Background: Contrasting 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.

TNF-α has long been regarded as a proimmune cytokine involved in antimicrobial type 1 immunity. However, the precise role of TNF-α in antimicrobial type 1 immunity remains poorly understood. We found that TNF-α-deficient (TNF -/-) mice quickly succumbed to respiratory failure following lung infection with replication-competent mycobacteria, because of apoptosis and necrosis of granuloma and lung structure. Tissue destruction was a result of an uncontrolled type 1 immune syndrome characterized by expansion of activated CD4 and CD8 T cells, increased frequency of antigen-specific T cells, and overproduction of IFN-γ and IL-12. Depletion of CD4 and CD8 T cells decreased IFN-γ levels, prevented granuloma and tissue necrosis, and prolonged the survival of TNF -/-hosts. Early reconstitution of TNF-α by gene transfer reduced the frequency of antigen-specific T cells and improved survival. TNF-α controlled type 1 immune activation at least in part by suppressing T cell proliferation, and this suppression involved both TNF receptor p55 and TNF receptor p75. Heightened type 1 immune activation also occurred in TNF -/-mice treated with dead mycobacteria, live replication-deficient mycobacteria, or mycobacterial cell wall components. Our study thus identifies TNF-α as a type 1 immunoregulatory cytokine whose primary role, different from those of other type 1 cytokines, is to keep an otherwise detrimental type 1 immune response in check.

Septic systems that are built in compliance with regulations are generally not expected to be the cause of groundwater borne disease outbreaks, especially in areas with thick vadose zones. However, this case study demonstrates that a disease outbreak can occur in such a setting and outlines the combination of epidemiological, microbiological, and hydrogeological methods used to confirm the source of the outbreak. In early June 2007, 229 patrons and employees of a new restaurant in northeastern Wisconsin were affected by acute gastroenteritis; 6 people were hospitalized. Epidemiological case‐control analysis indicated that drinking the restaurant's well water was associated with illness (odds ratio = 3.2, 95% confidence interval = 0.9 to 11.4, P = 0.06). Microbiological analysis (quantitative reverse transcription‐polymerase chain reaction) measured 50 genomic copies per liter of norovirus genogroup I in the well water. Nucleotide sequencing determined the genotype as GI.2 and further showed the identical virus was present in patrons' stool specimens and in the septic tank. Tracer tests using dyes injected at two points in the septic system showed that effluent was traveling from the tanks (through a leaking fitting) and infiltration field to the well in 6 and 15 d, respectively. The restaurant septic system and well (85‐m deep, in a fractured dolomite aquifer) both conformed to state building codes. The early arrival of dye in the well, which was 188 m from the septic field and located beneath a 35‐m thick vadose zone, demonstrates that in highly vulnerable hydrogeological settings, compliance with regulations may not provide adequate protection from fecal pathogens.

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.

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