Mineral Surfaces as Agents of Environmental Proteolysis: Mechanisms and Controls

The bottleneck in the turnover of soil organic matter (SOM) is the conversion of large molecular compounds into smaller compounds that can be transported through a cell membrane of a microbe for processing. Once inside the cell, organic compounds can be converted into biomass or be respired. The microbial depolymerization of SOM by microbes is catalyzed by extracellular enzymes. SOM is intimately associated with the mineral matrix, which can affect turnover by interfering with the accessibility of OM or the function of extracellular enzymes. Interactions with the mineral matrix have been primarily associated as a protective mechanism of SOM against microbial degradation. But it has been observed that soil minerals can participate in the chemical degradation of organic compounds This dissertation attempts to address whether soil minerals have the capacity to chemically modify or break down proteins in order to infer whether the mineral matrix has the capacity to alter extracellular enzymes in soil. The following research aims to identify what conditions are conducive to protein modifications by mineral interactions. The first research chapter explored how mineral surfaces can switch from sorbents to reactants towards proteins under a gradient of increasing energy similar to fireline intensities experienced in wildfires. The second research chapter observed the mechanisms responsible for proteolysis and the locations of cleavage by minerals. The last research chapter revealed that inserting an amino acid trimer to a model protein was sufficient in altering protein-mineral interactions such as adsorption and fragmentation. Together this work provides evidence to expand the role of protein-mineral interactions to include the degradative functionality of minerals in the cycling of SOM

Testing Extractants to Study How Protein Interacts with Iron Oxide Minerals

The goals of this experiment highlighted in this poster were to find a suitable extractant to extract protein adsorbed onto iron oxide minerals and to determine whether those minerals can modify protein. Data obtained from this experiment provides crucial background information to study the effects hydrogen peroxide has on protein in the presence of an iron oxide mineral. We found in this experiment that Sodium dodecyl sulfate and Guanidine Hydrochloride were able to extract some of the protein off of iron oxide minerals. Additionally, NMR spectroscopy was used to analyze the protein for any modification revealed that the extracted protein remained unchanged

Substrate concentration and enzyme allocation can affect rates of microbial decomposition

Abstract. A large proportion of the world's carbon is stored as soil organic matter (SOM). However, the mechanisms regulating the stability of this SOM remain unclear. Recent work suggests that SOM may be stabilized by mechanisms other than chemical recalcitrance. Here, we show that the mineralization rate of starch, a plant polymer commonly found in litter and soil, is concentration dependent, such that its decomposition rate can be reduced by as much as 50% when composing less than ;10% of SOM. This pattern is largely driven by low activities of starch-degrading enzymes and low inducibility of enzyme production by microbial decomposers. The same pattern was not observed for cellulose and hemicellulose degradation, possibly because the enzymes targeting these substrates are expressed at constitutively high levels. Nevertheless, given the heterogeneous distribution of SOM constituents, our results suggest a novel low-concentration constraint on SOM decomposition that is independent of chemical recalcitrance. These results may help explain the stability of at least some SOM constituents, especially those that naturally exist in relatively low concentrations in the soil environment

Protein–Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure

Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na⁺-montmorillonite (001), Ca²⁺-montmorillonite (001), goethite (100), and Na⁺-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, 4-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvated structure without these mineral surfaces present. Over the Na⁺ -birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation

SoDaH: the SOils DAta Harmonization database, an open-source synthesis of soil data from research networks, version 1.0

Data collected from research networks present opportunities to test theories and develop models about factors responsible for the long-term persistence and vulnerability of soil organic matter (SOM). Synthesizing datasets collected by different research networks presents opportunities to expand the ecological gradients and scientific breadth of information available for inquiry. Synthesizing these data is challenging, especially considering the legacy of soil data that have already been collected and an expansion of new network science initiatives. To facilitate this effort, here we present the SOils DAta Harmonization database (SoDaH; https://lter.github.io/som-website, last access: 22 December 2020), a flexible database designed to harmonize diverse SOM datasets from multiple research networks. SoDaH is built on several network science efforts in the United States, but the tools built for SoDaH aim to provide an open-access resource to facilitate synthesis of soil carbon data. Moreover, SoDaH allows for individual locations to contribute results from experimental manipulations, repeated measurements from long-term studies, and local- to regional-scale gradients across ecosystems or landscapes. Finally, we also provide data visualization and analysis tools that can be used to query and analyze the aggregated database. The SoDaH v1.0 dataset is archived and available at https://doi.org/10.6073/pasta/9733f6b6d2ffd12bf126dc36a763e0b4 (Wieder et al., 2020)

Substrate concentration constraints on microbial decomposition

Soil organic carbon is chemically heterogeneous, and microbial decomposers face a physiological challenge in metabolizing the diverse array of compounds present in soil. Different classes of polymeric compounds may require specialized enzymatic pathways for degradation, each of which requires an investment of microbial resources. Here we tested the resource allocation hypothesis, which posits that decomposition rates should increase once substrate concentrations are sufficient to overcome biochemical investment costs. We also tested the alternative hypothesis that mixing different substrates increases resource acquisition through priming effects involving generalist enzymes. Using a microcosm approach, we varied the soil concentration of seven distinct substrates individually and in mixture. We found that the percent carbon respired from starch, cellulose, chitin, and the mixture was significantly reduced at the lowest substrate concentration. The activities of β-glucosidase and N-acetyl-glucosaminidase that target cellulose and chitin, respectively, were also significantly lower at the lowest concentrations of their target substrates. However, we did not observe parallel declines in enzyme activity with starch or the mixture. Some enzymes, such as β-xylosidase, were consistent with specialist strategies because they showed the highest activity in the presence of their target substrate. Other enzymes were more generalist, with activity observed across multiple substrates. Together, these results suggest that the costs of biochemical machinery limit microbial decomposition of substrates at low concentration. The presence of enzymes with low substrate specificity was not sufficient to overcome this constraint for some substrates. Concentration constraints driven by microbial allocation patterns may be common in mineral soil and could be represented in new biogeochemical models based on microbial physiology

Substrate concentration constraints on microbial decomposition

Soil organic carbon is chemically heterogeneous, and microbial decomposers face a physiological challenge in metabolizing the diverse array of compounds present in soil. Different classes of polymeric compounds may require specialized enzymatic pathways for degradation, each of which requires an investment of microbial resources. Here we tested the resource allocation hypothesis, which posits that decomposition rates should increase once substrate concentrations are sufficient to overcome biochemical investment costs. We also tested the alternative hypothesis that mixing different substrates increases resource acquisition through priming effects involving generalist enzymes. Using a microcosm approach, we varied the soil concentration of seven distinct substrates individually and in mixture. We found that the percent carbon respired from starch, cellulose, chitin, and the mixture was significantly reduced at the lowest substrate concentration. The activities of β-glucosidase and N-acetyl-glucosaminidase that target cellulose and chitin, respectively, were also significantly lower at the lowest concentrations of their target substrates. However, we did not observe parallel declines in enzyme activity with starch or the mixture. Some enzymes, such as β-xylosidase, were consistent with specialist strategies because they showed the highest activity in the presence of their target substrate. Other enzymes were more generalist, with activity observed across multiple substrates. Together, these results suggest that the costs of biochemical machinery limit microbial decomposition of substrates at low concentration. The presence of enzymes with low substrate specificity was not sufficient to overcome this constraint for some substrates. Concentration constraints driven by microbial allocation patterns may be common in mineral soil and could be represented in new biogeochemical models based on microbial physiology

Substrate concentration constraints on microbial decomposition

Soil organic carbon is chemically heterogeneous, and microbial decomposers face a physiological challenge in metabolizing the diverse array of compounds present in soil. Different classes of polymeric compounds may require specialized enzymatic pathways for degradation, each of which requires an investment of microbial resources. Here we tested the resource allocation hypothesis, which posits that decomposition rates should increase once substrate concentrations are sufficient to overcome biochemical investment costs. We also tested the alternative hypothesis that mixing different substrates increases resource acquisition through priming effects involving generalist enzymes. Using a microcosm approach, we varied the soil concentration of seven distinct substrates individually and in mixture. We found that the percent carbon respired from starch, cellulose, chitin, and the mixture was significantly reduced at the lowest substrate concentration. The activities of β-glucosidase and N-acetyl-glucosaminidase that target cellulose and chitin, respectively, were also significantly lower at the lowest concentrations of their target substrates. However, we did not observe parallel declines in enzyme activity with starch or the mixture. Some enzymes, such as β-xylosidase, were consistent with specialist strategies because they showed the highest activity in the presence of their target substrate. Other enzymes were more generalist, with activity observed across multiple substrates. Together, these results suggest that the costs of biochemical machinery limit microbial decomposition of substrates at low concentration. The presence of enzymes with low substrate specificity was not sufficient to overcome this constraint for some substrates. Concentration constraints driven by microbial allocation patterns may be common in mineral soil and could be represented in new biogeochemical models based on microbial physiology