Scott C Alexander

Using pyrosequencing to shed light on deep mine microbial ecology

BackgroundContrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology.ResultsComparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the samples were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date.ConclusionWe anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.

Classification of Thermal Patterns at Karst Springs and Cave Streams

Thermal patterns of karst springs and cave streams provide potentially useful information concerning aquifer geometry and recharge. Temperature monitoring at 25 springs and cave streams in southeastern Minnesota has shown four distinct thermal patterns. These patterns can be divided into two types: those produced by flow paths with ineffective heat exchange, such as conduits, and those produced by flow paths with effective heat exchange, such as small fractures and pore space. Thermally ineffective patterns result when water flows through the aquifer before it can equilibrate to the rock temperature. Thermally ineffective patterns can be either event-scale, as produced by rainfall or snowmelt events, or seasonal scale, as produced by input from a perennial surface stream. Thermally effective patterns result when water equilibrates to rock temperature, and the patterns displayed depend on whether the aquifer temperature is changing over time. Shallow aquifers with seasonally varying temperatures display a phase-shifted seasonal signal, whereas deeper aquifers with constant temperatures display a stable temperature pattern. An individual aquifer may display more than one of these patterns. Since karst aquifers typically contain both thermally effective and ineffective routes, we argue that the thermal response is strongly influenced by recharge mode.

Lattice-Boltzmann Simulations of Carbonate Systems

Carbonate bedrocks encompass a vast range of primary porosities and permeabilities, which are further modified by the addition of secondary porosities as a result of fissure, fracture, and conduit development. The wide variety of primary and initial secondary porosities found in carbonates further complicate the already difficult task of modeling speleogenic processes. Understanding carbonate dissolution requires consideration of the aqueous speciation of a host of chemical elements (e.g., H, O, C, Ca, Mg, and S). It also requires simultaneous solution for the complex, typically non-Darcian, flow field over a wide range of spatial and temporal scales as the flow field affects the degree of advection and diffusion of the chemical species to and from the host rock. Lattice-Boltzmann methods are particularly suited to modeling the complex fluid dynamics involved in carbonate dissolution. Lattice-Boltzmann simulations are adept at reproducing complex and changing boundary geometries, as well as turbulent and laminar flows, multiphase-multicomponent flow, and buoyancy-induced convection due to solute and thermal gradients. Here, we present some preliminary numerical models, using lattice-Boltzmann simulations, to reproduce permeability development over a range of length and time scales for two different karst systems: continental Paleozoic systems and modern carbonate platforms.

Spring Characterization Methods & Springshed Mapping

A summary of springshed delineation techniques using the integration of historic dye tracing information, borehole geophysics and chemistry measurements. Fountain, Mahoney, Waterhole, Wykoff, Starless River and Cold Spring springshed delineations included. Interpretations are subject to change as new traces and information becomes available. A collaborative effort between the University of Minnesota and the Department of Natural Resources.

Dye tracing within the St. Lawrence confining unit in Southeastern Minnesota

A single trace near the Fillmore-Winona County Border near the City of Rushford, Fillmore County, Minnesota. The trace began in Winona County and did not cross the county boundary. Primary goal of the study was to delineate the springshed feeding a cluster of trout streams. A collaborative effort between the Minnesota Department of Natural Resources and the University of Minnesota.

Dye Tracing Sewage Lagoon Discharge in a Sandstone Karst, Askov, Minnesota

Two dye traces in 2005. Report includes geological and hydrogeological site descriptions, injection and sampling methods and a detailed interpretation including site figure with inferred groundwater flow paths and relationships to the Hinckley Fault system.

Springshed Mapping in Support of Watershed Management

Fillmore County has been the focal point of dye tracing efforts in Minnesota for several decades. In 1995, a 1:100,000, county-scale springshed map was published. At the county scale, we primarily delineated springsheds greater than 500 hectares. After that project was completed, dye-tracing efforts continued and focused on the South Branch Root River (SBRR) springshed in the western part of the county. At the scale of the SBRR springshed (about 20% of the county), we expanded the boundaries of the large springsheds but also located and refined the boundaries of springsheds that are less than 200 hectares. We found one previously unmapped small springshed (Meyers springshed), documented complex flow boundaries between a large springshed (11. Canfield) and an adjacent small springshed (26. Rainy), and expanded the boundaries of four other springsheds. The small springsheds present a new opportunity for karst watershed research, monitoring and management. The small springsheds are often dominated by one or a few land uses, which permit simpler, more evident identification of the causes of water quality degradation.

Dye Trace Study of a New Septic System in Door County, Wisconsin

A professionally designed, installed and inspected conforming waste water treatment system and a conforming water supply well were installed at a new restaurant in rural Door County, Wisconsin. In the two weeks following the opening of the restaurant, over 250 people became ill with viral gastroenteritis. Testing of the new, conforming well at the restaurant found contamination with a viral agent causing the illnesses. Stool samples of ill individuals had positive test results for norovirus, campylobacter and salmonella. Following the installation of a multi-stage water treatment system on the well, the restaurant re-opened and no further illness has occurred. The raw water from the well continues to show evidence of human waste contamination. A dual dye trace was conducted to identify possible rapid connections between the waste water treatment system and the water supply well. Dye injected in the dosing chamber that feeds the system drain field began to appear in the water supply well after fifteen days. The appearance of this dye is a measure of the flow through time from the dosing chamber to the water supply well. A second dye injected into a toilet in one of the restaurants restrooms began to appear in the water supply well after six days. The rapid appearance of this latter dye indicates a leak in the plumbing system before the effluent reaches the dosing chamber. Both dyes reached off site private wells about one-half mile down gradient in about three months and document a natural gradient groundwater flow velocity of about three kilometers per year. These results in a new conforming rural waste water disposal system call into question the efficacy of the current construction standards, guidelines and siting practices for large on-site waste water disposal treatment systems in karst.

The Sandstone Karst of Pine County, Minnesota

Others have developed broader definitions. In his treatment of some puzzling features on sandstone, Jennings (1983) defines karst as the result of “the process, solution, which is thought to be critical (but not necessarily dominant) in the development of the landforms and drainage characteristics of karst.” He defines pseudokarst as “country with resemblances to karst, which are due to other processes.”

Goliath’s Cave, Minnesota: Epigenic Modification and Extension of Pre-Existing Hypogenic Conduits

Introduction The Devonian, Ordovician, and Cambrian sedimentary rocks of southeast Minnesota (Mossler, 2008) host a variety of caves, sinkholes, sinking streams, blind valleys, large springs, and other karst features. The formations are relatively flat-lying, dip regionally to the southwest at a few m/km, and have been above sea level and subject to erosion since mid-Cretaceous time. All of southeast Minnesota has been glaciated several times during the Pleistocene but has not been covered with ice during the last two major glacial cycles. The highest concentration of karst features is in Fillmore County along the southern border of Minnesota. Fillmore County contains more mapped karst features than all of the rest of Minnesota combined (Gao et al., 2005).