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Chapter 5.1.6 : Environmental Systems Microbiology of Contaminated Environments

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Environmental Systems Microbiology of Contaminated Environments, Page 1 of 2

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Abstract:

Environmental Systems Microbiology is well positioned to move forward in dynamic complex system analysis probing new questions and developing new insight into the function, robustness and resilience in response to anthropogenic perturbations. Recent studies have demonstrated that natural bacterial communities can be used as quantitative biosensors in both groundwater and deep ocean water, predicting oil concentration from the Gulf of Mexico Deep Water Horizon spill and from groundwater at nuclear production waste sites (16, 17, 25). Since the first demonstration of catabolic gene expression in soil remediation (34) it has been clear that extension beyond organismal abundance to process and function of microbial communities as a whole using the whole suite of omic tools available to the post genomic era. Metatranscriptomics have been highlighted as a prime vehicle for understanding responses to environmental drivers (35) in complex systems and with rapidly developing metabolomics, full functional understanding of complex community biogeochemical cycling is an achievable goal. Perhaps more exciting is the dynamic nature of these systems and their complex adaptive strategies that may lead to new control paradigms and emergence of new states and function in the course of a changing environment.

Citation: Hazen T, Sayler G. 2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.6
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FIGURE 1

Bottom-up approach balanced with a top-down approach from systems ecology that aims to capture the dynamics and variations within a system. doi:10.1128/9781555818821.ch5.1.6.f1

Citation: Hazen T, Sayler G. 2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.6
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FIGURE 2

Environmental systems microbiology framework. doi:10.1128/9781555818821.ch5.1.6.f2

Citation: Hazen T, Sayler G. 2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.6
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FIGURE 3

Biases associated with nucleic acid analyses (reused from ( ), with permission). doi:10.1128/9781555818821.ch5.1.6.f3

Citation: Hazen T, Sayler G. 2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.6
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FIGURE 4

Different levels of analyses that can be performed and examples of analytical methods that can be used (reused from ( ), with permission). doi:10.1128/9781555818821.ch5.1.6.f4

Citation: Hazen T, Sayler G. 2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.6
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FIGURE 5

Examples of critical measurements made during the Deepwater Horizon oil spill ( ). An environmental systems microbiology approach was used by performing analyses at different scales, measurements, and methods. doi:10.1128/9781555818821.ch5.1.6.f5

Citation: Hazen T, Sayler G. 2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.6
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FIGURE 6

Flow chart for ESM study at Oak Ridge National Laboratory Field Site ( ). doi:10.1128/9781555818821.ch5.1.6.f6

Citation: Hazen T, Sayler G. 2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.6
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FIGURE 7

Bacterial DNA can be used to quantitatively predict many geochemical features. Besides classification, we can use 16S sequence data to predict quantitative values for a variety of geochemical measurements at each well sampled. Correlation coefficient (Kendall's tau) between true and predicted values. Eighteen of these correlations are highly significant ( < 0.0001, indicated by •), 8 are significant ( < 0.01, indicated by o), and 12 of these correlations are not significant (reused from ( ), with permission). doi:10.1128/9781555818821.ch5.1.6.f7

Citation: Hazen T, Sayler G. 2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.6
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FIGURE 8

Single organism living is an isolation mechanism for survival. Metabolic networks determined from metagenomic sequencing. Metabolic models and stable isotopic analyses of geochemistry determined sources nutrients and energy ( ). doi:10.1128/9781555818821.ch5.1.6.f8

Citation: Hazen T, Sayler G. 2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.6
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FIGURE 9

Single-cell sequence of oceanospiralle dominant strain in the Deep Water Horizon oil spill. doi:10.1128/9781555818821.ch5.1.6.f9

Citation: Hazen T, Sayler G. 2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.6
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FIGURE 10

SLiME predictions for groundwater and deep sea contaminants (reused from ( ), with permission). doi:10.1128/9781555818821.ch5.1.6.f10

Citation: Hazen T, Sayler G. 2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.6
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Tables

Generic image for table
TABLE 1

Prioritization of measurements for a typical ESM, data types, measurement types, data formats, and highest priority data (arranged by columns). Data priority established by importance to hypothesis testing.

Citation: Hazen T, Sayler G. 2016. Environmental Systems Microbiology of Contaminated Environments, p 5.1.6-1-5.1.6-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.6

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