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Title: Multiple element isotope probes, NanoSIMS, and the functional genomics of microbial carbon cycling in soils in response to chronic climatic change

Abstract

In this project, we developed an innovative and groundbreaking technique, quantitative stable isotope probing, a technique that uses density separation of nucleic acids as a quantitative measurement technique. This work is substantial because it advances SIP beyond the qualitative technique that has dominate the field for years. The first methods paper was published in Applied and Environmental Microbiology (Hungate et al. 2015), and this paper describes the mathematical model underlying the quantitative interpretation. A second methods paper (Schwartz et al. 2015) provides a conceptual overview of the method and its application to research problems. A third methods paper was just published (Koch et al. 2018), in which we develop the quantitative model combining sequencing and isotope data to estimate actual rates of microbial growth and death in natural populations. This work has met much enthusiasm in scientific presentations around the world. It has met with equally enthusiastic resistance in the peerreview process, though our record of publication to date argues that people are accepting the merits of the approach. The skepticism and resistance are also potentially signs that this technique is pushing the field forward, albeit with some of the discomfort that accompanies extrapolation. Part of this is a culturalmore » element in the field – the field of microbiology is not accustomed to the assumptions of ecosystem science. Research conducted in this project has pushed the philosophical perspective that major advances can occur when we advocate a sound merger between the traditions of strong inference in microbiology with those of grounded scaling in ecosystem science.« less

Authors:
 [1]
  1. Northern Arizona Univ., Flagstaff, AZ (United States)
Publication Date:
Research Org.:
Northern Arizona Univ., Flagstaff, AZ (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division
OSTI Identifier:
1430129
Report Number(s):
NAU_DOE_GS002
DOE Contract Number:
SC0010579; FOA0000866
Resource Type:
Technical Report
Resource Relation:
Related Information: Cites 10.1128/AEM.0228015Cites 10.1038/ismej.2016.28Cites 10.1016/j.copbio.2016.03.003Cites 10.1111/17582229.12475Cites 10.1038/ismej.2017.43Cites 10.1016/j.apsoil.2017.10.034Cites 10.1111/14622920.14051Cites 10.1128/AEM.0244117
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; 46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND TECHNOLOGY; microbial ecology; soil; stable isotopes; carbon cycling; bioinformatics; community ecology; quantitative stable isotope probing

Citation Formats

Hungate, Bruce. Multiple element isotope probes, NanoSIMS, and the functional genomics of microbial carbon cycling in soils in response to chronic climatic change. United States: N. p., 2018. Web. doi:10.2172/1430129.
Hungate, Bruce. Multiple element isotope probes, NanoSIMS, and the functional genomics of microbial carbon cycling in soils in response to chronic climatic change. United States. doi:10.2172/1430129.
Hungate, Bruce. Sat . "Multiple element isotope probes, NanoSIMS, and the functional genomics of microbial carbon cycling in soils in response to chronic climatic change". United States. doi:10.2172/1430129. https://www.osti.gov/servlets/purl/1430129.
@article{osti_1430129,
title = {Multiple element isotope probes, NanoSIMS, and the functional genomics of microbial carbon cycling in soils in response to chronic climatic change},
author = {Hungate, Bruce},
abstractNote = {In this project, we developed an innovative and groundbreaking technique, quantitative stable isotope probing, a technique that uses density separation of nucleic acids as a quantitative measurement technique. This work is substantial because it advances SIP beyond the qualitative technique that has dominate the field for years. The first methods paper was published in Applied and Environmental Microbiology (Hungate et al. 2015), and this paper describes the mathematical model underlying the quantitative interpretation. A second methods paper (Schwartz et al. 2015) provides a conceptual overview of the method and its application to research problems. A third methods paper was just published (Koch et al. 2018), in which we develop the quantitative model combining sequencing and isotope data to estimate actual rates of microbial growth and death in natural populations. This work has met much enthusiasm in scientific presentations around the world. It has met with equally enthusiastic resistance in the peerreview process, though our record of publication to date argues that people are accepting the merits of the approach. The skepticism and resistance are also potentially signs that this technique is pushing the field forward, albeit with some of the discomfort that accompanies extrapolation. Part of this is a cultural element in the field – the field of microbiology is not accustomed to the assumptions of ecosystem science. Research conducted in this project has pushed the philosophical perspective that major advances can occur when we advocate a sound merger between the traditions of strong inference in microbiology with those of grounded scaling in ecosystem science.},
doi = {10.2172/1430129},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Sat Mar 24 00:00:00 EDT 2018},
month = {Sat Mar 24 00:00:00 EDT 2018}
}

Technical Report:

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