Data

This data contains data from 90-day long incubation study which aimed to look at the soil moisture-texture relationship on soil organic carbon (SOC) cycling. Soils were collected from three distinct soil textures from mixed forests in 2017: sandy (Georgia, 2017-05-01), loamy (Missouri, 2017-06-14) and clayey (Texas, December 2017) were incubated at different soil moisture levels (air-dried, 25% water holding capacity (WHC), 50% WHC, 100% WHC and 175% WHC) at room temperature for a period of 90 days. Files contain microbial respiration, active and slow SOC pools, and their respective mineralization rates, extractable organic carbon (C), and C-acquiring extracellular enzymes. Findings from these data were used in Singh et al. (2021). This study aimed to examine the interactive effect of soil moisture and texture on SOC mineralization. Soil samples of three distinct textures (sandy, loamy, and clayey) were collected from mixed forests of Georgia, Missouri, and Texas, respectively. Soil cores of 5 cm diameter were collected from numerous random locations at each site from 0-15 cm depth after scraping the litter layer and mixed thoroughly to obtain a composite sample per site. Three additional soil cores were collected to determine the WHC using pressure plate extractors. Soil samples were composited, and triplicate soil samples were incubated in mason jars for a period of 90 days at room temperature under different moisture regimes: air dried, 25% WHC, 50% WHC, at WHC and 100% saturation. Soil respiration was measured weekly, and destructive sampling was conducted at 1, 15, 60, and 90 days to determine extractable organic C, C acquiring enzyme activity, and active and slow SOC pools with their respective mineralization rates. The C acquiring enzyme activity was the total activity of α-glucosidase, β-glucosidase, cellobiohydrolase, and β-xylosidase enzymes. Gas samples for microbial respiration measurements were collected from headspace of incubation jars through the sampling ports on the lids and then analyzed using a Shimadzu Gas Chromatograph (GC-2014). Prior to sampling, the vials were evacuated. Blank correction was also done by collecting gas samples from empty incubation jars. Double pool exponential decay model was used in SigmaPlot to determine the active and slow SOC pools and their mineralization rates (Farrar et al., 2012; Jagadamma et al., 2014). The C-acquiring extracellular enzymes were measured using the microplate method by German et al., (2011). Microbial community structure was determined using the phospholipid fatty acid (PLFA) and neutral lipid fatty acid (NLFA) analyses (Buyer and Sasser, 2012). This dataset has seven data files provided in comma-separate (*.csv) format. Additional metadata are provided: seven data dictionaries and a file-level metadata file in comma separate (*.csv) format and a user guide in PDF (*.pdf) format.

Carbon acquiring enzyme activity↗
DOE OSTI2021

Proline hydroxylase domain-containing enzymes regulate calcium levels in cardiomyocytes by TRPA1 ion channel

Highlights: • PHD induces calcium release from cardiomyocytes through ryanodine channel. • PHD activates TRPA1 to induce extracellular calcium ions into the cell and further activate the ryanodine channel. • TRPA1 is involved in the regulation of PHD-Ca2+-AMPK signaling pathway. The proline hydroxylase domain-containing enzymes (PHDs) acts as cellular oxygen sensors, inducing a series of responses to hypoxia, especially during the regulation of metabolism and energy homeostasis. The increase of Ca{sup 2+} in cardiomyocytes, induced by the opening of PHD signaling pathway, is the key initiation signal necessary for the PHD-mediated regulation of the energy metabolism pathway, but the underlying molecular mechanism remains incompletely understood. This study used PHD inhibitors (PHIs) and PHD2-specific RNA interference (PHD2shRNA) to inhibit PHD signals in cardiomyocytes to explore whether transient receptor potential ankyrin 1 (TRPA1) is involved in the regulation of calcium ion influx in the PHD activation pathway associated with to AMP-activated protein kinase (AMPK). The Fluo-3AM probe was used to measure changes in free intracellular calcium ion concentrations, and Western blot analysis was used to detect the levels of phosphorylated (P)-AMPK, TRPA1, and P–Ca{sup 2+}/calmodulin-dependent protein kinase Ⅱ (CaMKⅡ) levels. The PHI-mediated inhibition of PHD resulted in an increase in free Ca{sup 2+} fluorescence in cardiomyocytes, which activated AMPK, TRPA1, and CaMKⅡ. The TRPA1 inhibitor HC030031, the CaMKII inhibitor KN93, and a ryanodine inhibitor (Ryanodine) were all able to inhibit the PHI-induced increase in intracellular Ca{sup 2+} and AMPK activation. Both PHIs and PHD2shRNA were able to effectively activate CaMKII and TRPA1. However, an inositol 1,4,5-triphosphate receptor (IP3R) inhibitor and the protein kinase A (PKA) inhibitor H89 did not significantly inhibit the PHI-induced increase in intracellular Ca{sup 2+} and AMPK activation. These results indicated that PHD might activate the CaMKⅡ pathway through the TRPA1 ion channel, inducing the release of calcium from the sarcoplasmic reticulum through ryanodine receptor 2 (RyR2), activating AMPK to initiate the protective effects of hypoxia in cardiomyocytes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A Multiomic Approach to Understand How Pleurotus eryngii Transforms Non-Woody Lignocellulosic Material

Pleurotus eryngii is a grassland-inhabiting fungus of biotechnological interest due to its ability to colonize non-woody lignocellulosic material. Genomic, transcriptomic, exoproteomic, and metabolomic analyses were combined to explain the enzymatic aspects underlaying wheat–straw transformation. Up-regulated and constitutive glycoside–hydrolases, polysaccharide–lyases, and carbohydrate–esterases active on polysaccharides, laccases active on lignin, and a surprisingly high amount of constitutive/inducible aryl–alcohol oxidases (AAOs) constituted the suite of extracellular enzymes at early fungal growth. Higher enzyme diversity and abundance characterized the longer-term growth, with an array of oxidoreductases involved in depolymerization of both cellulose and lignin, which were often up-regulated since initial growth. These oxidative enzymes included lytic polysaccharide monooxygenases (LPMOs) acting on crystalline polysaccharides, cellobiose dehydrogenase involved in LPMO activation, and ligninolytic peroxidases (mainly manganese-oxidizing peroxidases), together with highly abundant H2O2-producing AAOs. Interestingly, some of the most relevant enzymes acting on polysaccharides were appended to a cellulose-binding module. This is potentially related to the non-woody habitat of P. eryngii (in contrast to the wood habitat of many basidiomycetes). Additionally, insights into the intracellular catabolism of aromatic compounds, which is a neglected area of study in lignin degradation by basidiomycetes, were also provided. The multiomic approach reveals that although non-woody decay does not result in dramatic modifications, as revealed by detailed 2D-NMR and other analyses, it implies activation of the complete set of hydrolytic and oxidative enzymes characterizing lignocellulose-decaying basidiomycetes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1988

Molecular and cellular aspects of calcium action in plants

Calcium is known to be a second messenger in many developmental processes in animal systems, but it has only recently become evident that Ca is an important intracellular messenger in plants as well. The level of free Ca concentration in the cytoplasm is extremely low, and it is influenced by extracellular signals such as light, gravity, and hormones. Investigations from our laboratory indicated that Ca and its binding protein, calmodulin, play an important role in stimulus-response coupling by regulating enzyme activities, especially through protein phosphorylation. In vivo and in vitro protein phosphorylation studies have revealed Ca-dependent changes in various plant tissues. We have also been able to influence various physiological processes such as cell elongation, abscission, senescence, and tuberization by altering extracellular and intracellular Ca levels. Other examples of Ca-mediated processes in plants are as follows: a) cell division, b) geotropism, c) protoplasmic streaming, d) stomatal control, e) chloroplast movement, f) secretion, g) hormone-dependent changes, h) enzyme activation, and i) protein phosphorylation.

NASA Program Space Biology↗
DOE OSTI2023

Highly Stable Fe/Co-TPY-MIL-88(NH 2 ) Metal–Organic Framework (MOF) in Enzymatic Cascade Reactions for Chemiluminescence-Based Detection of Extracellular Vesicles

Metal-Organic Frameworks (MOFs) can deliver many advantages when acting as enzyme mimics to assist with signal amplification in molecular detection: they have abundant active catalytic sites per unit volume of the material; their structures and elemental compositions are highly tunable, and their high specific surface area and porous property can assist with target separation and enrichment. In the present work, we have demonstrated that, by adding the pore partition agent, 2,4,6-tris(4-pyridyl)pyridine (TPY) during synthesis of the bimetallic Fe/Co-MIL-88(NH 2 ) MOF to block the open metal sites, a highly porous MOF of Fe/Co-TPY-MIL-88(NH 2 ) can be produced. This material also exhibits high stability in basic solutions and biofluids and possesses high peroxidase-mimicking activity, which can be utilized to produce long-lasting chemiluminescence (CL) from luminol and H 2 O 2 . Moreover, acting as the peroxidase-mimic, the Fe/Co-TPY-MIL-88(NH 2 ) MOF can form the enzymatic cascade with glucose oxidase (GOx) for biomarker detection. Further, when applied to detect extracellular vesicles (EVs), the MOF material and GOx are brought to the proximity on the EVs through two surface proteins, which triggers the enzyme cascade to produce high CL from glucose and luminol. EVs within the concentration range of 5 × 10 5 - 4 ×10 7 particles/mL can be detected, and the method can be used to analyze EV contents in human serum without sample preparation and EV purification. Overall, our work demonstrates that the high versatility and tunability of the MOF structures could bring in significant benefits to biosensing and enable ultrasensitive detection of biomarkers with judicious material designs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

Monoclonal Antibody Testing for Cancer Metastasis

Malignant cells are characterized by the ability to invade surrounding normal tissues. Tumor invasion is abetted by proteolytic enzymes that have been correlated with recurrent disease and metastasis. These enzymes are involved in a cascade of proteolytic interactions with other enzymes and inhibitors which allow cancer cells to dissolve surrounding extracellular matrix, thereby enabling the cells to rapidly invade adjacent tissues and migrate to metastatic sites distant from the primary tumor. Among these proteases are the plasminogen activators (PA), collagenase IV, faminase, and in some cases cathepsin D, which together mediate key steps in the invasion process of metastasis. Cells which have the selective advantage for invasion and metastasis are those capable of regulating their proteolytic activity and proliferation. Cells in the process of invasion would be probably down-regulated for proliferation, but subsequent to attachment and adhesion at a distant site, would then be in a proliferative mode, up-regulating DNA replication. Urokinase (uPA) can be present in the tissues in several molecular forms. The inactive proenzyme is a single chain protein (scuPA) that is cleaved at Lys. 158 to form the double chain, high molecular weight active form (HMW-uPA) of 54 kD. A low molecular weight form (LMW-uPA) can also be produced by cleavage of the HMW-U PA at Lys. 135 - Lys. 136 giving a 35 kD active enzyme. Recently, it has been shown that the HMW active form of urokinase, bound to the tumor cell membrane, is responsible for the local lysis of the extracellular matrix, hence the tissue invasion mechanism for metastasis (Andreasen et al, 19861. Receptor- (membrane) bound uPA is twice as efficient (catalytically) as free fluid-phase uPA. Tho unbound uPA and the LMW form is not responsible for most of the local dissolution of extracellular matrix in the immediate vicinity of the metastatic tumor cell. High levels of urokinase (greater than 3.49 ng/mg of total protein) extracted from breast tumor tissues have recently been shown, together with plasminogen activator inhibitor 1 (PAI-1), to be a good prognostic indicator for high risk of recurrence and shorter patient survival times. In this project, we have attempted to develop immunocytochemical methodologies for the clinical assessment of the expression of urokinase plasminogen activator, which has been implicated to be important for initial steps in tumor invasion, and to relate it to cell proliferation and DNA replication at the single-cell level.

Source record↗
DOE OSTI2024

Reactive transport modeling of organic carbon degradation in marine methane hydrate systems

Abstract Natural methane hydrate has often been observed in sand layers that contain no particulate organic carbon (POC), but are surrounded by organic-rich, fine-grained marine muds. In this paper, we develop a reactive transport model (RTM) of a microbially-mediated set of POC degradation reactions, including hydrolysis of POC driven by extracellular enzymes, fermentation of the resulting high-molecular weight dissolved organic carbon (HMW-DOC), and methanogenesis that consumes low-molecular weight dissolved organic carbon (LMW-DOC). These processes are mediated by two groups of microbes, fermenters and methanogens that are heterogeneously distributed in different lithologies, with the largest numbers of microbes in the large pores of coarse-grained layers. We find that the RTM can reproduce methane hydrate occurrences observed in two different geological environments, at Walker Ridge Site 313-H (Gulf of Mexico) and IODP Site U1325 (Cascadia Margin). We also find that microbes can degrade POC even if they are physically separated, as extracellular enzymes and DOC can diffuse away from where they are produced by microbes. Microbial activity is highest at relatively early times after burial at shallow depths and near lithological boundaries, where concentration gradients transport solutes to intervals that contain the most microbes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗