March 29, 2018

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Andrea Rocha Co-authors Article on Soil Metabolites for Frontiers in Microbiology

Andrea Rocha (Tennessee) co-authored an article entitled "Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites" that was published in Frontiers in Microbiology on December 22, 2017.

Her co-authors were Stefan Jenkins, Tami L. Swenson, Rebecca Lau, Alex Aaring, Terry C. Hazen, Romy Chakraborty, and Trent R. Northen.

Andrea is a Senior Staff Scientist based in Tennessee focused on leading-edge research using an array of geochemical, microbial, computational, and genomics techniques within the areas of environmental microbiology, computational biology, and engineering science. She has proven success helping clients by spearheading projects, leading multi-disciplinary teams toward project completion, establishing collaborations across organizations and United States Department of Energy (DOE) National Laboratories. Andrea's specific areas of expertise include the application of molecular technologies for defining and managing environmental processes; the utilization of computational biology tools for characterization of potentially key microbial metabolic processes involved in bioremediation and bioenergy; and the implementation of newly developed biotechnology for microbial detection and assessment.

Frontiers in Microbiology is a leading journal in its field, publishing rigorously peer-reviewed research across the entire spectrum of microbiology. This multidisciplinary open-access journal is at the forefront of disseminating and communicating scientific knowledge and impactful discoveries to researchers, academics, clinicians and the public worldwide.


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.

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