Microbes in iron and sulfurrich environments

AMDs are seminatural environments rich in extremophiles and are created as a result of mining and the exposure of predominantly ferrous iron in pyrite (FeS2) to the oxygen-rich atmosphere (Baker and Banfield, 2003; Druschel et al., 2004). Iron is one of the most abundant elements in Earth's crust and exists naturally in two oxidative states, ferrous (Fe2+) and ferric (Fe3+). In nature, these two forms cycle as a result of reduction and oxidation by microorganisms and abiotic geochemical processes. The reduction of Fe3+ to Fe2+ occurs in anoxic environments, with organic compounds in these environments acting as the electron donor. In contrast, the oxidation occurs in oxygenic environment with O2 as the electron acceptor. Several groups of chemolithotrophic organisms (e.g., A. ferrooxidans) actively participate in the oxidation reaction, and thrive in such environments by oxidizing large amounts of ferrous iron (Baker and Banfield, 2003).

Within AMD environments there is continuous cycling of sulfur species, which plays a major role in energy production and the maintenance of the microbial community (Elshahed et al., 2003). The transformation of reduced sulfur (sulfide) to oxidized forms (sulfate) via various intermediate forms represents an important energy-yielding pathway for chemo-synthetic microorganisms (Ehrlich, 1996). Sulfur compounds are among the most energy-rich inorganic chemical compounds available to microorganisms. From sulfide to sulfate a total of eight electrons can be exchanged in a stepwise manner to yield not only energy for the organisms but also a wide variety of mineral products, which, in turn, can often undergo redox transformations of their own. Since a wide array of microorganisms is able to oxidize and reduce sulfur, the microbial community structure of sulfur-rich habitats is clearly influenced by the prevalent environmental conditions at a specific site, for example pH; temperature; sulfide, sulfur, or sulfate concentrations; redox conditions; presence of other electron acceptors; light availability; and organic content. Members of the genus Acidithiobacillus were the first sulfur-oxidizing isolates from AMD environments, and there have been a large number of publications detailing sulfur cycling by A. ferrooxidans (Nordstrom and Southam, 1997 and references therein).

AMD systems have many microbial niches due to variations in temperature, ionic strength, and pH, and this results in habitats being restricted to a few, specific species. It has been reported using 16S rDNA and fluorescent in situ hybridization (FISH) analysis that only a handful of prokaryotic taxa make up the community in any specific microenvironment within an AMD system (Bond and Banfield, 2001; Druschel et al., 2004). This low diversity has also been noted using culture-based approaches (Johnson et al., 2001). Metagenomic analyses of a biofilm from an AMD system at Iron Mountain (California) have provided important insights into the microbial community structure in such systems (Tyson et al., 2004). From the resulting 78 Mb of sequence obtained, the genomes of the dominant species were constructed. Bioin-formatics analyses of the metagome sequence data showed that a Leptos-pirillum group III strain was found to contain genes homologous to those for biological nitrogen fixation. This information subsequently led to the design of a selective isolation strategy that allowed the isolation of this organism (Allen and Banfield, 2005). In addition, genes involved in essential pathways (such as nitrogen and carbon dioxide fixation and iron metabolism) were revealed. A proteomic analysis of this community identified an abundant novel protein, a cytochrome, as an essential component to iron oxidation and AMD formation (Ram et al., 2005) However, with the exception of studies that target low-complexity environments such as the acid mine habitat (Tyson et al., 2004), the assembly of complete microbial genome from metagenomic data remains a major technical challenge as a result of the immense diversity of many natural samples (Torsvik et al, 1998).

In addition to AMD environments, both cold sulfide springs and deep-sea hydrothermal vents are sulfur-rich environments. A study of a cold sulfide spring emanating from a dolomite/gypsum host rock in a temporal climate region showed that sulfate-reducing bacteria living in micro-bial communities on the solid walls of the rock strata were responsible for reducing the sulfate to H2S so that the waters emerged were highly charged with this reduced form of sulfur and highly anoxic (Douglas and Douglas, 2000, 2001). Sulfide in the springwater is then oxidized microbially to elemental sulfur by a microbial biofilm, and in the spring mouth itself, sulfur is oxidized by photosynthetic microorganisms (purple sulfur bacteria and green sulfur bacteria) that use the sulfide as an electron donor for photosynthesis, depositing sulfur in elemental form.

Deep-sea hydrothermal vents are important in global biogeochemical cycles as they provide an environment at the seafloor that allows microorganisms to flourish. As hot, acidic, and reduced hydrothermal fluids mix with cold, alkaline, and oxygenated seawater, minerals precipitate to form porous sulfide-sulfate deposits. These environments have been a major source of novel and phylogenetically deeply branched hyperther-mophiles, many belonging to the archaeal domain (Takai and Horikoshi, 1999; Takai et al., 2001). It has been proposed that fluid pH in the actively venting sulfide structures is generally low (pH < 4.5) (Reysenbach et al., 2006), yet no extreme thermoacidophile has been isolated from vent deposits. Archaea have been found to make up as much as 33-50% of the total microbial community in deep-sea hydrothermal vent environments based on 16S rDNA probing and whole-cell hybridization (Nercessian et al., 2003) and are able to occupy the highest temperature niches within the vent environment (Schrenk et al., 2003; Takai et al., 2001). Studies of microbial communities inhabiting mature hydrothermal vent environments, including those inhabiting in situ settling devices, have shown differences in microbial community composition among vents in a single system, as well as temporal changes in the diversity of the microbial community of the order of days (Guezennec et al., 1998; Nercessian et al., 2003; Reysenbach et al., 2006) to years (Huber et al., 2002; McCliment et al., 2006).

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