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Fields, Matthew

Fields MatthewMontana State University
Deputy Director,
Environmental Microbiology
[email protected]
(406) 994-7340


Matthew Fields, as the Environmental Component Deputy Director, studies environmental signals that are sensed by cells to mediate control over physiology and modes of growth. Matthew Fields is an associate professor in the Department of Microbiology at Montana State University. His lab is in the Center for Biofilm Engineering, and he is also associated with the Thermal Biology Institute and the Energy Research Institute at Montana State University. He is also an Adjunct Research Fellow at the National Center for Genome Resources in Santa Fe, NM. His laboratory uses molecular ecology to study microbial communities associated with different environments in the field that include subsurface sediments, groundwater, coal, and industrial environments. Laboratory work includes sulfate-reducing bacteria, methanogens, and lipid-producing algae, and these types of organisms are important to bioremediation, metal corrosion, and biofuel production, respectively. Ultimately, a driving question is to understand the relationships between structure and function at different scales of biology, and we use a model sulfate-reducing bacterium (Desulfovibrio) to understand ecological and physiological responses. An improved understanding of structure/function relationships will allow predictive modeling and design for a variety of natural and engineered systems. Matthew is the lead on the MicroParticle Mesogenomics Campaign.

Chakraborty, Romy

Chakraborty, RomyLawrence Berkeley National Lab
Earth Sciences
Principle Investigator
[email protected]
(510) 486-4091

Romy Chakraborty is a Principal Investigator of a discovery project in the Environmental component. Her lab is involved in high throughput isolation and characterization of metal-oxidizing and nitrate-reducing microbial isolates and microbial communities from the Oakridge FRC site. Her lab provides strains and isolates to members of the Environmental, Physiology and Biotechnology components.

Hazen, Terry

Hazen TerryUniversity of Tennessee
Director, Environmental Microbiology
[email protected]
(707) 631-6763

Terry Hazen, the Environmental Component Director, has a background in environmental microbiology, especially as it relates to bioremediation and bacterial stress. Terry maintains close collaboration with the executive and project leads in administration, management and operations of the project with a particular focus on accomplishing the goals and deliverables. Terry’s work anchors several of ENIGMA’s ongoing campaigns; He supervises field activities for the overall SFA.

Elias, Dwayne

Elias Dwayne, PHDOak Ridge National
Lab Principal Investigator
[email protected]
(865) 574-0956

Dwayne Elias, a Principal Investigator in the Environmental Component has a background in microbial physiology and ecology, especially as it relates to bioremediation and bacterial communities. His primary research interests focus on microbial physiology and ecology including Biochemical pathway elucidation and characterization within bacteria, Systems biology studies, Elucidation of the function of hypothetical genes, and Microbial interactions. Dwayne is the lead on the Synthetic Ecological Theory Campaign.

Zhou, Jizhong (Joe)

Zhou Jizhong JoeUniversity of Oklahoma
Principal Investigator
[email protected]
(405) 325-6073

Jizhong Zhou has expertise in molecular biology, microbial genomics, microbial ecology, molecular evolution, theoretical ecology, metagenomics, and genomic technologies, as well as array-based bioinformatics for environmental studies. He has pioneered the development of array-based genomic technologies for environmental studies. His lab is involved in multiple EMC campaigns.

Complete genome sequence of Pseudomonas stutzeri strain RCH2

Chakraborty, RomyDr. Chakraborty and a team of ENIGMA researchers have published the complete genome sequence of P. stutzeri strain RCH2 using targeted enrichment to isolate the microbe from samples at Hanford 100 H area; where hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and groundwater. The Pseudomonas strain RCH2 is now a model nitrate-reducing organism for ENIGMA due to its ability to reduce Cr(VI) and Fe(III) under denitrifying and oxic conditions.

Global genome comparisons of strain RCH2 with six other fully sequenced P. stutzeri strains revealed strain RCH2 has an additional 244 genes, some of which are involved in chemotaxis, Flp pilus biogenesis, and pyruvate/2-oxoglutarate complex formation.

Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Chakraborty R, Woo H, Dehal P, Walker R, Zemla M, Auer M, Goodwin LA, Kazakov A, Novichkov P, Arkin A.P, Hazen TC. Standards in Genomic Sciences (2017) 12:23; DOI: 10.1186/s40793-017-0233-7

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation


A collaboration of researchers at Johns Hopkins University, Colorado State University, The University of Tennessee, The Lawrence Berkley National Laboratory, The Massachusetts Institute of Technology, The University of Oklahoma and the University of Georgia, Oak Ridge National Laboratory researchers in the Bioscience Division for the ENIGMA have released an article in Environmental Science and Technology.

They have developed a novel in-field bioreactor system for closely approximating in-situ conditions and monitoring the response of the groundwater microbial communities to geochemical manipulation beyond the bulk phase of traditional systems.  The effect of contaminants on the diversity, structure, function, and biotransformation capabilities of groundwater microbial communities have been studied at the Oak Ridge Field Research Center (ORFRC), but only provided limited data linking geochemistry to microbial community structure and ecological function.  “The advantage of this new system is that these bioreactors are much smaller and can be mobile, which allows for greater experimental replication and flexibility. We have also incorporated both the free-living or planktonic organisms as well as those in biofilms in the same vessel so we can monitor both simultaneously” said Dwayne Elias the lead researcher on the study. Due to the constant influx of native groundwater, in situ conditions can be maintained for considerable lengths of time as opposed to closed microcosms. “Not only can we monitor the site conditions for long periods, but we can also introduce perturbations to some of the bioreactors and observe the community response as compared to the ongoing, actual site condition bioreactors, which we hope can inform site and risk management decisions in the future”, Elias said.

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. (2017). King, A.J., S.P. Preheim, K.L. Bailey, M.S. Robeson II, T. Roy Chowdhury, B.R. Crable, R.A. Hurt Jr., T. Mehlhorn, K.A. Lowe, T.J. Phelps, A.V. Palumbo, C.C. Brandt, S.D. Brown, M. Podar, P. Zhang, W.A. Lancaster, F. Poole, D.B. Watson, M.W. Fields, J.M. Chandonia, E.J. Alm, J. Zhou, M.W.W. Adams, T.C. Hazen, A.P. Arkin, and D.A. Elias. Environ. Sci. Technol.  51 (5), pp 2879–2889(DOI: 10.1021/acs.est.6b04751).


  • Successfully monitored microbial community for >16 weeks with reproducible community responses to repeated perturbations.
  • Provides evidence of stochastic microbial community assembly.
  • Ties the lab to the field by providing a technology for testing lab-based hypotheses in the field.

Predicting metabolic properties using dynamic substrate preference

Predicting-metabolic-properties-using-dynamic-substrate-preference (1)Exometabolomic profiling was used to examine the time-varying substrate depletion from a mixture of 19 amino acids and glucose by two Pseudomonads and one Bacillus FRC isolates. ENIGMA researchers at Lawrence Berkeley National Lab examined if the first substrates depleted resulted in maximal growth rate, or related to growth medium or biomass composition and found surprisingly few correlations. We also modeled patterns of substrate depletion, and these models were used to examine if substrate usage preferences and substrate depletion kinetics of three microbial isolates can be used to predict the metabolism of the pooled isolates in co-culture.  We found that most of the substrates fit the model predictions, indicating that the microbes are not altering their behaviors for these substrates in the presence of competitors. Compounds that deviate from the model highlight substrates that could be involved in species-species interactions within the consortium.


  • Time-resolved resource usage of strains grown alone was used to formulate models for substrate usage in a co-culture setting, assuming no overt competition between the strains for the substrate
  • The model accurately predicted mixed-culture substrate depletion for about half of the resources provided in the medium
  • Deviation from the models indicate resources of interest to study further
  • This study serves as a proof-of-principle for a method to identify critical resources in a more complex environment

Dynamic substrate preferences predict the metabolic properties of a simple microbial consortium. Erbilgin O, Bowen BP, Kosina SM, Jenkins S, Lau RK, Northen TR. 2017 BMC Bioinformatics 18:57 DOI: 10.1186/s12859-017-1478-2

Uranium binding complex a potential tool for environmental sequestration of uranium



Purification of uranium binding complex from Pelosinus Strain UFO1. The uranium-binding complex was purified from the membrane fraction by two column chromatography steps A) (anion exchange (DEAE FF) and B) size exclusion (Superose 6)). After the fractionation steps, fractions were analyzed for protein (blue), uranium (red), and phosphorus (green). The flow through fraction from column 1 was used for the second purification step and is denoted by a box. C) The denaturing gel image for purified UBC from fraction 6 of the Superose 6 column (arrow) is shown. The uranium binding complex binds 3.3 U(IV) atoms/ protein complex

Widespread uranium contamination from industrial sources poses hazards to human health and the environment. ENIGMA researchers from University of Georgia and Lawrence Berkeley National Lab identified a highly abundant uranium-binding complex (UBC) from Pelosinus sp. strain UFO1.  The complex makes up the primary protein component of the S-layer of strain UFO1 and binds 3.3 atoms of U(IV) per heterodimer. While other bacteria have been shown to bind U(VI) on their S-layer, this is the first demonstrated example of U(IV) being bound by an S-layer complex. UBC provides a potential tool for the microbiological sequestration of uranium to clean up contaminated environments


  • Identified an S-layer complex capable of binding U(IV).
  • Characterized the uranium binding stoichiometry of the uranium binding complex.
  • This uranium binding complex could provide a potential tool for environmental sequestration of uranium.

A Highly Expressed High Molecular Weight S-Layer Complex of Pelosinus Strain UFO1 Binds Uranium. (2017). Thorgersen, M.P., W.A. Lancaster, L. Rajeev, X. Ge, B.J. Vaccaro, F.L. Poole, A.P. Arkin, A. Mukhopadhyay, M.W. Adams. Appl. Environ. Microbiol. 83: (DOI: 10.1128/AEM.03044-16).

Rapid Detection of Microbial Cell Abundance in Aquatic Systems



(A) Overview of approach. To provide proof of principle, capacitance measurements from laboratory-sourced batch culture and environmentally-sourced samples were obtained using silicon wafer-based capacitive sensor

ENIGMA post doctoral fellow developed the application of ACEK-enhanced capacitive sensing technology as a rapid screening tool for the detection and quantification of microbial abundance in aquatic environments, such as groundwater wells at our Oak Ridge field site. As proof of principle, she applied the tool to samples from ORNL and the Great Australian Bight.

New Science & Significance

  • Results demonstrate that ACEK capacitance-based sensing can detect and determine microbial cell counts throughout cellular concentrations typically encountered in naturally occurring microbial communities (103-106 cells/mL).
  • This work provides a foundation for understanding the limits of capacitance-based sensing in natural environmental samples and supports future efforts focusing on evaluating the robustness ACEK capacitance-based within aquatic environments.

Rapid Detection of Microbial Cell Abundance in Aquatic Systems. Rocha, A.M., Q. Yuan, D. Close, K. B. O’Dell, J. L. Fortney, J. Wu, and T.C. Hazen. (2016)

Biosensors and Bioelectronics Volume 85, 15 November 2016, Pages 915–923. [doi]10.1016/j.bios.2016.05.098

Digital Droplet Multiple Displacement Amplification



Fig. 1. The working principles of ddMDA. The ddMDA procedure partitions E.coli sample into millions of picoliter droplets(A) and amplification in each droplet occur independently from the other droplets(B). At ddMDA endpoint, each droplet contains a discrete hyper-branched MDA product(C). Scale bar =100µm. Fig. 2. Comparison of whole-genome coverage of assembled contigs mapped to E. coli K-12 genome for ddMDA and tube MDA. (A) From the outermost circle, ddMDA for 100 pg/µL, tube MDA for 100 pg/µL, 10 pg/µL, and 10 pg/µL and (B) ddMDA for 1 pg/µL, tube MDA for 1 pg/µL, 0.1 pg/µL, and 0.1 pg/µL, respectively. GC contents in black and genomic DNA in green as a reference.

  • The ddMDA technique enabled significantly lower bias and non-specific amplification than conventional MDA thus achieving more uniform coverage of amplification over the entire genome
  • This technique can be a powerful tool for genomic studies where DNA samples are limited such as single cells, microaggregates, and uncultured microbes from many different environments

Digital Droplet Multiple Displacement Amplification (ddMDA) for whole-genome sequencing of limited DNA samples (2016) Rhee, M., Light, Y.K., Meagher, R.J., and Singh, A.K. Plos One [doi]10.1371/journal.pone.0153699

Preferential oxidation of microbial-mediated reduced sulfur by nitrate limits the in situ mobility of uranium



Conceptual model of subsurface reactions: reduced sulfur-bearing species preferentially oxidized by nitrate, U(IV) oxidization is limited Field data demonstrating nitrate-reduction primarily coupled to sulfur oxidation, U(IV) oxidization was secondary. Background U(VI) was 5 μM. Background SO42- was 1 mM.

Reoxidation and mobilization of previously reduced and immobilized uranium by dissolved-phase oxidants poses a significant challenge for remediating uranium-contaminated groundwater. Preferential oxidation of reduced sulfur-bearing species, as opposed to reduced uranium-bearing species, has been demonstrated to limit the mobility of uranium at the laboratory scale yet field-scale investigations are lacking. In this study, the mobility of uranium in the presence of nitrate oxidant was investigated in a shallow groundwater system after establishing conditions conducive to uranium reduction and the formation of reduced sulfur-bearing species. A series of three injections of groundwater (200 L) containing U(VI) (5 μM) and amended with ethanol (40 mM) and sulfate (20 mM) were conducted in ten test wells in order to stimulate microbial-mediated reduction of uranium and the formation of reduced sulfur-bearing species. Simultaneous push‐pull tests were then conducted in triplicate well clusters to investigate the mobility of U(VI) under three conditions: 1) high nitrate (120 mM), 2) high nitrate (120 mM) with ethanol (30 mM), and 3) low nitrate (2 mM) with ethanol (30 mM). Dilution-adjusted breakthrough curves of ethanol, nitrate, nitrite, sulfate, and U(VI) suggested that nitrate reduction was predominantly coupled to the oxidation of reduced-sulfur bearing species, as opposed to the reoxidation of U(IV), under all three conditions for the duration of the 36-day tests. The amount of sulfate, but not U(VI), recovered during the push‐pull tests was substantially more than injected, relative to bromide tracer, under all three conditions and further suggested that reduced sulfur-bearing species were preferentially oxidized under nitrate-reducing conditions. However, some reoxidation of U(IV) was observed under nitrate-reducing conditions and in the absence of detectable nitrate and/or nitrite. This suggested that reduced sulfur-bearing species may not be fully effective at limiting the mobility of uranium in the presence of dissolved and/or solid-phase oxidants. The results of this field study confirmed those of previous laboratory studies which suggested that reoxidation of uranium under nitrate-reducing conditions can be substantially limited by preferential oxidation of reduced sulfur-bearing species.


  • Test the in situ mobility of uranium in the presence of nitrate oxidant following uranium- and sulfate-reducing conditions

New Science

  • Conducted the first ever field-scale co-injection of ethanol and sulfate to form reduced sulfur-bearing species (S0, FeS, FeS2, MnS) at a uranium-contaminated site
  • Subsequent injection of nitrate oxidant and periodic extraction of groundwater demonstrated substantial oxidation of reduced sulfur-bearing species as opposed to reduced/immobilized uranium
  • Confirmed previous laboratory studies by demonstrating preferential oxidation of reduced sulfur by nitrate can limit the in situ mobility of uranium


  • Establishing sulfate-reducing conditions following U(VI) reduction can substantially limit the extent of uranium mobility in the presence of nitrate oxidant

Paradis CJ, Jagadamma S, Watson DB, McKay LD, Hazen TC, Park M, Istok JD (2016) In situ mobility of uranium in the presence of nitrate following sulfate-reducing conditions. Journal of Contaminant Hydrology 187:55-64. doi: