Faculty & Staff

  • Image of Erica L-W Majumder

    Erica L-W Majumder

    Assistant Professor of Bacteriology

    5550 Microbial Sciences Building
    Office: (608) 262-8106
    Lab: (608) 265-2024

Start and Promotion Dates

  • Assistant Professor: 2021


B.A. with Honors, Chemistry (ACS approved), Drury University 2010
Ph.D. Chemistry, Bioinorganic, Washington University in St. Louis 2015
Postdoctoral Research: University of Missouri-Columbia and The Scripps Research Institute

Areas of Study

Anaerobic metabolism, electron transfer, microbe-metal interactions, waste stream bioconversion to inorganic or polymer products, microbe-plastic interactions, contaminant biodegradation, metabolomics, activity of microbial chemistries

Research Overview

The Majumder Lab employs ‘omics-guided biochemistry to study the mechanisms and consequences of microbial inorganic metabolisms on environmental and human health.  We achieve this by investigating 1) Organismal response to perturbations in its environment, 2) Gene and metabolite function in situ, 3) Environmental applications of novel microbial chemistries.

Theme 1: Plastics
We recognize that one of the primary limitations of the big data era to understand complex biological systems is the reliance on incomplete genome annotations. Current genome annotations do not account for the multiplicity of functions one gene may perform nor do they include atypical metabolic pathways. We use genomics, enzymology and metabolomics-based technologies to determine the roles for specific genes, enzymes and metabolites in different conditions such as (1) bioplastic-precursor synthesis from waste carbon sources, (2) degradation of recalcitrant plastics in the environment, and (3) the ecology of the interactions between microplastics and Harmful Algal Blooms. 

Theme 2: Metals
As more and more organisms are sequenced and cultured, we are learning about an increasing range of microbial metabolisms and chemistries, especially from anaerobic bacteria. After determining these novel chemical capabilities, we can apply this knowledge and these microbes for greener solutions. Initial efforts in this theme are focused on the electron transfer and bioinorganic synthetic capabilities of anaerobes towards (1) enhanced wastewater treatment and (2) electricity production in photobioelectrochemical calls. 

Theme 3: Non-metal (Sulfur, Nitrogen, Phosphorus) Metabolites
One of the primary lessons the scientific community learned from the human genome and earth microbiome projects is that genome information alone cannot sufficiently explain observed phenotypes and that environmental factors are a significant, if not the main driving factor affecting phenotype presentation. Using a systems-level combination of genomics, metabolomics and biochemistry, we aim to elucidate the mechanisms of how environmental factors cause changes to an organism’s metabolism and result in the observed phenotype. Potential projects focused on this theme are (1) investigating the contributions of metabolism to prognosis in tick-borne diseases like Lyme’s, and (2) the effect of metal contamination on sulfur metabolism of the gut microbiome.

Connections across themes:
We anticipate cross-talk between the themes as genetic tools, mass spectrometry methods, and data analysis pipelines developed in one theme will be applicable in others.

Lab Personnel

Picture of Chatman
Chamia Chatman
Grad Student
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Liyuan (Joanna) Hou
Picture of Mejia
Robbie Mejia
Grad Student
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Hans Nielsen-Fox
Research Tech
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Grad Student
Picture of Shatara
Fuad Shatara
Grad Student

Research Papers

  • Thorgersen MP, Xue J, Majumder ELW, Trotter VV, Ge X, Poole FL, Owens TK, Lui LM, Nielsen TN, Arkin AP, Deutschbauer AM, Siuzdak G, Adams MWW (2021) Deciphering Microbial Metal Toxicity Responses via Random Bar Code Transposon Site Sequencing and Activity-Based Metabolomics. Applied and environmental microbiology 87((21)):e0103721 PMC8516053 · Pubmed · DOI

    No abstract available.

  • Lui LM, Majumder EL, Smith HJ, Carlson HK, von Netzer F, Fields MW, Stahl DA, Zhou J, Hazen TC, Baliga NS, Adams PD, Arkin AP (2021) Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. Frontiers in microbiology 12:642422 PMC8024649 · Pubmed · DOI

    No abstract available.

  • Otwell AE, Carr AV, Majumder ELW, Ruiz MK, Wilpiszeski RL, Hoang LT, Webb B, Turkarslan S, Gibbons SM, Elias DA, Stahl DA, Siuzdak G, Baliga NS (2021) Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification. mSystems 6((1)): PMC7883540 · Pubmed · DOI

    No abstract available.

  • Hou L, Majumder EL (2021) Potential for and Distribution of Enzymatic Biodegradation of Polystyrene by Environmental Microorganisms. Materials (Basel, Switzerland) 14((3)): PMC7864516 · Pubmed · DOI

    No abstract available.

  • Majumder EL, Billings EM, Benton HP, Martin RL, Palermo A, Guijas C, Rinschen MM, Domingo-Almenara X, Montenegro-Burke JR, Tagtow BA, Plumb RS, Siuzdak G (2021) Cognitive analysis of metabolomics data for systems biology. Nature protocols 16((3)):1376-1418 · Pubmed · DOI

    No abstract available.

  • Guijas C, Montenegro-Burke JR, Cintron-Colon R, Domingo-Almenara X, Sanchez-Alavez M, Aguirre CA, Shankar K, Majumder EL, Billings E, Conti B, Siuzdak G (2020) Metabolic adaptation to calorie restriction. Science signaling 13((648)): PMC7580877 · Pubmed · DOI

    No abstract available.

  • Moon JW, Paradis CJ, Joyner DC, von Netzer F, Majumder EL, Dixon ER, Podar M, Ge X, Walian PJ, Smith HJ, Wu X, Zane GM, Walker KF, Thorgersen MP, Poole Ii FL, Lui LM, Adams BG, De León KB, Brewer SS, Williams DE, Lowe KA, Rodriguez M, Mehlhorn TL, Pfiffner SM, Chakraborty R, Arkin AP, Wall JD, Fields MW, Adams MWW, Stahl DA, Elias DA, Hazen TC (2020) Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer. Chemosphere 255:126951 · Pubmed · DOI

    No abstract available.

  • Krantz GP, Lucas K, Wunderlich EL, Hoang LT, Avci R, Siuzdak G, Fields MW (2019) Bulk phase resource ratio alters carbon steel corrosion rates and endogenously produced extracellular electron transfer mediators in a sulfate-reducing biofilm. Biofouling 35((6)):669-683 · Pubmed · DOI

    G20 biofilms were cultivated on 316 steel, 1018 steel, or borosilicate glass under steady-state conditions in electron-acceptor limiting (EAL) and electron-donor limiting (EDL) conditions with lactate and sulfate in a defined medium. Increased corrosion was observed on 1018 steel under EDL conditions compared to 316 steel, and biofilms on 1018 carbon steel under the EDL condition had at least twofold higher corrosion rates compared to the EAL condition. Protecting the 1018 metal coupon from biofilm colonization significantly reduced corrosion, suggesting that the corrosion mechanism was enhanced through attachment between the material and the biofilm. Metabolomic mass spectrometry analyses demonstrated an increase in a flavin-like molecule under the 1018 EDL condition and sulfonates under the 1018 EAL condition. These data indicate the importance of S-cycling under the EAL condition, and that the EDL is associated with increased biocorrosion indirect extracellular electron transfer mediated by endogenously produced flavin-like molecules.

  • Domingo-Almenara X, Montenegro-Burke JR, Guijas C, Majumder EL, Benton HP, Siuzdak G (2019) Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics. Analytical chemistry 91((5)):3246-3253 PMC6637741 · Pubmed · DOI

    No abstract available.

  • Ge X, Vaccaro BJ, Thorgersen MP, Poole FL, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, Hazen TC, Adams MWW (2018) Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle. Environmental microbiology 21((1)):152-163 · Pubmed · DOI

    No abstract available.

  • Majumder EL, Wolf BM, Liu H, Berg RH, Timlin JA, Chen M, Blankenship RE (2017) Subcellular pigment distribution is altered under far-red light acclimation in cyanobacteria that contain chlorophyll f. Photosynthesis research 134((2)):183-192 · Pubmed · DOI

    No abstract available.

  • Huan T, Forsberg EM, Rinehart D, Johnson CH, Ivanisevic J, Benton HP, Fang M, Aisporna A, Hilmers B, Poole FL, Thorgersen MP, Adams MWW, Krantz G, Fields MW, Robbins PD, Niedernhofer LJ, Ideker T, Majumder EL, Wall JD, Rattray NJW, Goodacre R, Lairson LL, Siuzdak G (2017) Systems biology guided by XCMS Online metabolomics. Nature methods 14((5)):461-462 PMC5933448 · Pubmed · DOI

    No abstract available.

  • Majumder EL, Wall JD (2017) Bio-transformations of Uranium: Chemical or Biological Processes? Open journal of inorganic chemistry 7((2)): · DOI

    No abstract available.

  • Majumder EL, Olsen JD, Qian P, Collins AM, Hunter CN, Blankenship RE (2015) Supramolecular organization of photosynthetic complexes in membranes of Roseiflexus castenholzii. Photosynthesis research 127((1)):117-30 · Pubmed · DOI

    The photosynthetic membranes of the filamentous anoxygenic phototroph Roseiflexus castenholzii have been studied with electron microscopy, atomic force microscopy, and biochemistry. Electron microscopy of the light-harvesting reaction center complex produced a 3D model that aligns with the solved crystal structure of the RC-LH1 from Thermochromatium tepidum with the H subunit removed. Atomic force microscopy of the whole membranes yielded a picture of the supramolecular organization of the major proteins in the photosynthetic electron transport chain. The results point to a loosely packed membrane without accessory antenna proteins or higher order structure.

  • Zhang Y, Majumder EL, Yue H, Blankenship RE, Gross ML (2014) Structural analysis of diheme cytochrome c by hydrogen-deuterium exchange mass spectrometry and homology modeling. Biochemistry 53((35)):5619-30 PMC4159202 · Pubmed · DOI

    A lack of X-ray or nuclear magnetic resonance structures of proteins inhibits their further study and characterization, motivating the development of new ways of analyzing structural information without crystal structures. The combination of hydrogen-deuterium exchange mass spectrometry (HDX-MS) data in conjunction with homology modeling can provide improved structure and mechanistic predictions. Here a unique diheme cytochrome c (DHCC) protein from Heliobacterium modesticaldum is studied with both HDX and homology modeling to bring some definition of the structure of the protein and its role. Specifically, HDX data were used to guide the homology modeling to yield a more functionally relevant structural model of DHCC.

  • Gao X, Majumder EW, Kang Y, Yue H, Blankenship RE (2013) Functional analysis and expression of the mono-heme containing cytochrome c subunit of Alternative Complex III in Chloroflexus aurantiacus. Archives of biochemistry and biophysics 535((2)):197-204 · Pubmed · DOI

    The filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus possesses an unusual electron transfer complex called Alternative Complex III instead of the cytochrome bc or bf type complex found in nearly all other known groups of phototrophs. Earlier work has confirmed that Alternative Complex III behaves as a menaquinol:auracyanin oxidoreductase in the photosynthetic electron transfer chain. In this work, we focus on elucidating the contribution of individual subunits to the overall function of Alternative Complex III. The monoheme subunit ActE has been expressed and characterized in Escherichia coli. A partially dissociated Alternative Complex III missing subunit ActE and subunit ActG was obtained by treatment with the chaotropic agent KSCN, and was then reconstituted with the expressed ActE. Enzymatic activity of the partially dissociated Alternative Complex III was greatly reduced and was largely restored in the reconstituted complex. The redox potential of the heme in the recombinant ActE was +385mV vs. NHE, similar to the highest potential heme in the intact complex. The results strongly suggest that the monoheme subunit, ActE, is the terminal electron carrier for Alternative Complex III.

  • Majumder EL, King JD, Blankenship RE (2013) Alternative Complex III from phototrophic bacteria and its electron acceptor auracyanin. Biochimica et biophysica acta 1827((11-12)):1383-91 · Pubmed · DOI

    Alternative Complex III (ACIII) is a multisubunit integral membrane protein electron transfer complex that is proposed to be an energy-conserving functional replacement for the bacterial cytochrome bc1 or b6f complexes. Clues to the structure and function of this novel complex come from its relation to other bacterial enzyme families. The ACIII complex has menaquinone: electron acceptor oxidoreductase activity and contains protein subunits with multiple Fe-S centers and c-type hemes. ACIII is found in a diverse group of bacteria, including both phototrophic and nonphototrophic taxa. In the phototrophic filamentous anoxygenic phototrophs, the electron acceptor is the small blue copper protein auracyanin instead of a soluble cytochrome. Recent work on ACIII and the copper protein auracyanin is reviewed with focus on the photosynthetic systems and potential electron transfer pathways and mechanisms. Taken together, the ACIII complexes constitute a unique system for photosynthetic electron transfer and energy conservation. This article is part of a Special Issue entitled: Respiratory Complex III and related bc complexes.

  • Badhwar J, Karri S, Cass CK, Wunderlich EL, Znosko BM (2007) Thermodynamic characterization of RNA duplexes containing naturally occurring 1 x 2 nucleotide internal loops. Biochemistry 46((50)):14715-24 · Pubmed · DOI

    Thermodynamic data for RNA 1 x 2 nucleotide internal loops are lacking. Thermodynamic data that are available for 1 x 2 loops, however, are for loops that rarely occur in nature. In order to identify the most frequently occurring 1 x 2 nucleotide internal loops, a database of 955 RNA secondary structures was compiled and searched. Twenty-four RNA duplexes containing the most common 1 x 2 nucleotide loops were optically melted, and the thermodynamic parameters DeltaH degrees , DeltaS degrees , DeltaG degrees 37, and TM for each duplex were determined. This data set more than doubles the number of 1 x 2 nucleotide loops previously studied. A table of experimental free energy contributions for frequently occurring 1 x 2 nucleotide loops (as opposed to a predictive model) is likely to result in better prediction of RNA secondary structure from sequence. In order to improve free energy calculations for duplexes containing 1 x 2 nucleotide loops that do not have experimental free energy contributions, the data collected here were combined with data from 21 previously studied 1 x 2 loops. Using linear regression, the entire dataset was used to derive nearest neighbor parameters that can be used to predict the thermodynamics of previously unmeasured 1 x 2 nucleotide loops. The DeltaG degrees 37,loop and DeltaH degrees loop nearest neighbor parameters derived here were compared to values that were published previously for 1 x 2 nucleotide loops but were derived from either a significantly smaller dataset of 1 x 2 nucleotide loops or from internal loops of various sizes [Lu, Z. J., Turner, D. H., and Mathews, D. H. (2006) Nucleic Acids Res. 34, 4912-4924]. Most of these values were found to be within experimental error, suggesting that previous approximations and assumptions associated with the derivation of those nearest neighbor parameters were valid. DeltaS degrees loop nearest neighbor parameters are also reported for 1 x 2 nucleotide loops. Both the experimental thermodynamics and the nearest neighbor parameters reported here can be used to improve secondary structure prediction from sequence.