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Chapter 5.2.2 : Experimental Geomicrobiology: From Field to Laboratory

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Experimental Geomicrobiology: From Field to Laboratory, Page 1 of 2

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Abstract:

Geomicrobiology involves the study of microbes that rely on certain geochemical conditions and substrates for growth and survival. Field and laboratory methods need to be carefully considered in order to thoroughly understand unique biogeochemical environments. Choices of field site as well as culture-dependent and culture-independent approaches are central to the study of systems where geomicrobiological processes such as metal oxidation, reduction, and adsorption predominate. We describe general considerations for fieldwork including choice of site, safety issues, and sampling options. Development of powerful ‘omics’ approaches such as metaproteomics and metagenomics now allow researchers to more fully understand complex geomicrobiological phenomena from the molecular to ecosystem scales. Examples are presented where combined 'omics' analyses have shown what biogeochemical processes are occurring and how these influence the geochemical environment. When combined with geochemical analyses, microbiological data from a given system can reveal what key metal transformation processes are occurring, their relative importance in the environment, and the ultimate impact that microbes have on the geochemistry of a system. This chapter serves as a practical guide for initiating and developing a variety of geomicrobiology projects, and can be used in conjunction with microbiology courses and teaching laboratories where questions regarding microbial transformation of metals are being explored.

Citation: Magnuson T, Ledbetter R. 2016. Experimental Geomicrobiology: From Field to Laboratory, p 5.2.2-1-5.2.2-7. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.2.2
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Image of FIGURE 1
FIGURE 1

Example of a “bug trap” deployed in Worswick Hot Springs, ID. The stainless steel chamber is loaded with 5 mm diameter glass beads, which become colonized over the next 24 h. The device was recovered and returned to the laboratory, after which the beads were removed and used to inoculate agar plates of growth medium. Mineral substrates such as iron oxides can be placed in the device to select for iron-transforming organisms. The bug trap was donated to Dr. Tim Magnuson by Dr. Brent Peyton, Montana State University. doi:10.1128/9781555818821.ch5.2.2.f1

Citation: Magnuson T, Ledbetter R. 2016. Experimental Geomicrobiology: From Field to Laboratory, p 5.2.2-1-5.2.2-7. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.2.2
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Image of FIGURE 2
FIGURE 2

Custom-built biofilm cultivation apparatus. Fresh sterile medium is delivered to the chamber via a peristaltic pump, through a drip chamber that prevents back colonization into the pump and medium vessel. The chamber is inoculated through injection ports, and gas mixes can be delivered. Once adequate biofilm formation is evident, the growth surfaces (e.g., glass, hematite, stainless steel) can be removed and biofilm material harvested. doi:10.1128/9781555818821.ch5.2.2.f2

Citation: Magnuson T, Ledbetter R. 2016. Experimental Geomicrobiology: From Field to Laboratory, p 5.2.2-1-5.2.2-7. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.2.2
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Image of FIGURE 3
FIGURE 3

Workflow for conducting combined proteomic and genomic interrogation of pure cultures or natural biofilms of metal-transforming microbes. Using combined omics techniques, a considerable amount of information can be generated regarding the presence of metal-transforming genes and enzymes. doi:10.1128/9781555818821.ch5.2.2.f3

Citation: Magnuson T, Ledbetter R. 2016. Experimental Geomicrobiology: From Field to Laboratory, p 5.2.2-1-5.2.2-7. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.2.2
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