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. 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 isolatesmore »
- Authors:
-
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology; Zymergen, Emeryville, CA (United States)
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Geosyntec Consultants, Knoxville, TN (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth and Environmental Sciences
- 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
- 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 Laboratory (LBNL), Berkeley, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- 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. https://doi.org/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. https://doi.org/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. 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 = {Fri Dec 22 00:00:00 EST 2017},
month = {Fri Dec 22 00:00:00 EST 2017}
}
Web of Science
Works referenced in this record:
The Use of Carbon Substrate Utilization Patterns in Environmental and Ecological Microbiology
journal, March 1998
- Konopka, A.; Oliver, L.; Jr., R. F. Turco,
- Microbial Ecology, Vol. 35, Issue 2
Influence of vegetation on low-molecular-weight carboxylic acids in soil solution—a review
journal, February 2001
- Strobel, Bjarne W.
- Geoderma, Vol. 99, Issue 3-4
Exometabolite niche partitioning among sympatric soil bacteria
journal, September 2015
- Baran, Richard; Brodie, Eoin L.; Mayberry-Lewis, Jazmine
- Nature Communications, Vol. 6, Issue 1
MassBank: a public repository for sharing mass spectral data for life sciences
journal, July 2010
- Horai, Hisayuki; Arita, Masanori; Kanaya, Shigehiko
- Journal of Mass Spectrometry, Vol. 45, Issue 7
The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter
journal, February 2002
- Kögel-Knabner, I.
- Soil Biology and Biochemistry, Vol. 34, Issue 2
Molecular Composition and Biodegradability of Soil Organic Matter: A Case Study Comparing Two New England Forest Types
journal, June 2014
- Ohno, Tsutomu; Parr, Thomas B.; Gruselle, Marie−Cécile I.
- Environmental Science & Technology, Vol. 48, Issue 13
Competitive sorption of microbial metabolites on an iron oxide mineral
journal, November 2015
- Swenson, Tami L.; Bowen, Benjamin P.; Nico, Peter S.
- Soil Biology and Biochemistry, Vol. 90
Soil Organic C:N vs. Water-Extractable Organic C:N
journal, January 2012
- Haney, Richard L.; Franzluebbers, Alan. J.; Jin, Virginia. L.
- Open Journal of Soil Science, Vol. 02, Issue 03
An extraction method for measuring soil microbial biomass C
journal, January 1987
- Vance, E. D.; Brookes, P. C.; Jenkinson, D. S.
- Soil Biology and Biochemistry, Vol. 19, Issue 6
Dissolved organic nitrogen dynamics in a Mediterranean vineyard soil
journal, August 2006
- Christou, M.; Avramides, E. J.; Jones, D. L.
- Soil Biology and Biochemistry, Vol. 38, Issue 8
Dissolved organic nitrogen in contrasting agricultural ecosystems
journal, August 2005
- Christou, M.; Avramides, E. J.; Roberts, J. P.
- Soil Biology and Biochemistry, Vol. 37, Issue 8
Changing microbial substrate use in Arctic tundra soils through a freeze-thaw cycle
journal, August 2005
- Schimel, Joshua P.; Mikan, Carl
- Soil Biology and Biochemistry, Vol. 37, Issue 8
A comparison of extraction procedures for water-extractable organic matter in soils: Comparison of WEOM extraction procedures
journal, June 2014
- Guigue, J.; Mathieu, O.; Lévêque, J.
- European Journal of Soil Science, Vol. 65, Issue 4
Response of osmolytes in soil to drying and rewetting
journal, March 2014
- Warren, Charles R.
- Soil Biology and Biochemistry, Vol. 70
METLIN: A Metabolite Mass Spectral Database
journal, January 2005
- Smith, Colin A.; Maille, Grace O??; Want, Elizabeth J.
- Therapeutic Drug Monitoring, Vol. 27, Issue 6
Process-based isotope partitioning of winter soil respiration in a subalpine ecosystem reveals importance of rhizospheric respiration
journal, July 2014
- Tucker, Colin L.; Young, Jessica M.; Williams, David G.
- Biogeochemistry, Vol. 121, Issue 2
Carbohydrate and amino acid composition of dissolved organic matter leached from soil
journal, November 2007
- Fischer, Holger; Meyer, Axel; Fischer, Klaus
- Soil Biology and Biochemistry, Vol. 39, Issue 11
Microbial Community Dynamics Associated with Rhizosphere Carbon Flow
journal, November 2003
- Butler, J. L.; Williams, M. A.; Bottomley, P. J.
- Applied and Environmental Microbiology, Vol. 69, Issue 11
FiehnLib: Mass Spectral and Retention Index Libraries for Metabolomics Based on Quadrupole and Time-of-Flight Gas Chromatography/Mass Spectrometry
journal, December 2009
- Kind, Tobias; Wohlgemuth, Gert; Lee, Do Yup
- Analytical Chemistry, Vol. 81, Issue 24
Staphylococcus aureus metabolic response to changing environmental conditions – A metabolomics perspective
journal, May 2014
- Liebeke, Manuel; Lalk, Michael
- International Journal of Medical Microbiology, Vol. 304, Issue 3-4
Metabolic Footprinting of Mutant Libraries to Map Metabolite Utilization to Genotype
journal, October 2012
- Baran, Richard; Bowen, Benjamin P.; Price, Morgan N.
- ACS Chemical Biology, Vol. 8, Issue 1
Comparison of Whole-Cell Fatty Acid (MIDI) or Phospholipid Fatty Acid (PLFA) Extractants as Biomarkers to Profile Soil Microbial Communities
journal, February 2013
- Fernandes, Marcelo F.; Saxena, Jyotisna; Dick, Richard P.
- Microbial Ecology, Vol. 66, Issue 1
How Pseudomonas aeruginosa adapts to various environments: a metabolomic approach: Metabolic adaptation of Pseudomonas aeruginosa
journal, February 2010
- Frimmersdorf, Eliane; Horatzek, Sonja; Pelnikevich, Anya
- Environmental Microbiology, Vol. 12, Issue 6
High diversity of small organic N observed in soil water
journal, February 2013
- Warren, Charles R.
- Soil Biology and Biochemistry, Vol. 57
Metabolic Phenotyping in Health and Disease
journal, September 2008
- Holmes, Elaine; Wilson, Ian D.; Nicholson, Jeremy K.
- Cell, Vol. 134, Issue 5
Persistence of soil organic matter as an ecosystem property
journal, October 2011
- Schmidt, Michael W. I.; Torn, Margaret S.; Abiven, Samuel
- Nature, Vol. 478, Issue 7367
Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil
journal, May 2006
- Jones, D.; Willett, V.
- Soil Biology and Biochemistry, Vol. 38, Issue 5
Episodic rewetting enhances carbon and nitrogen release from chaparral soils
journal, December 2005
- Miller, A.; Schimel, J.; Meixner, T.
- Soil Biology and Biochemistry, Vol. 37, Issue 12
Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism
journal, April 2016
- Bouskill, Nicholas J.; Wood, Tana E.; Baran, Richard
- Frontiers in Microbiology, Vol. 7
Ultrahigh Resolution Mass Spectrometry and Indicator Species Analysis to Identify Marker Components of Soil- and Plant Biomass-Derived Organic Matter Fractions
journal, November 2010
- Ohno, Tsutomu; He, Zhongqi; Sleighter, Rachel L.
- Environmental Science & Technology, Vol. 44, Issue 22
Bioavailability of water extractable organic carbon fractions in forest and agricultural soil profiles
journal, June 1996
- Boyer, J. N.; Groffman, P. M.
- Soil Biology and Biochemistry, Vol. 28, Issue 6
Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments
journal, May 2015
- Thorgersen, Michael P.; Lancaster, W. Andrew; Vaccaro, Brian J.
- Applied and Environmental Microbiology, Vol. 81, Issue 15
Physiological roles of trehalose in bacteria and yeasts: a comparative analysis
journal, September 2000
- Argüelles, Juan Carlos
- Archives of Microbiology, Vol. 174, Issue 4
Untargeted soil metabolomics methods for analysis of extractable organic matter
journal, January 2015
- Swenson, Tami L.; Jenkins, Stefan; Bowen, Benjamin P.
- Soil Biology and Biochemistry, Vol. 80
HMDB 3.0—The Human Metabolome Database in 2013
journal, November 2012
- Wishart, David S.; Jewison, Timothy; Guo, An Chi
- Nucleic Acids Research, Vol. 41, Issue D1
Nutritional flexibility of oligotrophic and copiotrophic Antarctic bacteria with respect to organic substrates
journal, January 1989
- Upton, A. C.; Nedwell, D. B.
- FEMS Microbiology Letters, Vol. 62, Issue 1
Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys: Cultivation of soil bacteria
journal, November 2002
- Sait, Michelle; Hugenholtz, Philip; Janssen, Peter H.
- Environmental Microbiology, Vol. 4, Issue 11
Plant species affect the concentration of free sugars and free amino acids in different types of soil
journal, October 2002
- Hertenberger, Gerhard; Zampach, Peter; Bachmann, Gert
- Journal of Plant Nutrition and Soil Science, Vol. 165, Issue 5
MassBank: a public repository for sharing mass spectral data for life sciences
journal, July 2010
- Horai, Hisayuki; Arita, Masanori; Kanaya, Shigehiko
- Journal of Mass Spectrometry, Vol. 45, Issue 7
Physiological roles of trehalose in bacteria and yeasts: a comparative analysis
journal, December 2000
- Argüelles, C.
- Archives of Microbiology, Vol. 174, Issue 6
The Use of Carbon Substrate Utilization Patterns in Environmental and Ecological Microbiology
journal, March 1998
- Konopka, A.; Oliver, L.; Jr., R. F. Turco,
- Microbial Ecology, Vol. 35, Issue 2
Process-based isotope partitioning of winter soil respiration in a subalpine ecosystem reveals importance of rhizospheric respiration
journal, July 2014
- Tucker, Colin L.; Young, Jessica M.; Williams, David G.
- Biogeochemistry, Vol. 121, Issue 2
An extraction method for measuring soil microbial biomass C
journal, January 1987
- Vance, E. D.; Brookes, P. C.; Jenkinson, D. S.
- Soil Biology and Biochemistry, Vol. 19, Issue 6
Bioavailability of water extractable organic carbon fractions in forest and agricultural soil profiles
journal, June 1996
- Boyer, J. N.; Groffman, P. M.
- Soil Biology and Biochemistry, Vol. 28, Issue 6
Metabolic Phenotyping in Health and Disease
journal, September 2008
- Holmes, Elaine; Wilson, Ian D.; Nicholson, Jeremy K.
- Cell, Vol. 134, Issue 5
Staphylococcus aureus metabolic response to changing environmental conditions – A metabolomics perspective
journal, May 2014
- Liebeke, Manuel; Lalk, Michael
- International Journal of Medical Microbiology, Vol. 304, Issue 3-4
Changing microbial substrate use in Arctic tundra soils through a freeze-thaw cycle
journal, August 2005
- Schimel, Joshua P.; Mikan, Carl
- Soil Biology and Biochemistry, Vol. 37, Issue 8
Dissolved organic nitrogen in contrasting agricultural ecosystems
journal, August 2005
- Christou, M.; Avramides, E. J.; Roberts, J. P.
- Soil Biology and Biochemistry, Vol. 37, Issue 8
Episodic rewetting enhances carbon and nitrogen release from chaparral soils
journal, December 2005
- Miller, A.; Schimel, J.; Meixner, T.
- Soil Biology and Biochemistry, Vol. 37, Issue 12
Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil
journal, May 2006
- Jones, D.; Willett, V.
- Soil Biology and Biochemistry, Vol. 38, Issue 5
Dissolved organic nitrogen dynamics in a Mediterranean vineyard soil
journal, August 2006
- Christou, M.; Avramides, E. J.; Jones, D. L.
- Soil Biology and Biochemistry, Vol. 38, Issue 8
Carbohydrate and amino acid composition of dissolved organic matter leached from soil
journal, November 2007
- Fischer, Holger; Meyer, Axel; Fischer, Klaus
- Soil Biology and Biochemistry, Vol. 39, Issue 11
High diversity of small organic N observed in soil water
journal, February 2013
- Warren, Charles R.
- Soil Biology and Biochemistry, Vol. 57
Competitive sorption of microbial metabolites on an iron oxide mineral
journal, November 2015
- Swenson, Tami L.; Bowen, Benjamin P.; Nico, Peter S.
- Soil Biology and Biochemistry, Vol. 90
FiehnLib: Mass Spectral and Retention Index Libraries for Metabolomics Based on Quadrupole and Time-of-Flight Gas Chromatography/Mass Spectrometry
journal, December 2009
- Kind, Tobias; Wohlgemuth, Gert; Lee, Do Yup
- Analytical Chemistry, Vol. 81, Issue 24
Metabolic Footprinting of Mutant Libraries to Map Metabolite Utilization to Genotype
journal, October 2012
- Baran, Richard; Bowen, Benjamin P.; Price, Morgan N.
- ACS Chemical Biology, Vol. 8, Issue 1
Molecular Composition and Biodegradability of Soil Organic Matter: A Case Study Comparing Two New England Forest Types
journal, June 2014
- Ohno, Tsutomu; Parr, Thomas B.; Gruselle, Marie−Cécile I.
- Environmental Science & Technology, Vol. 48, Issue 13
Persistence of soil organic matter as an ecosystem property
journal, October 2011
- Schmidt, Michael W. I.; Torn, Margaret S.; Abiven, Samuel
- Nature, Vol. 478, Issue 7367
HMDB 3.0—The Human Metabolome Database in 2013
journal, November 2012
- Wishart, David S.; Jewison, Timothy; Guo, An Chi
- Nucleic Acids Research, Vol. 41, Issue D1
METLIN: A Metabolite Mass Spectral Database
journal, January 2005
- Smith, Colin A.; Maille, Grace O??; Want, Elizabeth J.
- Therapeutic Drug Monitoring, Vol. 27, Issue 6
Nutritional flexibility of oligotrophic and copiotrophic Antarctic bacteria with respect to organic substrates
journal, January 1989
- Upton, A. C.; Nedwell, D. B.
- FEMS Microbiology Letters, Vol. 62, Issue 1
A new medium for the enumeration and subculture of bacteria from potable water.
journal, January 1985
- Reasoner, D. J.; Geldreich, E. E.
- Applied and Environmental Microbiology, Vol. 49, Issue 1
Laboratory Cultivation of Widespread and Previously Uncultured Soil Bacteria
journal, December 2003
- Joseph, S. J.; Hugenholtz, P.; Sangwan, P.
- Applied and Environmental Microbiology, Vol. 69, Issue 12
Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism
journal, April 2016
- Bouskill, Nicholas J.; Wood, Tana E.; Baran, Richard
- Frontiers in Microbiology, Vol. 7
Works referencing / citing this record:
Evaluation of an untargeted nano-liquid chromatography-mass spectrometry approach to expand coverage of low molecular weight dissolved organic matter in Arctic soil
journal, April 2019
- Ladd, Mallory P.; Giannone, Richard J.; Abraham, Paul E.
- Scientific Reports, Vol. 9, Issue 1