General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
Abstract
When exposed at Earth’s surface, rocks are out of thermodynamic equilibrium with respect to their environment. This disequilibrium drives the chemical transformation, or weathering, of these rocks into soils and governs the chemical composition of natural waters and the atmosphere. Over geologic timescales, complex feedbacks associated with weathering processes are presumed to regulate the concentrations of CO₂ and O₂ in the atmosphere with profound implications for the habitability of the planet. However, a mechanistic understanding of how biologic, tectonic, and climatic conditions interact to control weathering fluxes has remained elusive. In part, our understanding of weathering processes is hindered by the fact that they operate continuously over an enormous range of spatial (atomic to global) and temporal (microseconds to millions of years) scales, but we can only make measurements over discrete ranges of these values. While each scale of observation available offers unique insights, it is often difficult to link observations made at different scales. For my Ph.D., I focused on three distinct projects that span the range of observable scales in order to better understand the links between chemical weathering and long-term biogeochemical cycles. ❧ Chapter 2: Laboratory insights into microbial mineral dissolution. Rocks and minerals represent a major reservoir of bio-essential nutrients. While abundant, some of these lithogenic nutrients, like iron, are not readily bio-available. As a result, many organisms produce metal-binding ligands to scavenge these trace nutrients from the environment. Using targeted laboratory experiments with live microbial cultures and purified microbial ligands, I explored efficacy by which microbes can access trace nutrients from common silicate minerals (Torres et al., in prep). In addition to providing insight into biological nutrient scavenging strategies, this work also provides the basic research necessary to develop microbe-based CO₂ sequestration techniques since the dissolution of silicate minerals for nutrient acquisition also sequesters CO₂. ❧ Chapters 3 & 4: Geomorphic control on the hydrology and carbon budget of weathering. Erosional processes and hydrology are known to influence chemical weathering rates by controlling the timescales over which minerals react. Accurately describing the complex linkages between weathering, erosion, and hydrology observed in natural environments remains a major research challenge. To help address this problem, a major part of my Ph.D. was focused on characterizing how chemical weathering and hydrology are coupled in distinct erosional environments. This work combines hydrologic monitoring, solute chemistry, and water isotope analyses in order to robustly document how water is stored in catchments and link this to measured solute fluxes from chemical weathering (Clark et al., 2014; Torres et al., 2015). The results of this study are intriguing in that the hydrological control of weathering was found to vary predictably with the erosional regime, which has important implications for how changes in tectonic activity affect global weathering fluxes. ❧ By affecting the timescales over which weathering reactions occur, erosional processes also influence which minerals react due to the intrinsic variability in the reaction rates of different minerals. Rapid erosion rates favor the oxidation of sulfide minerals relative to the dissolution of silicate minerals, which leads to the release of CO₂ into the ocean-atmosphere system. To trace sulfide oxidation and its effect on the carbon budget, I combined multiple isotopic systems (e.g., S, C, and Sr) with major and trace element analyses (Torres et al., in prep). By making observations in catchments with diverse erosional regimes, it was possible to interrogate how sulfide oxidation fluxes relate to erosional processes. My results showed that sulfide oxidation dominates in rapidly eroding environments and leads to the significant release of CO₂. This is in contrast to more slowly eroding environments, where CO₂ consumption during silicate weathering dominates. ❧ Chapter 5: The evolution of the Cenozoic carbon cycle. My research on sulfide oxidation in modern systems suggested a link between tectonic uplift and the carbon budget of weathering processes with important implications for the long-term carbon cycle. To test this hypothesis, I incorporated the effects of sulfide-oxidation driven CO₂ release into a model of the Cenozoic carbon cycle. The Cenozoic carbon cycle has long plagued geochemists as isotopic records suggest changes in weathering fluxes that appear to be inconsistent with the requirement of mass balance in the long-term carbon cycle. By incorporating sulfide oxidation as a CO₂ source, I was able to provide a novel solution to the “Cenozoic isotope-weathering paradox” (Torres et al., 2014).