Environmental Molecular Sciences Laboratory

A DOE Office of Science User Facility

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Virtual Tour

Welcome to EMSL's virtual tours. Here you will be able to virtually facilities within EMSL's user program.

Easy Navigation
You can zoom and pan 360-degrees at each tour stop. Major stops include symbols indicating different types of information that provide greater detail about the location.

The symbols include:
• A "star" – provides an overview of the capability of that lab.
• A "video camera" – indicates a video featuring an EMSL expert explaining that laboratory and capabilities available to EMSL users.
• A "paragraph" – takes you to additional materials, such as science highlights and brochures.

EMSL EMSL building
This tour includes an overview from former EMSL Director Allison Campbell and features four laboratories within EMSL. You can see firsthand 11 of its state-of-the-art instruments and hear from EMSL experts.

The laboratories featured include:
• Nuclear Magnetic Resonance
• Surface Science
• High-Sensitivity Laser Imaging
• Ion Mobility Mass Spectrometry

This tour includes six laboratories. On this tour, you will hear from Nancy Hess, EMSL Science Theme lead for Terrestrial Subsurface Ecosystems, and EMSL experts.

The laboratories featured include:
• Nuclear Magnetic Resonance and Electron Magnetic Resonance – NMR/EPR
• Transmission Electron Microscopy – TEM
• Scanning Electron Microscopy – SEM
• Electron Microprobe and Scanning Probe Microscopy – EMP/SPM
• X-ray Photoelectron Spectrometry – XPS
• Sample Receiving and Preparation/Analytical Chemistry

Instruments

Highlighted Research Applications EMSL’s suite of NMR metabolomics and metabolic flux analysis capabilities enables EMSL users to probe the...
Custodian(s): David Hoyt

Science Highlights

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Instruments

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Related Videos

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Welcome to EMSL's virtual tours. Here you will be able to virtually facilities within EMSL's user program.

Easy Navigation
You can zoom and pan 360-degrees at each tour stop. Major stops include symbols indicating different types of information that provide greater detail about the location.

The symbols include:
• A "star" – provides an overview of the capability of that lab.
• A "video camera" – indicates a video featuring an EMSL expert explaining that laboratory and capabilities available to EMSL users.
• A "paragraph" – takes you to additional materials, such as science highlights and brochures.

EMSL EMSL building
This tour includes an overview from former EMSL Director Allison Campbell and features four laboratories within EMSL. You can see firsthand 11 of its state-of-the-art instruments and hear from EMSL experts.

The laboratories featured include:
• Nuclear Magnetic Resonance
• Surface Science
• High-Sensitivity Laser Imaging
• Ion Mobility Mass Spectrometry

This tour includes six laboratories. On this tour, you will hear from Nancy Hess, EMSL Science Theme lead for Terrestrial Subsurface Ecosystems, and EMSL experts.

The laboratories featured include:
• Nuclear Magnetic Resonance and Electron Magnetic Resonance – NMR/EPR
• Transmission Electron Microscopy – TEM
• Scanning Electron Microscopy – SEM
• Electron Microprobe and Scanning Probe Microscopy – EMP/SPM
• X-ray Photoelectron Spectrometry – XPS
• Sample Receiving and Preparation/Analytical Chemistry

Metabolic effects of vitamin B12 on physiology, stress resistance, growth rate and biomass productivity of Cyanobacterium

Abstract: 

Although synthesized only by bacteria and archaea, cobalamin (vitamin B12) is essential for virtually all living cells. One major function is its role in methionine synthesis, as a co-factor in for the B12-dependent methionine synthase MetH. However, large number of microbes avoid requirements for B12 by encoding cobalamin-independent enzymes, such as the B12-independent methionine synthase MetE. Ineterestingly, many such microbes retain transporters for exogenous B12, produced by neighboring microbes. We hypothesise that selection for retention of B12 transport suggests preservation of unrevealed but critical roles for cobalamin in photoautotroph fitness. To identify the impacts of B12 on photoautorophic metabolism, we studied the physiological and transcriptional adaptation of Cyanobacterium stanieri HL-69 to varying irradiance and oxidative stress in the presence and absence of B12. The metabolic flexibility of C. stanieri, which possesses both MetH and MetE, alows comparative analysis of cobalamin impacts on its global metabolism. As anticipated, B12 availability governed transcription of cobalamin transporter btuB, metH and a number of genes involved in the methionine-folate cycle. Surprisingly, however, B12 impacted the cell integrity and growth rate of C. stanieri under conditions of likely oxidative stress due to biofilm growth or under high partial pressures of O2. Furthermore, C. stanieri response to B12 globally rewired cellular metabolic networks, including nitrogen metabolism, energy metabolism, and redox homeostasis and oxidative stress response. These findings demonstrate previously-unappreciated roles for B12 metabolism beyond methionine synthesis and reveal how interactions with cobalamin-producing heterotrophs may affect phytoplankton function and dynamics in natural microbial communities.
Importance
Cobalamin cross-feeding is recognised as a key factor promoting establishment of complex microbial systems. However, the lack of understanding regarding B12 impacts on photoautotroph metabolism hinders our ability to predict structure-function relationships in phytoplankton communities. Our data suggesting B12’s irrelevance to C. stanieri’s growth rate in the absence of oxygen stress may explain the loss of B12 synthesis genes from its genome. However, B12 impacts on fitness during periodic exposures to elevated pO2 in the diffusion-limited environment of a phototrophic microbial mat suggests a rationale for retention of B12-dependent processes and transport in C. stanieri. Furthermore, this study reveals that B12 availability exerts far-reaching impacts on C. stanieri metabolism, such as in redox homeostasis and oxidative stress response. Finally, understanding the mechanisms underlying the protective effect of cobalamin against oxidative stress may help explain the high robustness of phototrophic microbial communities and suggests strategies for engineering more efficient bioprocesses.

Citation: 
Bohutskyi P., R.S. McClure, E.A. Hill, W.C. Nelson, W.B. Chrisler, J. Nunez, and R.S. Renslow, et al. 2019. "Metabolic effects of vitamin B12 on physiology, stress resistance, growth rate and biomass productivity of Cyanobacterium stanieri planktonic and biofilm cultures." <i>Algal Research</i> 42. PNNL-SA-136164. doi:10.1016/j.algal.2019.101580
Authors: 
Bohutskyi
Pavlo;McClure
Ryan S;Hill
Eric A;Nelson
William C;Chrisler
William B;Nunez
Jamie;Renslow
Ryan S;Charania
M.;Lindemann
Steve;Beliaev
Alex S
Facility: 

A Phenotarget Approach for Identifying an Alkaloid Interacting with the Tuberculosis Protein Rv1466

Abstract: 

In recent years, there has been a revival of interest in phenotypic-based drug discovery (PDD) due to target-based drug discovery (TDD) falling below expectations. Both PDD and TDD have their unique advantages and should be used as complementary methods in drug discovery. The PhenoTarget approach combines the strengths of the PDD and TDD approaches. Phenotypic screening is conducted initially to detect cellular active components and the hits are then screened against a panel of putative targets. This PhenoTarget protocol can be equally applied to pure compound libraries as well as natural product fractions. Here we described the use of the PhenoTarget approach to identify an anti-tuberculosis lead compound. Fractions from Polycarpa aurata were identified with activity against Mycobacterium tuberculosis H37Rv. Native magnetic resonance mass spectrometry (MRMS) against a panel of 37 proteins from Mycobacterium proteomes showed that a fraction from a 95% ethanol re-extraction specifically formed a protein-ligand complex with Rv1466, a putative uncharacterized Mycobacterium tuberculosis protein. The natural product responsible was isolated and characterized to be polycarpine. The molecular weight of the ligand bound to Rv1466, 233 Da, was half the molecular weight of polycarpine less one proton, indicating that polycarpine formed a covalent bond with Rv1466.

Citation: 
Xie Y., Y. Feng, A. Di Capua, T. Mak, G.W. Buchko, P.J. Myler, and M. Lui, et al. 2020. "A Phenotarget Approach for Identifying an Alkaloid Interacting with the Tuberculosis Protein Rv1466." <i>Marine Drugs</i> 18, no. 3:149. PNNL-SA-150251. doi:10.3390/md18030149
Authors: 
Buchko
Garry W;Myler
Peter J;Quinn
Ronald J;Lui
Miaomiao;Mak
Tin;Feng
Yunjiang;Xie
Yan;Di Capua
Angela
Capabilities: 
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Crystal structure of a hemerythrin-like protein from Mycobacterium kansasii and homology model of the orthologous Rv2633c

Abstract: 

Pathogenic and opportunistic mycobacteria have a distinct class of non-heme di-iron hemerythrin-like proteins (HLPs). The first to be isolated was the Rv2633c protein, which plays a role in infection by Mycobacterium tuberculosis (Mtb), but could not be crystallized. This work presents the first crystal structure of an ortholog of Rv2633c, the mycobacterial HLP from Mycobacterium kansasii (Mka). This structure differs from those of hemerythrins and other known HLPs. It is comprised of five ??-helices, whereas all other HLP domains have four. In contrast to other HLPs, the HLP domain is not fused to an additional protein domain. The residues ligating and surrounding the di-iron site are also unique among HLPs. Notably; a tyrosine occupies the position normally held by one of the histidine ligands in hemerythrin. This structure was used to construct a homology model of Rv2633c. The structure of five ??-helices is conserved and the di-iron site ligands are identical in Rv2633c. Two residues near the ends of helices in the Mka HLP structure are replaced with prolines in Rv2633c model. This may account for structural perturbations that decrease the solubility of Rv2633c relative to Mka HLP. Clusters of residues that differ in charge or polarity between Rv2633c and Mka HLP that point outward from the helical core could reflect a specificity for potential differential interactions with other protein partners in vivo, which are related to function. The Mka HLP exhibited weaker catalase activity than Rv2633c. Evidence was obtained for interaction of Mka HLP irons with nitric oxide.

Citation: 
Ma Z., J. Abendroth, G.W. Buchko, K.H. Rohde, and V.L. Davidson. 2020. "Crystal structure of a hemerythrin-like protein from Mycobacterium kansasii and homology model of the orthologous Rv2633c protein of M. tuberculosis." <i>Biochemical Journal</i> 477, no. 2:567-581. PNNL-SA-147766. doi:10.1042/BCJ20190827
Authors: 
Ma
Zhongxin;Abendroth
Jan;Buchko
Garry W;Rohde
Kyle H;Davidson
Victor L
Capabilities: 
Facility: 

Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery

Abstract: 

Although the etiology of obesity is not well-understood, genetic, environmental, and microbiome elements are recognized as contributors to this rising pandemic. For morbid obesity, Roux-en-Y gastric bypass (RYGB) surgery alters the fecal microbiome, but data are sparse on temporal and spatial changes in the microbiome and metabolome. We characterized the structure and metabolism of the microbial communities in the gut lumen and on mucosal surfaces in morbidly obese individuals before and after RYGB surgery, and we compared our longitudinal cohort to a previously studied cross-sectional one. RYGB concurrently changed the gut microbiome and led to improvements of obesity comorbidities. Changes in the gut microbiome were reflected in the metabolome, including fermentation products and bile acids. The effects persisted 12 months post-surgery, and the microbiomes and metabolomes were similar to those found for the cross-sectional RYGB cohort. Thus, RYGB surgery had profound and persistent impacts on the intestinal microbiome and metabolome.

Citation: 
Ilhan Z.E., J.K. DiBaise, S.E. Dautel, N.G. Isern, Y. Kim, D.W. Hoyt, and A.A. Schepmoes, et al. 2020. "Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery." <i>NPJ Biofilms and Microbiomes</i> 6, no. 1:Article No. 12. PNNL-SA-133750. doi:10.1038/s41522-020-0122-5
Authors: 
Heather Brewer,
Hoyt, David W
Ilhan
Zehra E;Dautel
Sydney E;Kim
Young-Mo;DiBaise
John K;Brewer
Heather M;Weitz
Karl K;Kang
Dae Wook;Isern
Nancy G;Hoyt
David W;Metz
Thomas O;Crowell
Michael;Schepmoes
Athena A;Rittmann
Bruce E;Krajmalnik-Brown
Rosa
Capabilities: 
Facility: 

Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp.

Abstract: 

Bacterial Halanaerobium strains become the dominant persisting microbial
community member in produced fluids across geographically distinct hydraulically
fractured shales. Halanaerobium is believed to be inadvertently introduced into
this environment during the drilling and fracturing process and must therefore tolerate
large changes in pressure, temperature, and salinity. Here, we used a Halanaerobium
strain isolated from a natural gas well in the Utica Point Pleasant formation to
investigate metabolic and physiological responses to growth under high-pressure
subsurface conditions. Laboratory incubations confirmed the ability of Halanaerobium
congolense strain WG8 to grow under pressures representative of deep shale
formations (21 to 48 MPa). Under these conditions, broad metabolic and physiological
shifts were identified, including higher abundances of proteins associated with
the production of extracellular polymeric substances. Confocal laser scanning microscopy
indicated that extracellular polymeric substance (EPS) production was associated
with greater cell aggregation when biomass was cultured at high pressure.
Changes in Halanaerobium central carbon metabolism under the same conditions
were inferred from nuclear magnetic resonance (NMR) and gas chromatography
measurements, revealing large per-cell increases in production of ethanol, acetate,
and propanol and cessation of hydrogen production. These metabolic shifts were associated
with carbon flux through 1,2-propanediol in response to slower fluxes of
carbon through stage 3 of glycolysis. Together, these results reveal the potential for
bioclogging and corrosion (via organic acid fermentation products) associated with
persistent Halanaerobium growth in deep, hydraulically fractured shale ecosystems,
and offer new insights into cellular mechanisms that enable these strains to dominate
deep-shale microbiomes.
IMPORTANCE The hydraulic fracturing of deep-shale formations for hydrocarbon recovery
accounts for approximately 60% of U.S. natural gas production. Microbial activity
associated with this process is generally considered deleterious due to issues
associated with sulfide production, microbially induced corrosion, and bioclogging in
the subsurface. Here we demonstrate that a representative Halanaerobium species,
frequently the dominant microbial taxon in hydraulically fractured shales, responds
to pressures characteristic of the deep subsurface by shifting its metabolism to generate
more corrosive organic acids and produce more polymeric substances that
cause “clumping” of biomass. While the potential for increased corrosion of steel infrastructure and clogging of pores and fractures in the subsurface may significantly
impact hydrocarbon recovery, these data also offer new insights for microbial control
in these ecosystems.

Citation: 
Booker A.E., D.W. Hoyt, T. Meulia, E.K. Eder, C.D. Nicora, S.O. Purvine, and R. Daly, et al. 2019. "Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp." <i>Applied and Environmental Microbiology</i> 85, no. 12:e00018-19. PNNL-SA-144542. doi:10.1128/AEM.00018-19
Authors: 
Booker
Anne Elizabeth;Hoyt
David W;Meulia
Tea;Eder
Elizabeth K;Nicora
Carrie D;Purvine
Samuel O;Daly
Rebecca;Moore
Joseph D;Wunch
Kenneth;Pfiffner
Susan M;Lipton
Mary S;Mouser
Paula J;Wrighton
Kelly C;Wilkins
Michael James
Capabilities: 
Facility: 

Spatiotemporal Transformation in the Alkaloid Profile of Pinus Roots in Response to Mycorrhization

Abstract: 

The development of ectomycorrhizae (EM), a symbiotic association between roots of woody gymnosperms (e.g., Pinaceae) and ectomycorrhizal fungi (EMF), involves dramatic changes in root and hyphal morphology and biochemistry which are tightly regulated in response to molecular signals (Martin & Hilbert, 1991; Isidorov et al., 2008; Liao et al., 2016). There is emerging evidence that secondary metabolites (SM), in particular flavonoids, terpenes, phytohormones, and sterols can affect EM colonization (Hanna & Patrycja, 2011).

Citation: 
Velickovic D., H. Liao, R. Vilgalys, R.K. Chu, and C.R. Anderton. 2019. "Spatiotemporal Transformation in the Alkaloid Profile of Pinus Roots in Response to Mycorrhization." <i>Journal of Natural Products</i> 82, no. 5:1382-1386. PNNL-SA-140336. doi:10.1021/acs.jnatprod.8b01050
Authors: 
Velickovic
Dusan;Liao
Hui-Ling;Vilgalys
Rytas;Chu
Rosalie K;Anderton
Christopher R
Capabilities: 
Facility: 

In Situ and Ex Situ NMR for Battery Research

Abstract: 

A rechargeable battery stores readily convertible chemical energy to operate a variety of devices such as mobile phones, laptop computers, and electric automobiles, etc. A battery generally consists of four components, i.e., a cathode, an anode, a separator and electrolytes. The properties of these components jointly determine the safety, the lifetime, and the electrochemical performance, include but not limited to the power density and the charge, recharge time/rate associated with a battery system. Extensive amount of research is thus dedicated to understand the physical and chemical properties associated with each of the four components aimed at developing new generations of battery systems with greatly enhanced safety and electrochemical performance while at significantly reduced cost for large scale applications. Advanced characterization tools are prerequisite to fundamentally understand battery materials. Considering that some of the key electrochemical processes can only exist under in situ conditions, thus, can only be captured under a working battery conditions when electric wires are attached and current and voltage applied, in situ detection is critical. NMR, a non-invasive and atomic specific tool, is capable of detecting all phases, including crystalline, amorphous, liquid and gaseous phases simultaneously and is ideal for in situ detection on a working battery system. Ex situ NMR on the other hand can provide more detailed molecular or structural information on stable species with better spectral resolution and sensitivity. The combination of in situ and ex situ NMR, thus, offers a powerful tool for investigating the detailed electrochemistry in batteries.

Citation: 
Hu J.Z., N.R. Jaegers, M.Y. Hu, and K.T. Mueller. 2018. "In Situ and Ex Situ NMR for Battery Research." <i>Journal of Physics: Condensed Matter</i> 30, no. 46:Article No. 463001. PNNL-SA-134425. doi:10.1088/1361-648X/aae5b8
Authors: 
Hu
Jian Z;Jaegers
Nicholas R;Hu
Mary Y;Mueller
Karl T
Facility: 

Studying Salmonellae and Yersiniae Host–Pathogen Interactions Using Integrated ‘Omics and Modeling

Abstract: 

Salmonella and Yersinia are two distantly related genera containing species with wide host-range specificity and pathogenic capacity. The metabolic complexity of these organisms facilitates robust lifestyles both outside of and within animal hosts. Using a pathogen-centric systems biology approach, we are combining a multi-omics (transcriptomics, proteomics, metabolomics) strategy to define properties of these pathogens under a variety of conditions including those that mimic the environments encountered during pathogenesis. These high-dimensional omics datasets are being integrated in selected ways to improve genome annotations, discover novel virulence-related factors, and model growth under infectious states. We will review the evolving technological approaches toward understanding complex microbial life through multi-omic measurements and integration, while highlighting some of our most recent successes in this area.

Citation: 
Ansong C.K., C.K. Ansong, B.L. Deatherage, D.R. Hyduke, B. Schmidt, J.E. McDermott, and M.B. Jones, et al. 2012. "Studying Salmonellae and Yersiniae Host–Pathogen Interactions Using Integrated ‘Omics and Modeling." <i>Current Topics in Microbiology and Immunology</i> 363. PNNL-SA-135981. doi:10.1007/82_2012_247
Authors: 
Li
Jie;Niemann
George;Deatherage
Barbara Louise;Kim
Young-Mo;Ansong
Charles K;Brown
Roslyn N;Charusanti
Pep;Nakayasu
Ernesto S;Ansong
Charles K;Peterson
Scott;Jones
Marcus B;McDermott
Jason E;Mcateer
Kathleen;Metz
Thomas O;Kidwai
Afshan S;Adkins
Joshua N;Schmidt
Brian;Palsson
Bernhard Orn;Heffron
Fred;Chauhan
Sadhana;Smith
Richard D;Hyduke
Daniel R;Motin
Vladimir L
Capabilities: 
Facility: 

Genome-centric View of Carbon Processing in Thawing Permafrost

Abstract: 

As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. However, accurate prediction of carbon gas emissions produced from thawing permafrost is limited by our understanding of the resident microbial communities and their associated carbon metabolism. Here, metagenomic sequencing of 214 samples from intact, thawing and thawed sites collected over three years enabled the recovery of 1,529 metagenome-assembled genomes (MAGs), including many from phyla with poor genomic representation. These genomes were shown to broadly reflect the diversity of this complex ecosystem with genus-level representatives recovered for >60% of the community, constituting a two orders of magnitude increase in the number of genomes available for understanding carbon processing in this environment. Metabolic reconstruction, supported by metatranscriptomic and metaproteomic data, revealed key populations involved in organic matter degradation, including bacteria encoding a pathway for xylose degradation only previously identified in fungi. Combined analysis of the microbial communities and geochemical data highlighted lineages correlated with the production of greenhouse gases and suggest novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in each stage of carbon processing, providing key information for predicting the impact of climate change on these systems.

Citation: 
Woodcroft B.J., C.M. Singleton, J. Boyd, P.N. Evans, J.B. Emerson, A.A. Zayed, and R.D. Hoelzle, et al. 2018. "Genome-centric View of Carbon Processing in Thawing Permafrost." <i>Nature</i> 560, no. 7716:49-54. PNNL-SA-134955. doi:10.1038/s41586-018-0338-1
Authors: 
Mccalley
Carmody K;Saleska
Scott;Hoelzle
Robert D;Evans
Paul N;Rich
Virginia;Zayed
Ahmed A;Lamberton
Timothy O;Woodcroft
Benjamin J;Emerson
Joanne B;Wilson
Rachel M;Chanton
Jeffrey;Frolking
Steve;Tyson
Gene W;Nicora
Carrie D;Singleton
Caitlin M;Boyd
Joel;Purvine
Samuel O;Li
Changsheng;Hodgkins
Suzanne;Crill
Patrick M
Facility: 

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured

Abstract: 

Hydraulic fracturing is one of the industrial processes behind the surging natural gas output in the United States. This technology inadvertently creates an engineered microbial ecosystem thousands of meters below Earth’s surface. Here, we used laboratory reactors to perform manipulations of persisting shale microbial communities that are currently not feasible in field scenarios. Metaproteomic and metabolite findings from the laboratory were then corroborated using regression based modeling performed on metagenomic and metabolite data from more than 40 produced fluids from five hydraulically fractured shale wells. Collectively, our findings show that Halanaerobium, Geotoga, and Methanohalophilius strain abundances predict a significant fraction of nitrogen and carbon metabolites in the field. Our laboratory findings also exposed cryptic predatory, cooperative, and competitive interactions that impact microorganisms across fractured shales. Scaling these results from the laboratory to the field identified mechanisms underpinning biogeochemical reactions, yielding knowledge that can be harnessed to potentially increase energy yields and inform management practices in hydraulically fractured shales.

Citation: 
Borton M., D.W. Hoyt, S. Roux, R. Daly, S. Welch, C.D. Nicora, and S.O. Purvine, et al. 2018. "Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales." <i>Proceedings of the National Academy of Sciences of the United States of America</i> 115, no. 28:E6585-E6594. PNNL-SA-134972. doi:10.1073/pnas.1800155115
Authors: 
Wolfe
Richard;Sharma
Shikha;Hanson
Andrea J;Lipton
Mary S;Borton
Mikalya;Carr
Timothy R;Daly
Rebecca;Purvine
Samuel O;Eder
Elizabeth K;Sheets
Julia;Roux
Simon;Hoyt
David W;Cole
David R;Welch
Susan;Morgan
David M;Wrighton
Kelly Catherine;Mouser
Paula J;Wilkins
Michael J;Nicora
Carrie D
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