Carbon utilization

Abstract: Mine tailings disposal sites from either inactive or abandoned mine sites are prevalent in arid and semiarid regions throughout the world. Major areas include northern Mexico and the Western United States, the Pacific coast of South America (Chile and Peru), southwestern Spain, western India, South Africa, and Australia (Munshower 1994; Tordoff et al. 2000). The global impact of such mine tailings disposal sites is enormous, as unreclaimed mining sites generally remain unvegetated for tens to hundreds of years, and exposed tailings can spread over tens of hectares via eolian dispersion and water erosion [Gonzalez and Gonzalez-Chavez 2006; Morris et al. 2003; Munshower 1994; U.S. Environmental Protection Agency (U.S. EPA) 2004; Warhurst 2000]. Mine tailings, or mill tailings, are the materials remaining after extraction and beneficiation of ores. What prevents the natural revegetation of mine tailings? It is generally a combination of factors beginning with metal toxicity. Tailings are characterized by elevated concentrations of metals such as arsenic, cadmium, copper, manganese, lead, and zinc (1–50 g/kg) (Boulet and Larocque 1998; Bradshaw et al. 1978; Walder and Chavez 1995). Further, tailings contain no organic matter or macronutrients, and usually exhibit acidic pH, although some tailings may be alkaline (Johnson and Bradshaw 1977; Krzaklewski and Pietrzykowski 2002). For these reasons, tailings remain without normal soil structure and support a severely stressed heterotrophic microbial community (Mendez et al. 2007; Southam and Beveridge 1992). Hence, the microbial community is extremely low in species richness and carbon utilization diversity compared with uncontaminated soil (Moynahan et al. 2002). Furthermore, autotrophic iron- and sulfur-oxidizing bacteria dominate the microbial community in mine tailings and are associated with plant death in acidic tailings (Schippers et al. 2000). In arid and semiarid regions, plant establishment on mine tailings is further impeded by a number of physicochemical factors including extreme temperatures especially at the tailings surface, low precipitation, and high winds. These factors contribute to the development of extremely high salt concentrations ranging up to 22 dS/m due to high evaporation and low water infiltration (Munshower 1994).

Abstract: 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. Comparisons 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. We 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.

Abstract: The lactic acid bacterium Streptococcus thermophilus is widely used for the manufacture of yogurt and cheese. This dairy species of major economic importance is phylogenetically close to pathogenic streptococci, raising the possibility that it has a potential for virulence. Here we report the genome sequences of two yogurt strains of S. thermophilus. We found a striking level of gene decay (10% pseudogenes) in both microorganisms. Many genes involved in carbon utilization are nonfunctional, in line with the paucity of carbon sources in milk. Notably, most streptococcal virulence-related genes that are not involved in basic cellular processes are either inactivated or absent in the dairy streptococcus. Adaptation to the constant milk environment appears to have resulted in the stabilization of the genome structure. We conclude that S. thermophilus has evolved mainly through loss-of-function events that remarkably mirror the environment of the dairy niche resulting in a severely diminished pathogenic potential.