R-3 Repository :: Browsing by Author "Masiello, Caroline A."

Browsing by Author "Masiello, Caroline A."

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A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology
(American Chemical Society, 2022) Sridhar, Swetha; Ajo-Franklin, Caroline M.; Masiello, Caroline A.
Microbial biosensors sense and report exposures to stimuli, thereby facilitating our understanding of environmental processes. Successful design and deployment of biosensors hinge on the persistence of the microbial host of the genetic circuit, termed the chassis. However, model chassis organisms may persist poorly in environmental conditions. In contrast, non-model organisms persist better in environmental conditions but are limited by other challenges, such as genetic intractability and part unavailability. Here we identify ecological, metabolic, and genetic constraints for chassis development and propose a conceptual framework for the systematic selection of environmental biosensor chassis. We identify key challenges with using current model chassis and delineate major points of conflict in choosing the most suitable organisms as chassis for environmental biosensing. This framework provides a way forward in the selection of biosensor chassis for environmental synthetic biology.
A zero-dimensional view of atmospheric degradation of levoglucosan (LEVCHEM_v1) using numerical chamber simulations
(Copernicus Publications, 2021) Suciu, Loredana G.; Griffin, Robert J.; Masiello, Caroline A.
Here, we developed a zero-dimensional (0-D) modeling framework (LEVCHEM_v1) to provide insights into the atmospheric degradation of a key tracer emitted during biomass burning – levoglucosan (LEV), while additionally exploring its effects on the dynamics of secondary organic aerosols (SOA) and other gases. For this, we updated existing chemical mechanisms (homogeneous gas-phase chemistry and heterogeneous chemistry) in the BOXMOXv1.7 model to include the chemical degradation of LEV and its intermediary degradation products in both phases (gas and aerosol). In addition, we added a gas-particle partitioning mechanism to the model to account for the effect of evaporation and condensation on the phase-specific concentrations of LEV and its degradation products. Comparison of simulation results with measurements from various chamber experiments (spanning summer and winter conditions) show that the degradation timescale of LEV varied by phase, with gas-phase degradation occurring over ∼1.5–5 d and aerosol-phase degradation occurring over ∼8–36 h. These relatively short timescales suggest that most of the initial LEV concentration can be lost chemically or deposited locally before being transported regionally. We varied the heterogeneous reaction rate constant in a sensitivity analysis (for summer conditions only) and found that longer degradation timescales of LEV are possible, particularly in the aerosol phase (7 d), implying that some LEV may be transported regionally. The multiphase chemical degradation of LEV has effects on SOA and other gases. Several first- or second-generation products resulted from its degradation; most of the products include one or two carbonyl groups, one product contains a nitrate group, and a few products show the cleavage of C−C bonds. The relative importance of the products varies depending on the phase and the timing of the maximum concentration achieved during the simulation. Our estimated secondary organic aerosol SOA yields (4 %–32 %) reveal that conversion of LEV to secondary products is significant and occurs rapidly in the studied scenarios. LEV degradation affected other gases by increasing the concentrations of radicals and decreasing those of reactive nitrogen species. Decreases of the mixing ratios of nitrogen oxides appear to drive a more rapid increase in ozone compared with changes in volatile organic compounds levels. An important next step to confirm longer degradation timescales will be to extend the evaluation of the modeled LEV degradation beyond 3–6 h by using more extensive data from chambers and, possibly, from fire plumes. The mechanism developed here can be used in chemical transport models applied to fire plumes to trace LEV and its degradation products from source to deposition, to assess their atmospheric implications and to answer questions relevant to fire tracing, carbon and nitrogen cycling, and climate.
Aged black carbon in marine sediments and sinking particles
(Wiley, 2014) Coppola, Alysha I.; Ziolkowski, Lori A.; Masiello, Caroline A.; Druffel, Ellen R.M.
We report measurements of oceanic black carbon (BC) to determine the sources of BC to abyssal marine sediments in the northeast Pacific Ocean. We find that the average 14C age of BC is older (by 6200 ± 2200 14C years) than that of the concurrently deposited non-BC sedimentary organic carbon. We investigate sources of aged BC to sediments by measuring a sample of sinking particulate organic carbon (POC) and find that POC may provide the main transport mechanism of BC to sediments. We suggest that aged BC is incorporated into POC from a combination of resuspended sediments and sorption of ancient dissolved organic carbon BC onto POC. Our BC flux estimate represents ~8–16% of the global burial flux of organic carbon to abyssal sediments and constitutes a minimum long-term removal estimate of 6–32% of biomass-derived BC using the present day emission flux.
Agroecosystem modeling of reactive nitrogen emissions from U.S. agricultural soils with carbon amendments
(Springer Nature, 2023) Luo, Lina; Cohan, Daniel S.; Masiello, Caroline A.; Lychuk, Taras E.; Gao, Xiaodong
Fertilizer-intensive agriculture is a leading source of reactive nitrogen (Nr) emissions that damage climate, air quality, and human health. Biochar has long been studied as a soil amendment, but its influence on Nr emissions remains insufficiently characterized. More recently, the pyrolysis of light hydrocarbons has been suggested as a source of hydrogen fuel, resulting in a solid zero-valent carbon (ZVC) byproduct whose impact on soil emissions has yet to be tested. We incorporate carbon amendment algorithms into an agroecosystem model to simulate emission changes in the year following the application of biochar or ZVC to the US. fertilized soils. Our simulations predicted that the impacts of biochar amendments on Nr emissions would vary widely (− 17% to + 27% under 5 ton ha−1 applications, − 38% to + 18% under 20 ton ha−1 applications) and depend mostly on how nitrification is affected. Low-dose biochar application (5 ton ha−1) stimulated emissions of all three nitrogen species in 75% of simulated agricultural areas, while high-dose applications (20 ton ha−1) mitigated emissions in 76% of simulated areas. Applying zero-valent carbon at 20 ton ha−1 exhibited similar effects on nitrogen emissions as biochar applications at 5 ton ha−1. Biochar amendments are most likely to mitigate emissions if applied at high rates in acidic soils (pH < 5.84) with low organic carbon (< 55.9 kg C ha−1) and inorganic nitrogen (< 101.5 kg N ha−1) content. Our simulations could inform where the application of carbon amendments would most likely mitigate Nr emissions and their associated adverse impacts.
Artificial Soils Reveal Individual Factor Controls on Microbial Processes
(American Society for Microbiology, 2022) Del Valle, Ilenne; Gao, Xiaodong; Ghezzehei, Teamrat A.; Silberg, Jonathan J.; Masiello, Caroline A.
Soil matrix properties influence microbial behaviors that underlie nutrient cycling, greenhouse gas production, and soil formation. However, the dynamic and heterogeneous nature of soils makes it challenging to untangle the effects of different matrix properties on microbial behaviors. To address this challenge, we developed a tunable artificial soil recipe and used these materials to study the abiotic mechanisms driving soil microbial growth and communication. When we used standardized matrices with varying textures to culture gas-reporting biosensors, we found that a Gram-negative bacterium (Escherichia coli) grew best in synthetic silt soils, remaining active over a wide range of soil matric potentials, while a Gram-positive bacterium (Bacillus subtilis) preferred sandy soils, sporulating at low water potentials. Soil texture, mineralogy, and alkalinity all attenuated the bioavailability of an acyl-homoserine lactone (AHL) signaling molecule that controls community-level microbial behaviors. Texture controlled the timing of AHL sensing, while AHL bioavailability was decreased ~105-fold by mineralogy and ~103-fold by alkalinity. Finally, we built artificial soils with a range of complexities that converge on the properties of one Mollisol. As artificial soil complexity increased to more closely resemble the Mollisol, microbial behaviors approached those occurring in the natural soil, with the notable exception of organic matter.
Biochar and Microbial Signaling: Production Conditions Determine Effects on Microbial Communication
(American Chemical Society, 2013) Masiello, Caroline A.; Chen, Ye; Gao, Xiaodong; Liu, Shirley; Cheng, Hsiao-Ying; Bennett, Matthew R.; Rudgers, Jennifer A.; Wagner, Daniel S.; Zygourakis, Kyriacos; Silberg, Jonathan J.
Charcoal has a long soil residence time, which has resulted in its production and use as a carbon sequestration technique (biochar). A range of biological effects can be triggered by soil biochar that can positively and negatively influence carbon storage, such as changing the decomposition rate of organic matter and altering plant biomass production. Sorption of cellular signals has been hypothesized to underlie some of these effects, but it remains unknown whether the binding of biochemical signals occurs, and if so, on time scales relevant to microbial growth and communication. We examined biochar sorption of N-3-oxo-dodecanoyl-L-homoserine lactone, an acyl-homoserine lactone (AHL) intercellular signaling molecule used by many gram-negative soil microbes to regulate gene expression. We show that wood biochars disrupt communication within a growing multicellular system that is made up of sender cells that synthesize AHL and receiver cells that express green fluorescent protein in response to an AHL signal. However, biochar inhibition of AHL-mediated cell–cell communication varied, with the biochar prepared at 700 °C (surface area of 301 m2/g) inhibiting cellular communication 10-fold more than an equivalent mass of biochar prepared at 300 °C (surface area of 3 m2/g). These findings provide the first direct evidence that biochars elicit a range of effects on gene expression dependent on intercellular signaling, implicating the method of biochar preparation as a parameter that could be tuned to regulate microbial-dependent soil processes, like nitrogen fixation and pest attack of root crops.
Biochar particle size, shape, and porosity act together to influence soil water properties
(Public Library of Science, 2017) Liu, Zuolin; Dugan, Brandon; Masiello, Caroline A.; Gonnermann, Helge M.
Many studies report that, under some circumstances, amending soil with biochar can improve field capacity and plant-available water. However, little is known about the mechanisms that control these improvements, making it challenging to predict when biochar will improve soil water properties. To develop a conceptual model explaining biochar’s effects on soil hydrologic processes, we conducted a series of well constrained laboratory experiments using a sand matrix to test the effects of biochar particle size and porosity on soil water retention curves. We showed that biochar particle size affects soil water storage through changing pore space between particles (interpores) and by adding pores that are part of the biochar (intrapores). We used these experimental results to better understand how biochar intrapores and biochar particle shape control the observed changes in water retention when capillary pressure is the main component of soil water potential. We propose that biochar’s intrapores increase water content of biochar-sand mixtures when soils are drier. When biochar-sand mixtures are wetter, biochar particles’ elongated shape disrupts the packing of grains in the sandy matrix, increasing the volume between grains (interpores) available for water storage. These results imply that biochars with a high intraporosity and irregular shapes will most effectively increase water storage in coarse soils.
Biochar-Induced Changes in Soil Hydraulic Conductivity and Dissolved Nutrient Fluxes Constrained by Laboratory Experiments
(Public Library of Science, 2014) Barnes, Rebecca T.; Gallagher, Morgan E.; Masiello, Caroline A.; Liu, Zuolin; Dugan, Brandon
The addition of charcoal (or biochar) to soil has significant carbon sequestration and agronomic potential, making it important to determine how this potentially large anthropogenic carbon influx will alter ecosystem functions. We used column experiments to quantify how hydrologic and nutrient-retention characteristics of three soil materials differed with biochar amendment. We compared three homogeneous soil materials (sand, organic-rich topsoil, and clay-rich Hapludert) to provide a basic understanding of biochar-soil-water interactions. On average, biochar amendment decreased saturated hydraulic conductivity (K) by 92% in sand and 67% in organic soil, but increased K by 328% in clay-rich soil. The change in K for sand was not predicted by the accompanying physical changes to the soil mixture; the sand-biochar mixture was less dense and more porous than sand without biochar. We propose two hydrologic pathways that are potential drivers for this behavior: one through the interstitial biochar-sand space and a second through pores within the biochar grains themselves. This second pathway adds to the porosity of the soil mixture; however, it likely does not add to the effective soil K due to its tortuosity and smaller pore size. Therefore, the addition of biochar can increase or decrease soil drainage, and suggests that any potential improvement of water delivery to plants is dependent on soil type, biochar amendment rate, and biochar properties. Changes in dissolved carbon (C) and nitrogen (N) fluxes also differed; with biochar increasing the C flux from organic-poor sand, decreasing it from organic-rich soils, and retaining small amounts of soil-derived N. The aromaticity of C lost from sand and clay increased, suggesting lost C was biochar-derived; though the loss accounts for only 0.05% of added biochar-C. Thus, the direction and magnitude of hydraulic, C, and N changes associated with biochar amendments are soil type (composition and particle size) dependent.
Broadening theories of soils genesis: Insights from Tanzania and simple models
(2007) Little, Mark Gabriel; Lee, Cin-Ty A.; Luttge, Andreas; Tomson, Mason B.; Anderson, John B.; Ewing, Maurice W.; Masiello, Caroline A.
Three basic assumptions of soil formation are challenged herein: the degree of chemical weathering decreases with depth; increased physical weathering due to high topographical gradients causes an increase in chemical weathering; and the mineral soil derives from the transformation of in situ parent material. The first part presents an investigation into the degree and nature of chemical weathering during soil formation on a volcanic substrate on Mt. Kilimanjaro in northern Tanzania. The degree of weathering was found to increase with depth in the soil profile. Observations show that the upper and lower layers of the weathering profile have undergone different weathering histories. The presence of a buried paleosol or enhanced weathering due to lateral subsurface water flow may explain the observations, the latter having novel implications for the transport of dissolved cations to the ocean. The second part presents a model to test the link between chemical weathering associated with soil formation and erosion associated with mass wasting. The predicted ratios suspended/dissolved ratios, however, are all higher than observed in rivers, the discrepancy worsening with increasing topographic relief. This discrepancy arises from the fact that in regions of high relief, mass wasting are so high that soil mantles do not reside on hillslopes long enough to allow for significant chemical weathering. The discrepancy between the model and observations can be explained by: over-estimate of predicted suspended load; absence of chemical weathering of deltaic/alluvial sediments from the model; or chemical weathering associated with groundwater weathering. The third part presents data from a sequential extraction on a basaltic soil from Mt. Meru in Northern Tanzania. The behavior of relatively immobile elements is consistent with soil formation being accompanied by mass loss due to chemical weathering. However, superimposed on this mass loss appears to be enrichment of most elements measured. These data suggest that the surface of the Meru soil columns may have experienced "re-fertilization" by the deposition of volcanic ash.
Carbon sequestration potential and physicochemical properties differ between wildfire charcoals and slow-pyrolysis biochars
(Springer Nature, 2017) Santín, Cristina; Doerr, Stefan H.; Merino, Agustin; Bucheli, Thomas D.; Bryant, Rob; Ascough, Philippa; Gao, Xiaodong; Masiello, Caroline A.
Pyrogenic carbon (PyC), produced naturally (wildfire charcoal) and anthropogenically (biochar), is extensively studied due to its importance in several disciplines, including global climate dynamics, agronomy and paleosciences. Charcoal and biochar are commonly used as analogues for each other to infer respective carbon sequestration potentials, production conditions, and environmental roles and fates. The direct comparability of corresponding natural and anthropogenic PyC, however, has never been tested. Here we compared key physicochemical properties (elemental composition, δ13C and PAHs signatures, chemical recalcitrance, density and porosity) and carbon sequestration potentials of PyC materials formed from two identical feedstocks (pine forest floor and wood) under wildfire charring- and slow-pyrolysis conditions. Wildfire charcoals were formed under higher maximum temperatures and oxygen availabilities, but much shorter heating durations than slow-pyrolysis biochars, resulting in differing physicochemical properties. These differences are particularly relevant regarding their respective roles as carbon sinks, as even the wildfire charcoals formed at the highest temperatures had lower carbon sequestration potentials than most slow-pyrolysis biochars. Our results challenge the common notion that natural charcoal and biochar are well suited as proxies for each other, and suggest that biochar’s environmental residence time may be underestimated when based on natural charcoal as a proxy, and vice versa.
Carbon Sequestration through Biochar Soil Amendment: Experimental studies and mathematical modeling
(2012-09-05) Sun, Hao; Zygourakis, Kyriacos; Masiello, Caroline A.; Chapman, Walter G.; Hockaday, William C.
Intentional amendment of soil with charcoal (called biochar) is a promising new approach to sequester atmospheric carbon dioxide and increase soil fertility. However, the environmental properties of biochars can vary with production conditions, making it challenging to engineer biochars that are simultaneously optimized for carbon sequestration, nutrient storage, and water-holding capacity. For this reason, I have undertaken a systematic study to (a) determine the pyrolysis conditions that lead to biochars with desired chemical and physical properties, and (b) find how these properties affect the water-holding capacity and nutrient adsorption in biochar-soil mixtures. First, a library of biochars was produced in a custom-built pyrolysis reactor under precisely controlled conditions. The chemical and physical structures of the produced biochars were characterized with various analytical techniques including 13C NMR, XPS, EA and BET pore surface analysis. My results suggest that the chemical composition and pore structure of biochars are determined not just by the maximum heat treatment temperature, but also by several other factors that include the pyrolysis heating rate, treatment time at the maximum temperature and particle size. I also tested a new approach that combines thermogravimetric reactivity measurements, diffusion-reaction theory and structural models to achieve a better characterization of the complicated multi-scale pore structure of biochars. The structural models treat biochars as porous solids having micro- and macropores of different shapes and exhibiting widely ranging pore-size distributions. Simulations results are then compared to experimental data to identify the presence of ordered or random pore networks and test their size distributions and connectivity. I then developed a multi-solid one-dimensional model that can use experimentally determined biochar properties to predict their field performance in beds packed with soil/biochar mixtures. The model used a system of coupled partial differential equations to describe the dynamic adsorption/elution of ammonium nitrate, a model fertilizer, in columns packed with biochar/soil mixtures and perfused with aqueous solutions of the fertilizer. The PDE system was solved using orthogonal collocation on finite elements. My chromatographic model accounted for all the important processes occurring in this system, including external mass transfer between the fluid phase and the solid particles, as well as intraparticle diffusion and adsorption of the solute on the pore surface area of the sorbents. To our knowledge, this is the first chromatographic model that accounted explicitly for the presence of two solid phases with widely different pore structures and adsorption capacities. A systematic parametric study was carried out to determine the importance of each system parameter. The adsorption equilibrium parameters and the intraparticle effective diffusivity of ammonium had the most significant effect on environmental performance. To complete the theoretical analysis, I also developed a model to describe the saturation and drainage of water from the packed column. The model accounted for all the important processes occurring in this system: (a) water exchange between the interstitial pore region and two different smaller pore regions and (b) water flow inside the larger pore region and the two different smaller pore regions. The transient mass balances led to a system of partial differential equations that was solved using block centered finite difference.
Charcoal Disrupts Soil Microbial Communication through a Combination of Signal Sorption and Hydrolysis
(American Chemical Society, 2016) Gao, Xiaodong; Cheng, Hsiao-Ying; Del Valle, Ilenne; Liu, Shirley; Masiello, Caroline A.; Silberg, Jonathan J.
The presence of charcoal in soil triggers a range of biological effects that are not yet predictable, in part because it interferes with the functioning of chemical signals that microbes release into their environment to communicate. We do not fully understand the mechanisms by which charcoal alters the biologically available concentrations of these intercellular signals. Recently, charcoal has been shown to sorb the signaling molecules that microbes release, rendering them ineffective for intercellular communication. Here, we investigate a second, potentially more important mechanism of interference: signaling-molecule hydrolysis driven by charcoal-induced soil pH changes. We examined the effects of 10 charcoals on the bioavailable concentration of an acyl-homoserine lactone (AHL) used by many Gram-negative bacteria for cell–cell communication. We show that charcoals decrease the level of bioavailable AHL through sorption and pH-dependent hydrolysis of the lactone ring. We then built a quantitative model that predicts the half-lives of different microbial signaling compounds in the presence of charcoals varying in pH and surface area. Our model results suggest that the chemical effects of charcoal on pH-sensitive bacterial AHL signals will be fundamentally distinct from effects on pH-insensitive fungal signals, potentially leading to shifts in microbial community structures.
Effect of freeze-thaw cycling on grain size of biochar
(Public Library of Science, 2018) Liu, Zuolin; Dugan, Brandon; Masiello, Caroline A.; Wahab, Leila M.; Gonnermann, Helge M.; Nittrouer, Jeffrey A.
Biochar may improve soil hydrology by altering soil porosity, density, hydraulic conductivity, and water-holding capacity. These properties are associated with the grain size distributions of both soil and biochar, and therefore may change as biochar weathers. Here we report how freeze-thaw (F-T) cycling impacts the grain size of pine, mesquite, miscanthus, and sewage waste biochars under two drainage conditions: undrained (all biochars) and a gravity-drained experiment (mesquite biochar only). In the undrained experiment plant biochars showed a decrease in median grain size and a change in grain-size distribution consistent with the flaking off of thin layers from the biochar surface. Biochar grain size distribution changed from unimodal to bimodal, with lower peaks and wider distributions. For plant biochars the median grain size decreased by up to 45.8% and the grain aspect ratio increased by up to 22.4% after 20 F-T cycles. F-T cycling did not change the grain size or aspect ratio of sewage waste biochar. We also observed changes in the skeletal density of biochars (maximum increase of 1.3%), envelope density (maximum decrease of 12.2%), and intraporosity (porosity inside particles, maximum increase of 3.2%). In the drained experiment, mesquite biochar exhibited a decrease of median grain size (up to 4.2%) and no change of aspect ratio after 10 F-T cycles. We also document a positive relationship between grain size decrease and initial water content, suggesting that, biochar properties that increase water content, like high intraporosity and pore connectivity large intrapores, and hydrophilicity, combined with undrained conditions and frequent F-T cycles may increase biochar breakdown. The observed changes in biochar particle size and shape can be expected to alter hydrologic properties, and thus may impact both plant growth and the hydrologic cycle.
Environmental conditions play a key role in controlling the composition and diversity of Colombian biocrust microbiomes
(Frontiers Media S.A., 2024) Giraldo-Silva, Ana; Masiello, Caroline A.
Drylands soils worldwide are naturally colonized by microbial communities known as biocrusts. These soil microbiomes render important ecosystem services associated with soil fertility, water holding capacity, and stability to the areas they cover. Because of the importance of biocrusts in the global cycling of nutrients, there is a growing interest in describing the many microbial configurations these communities display worldwide. However, comprehensive 16S rRNA genes surveys of biocrust communities do not exist for much of the planet: for example, in the continents of South America and the northern part of Africa. The absence of a global understanding of biocrust biodiversity has lead us to assign a general importance to community members that may, in fact, be regional. Here we report for the first time the presence of biocrusts in Colombia (South America) through 16S rRNA genes surveys across an arid, a semi-arid and a dry subtropical region within the country. Our results constitute the first glance of the Bacterial/Archaeal communities associated with South American biocrust microbiomes. Communities where cyanobacteria other than Microcoleus vaginatus prevail, despite the latter being considered a key species elsewhere, illustrate differentiable results in these surveys. We also find that the coastal biocrust communities in Colombia include halo-tolerant and halophilic species, and that niche preference of some nitrogen fixing organisms deviate from previously described global trends. In addition, we identified a high proportion (ranging from 5 to 70%, in average) of cyanobacterial sequences that did not match any formally described cyanobacterial species. Our investigation of Colombian biocrusts points to highly diverse communities with climatic regions controlling taxonomic configurations. They also highlight an extensive local diversity to be discovered which is central to better design management and restoration strategies for drylands soils currently undergoing disturbances due to land use and global warming. Finally, this field study highlights the need for an improved mechanistic understanding of the response of key biocrust community members to changes in moisture and temperature.
Forest soil carbon oxidation state and oxidative ratio responses to elevated CO2
(Wiley, 2015) Hockaday, William C.; Gallagher, Morgan E.; Masiello, Caroline A.; Baldock, Jeffrey A.; Iversen, Colleen M.; Norby, Richard J.
The oxidative ratio (OR) of the biosphere is the stoichiometric ratio (O2/CO2) of gas exchange by photosynthesis and respiration—a key parameter in budgeting calculations of the land and ocean carbon sinks. Carbon cycle-climate feedbacks could alter the OR of the biosphere by affecting the quantity and quality of organic matter in plant biomass and soil carbon pools. This study considers the effect of elevated atmospheric carbon dioxide concentrations ([CO2]) on the OR of a hardwood forest after nine growing seasons of Free-Air CO2 Enrichment. We measured changes in the carbon oxidation state (Cox) of biomass and soil carbon pools as a proxy for the ecosystem OR. The OR of net primary production, 1.039, was not affected by elevated [CO2]. However, the Cox of the soil carbon pool was 40% higher at elevated [CO2], and the estimated OR values for soil respiration increased from 1.006 at ambient [CO2] to 1.054 at elevated [CO2]. A biochemical inventory of the soil organic matter ascribed the increases in Cox and OR to faster turnover of reduced substrates, lignin and lipids, at elevated [CO2]. This implicates the heterotrophic soil community response to elevated [CO2] as a driver of disequilibrium in the ecosystem OR. The oxidation of soil carbon pool constitutes an unexpected terrestrial O2 sink. Carbon budgets constructed under the assumption of OR equilibrium would equate such a terrestrial O2 sink to CO2 uptake by the ocean. The potential for climate-driven disequilibriua in the cycling of O2 and CO2 warrants further investigation.
Impacts of biochar concentration and particle size on hydraulic conductivity and DOC leaching of biochar-sand mixtures
(Elsevier, 2016) Liu, Zuolin; Dugan, Brandon; Masiello, Caroline A.; Barnes, Rebecca T.; Gallagher, Morgan E.; Gonnermann, Helge
The amendment of soil with biochar can sequester carbon and alter hydrologic properties by changing physical and chemical characteristics of soil. To understand the effect of biochar amendment on soil hydrology, we measured the hydraulic conductivity (K) of biochar–sand mixtures as well as dissolved organic carbon (DOC) in leachate. Specifically, we assessed the effects of biochar concentration and particle size on K and amount of DOC in the soil leachate. To better understand how physical properties influenced K, we also measured the skeletal density of biochars and sand, and the bulk density, the water saturation, and the porosity of biochar–sand mixtures. Our model soil was sand (0.251–0.853 mm) with biochar rates from 2 to 10 wt% (g biochar/g total soil × 100%). As biochar (<0.853 mm) concentration increased from 0 to 10 wt%, K decreased by 72 ± 3%. When biochar particle size was equal to, greater than, and less than particle size of sand, we found that biochar in different particle sizes have different effects on K. For a 2 wt% biochar rate, K decreased by 72 ± 2% when biochar particles were finer than sand particles, and decreased by 15 ± 2% when biochar particles were coarser than sand particles. When biochar and sand particle size were comparable, we observed no significant effect on K. We propose that the decrease of K through the addition of fine biochar was because finer biochar particles filled spaces between sand particles, which increased tortuosity and reduced pore throat size of the mixture. The decrease of K associated with coarser biochar was caused by the bimodal particle size distribution, resulting in more compact packing and increased tortuosity. The loss of biochar C as DOC was related to both biochar rate and particle size. The cumulative DOC loss was 1350% higher from 10 wt% biochar compared to pure sand. This large increase reflected the very small DOC yield from pure sand. In addition, DOC in the leachate decreased as biochar particle size increased. For all treatments, the fraction of carbon lost as DOC ranged from 0.06 to 0.18 wt% of biochar. These experiments suggest that mixing sandy soils with biochar is likely to reduce infiltration rates, holding water near the surface longer with little loss of biochar-derived carbon to groundwater and streams.
Incorporation of Satellite Observations into Texas Ozone Attainment Modeling
(2014-04-15) Tang, Wei; Cohan, Daniel S.; Griffin, Robert J.; Masiello, Caroline A.; Pour-Biazar, Arastoo
Uncertain photolysis rates and nitrogen oxides (NOx) emission inventories impair the accuracy of ozone (O3) regulatory modeling. Satellite-observed clouds have been used to correct model-predicted photolysis rates, and satellite-constrained top-down NOx emissions have been used to identify and reduce uncertainties in bottom-up NOx emissions. However, studies on using multiple satellite-derived model inputs to improve O3 State Implementation Plan (SIP) modeling are rare. In this thesis, observations of clouds from the Geostationary Operational Environmental Satellite (GOES) and of NO2 from the Ozone Monitoring Instrument (OMI) are used to adjust the inputs to SIP modeling of O3 in Texas. The discrete Kalman filter (DKF) inversion approach is successfully applied with decoupled direct method (DDM) sensitivities in the Comprehensive Air Quality Model with extensions (CAMx) model to adjust Texas NOx emissions in designated emission regions and categories to better match OMI NO2 data. The NO2 vertical column densities (VCD) gap between OMI and CAMx over rural areas is alleviated by adding missing lightning and aviation and underestimated soil NOx emissions to the base regulatory emission inventory and further reduced by increasing modeled NOx lifetime and adding an artificial NO2 layer in the upper troposphere. The region-based DKF inversion using OMI NO2 tends to scale up NOx emissions in most regions, which conflicts with the inversion results using ground NO2 measurements and fails to improve the ground-level O3 simulations. The sector-based DKF inversion using OMI NO2 suggests scaling down area and non-road NOx emissions by 50%, leading to approximately 2-5ppb decrease in ground 8-h O3 concentrations, and improving both hourly ground-level NO2 and O3 simulations by reducing biases by 0.25 and 0.04 and errors by 0.13 and 0.04, respectively. Finally, using both GOES-derived photolysis rates and OMI-constrained NOx emissions reduces modeled bias and error by 0.05, and increases the model correlations in simulating ground O3 measurements and makes O3 more sensitive to NOx emissions in the O3 nonattainment areas.
Nitrogen, biochar, and mycorrhizae: Alteration of the symbiosis and oxidation of the char surface
(Elsevier, 2014) LeCroy, Chase; Masiello, Caroline A.; Rudgers, Jennifer A.; Hockaday, William C.; Silberg, Jonathan J.
In some cases amending soil with biochar improves fertility, although the exact mechanisms through which biochar alters soil processes are not well understood. In other cases, however, biochar amendment can have no effect on plant growth, or can have negative effects. When crop benefits occur, simultaneous amendment with biochar and mineral nutrients causes results that are not additive, suggesting that biochar may be capable of improving the efficiency of nutrient uptake by plants, but the mechanisms of this synergy remain unknown. One possible mechanism that has not been fully explored is alterations to the plant-mycorrhizal fungus mutualism, a relationship that occurs in most land plants. In a 4 week greenhouse experiment, we investigated possible effects of the presence of biochar, mycorrhizal fungi, and nitrogen fertilizer on sorghum seedling growth. Results indicated that the combined treatment of biochar, mycorrhizal fungi, and high nitrogen decreased aboveground plant biomass by 42% relative to the mycorrhizae and high nitrogen treatment, while simultaneously promoting mycorrhizal root colonization. This is evidence for an induced parasitism of the mycorrhizal fungus in the presence of nitrogen and biochar within the 4 week timescale of our experiments. Using x-ray photoelectron spectroscopy, we found evidence of increased surface oxidation on biochar particles over the 4 weeks of our trial, consistent with sorption of labile, plant derived dissolved organic matter or char oxidation, either via biotic or abiotic processes. Biochar in soils with mycorrhizae but without sufficient nitrogen showed more surface oxidation than other treatment combinations, and showed a significantly greater fraction of surface carbon present in carbonyl (ﾖCdouble bond; length as m-dashO) functionalities. Our results suggest that soil nitrogen acts as a switch controlling the ability of char to influence the mycorrhizal symbiosis and, in turn, the degree to which the fungi oxidize the char surface.
Nonrandom seed dispersal by lemur frugivores: mechanism, patterns and impacts
(2015-04-23) Razafindratsima, Onja Harinala Franckline Eva; Dunham, Amy E.; Rudolf, Volker H. W.; Siemann, Evan; Masiello, Caroline A.; Erhart, Elizabeth M.
Frugivores act as seed-dispersal agents in many ecosystems. Thus, understanding the roles and impacts of seed dispersal by frugivores is important to understand the structure and diversity maintenance of plant communities. Frugivore-mediated seed dispersal is behaviorally driven, generating nonrandom patterns of seed dispersion; but, we know relatively little about how this might affect plant populations or communities. I examined how frugivores affected plants from the individual level to the population and community levels. To do this, I used modeling, trait-based and phylogenetic approaches combined with field observations and experiments, focusing on seed dispersal by three frugivorous lemur species in the biodiverse rainforest of Ranomafana National Park, Madagascar. An analysis of traits suggested that 84% of trees in Ranomafana are adapted for animal dispersal, of which more than 70% are dispersed by these three lemur species indicating their role as generalist dispersers. The distribution of fruit and seed size of bird-dispersed species was nested within the wide spectrum of size distribution associated with lemur dispersal. Nonrandom seed dispersal by these three frugivores increased per capita recruitment of the seeds of a long-lived canopy tree, Cryptocarya crassifolia, by four-fold compared with no dispersal, even though it was not an overall advantage compared to random dispersal. The three frugivores not only dispersed seeds away from parent and conspecific adult-trees, but also biased seed dispersal toward certain microhabitats. By using fruiting trees as seed dispersal foci, lemur frugivores structure the spatial associations between dispersed seeds and adult-trees nonrandomly, in terms of fruiting time, dispersal mode and phylogenetic relatedness. However, lemur-dispersed tree species were not more likely to be each other’s neighbors as adults. Interestingly, co-fruiting neighboring trees sharing lemur dispersers were more phylogenetically distant than expected by chance despite a phylogenetic signal in lemur dispersal mode, although there was no phylogenetic signal in the timing of fruiting among lemur-dispersed tree species. Results suggest an important link between frugivore foraging behavior and the spatial, temporal and phylogenetic patterning of seed dispersal. The critical role of frugivores in structuring seed dispersion and seed-adult plant associations has critical implications for plant-plant interactions, biodiversity patterns and community structure.
Parallelizing Interproscan with SLURM
(Rice University, 6/27/2023) Fulk, Emily M.; Goldman, Annelise L.; Momper, Lily; Heider, Clinton; Mulligan, John; Osburn, Magdalena; Masiello, Caroline A.; Silberg, Jonathan J.; Systems, Synthetic, and Physical Biology
This repository contains code to facilitate analysis of large numbers of proteins by Interproscan with minimum user oversight and efficient use of computational resources. It provides templates for parallelizing Interproscan with SLURM on the Rice NOTS computing cluster, following a high-throughput computing model.

Browsing by Author "Masiello, Caroline A."

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