Chapter 2 : From Geocycles to Genomes and Back

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This chapter discusses the ways a budding geomicrobiologist might embark on the quest to understand how microbial communities affect environment and to predict how they will respond in the face of environmental change. It introduces various methods geomicrobiologists have at their disposal to achieve this goal, including both traditional nonmolecular and molecular methods. It focuses on iron, which is one of the most ubiquitous and biogeochemically relevant metals in the environment. The chapter provides a brief review of the (bio)geochemistry of this element and describes Lake Matano, an iron-rich environment that is geochemically fascinating with respect to metal cycling. It presents the known-facts about Lake Matano and discusses how the traditional and the molecular microbiological approaches described can be used to gain insight into the manner in which microorganisms affect the biogeochemical cycling of iron and other elements in the environment. Once whole genomes of novel organisms from this environment would become available, bioinformatics provides powerful additional tools to search for metabolic key components that contribute to the biogeochemical cycling of iron and other elements in this environment.

Citation: Bose A, Kopf S, Newman D. 2011. From Geocycles to Genomes and Back, p 13-38. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch2
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Image of FIGURE 1

TEM and SEM of strain SW2 grown photoferrotrophically. (A) TEM image of strain SW2 grown photoferrotrophically for 5 days. Arrows indicate Fe(III) precipitates. Image previously published as Figure 4B in . (B) SEM of strain SW2 grown photoferrotrophically for 4 weeks showing the crystalline, regularly shaped Fe(III) precipitates. 10.1128/9781555817190.ch2.f1

Citation: Bose A, Kopf S, Newman D. 2011. From Geocycles to Genomes and Back, p 13-38. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch2
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Image of FIGURE 2

Simplified illustration of the coupling of the biogeochemical cycling of iron with the carbon, nitrogen, and sulfur cycles. Shown are interactions of the element cycles during mineral formation and dissolution (left column: arrows indicate precipitation, parentheses provide examples of mineral species), redox cycling (center column: arrows illustrate redox transformations coupled to iron oxidation/reduction, parentheses provide examples of the reduced and oxidized species involved), and enzymatic catalysis (right column: arrows indicate examples of iron-dependent metabolic processes for sulfur, carbon, and nitrogen, respectively). 10.1128/9781555817190.ch2.f2

Citation: Bose A, Kopf S, Newman D. 2011. From Geocycles to Genomes and Back, p 13-38. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch2
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Image of FIGURE 3

Simplified schematic illustrating the interactions of the iron cycle with other element cycles in Lake Matano. The oxic surface waters are shown with a white background, the anoxic monimolimion is shown in light grey. Penetration of sunlight and phototrophic transformations are indicated with dotted lines, nonphototrophic microbial transformations are indicated with solid lines, and precipitation and diffusion are shown by dashed lines. Coupled arrows, such as organic matter oxidation to carbon dioxide (<CHO> to CO) with sulfate reduction to hydrogen sulfide (SO to HS), illustrate closely linked redox transformations. Several hypothesized, but still insufficiently investigated potential processes in Lake Matano, such as photoferrotrophy and iron-dependent anaerobic methane oxidation, are highlighted with a question mark. 10.1128/9781555817190.ch2.f3

Citation: Bose A, Kopf S, Newman D. 2011. From Geocycles to Genomes and Back, p 13-38. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch2
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