A thermodynamically-based model for predicting microbial growth and community composition coupled to system geochemistry: Application to uranium bioreduction

Istok, Jonathan D.; Park, Melora M.; Michalsen, Mandy M.; Spain, Anne M.; Krumholz, Lee R.; Liu, Chongxuan; McKinley, James P.; Long, Philip E.; Roden, Eric E.; Peacock, Aaron D.; Baldwin, Brett R.

doi:10.1016/j.jconhyd.2009.07.004

Cited by 35 publications

(25 citation statements)

References 44 publications

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“…The consumption of acetate correlated with increases of CH 4 and CO 2 concentrations in previous incubation experiments suggested either acetoclastic methanogenesis or syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis, which are both consistent with isotopic analyses of CH 4 from the site (Throckmorton et al, 2015;Vaughn et al, 2016). Using reaction stoichiometry for acetoclastic methanogenesis and anaerobic respiration 15 through iron reduction (Istok et al, 2010), we estimated the amount of acetate being consumed by these parallel processes in the transition zone and permafrost (Fig. 8).…”

supporting

confidence: 78%

Impacts of temperature and soil characteristics on methane production and oxidation in Arctic polygonal tundra

Zheng¹,

Chowdhury²,

Yang³

et al. 2018

Preprint

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Methane (CH 4 ) oxidation mitigates CH 4 emission from soils. However, it is still highly uncertain whether soils in highlatitude ecosystems will function as a net source or sink for this important greenhouse gas. We investigated CH 4 production and oxidation potential in permafrost-affected soils from degraded ice-wedge polygons with carbon-rich soils at the Barrow Environmental Observatory, Utqiaġvik (Barrow) Alaska, USA. Frozen soil cores from flat and high-centered polygons were 25 sectioned into active layers, transition zones, and permafrost, and incubated at -2, +4 and +8°C to determine potential CH 4 production and oxidation rates. Organic acids produced by fermentation fueled methanogenesis and competing iron reduction processes responsible for most anaerobic respiration. Significant CH 4 oxidation was observed from the suboxic transition zone and permafrost of flat-centered polygon soil, which also exhibited higher CH 4 production rates during the incubations. Although CH 4 production showed higher temperature sensitivity than CH 4 oxidation, potential rates of CH 4 30 oxidation exceeded methanogenesis rates at each temperature. Assuming no diffusion limitation, our results suggest that CH 4Biogeosciences Discuss., https://doi.org/10.5194/bg-2017-566 Manuscript under review for journal Biogeosciences Discussion started: 29 January 2018 c Author(s) 2018. CC BY 4.0 License. 2 oxidation could offset CH 4 production and limit surface CH 4 emissions, in response to elevated temperature, and thus should be considered in model predictions of net CH 4 fluxes in Arctic polygonal tundra.

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supporting

confidence: 78%

Impacts of temperature and soil characteristics on methane production and oxidation in Arctic polygonal tundra

Zheng¹,

Chowdhury²,

Yang³

et al. 2018

Preprint

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“…Since biological oxidation and reduction can also occur, it makes sense to supplement databases of geochemical reactions with reactions mediated by microbial communities. Istok et al [77] supplemented tables of geochemical reactions with thermodynamic-based growth equations of microbes and then predicted laboratory and field interventions for the bioreduction of uranium. Likewise, Larowe et al [78] used thermodynamic modeling to evaluate and compare the driving forces responsible for microbial anaerobic methane oxidation across representative marine ecological sites and different consortia.…”

Section: Thermodynamically-based Modelsmentioning

confidence: 99%

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

et al. 2014

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Microorganisms in nature form diverse communities that dynamically change in structure and function in response to environmental variations. As a complex adaptive system, microbial communities show higher-order properties that are not present in individual microbes, but arise from their interactions. Predictive mathematical models not only help to understand the underlying principles of the dynamics and emergent properties of natural and synthetic microbial communities, but also provide key knowledge required for engineering them. In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can be potentially useful. We discuss a broad range of methods ranging from low-resolution supra-organismal to high-resolution individual-based modeling. Particularly, we highlight the integrative approaches that synergistically combine disparate methods. In conclusion, we provide our outlook for the key aspects that should be further developed to move microbial community modeling towards greater predictive power.

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“…The concentrations of enzymes that actually catalyze biogeochemical reactions are therefore the ideal variables to link microbial community functions with changes in the concentration of biogeochemical species (Philippot and Hallin, 2005;Rocca et al, 2014). While most biogeochemical species are readily quantified, the presence or relative abundance of the enzymes that catalyze their transformation are commonly inferred using surrogate variables such as biomass, functional genes or gene transcripts and apparent enzyme activities (Istok et al, 2010;Johnson, 2013;Moran et al, 2013;Reed et al, 2014).…”

Section: Prospect Of the New Technique In Environmental Microbiologymentioning

confidence: 99%

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes

Gao

Qian

et al. 2017

Environ Microbiol Rep

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Microbial enzymes catalytically drive biogeochemical processes in environments. The dynamic linkage between functional enzymes and biogeochemical species transformation has, however, rarely been investigated for decades because of the challenges to directly quantify enzymes in environmental samples. The diversity of microorganisms, the low amount of available biomass and the complexity of chemical composition in environmental samples represent the main challenges. To address the diversity challenge, we first identify several signature peptides that are conserved in the targeted enzymes with the same functionality across many phylogenetically diverse microorganisms using metagenome-based protein sequence data. Quantification of the signature peptides then allows estimation of the targeted enzyme abundance. To achieve analyses of the requisite sensitivity for complex environmental samples with low available biomass, we adapted a recently developed ultrasensitive targeted quantification technology, termed high-pressure high-resolution separations with intelligent selection and multiplexing (PRISM) by improving peptide separation efficiency and method detection sensitivity. Nitrate reduction dynamics catalyzed by dissimilatory and assimilatory enzymes in a hyporheic zone sediment was used as an example to demonstrate the application of the enzyme quantification approach. Together with the measurements of biogeochemical species, the approach enables investigating the dynamic linkage between functional enzymes and biogeochemical processes.

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A thermodynamically-based model for predicting microbial growth and community composition coupled to system geochemistry: Application to uranium bioreduction

Cited by 35 publications

References 44 publications

Impacts of temperature and soil characteristics on methane production and oxidation in Arctic polygonal tundra

Impacts of temperature and soil characteristics on methane production and oxidation in Arctic polygonal tundra

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes

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