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

Abstract

Microbially mediated biogeochemical processes are catalyzed by enzymes that control the transformation of carbon, nitrogen, and other elements in environment. The dynamic linkage between enzymes and biogeochemical species transformation has, however, rarely been investigated because of the lack of analytical approaches to efficiently and reliably quantify enzymes and their dynamics in soils and sediments. Herein, we developed a signature peptide-based technique for sensitively quantifying dissimilatory and assimilatory enzymes using nitrate-reducing enzymes in a hyporheic zone sediment as an example. Moreover, the measured changes in enzyme concentration were found to correlate with the nitrate reduction rate in a way different from that inferred from biogeochemical models based on biomass or functional genes as surrogates for functional enzymes. This phenomenon has important implications for understanding and modeling the dynamics of microbial community functions and biogeochemical processes in environments. Our results also demonstrate the importance of enzyme quantification for the identification and interrogation of those biogeochemical processes with low metabolite concentrations as a result of faster enzyme-catalyzed consumption of metabolites than their production. The dynamic enzyme behaviors provide a basis for the development of enzyme-based models to describe the relationship between the microbial community and biogeochemical processes.

Authors:
 [1];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [1];  [2];  [2];  [3]
  1. School of Environmental Studies, China University of Geosciences, Wuhan 430074 People's Republic of China
  2. Pacific Northwest National Laboratory, Richland, WA 99354 USA
  3. Pacific Northwest National Laboratory, Richland, WA 99354 USA; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055 People's Republic of China
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1406720
Report Number(s):
PNNL-SA-120732
Journal ID: ISSN 1758-2229; KP1702030
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Environmental Microbiology Reports
Additional Journal Information:
Journal Volume: 9; Journal Issue: 5; Journal ID: ISSN 1758-2229
Publisher:
Wiley-Blackwell
Country of Publication:
United States
Language:
English

Citation Formats

Li, Minjing, Gao, Yuqian, Qian, Wei-Jun, Shi, Liang, Liu, Yuanyuan, Nelson, William C., Nicora, Carrie D., Resch, Charles T., Thompson, Christopher, Yan, Sen, Fredrickson, James K., Zachara, John M., and Liu, Chongxuan. Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics. United States: N. p., 2017. Web. doi:10.1111/1758-2229.12558.
Li, Minjing, Gao, Yuqian, Qian, Wei-Jun, Shi, Liang, Liu, Yuanyuan, Nelson, William C., Nicora, Carrie D., Resch, Charles T., Thompson, Christopher, Yan, Sen, Fredrickson, James K., Zachara, John M., & Liu, Chongxuan. Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics. United States. doi:10.1111/1758-2229.12558.
Li, Minjing, Gao, Yuqian, Qian, Wei-Jun, Shi, Liang, Liu, Yuanyuan, Nelson, William C., Nicora, Carrie D., Resch, Charles T., Thompson, Christopher, Yan, Sen, Fredrickson, James K., Zachara, John M., and Liu, Chongxuan. Thu . "Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics". United States. doi:10.1111/1758-2229.12558.
@article{osti_1406720,
title = {Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics},
author = {Li, Minjing and Gao, Yuqian and Qian, Wei-Jun and Shi, Liang and Liu, Yuanyuan and Nelson, William C. and Nicora, Carrie D. and Resch, Charles T. and Thompson, Christopher and Yan, Sen and Fredrickson, James K. and Zachara, John M. and Liu, Chongxuan},
abstractNote = {Microbially mediated biogeochemical processes are catalyzed by enzymes that control the transformation of carbon, nitrogen, and other elements in environment. The dynamic linkage between enzymes and biogeochemical species transformation has, however, rarely been investigated because of the lack of analytical approaches to efficiently and reliably quantify enzymes and their dynamics in soils and sediments. Herein, we developed a signature peptide-based technique for sensitively quantifying dissimilatory and assimilatory enzymes using nitrate-reducing enzymes in a hyporheic zone sediment as an example. Moreover, the measured changes in enzyme concentration were found to correlate with the nitrate reduction rate in a way different from that inferred from biogeochemical models based on biomass or functional genes as surrogates for functional enzymes. This phenomenon has important implications for understanding and modeling the dynamics of microbial community functions and biogeochemical processes in environments. Our results also demonstrate the importance of enzyme quantification for the identification and interrogation of those biogeochemical processes with low metabolite concentrations as a result of faster enzyme-catalyzed consumption of metabolites than their production. The dynamic enzyme behaviors provide a basis for the development of enzyme-based models to describe the relationship between the microbial community and biogeochemical processes.},
doi = {10.1111/1758-2229.12558},
journal = {Environmental Microbiology Reports},
issn = {1758-2229},
number = 5,
volume = 9,
place = {United States},
year = {2017},
month = {7}
}

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