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Select publications

  1. Ontiveros-Valencia A, Penton CR, Krajmalnik-Brown R, Rittmann BE. Hydrogen-fed biofilm reactors reducing selenate and sulfate: Community structure and capture of elemental selenium within the biofilm.
    Biotechnol Bioeng. 2016 Jan 25. doi: 10.1002/bit.25945. [Epub ahead of print]

  2. Miceli JF III, Garcia-Peña I, Parameswaran P, Torres CI, Krajmalnik-Brown R. 2014. Combining microbial cultures for the efficient production of electricity from butyrate in a microbial electrochemical cell.  Bioresource Technology 169:169-174.

  3. Delgado AG, Kang D-W, Nelson KG, Fajardo-Williams D, Miceli JF III, Done HY, Popat SC, Krajmalnik-Brown R. 2014. Selective enrichment yields robust ethene-producing dechlorinating cultures from microcosms stalled at cis-dichloroethene. PLoS ONE 9(6): e100654. doi:10.1371/journal.pone.0100654.

  4. Ontiveros-Valencia A,Tang Y, Zhao, H-P,Friese D, Overstreet R, Smith J, Evans P, Rittmann BE, Krajmalnik-Brown R. in press. Pyrosequencing analysis yields comprehensive assessment of microbial communities in pilot-scale two-stage membrane biofilm reactors. Environmental Science & TechnologyDOI: 10.1021/es5012466.

  5. Ruiz V, Ilhan ZE, Kang D-W, Krajmalnik-Brown R, Buitrón G. 2014The source of inoculum plays a defining role in the development of MEC microbial consortia fed with acetic and propionic acid mixtures. Journal of Biotechnology 182-183:11-18.

  6. Ontiveros-Valencia A, Tang Y, Krajmalnik-Brown R, Rittmann BE. in press. Managing the interactions between sulfate- and perchlorate-reducing bacteria when using hydrogen-fed biofilms to treat a groundwater with a high perchlorate concentration. Water Research.

  7. Ekre, R., P.C. Johnson, B.E. Rittmann, and R. Krajmalnik-Brown. 2014. Method for Assessing Source Zone Natural Attenuation at Chlorinated Aliphatic Spill Sites. Groundwater Monitoring & Remediation 34(2):60-70.

  8. Zhao H-P, Ontiveros-Valencia A, Tang Y, Kim B-O, VanGinkel S, Friese D, Overstreet R, Smith J, Evans PJ, Krajmalnik-Brown R, Rittmann BE. 2014. Removal of multiple electron acceptors by pilot-scale, two-stage membrane biofilm reactors. Water Research 54:115-122.

  9. Delgado AG, Fajardo-Williams D, Popat SC, Torres CI, Krajmalnik-Brown R. 2014. Successful operation of continuous reactors at short retention times results in fast-rate, high-density Dehalococcoides dechlorinating cultures. Applied Microbiology and Biotechnology 98(6):2729-2737. pdf

  10. Badalamenti JP, Torres CI and Krajmalnik-Brown R. 2014. Coupling dark metabolism to electricity generation using photosynthetic cocultures. Biotechnology and Bioengineering 111(2):223-231.

  11. Ziv-El M, Kalinowski T,  Krajmalnik-Brown R, Halden RU. 2014. Simultaneous determination of chlorinated ethenes and ethene in groundwater using automated headspace solid phase microextraction. Journal of Chromatographic Science 52(2):137-142.


  1. Gilbert JA, Krajmalnik-Brown R,  Porazinska DL, Weiss SJ, Knight R. 2013. Toward effective probiotics for autism and other neurodevelopmental disorders. Cell 155(7):1446-1448.

  2. Ontiveros-Valencia A, Tang Y, Krajmalnik-Brown R, Rittmann BE, 2013. Perchlorate reduction from a highly contaminated groundwater in the presence of sulfate-reducing bacteria in a hydrogen-fed biofilm. Biotechnology and Bioengineering 110(12):3139-3147.

  3. Zhao H-P, Ontiveros-Valencia A, Tang Y, Kim B-O, Ilhan ZE, Krajmalnik-Brown R, Rittrnann BE. 2013. Using a two-stage hydrogen-based membrane biofilm reactor (MBfR) to achieve complete perchlorate reduction in the presence of nitrate and sulfate. Environmental Science & Technology 47(3):1565-1572.

  4. Zhao H-P, Ilhan ZE, Ontiveros-Valencia A, Tang Y, Rittmann BE, Krajmalnik-Brown R. 2013. Effects of multiple electron acceptors on microbial interactions in a hydrogen-based biofilm. Environmental Science & Technology 47(13):7396-7403.

  5. Badalamenti JP, Krajmalnik-Brown R, Torres CI. 2013. Generation of high current densities by pure cultures of anode-respiring Geoalkalibacter spp. under alkaline and saline conditions in microbial electrochemical cells. Mbio 4(3).

  6. Badalamenti JP, Torres CI, Krajmalnik-Brown R. 2013. Light-responsive current generation by phototrophically enriched anode biofilms dominated by green sulfur bacteria. Biotechnology and Bioengineering 110(4):1020-1027.

  7. Kang D-W, Park JG, Ilhan ZE, Wallstrom G, LaBaer J, Adams JB, Krajmalnik-Brown R. 2013. Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children. PLoS ONE 8(7).

  8. Tang Y, Krajmalnik-Brown R, Rittmann BE. 2013. Modeling trichloroethene reduction in a hydrogen-based biofilm. Water Science and Technology 68(5):1158-1163.

  9. Tang Y, Ontiveros-Valencia A, Feng L, Zhou C, Krajmalnik-Brown R, Rittmann BE. 2013. A biofilm model to understand the onset of sulfate reduction in denitrifying membrane biofilm reactors. Biotechnology and Bioengineering 110(3):763-772.

  10. Ontiveros-Valencia A, Ilhan ZE, Kang D-W, Rittmann B, Krajmalnik-Brown R. 2013. Phylogenetic analysis of nitrate- and sulfate-reducing bacteria in a hydrogen-fed biofilm. FEMS Microbiology Ecology 85(1):158-167.

  11. Young MN, Krajmalnik-Brown R, Liu W, Doyle ML, Rittmann BE. 2013. The role of anaerobic sludge recycle in improving anaerobic digester performance. Bioresource Technology 128:731-737.


  1. Ziv-El M, Delgado AG, Yao Y, Kang DW, Nelson KG, Halden RU, Krajmalnik-Brown R. 2012. Erratum to: Development and characterization of DehaloR^2, a novel anaerobic microbial consortium performing rapid dechlorination of TCE to ethene (vol 92, pg 1063, 2011). Applied Microbiology and Biotechnology 95(1):273-274.

  2. Ziv-El M, Popat SC, Cai K, Halden RU, Krajmalnik-Brown R, Rittmann BE. 2012. Managing methanogens and homoacetogens to promote reductive dechlorination of trichloroethene with direct delivery of H2 in a membrane biofilm reactor. Biotechnology and Bioengineering 109(9):2200-2210.

  3. Ziv-El M, Popat SC, Parameswaran P, Kang DW, Polasko A, Halden RU, Rittmann BE, Krajmalnik-Brown R. 2012. Using electron balances and molecular techniques to assess trichoroethene-induced shifts to a dechlorinating microbial community. Biotechnology and Bioengineering 109(9):2230-2239.

  4. Hartmann EM, Badalamenti JP, Krajmalnik-Brown R, Halden RU. 2012. Quantitative PCR for tracking the megaplasmid-borne biodegradation potential of a model sphingomonad. Applied and Environmental Microbiology 78(12):4493-4496.

  5. Ontiveros-Valencia A, Ziv-El M, Zhao H-P, Feng L, Rittmann BE, Krajmalnik-Brown R. 2012. Interactions between nitrate-reducing and sulfate-reducing bacteria coexisting in a hydrogen-fed biofilm. Environmental Science & Technology 46(20):11289-11298.

  6. Delgado AG, Parameswaran P, Fajardo-Williams D, Halden RU, Krajmalnik-Brown R. 2012. Role of bicarbonate as a pH buffer and electron sink in microbial dechlorination of chloroethenes. Microbial Cell Factories 11(128).

  7. Miceli JF, Parameswaran P, Kang DW, Krajmalnik-Brown R, Torres CI. 2012. Enrichment and analysis of anode-respiring bacteria from diverse anaerobic inocula. Environmental Science & Technology 46(18):10349-10355.

  8. Parameswaran P, Torres CI, Kang DW, Rittmann BE, Krajmalnik-Brown R. 2012. The role of homoacetogenic bacteria as efficient hydrogen scavengers in microbial electrochemical cells (MXCs). Water Science and Technology 65(1):1-6.

  9. Krajmalnik-Brown R, Ilhan Z-E, Kang D-W, DiBaise JK. 2012. Effects of gut microbes on nutrient absorption and energy regulation. Nutrition in Clinical Practice 27(2):201-214.

  10. Tang Y, Zhao H, Marcus AK, Krajmalnik-Brown R, Bruce ER. 2012. A steady-state biofilm model for simultaneous reduction of nitrate and perchlorate, part 1: Model development and numerical solution. Environmental Science & Technology 46(3):1598-1607.

  11. Tang Y, Zhao H, Marcus AK, Krajmalnik-Brown R, Bruce ER. 2012. A steady-state biofilm model for simultaneous reduction of nitrate and perchlorate, part 2: Parameter optimization and results and discussion. Environmental Science & Technology 46(3):1608-1615.


  1. Zhao H-P, Van Ginkel S, Tang Y, Kang D-W, Rittmann B, Krajmalnik-Brown R. 2011. Interactions between perchlorate and nitrate reductions in the biofilm of a hydrogen-based membrane biofilm reactor. Environmental Science & Technology 45(23):10155-10162.

  2. Ziv-El M, Delgado AG, Yao Y, Kang DW, Nelson KG, Halden RU, Krajmalnik-Brown R. 2011. Development and characterization of DehaloR^2, a novel anaerobic microbial consortium performing rapid dechlorination of TCE to ethene. Applied Microbiology and Biotechnology 92(5):1063-1071. pdf

  3. Parameswaran P, Torres CI, Lee HS, Rittmann BE, Krajmalnik-Brown R. 2011. Hydrogen consumption in microbial electrochemical systems (MXCs): The role of homo-acetogenic bacteria. Bioresource Technology 102(1):263-271.

  4. Garcia-Pena EI, Parameswaran P, Kang DW, Canul-Chan M, Krajmalnik-Brown R. 2011. Anaerobic digestion and co-digestion processes of vegetable and fruit residues: Process and microbial ecology. Bioresource Technology 102(20):9447-9455.

  5. Sheng J, Kim HW, Badalamenti JP, Zhou C, Sridharakrishnan S, Krajmalnik-Brown R, Rittmann BE, Vannela R. 2011. Effects of temperature shifts on growth rate and lipid characteristics of Synechocystis sp PCC6803 in a bench-top photobioreactor. Bioresource Technology 102(24):11218-11225.

  6. Torres CI, Ramakrishna S, Chiu C-A, Nelson KG, Westerhoff P, Krajmalnik-Brown R. 2011. Fate of sucralose during wastewater treatment. Environmental Engineering Science 28(5):325-331.


  1. Zhang HS, Ziv-El M, Rittmann BE, Krajmalnik-Brown R. 2010. Effect of dechlorination and sulfate reduction on the microbial community structure in denitrifying membrane-biofilm reactors. Environmental Science & Technology 44(13):5159-5164.

  2. Parameswaran P, Zhang HS, Torres CI, Rittmann BE, Krajmalnik-Brown R. 2010. Microbial community structure in a biofilm anode fed with a fermentable substrate: The significance of hydrogen scavengers. Biotechnology and Bioengineering 105(1):69-78.

  3. Torres CI, Marcus AK, Lee H-S, Parameswaran P, Krajmalnik-Brown R, Rittmann BE. 2010. A kinetic perspective on extracellular electron transfer by anode-respiring bacteria. FEMS Microbiology Reviews 34(1):3-17.


  1. Zhang H, Banaszak JE, Parameswaran P, Alder J, Krajmalnik-Brown R, Rittmann BE. 2009. Focused-Pulsed sludge pre-treatment increases the bacterial diversity and relative abundance of acetoclastic methanogens in a full-scale anaerobic digester. Water Research 43(18):4517-4526.

  2. Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, Yu Y, Parameswaran P, Crowell MD, Wing R, Rittmann BE and others. 2009. Human gut microbiota in obesity and after gastric bypass. Proceedings of the National Academy of Sciences of the United States of America 106(7):2365-2370.

  3. Lee H-S, Krajmalnik-Brown R, Zhang H, Rittmann BE. 2009. An electron-flow model can predict complex redox reactions in mixed-culture fermentative BioH2: Microbial ecology evidence. Biotechnology and Bioengineering 104(4):687-697.

  4. Parameswaran P, Torres CI, Lee HS, Krajmalnik-Brown R, Rittmann BE. 2009. Syntrophic interactions among anode respiring bacteria (ARB) and Non-ARB in a biofilm anode: Electron balances. Biotechnology and Bioengineering 103(3):513-523.

  5. Torres CI, Krajmalnik-Brown R, Parameswaran P, Marcus AK, Wanger G, Gorby YA, Rittmann BE. 2009. Selecting anode-respiring bacteria based on anode potential: Phylogenetic, electrochemical, and microscopic characterization. Environmental Science & Technology 43(24):9519-9524.


  1. Chung J, Krajmalnik-Brown R, Rittmann BE. 2008. Bioreduction of trichloroethene using a hydrogen-based membrane biofilm reactor. Environmental Science & Technology 42(2):477-483.

  2. Rittmann BE, Krajmalnik-Brown R, Halden RU. 2008. Pre-genomic, genomic and postgenomic study of microbial communities involved in bioenergy. Nature Reviews Microbiology 6(8):604-612.

  3. DiBaise JK, Zhang H, Crowell MD, Krajmalnik-Brown R, Decker GA, Rittmann BE. 2008. Gut microbiota and its possible relationship with obesity. Mayo Clinic Proceedings 83(4):460-469.


  1. Krajmalnik-Brown R, Sung Y, Ritalahti KM, Saunders FM, Löffler FE. 2007. Environmental distribution of the trichloroethene reductive dehalogenase gene (tceA) suggests lateral gene transfer among Dehalococcoides. FEMS Microbiology Ecology 59(1):206-214.


  1. He J, Sung Y, Krajmalnik-Brown R, Ritalahti KM, Löffler FE. 2005. Isolation and characterization of Dehalococcoides sp strain FL2, a trichloroethene (TCE)- and 1,2-dichloroethene-respiring anaerobe. Environmental Microbiology 7(9):1442-1450.

  2. Waller AS, Krajmalnik-Brown R, Löffler FE, Edwards EA. 2005. Multiple reductive-dehalogenase-homologous genes are simultaneously transcribed during dechlorination by Dehalococcoides-containing cultures. Applied and Environmental Microbiology 71(12):8257-8264.


  1. Hölscher T, Krajmalnik-Brown R, Ritalahti KM, von Wintzingerode F, Gorisch H, Löffler FE, Adrian L. 2004. Multiple nonidentical reductive-dehalogenase-homologous genes are common in Dehalococcoides. Applied and Environmental Microbiology 70(9):5290-5297.

  2. Krajmalnik-Brown R, Hölscher T, Thomson IN, Saunders FM, Ritalahti KM, Löffler FE. 2004. Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp strain BAV1. Applied and Environmental Microbiology 70(10):6347-6351.


  1. Lendvay JM, Löffler FE, Dollhopf M, Aiello MR, Daniels G, Fathepure BZ, Gebhard M, Heine R, Helton R, Shi J and others. 2003. Bioreactive barriers: A comparison of bioaugmentation and biostimulation for chlorinated solvent remediation. Environmental Science & Technology 37(7):1422-1431.

Book Chapters

Zhang H, Parameswaran P, Badalamenti JP, Rittmann BE, Krajmalnik-Brown R. Integrating high-throughput pyrosequencing and quantitative real-time PCR to analyze microbial communities. 2011. In High-Throughput Next Generation Sequencing, Methods in Molecular Biology 733:107-128.