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Title: Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites

Abstract

Exometabolomics enables analysis of metabolite utilization of low molecular weight organic substances by soil bacteria. Thus, environmentally-based defined media are needed to examine ecologically relevant patterns of substrate utilization. Here, we describe an approach for the construction of defined media using untargeted characterization of water soluble soil microbial metabolites from a saprolite soil collected from the Oak Ridge Field Research Center (ORFRC). To broadly characterize metabolites, both liquid chromatography mass spectrometry (LC/MS) and gas chromatography mass spectrometry (GC/MS) were used. With this approach, 96 metabolites were identified, including amino acids, amino acid derivatives, sugars, sugar alcohols, mono- and di-carboxylic acids, nucleobases, and nucleosides. From this pool of metabolites, 25 were quantified. Molecular weight cut-off filtration determined the fraction of carbon accounted for by the quantified metabolites and revealed that these soil metabolites have an uneven quantitative distribution (e.g., trehalose accounted for 9.9% of the < 1 kDa fraction). This quantitative information was used to formulate two soil defined media (SDM), one containing 23 metabolites (SDM1) and one containing 46 (SDM2). To evaluate the viability of the SDM, we examined the growth of 30 phylogenetically diverse soil bacterial isolates from the ORFRC field site. The simpler SDM1 supported the growth ofmore » 13 isolates while the more complex SDM2 supported 15 isolates. To investigate SDM1 substrate preferences, one isolate, Pseudomonas corrugata strain FW300-N2E2 was selected for a time-series exometabolomics analysis. Interestingly, it was found that this organism preferred lower-abundance substrates such as guanine, glycine, proline and arginine and glucose and did not utilize the more abundant substrates maltose, mannitol, trehalose and uridine. These results demonstrate the viability and utility of using exometabolomics to construct a tractable environmentally relevant media. We anticipate that this approach can be expanded to other environments to enhance isolation and characterization of diverse microbial communities.« less

Authors:
 [1];  [2];  [2];  [3];  [4];  [5];  [4];  [6]
  1. Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology; Zymergen, Emeryville, CA (United States)
  2. Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Geosyntec Consultants, Knoxville, TN (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth and Environmental Sciences
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil and Environmental Engineering, Dept. of Earth and Planetary Sciences and Dept. of Microbiology
  6. Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1432237
Alternate Identifier(s):
OSTI ID: 1468124
Grant/Contract Number:  
AC02-05CH11231; AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 8; Journal Issue: DEC; Related Information: © 2017 Jenkins, Swenson, Lau, Rocha, Aaring, Hazen, Chakraborty and Northen.; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; exometabolomics; liquid chromatography/mass spectrometry; gas chromatography/mass spectrometry; soil defined media; water extractable organic carbon

Citation Formats

Jenkins, Stefan, Swenson, Tami L., Lau, Rebecca, Rocha, Andrea M., Aaring, Alex, Hazen, Terry C., Chakraborty, Romy, and Northen, Trent R. Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites. United States: N. p., 2017. Web. doi:10.3389/fmicb.2017.02618.
Jenkins, Stefan, Swenson, Tami L., Lau, Rebecca, Rocha, Andrea M., Aaring, Alex, Hazen, Terry C., Chakraborty, Romy, & Northen, Trent R. Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites. United States. doi:10.3389/fmicb.2017.02618.
Jenkins, Stefan, Swenson, Tami L., Lau, Rebecca, Rocha, Andrea M., Aaring, Alex, Hazen, Terry C., Chakraborty, Romy, and Northen, Trent R. Fri . "Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites". United States. doi:10.3389/fmicb.2017.02618. https://www.osti.gov/servlets/purl/1432237.
@article{osti_1432237,
title = {Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites},
author = {Jenkins, Stefan and Swenson, Tami L. and Lau, Rebecca and Rocha, Andrea M. and Aaring, Alex and Hazen, Terry C. and Chakraborty, Romy and Northen, Trent R.},
abstractNote = {Exometabolomics enables analysis of metabolite utilization of low molecular weight organic substances by soil bacteria. Thus, environmentally-based defined media are needed to examine ecologically relevant patterns of substrate utilization. Here, we describe an approach for the construction of defined media using untargeted characterization of water soluble soil microbial metabolites from a saprolite soil collected from the Oak Ridge Field Research Center (ORFRC). To broadly characterize metabolites, both liquid chromatography mass spectrometry (LC/MS) and gas chromatography mass spectrometry (GC/MS) were used. With this approach, 96 metabolites were identified, including amino acids, amino acid derivatives, sugars, sugar alcohols, mono- and di-carboxylic acids, nucleobases, and nucleosides. From this pool of metabolites, 25 were quantified. Molecular weight cut-off filtration determined the fraction of carbon accounted for by the quantified metabolites and revealed that these soil metabolites have an uneven quantitative distribution (e.g., trehalose accounted for 9.9% of the < 1 kDa fraction). This quantitative information was used to formulate two soil defined media (SDM), one containing 23 metabolites (SDM1) and one containing 46 (SDM2). To evaluate the viability of the SDM, we examined the growth of 30 phylogenetically diverse soil bacterial isolates from the ORFRC field site. The simpler SDM1 supported the growth of 13 isolates while the more complex SDM2 supported 15 isolates. To investigate SDM1 substrate preferences, one isolate, Pseudomonas corrugata strain FW300-N2E2 was selected for a time-series exometabolomics analysis. Interestingly, it was found that this organism preferred lower-abundance substrates such as guanine, glycine, proline and arginine and glucose and did not utilize the more abundant substrates maltose, mannitol, trehalose and uridine. These results demonstrate the viability and utility of using exometabolomics to construct a tractable environmentally relevant media. We anticipate that this approach can be expanded to other environments to enhance isolation and characterization of diverse microbial communities.},
doi = {10.3389/fmicb.2017.02618},
journal = {Frontiers in Microbiology},
number = DEC,
volume = 8,
place = {United States},
year = {2017},
month = {12}
}

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