Selected Publications

PEER-REVIEWED JOURNAL ARTICLES (Graduate Students mentees underlined and bolded; Postdocs dash-underlined and bolded; undergraduate student underlined but not bolded)

  1. Fernandez-Baca, Cristina, P., Spirito, Catherine M., Bae, Justin S., Zsegletes, Zsofia M., Barott, Nathan, Sausele, Desiree J., Brooks, Yolanda M., Weller, Daniel L., and Richardson, Ruth E. (2021). Rapid qPCR-based water quality monitoring in New York State recreational waters. In Press.
  2. James, Andrew R., Lin, Janni, and Richardson, Ruth E. (2021). Relationship between peat type and microbial ecology in Sphagnum-containing peatlands of the Adirondack Mountains, New York, USA. Microbial Ecology. In Press
  3. Tentori, Egidio F. and Richardson, Ruth E. (2021) Methane monooxygenase transcripts as quantitative biomarkers of methanotrophic activity in Methylosinus trichosporium Applied and Environmental Microbiology. AEM.01048-20v1.
  4. Bora, Raaj R., Richardson, Ruth E. , and You, Fengqi. (2020) Resource recovery and waste-to-energy from wastewater sludge via thermochemical conversion technologies in support of circular economy: a comprehensive review. BMC Chemical Engineering 2, no. 1 (2020): 8.
  5. James, Andrew R., Joseph B. Yavitt, Stephen H. Zinder, and Ruth E. Richardson. Linking microbial sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study.” The ISME Journal, September 19, 2020.
  6. Tian, Xueyu, Richardson, Ruth E. , Tester, Jefferson W. , Lozano, José L. , and You, Fengqi. (2020). Retrofitting municipal wastewater treatment facilities toward a greener and circular economy by virtue of resource recovery: techno-economic analysis and life cycle assessment. ACS Sustainable Chemistry & Engineering 8, no. 36: 13823–37.
  7. James, Andrew R., and Richardson, Ruth E. (2020). Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate reducing conditions. FEMS Microbiology Ecology 96.
  8. Bora, Raaj.R., Tao, Y., Lehmann, Johannes, Tester, Jefferson W., Richardson, Ruth E., and You, Fengqi. (2020). Techno-economic feasibility and spatial analysis of thermochemical conversion pathways for regional poultry waste valorization. i. 8, 5763–5775.
  9. Brooks, Y.M., Spirito, C.M., Bae, J.S., Hong, A., Mosier, E.M., Sausele, D.J., Fernández-Baca, C. P., Epstein, J.L., Shapley, D.J., Goodman, L.B., Anderson, R.R., Glaser, A.L., Richardson, R.E., (2020) Fecal indicator bacteria, fecal source tracking markers, and pathogens detected in two Hudson River tributaries. Water Research, DOI: 10.1016/j.watres.2019.115342 .
  10. Fernández-Baca, Cristina P., Amir-Eldin, Omar, Reid ,Matthew C., and Richardson, Ruth E., 2020. Temporal lags in post-rain greenhouse gas cycling and fluxes from septic leach field soils and associated greenhouse gas cycling microbial populations. Journal of Sustainable Water in the Built Environment 6, no. 2 (May 1, 2020): 04020004.
  11. Heavner, Gretchen L. W., Cresten B. Mansfeldt, Michael J. Wilkins, Carrie D. Nicora, Garrett E. Debs, Elizabeth A. Edwards, and Ruth E. Richardson. (2019) Detection of Organohalide-Respiring Enzyme Biomarkers at a Bioaugmented TCE-Contaminated Field Site. Frontiers in Microbiology 10 (June).
  12. Fernández-Baca, Cristina P.; Amir-Eldin H Omar; Jesse T Pollard; Ruth E Richardson (2019) Microbial communities controlling methane and nutrient cycling in leach field soils. Water Research 151, 456–467.
  13. Brooks, Yolanda M, Erika A. Tenorio-Moncada, Nisarg Gohil, Yuqi Yu, Mynor R. Estrada-Mendez, Geovanny Bardales, and Ruth E. Richardson. (2018) Performance evaluation of gravity-fed water treatment systems in rural Honduras: verifying robust reduction of turbidity and Escherichia coli during wet and dry weather. American Journal of Tropical Medicine and Hygiene.  Doi:10.4269/ajtmh.17-0577.
  14. Otwell, Anne E, Callister, S.J., Sherwood, R.W., Zhang, S., Goldman, A.R., Smith, R.D., Richardson, R.E. (2018). Physiological and proteomic analyses of Fe(III)-reducing co-cultures of Desulfotomaculum reducens MI-1 and Geobacter sulfurreducens Geobiology. Sep;16(5):522-539. doi: 10.1111/gbi.12295.
  15. Heavner, G. L. W.; Mansfeldt, C. B.; Debs, G. E.; Hellerstedt, S. T.; Rowe, A. R.; Richardson, R. E. (2018) Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1. Microorganisms.  Feb 8;6(1). pii: E13. doi: 10.3390/microorganisms6010013.
  16. Richter, L. V.; Mansfeldt, C. B.; Kuan, M.; Cesare, A.; Menefee, S. T.; Richardson, R. E.; Ahner, B. A. (2018) Altered Microbiome Leads to Significant Phenotypic and Transcriptomic Differences in a Lipid Accumulating Chlorophyta. Environmental Science & Technology, 52 (12), pp 6854–6863. DOI: 10.1021/acs.est.7b06581
  17. Fernández-Baca, Cristina P, Truhlar, AM, Omar, A-E H, Rahm, BG, Walter, MT, and R.E. Richardson (2018) Methane and nitrous oxide cycling microbes in soils above septic leach fields: abundances with depth and correlations with net surface emissions. Science of the Total Environment, 640–641, 429–441.
  18. Brooks, Yolanda M., Shalean M. Collins, Patrick Mbullo, Godfred O. Boateng, Sera E. Young, and Ruth E. Richardson (2017) Evaluating human sensory perceptions and the Compartment Bag Test assays as proxies for the presence and concentration of Escherichia coli in drinking water in western Kenya: Suggestions for monitoring SDGs in low resource settings. American Journal of Tropical Medicine and Hygiene (Impact Factor: 2.453). doi:10.4269/ajtmh.16-0878. (featured in Editorial
  19. Greene, Charles H., Mark E. Huntley, Ian Archibal, Léda N. Gerber, Deborah L. Sills, Joe Granados, Jefferson W. Tester, Colin M. Beal, Michael J. Walsh, Robert R. Bidigare, Susan L. Brown, William P. Cochlan, Zackary I. Johnson, Xin Gen Lei, Stephen C. Machesky, D.G. Redalje, Ruth E. Richardson, Viswanath Kiron, Virginia Corless (2016) Microalgae: Climate, Energy, and Food Security from the Sea. Oceanography (IF=883). 29(4):8-13.
  20. Mansfeldt, Cresten B., Gretchen W. Heavner, Annette R. Rowe, Boris Hayete, Bruce Church, and Ruth E Richardson. (2016) Inferring gene networks for strains of Dehalococcoides highlights conserved relationships between genes encoding core catabolic and cell-wall structural proteins.  PLoS One (IF=3.057) 11(11): e0166234. doi: 10.1371/journal.pone.0166234.
  21. Mansfeldt, C.B., Richter, L.V., Ahner, B.A., Cochlan, W.P., Richardson, R.E. (2016) Use of De Novo Transcriptome Libraries to Characterize a Novel Oleaginous Marine Chlorella Species during the Accumulation of Triacylglycerols. PLoS One (IF=3.057).11, e0147527. doi:10.1371/journal.pone.0147527
  22. Otwell, A.E., Callister, S.J., Zink, E.M., Smith, R.D., Richardson, R.E. (2016) Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-positive Sulfate and Metal-reducing Bacterium. Frontiers in Microbiology (IF=4.265). doi:10.3389/fmicb.2016.00191
  23. Li, Z., Kim, D.D., Nelson, O.D., Otwell, A.E., Richardson, R.E., Callister, S.J., Lin, H. (2015) Molecular dissection of a putative iron reductase from Desulfotomaculum reducens MI-1. Biochemical and Biophysical Research Communications (IF=2.371) 467, 503–508. doi:10.1016/j.bbrc.2015.10.016
  24. Kostylev, M., Otwell, A.E., Richardson, R.E., Suzuki, Y. (2015) Cloning Should Be Simple: Escherichia coli DH5α-Mediated Assembly of Multiple DNA Fragments with Short End Homologies. PLoS One (IF=3.057). 10, e0137466. doi:10.1371/journal.pone.0137466
  25. Otwell, A.E., Sherwood, R.W., Zhang, S., Nelson, O.D., Li, Z., Lin, H., Callister, S.J., Richardson, R.E. (2015) Identification of proteins capable of metal reduction from the proteome of the Gram-positive bacterium Desulfotomaculum reducens MI-1 using an NADH-based activity assay: Metal reductases from Gram-positive metal reducer. Environmental Microbiology (IF=5.932). 17, 1977–1990. doi:10.1111/1462-2920.12673
  26. Mansfeldt, C.B., Logsdon, B.A., Debs, G.E., Richardson, R.E. (2015) SPINE: SParse eIgengene NEtwork Linking Gene Expression Clusters in Dehalococcoides mccartyi to Perturbations in Experimental Conditions. PLoS One (IF=3.057). 10, e0118404. doi:10.1371/journal.pone.0118404
  27. Rowe, A. R., B. Mansfeldt, G. L. Heavner, and Ruth E. Richardson. (2015) Relating mRNA and Protein Biomarker Levels in a Dehalococcoides and Methanospirillum-Containing Community. Applied Microbiology and Biotechnology (IF=3.376). 99 (5): 2313–27. doi:10.1007/s00253-014-6220-7.
  28. Mansfeldt, C.B., Rowe, A.R., Heavner, G.L.W., Zinder, S.H., Richardson, R.E. (2014) Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit. Applied and Environmental Microbiology (IF=3.823) 80, 6062–6072. doi:10.1128/AEM.02130-14
  29. Heavner, G.L.W., Rowe, A.R., Mansfeldt, C.B., Pan, J.K., Gossett, J.M., and Richardson, R.E. (2013) Molecular Biomarker-Based Biokinetic Modeling of a PCE-Dechlorinating and Methanogenic Mixed Culture. Environmental Science & Technology (IF=5.393). 47: 3724-3733.
  30. Matturro, B.(visiting scholar in RER lab), Heavner, G.L., Richardson, R.E., and Rossetti, S. (2013) Quantitative estimation of Dehalococcoides mccartyi at laboratory and field scale: Comparative study between CARD-FISH and Real Time PCR. Journal of Microbiological Methods (IF=1.857). 93: 127-133.
  31. Richardson, R.E. (2013) Genomic insights into organohalide respiration. Current Opinion in Biotechnology (IF=8.314). 24: 498-505.
  32. Rowe, A.R., Mansfeldt, C.B., Heavner, G.L., and Richardson, R.E. (2013) Methanospirillum Respiratory mRNA Biomarkers Correlate with Hydrogenotrophic Methanogenesis Rate during Growth and Competition for Hydrogen in an Organochlorine-Respiring Mixed Culture. Environmental Science & Technology (IF=5.393). 47: 372-381.
  33. Hug, L.A., Beiko, R.G., Rowe, A.R., Richardson, R.E., and Edwards, E.A. (2012) Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community. BMC Genomics (IF=3.867). 13.
  34. Rowe, A.R., Heavner, G.L., Mansfeldt, C.B., Werner, J.J., and Richardson, R.E. (2012) Relating Chloroethene Respiration Rates in Dehalococcoides to Protein and mRNA Biomarkers. Environmental Science & Technology (IF=5.393). 46: 9388-9397.
  35. Walter, RK, PH Lin, ME Edwards, and RE Richardson (2011) Investigation of Factors Affecting the Accumulation of Vinyl Chloride in Polyvinyl Chloride Piping Used in Drinking Water Distribution Systems. Water Research (IF=5.991). 45:2607-15.
  36. Powers, CA, NR Scott, and RE Richardson (2011) Performance of Microbial Fuel Cells With Dairy Manure as the Substrate and Combined with Anaerobic Digestion. Journal of Biological Engineering (IF=3.000). 3(3).
  37. Werner, JW, S Zhang, AC Ptak, BG Rahm, and RE Richardson. (2009) Absolute quantification of Dehalococcoides proteins: Enzyme bioindicators of chlorinated ethene dehalorespiration. Environmental Microbiology (IF=5.932). 11(10): p. 2687-97.
  38. Rowe, AR, BJ Lazar, RM Morris, and RE Richardson. (2008) Characterization of a dechlorinating mixed culture: community structure and comparisons of gene expression in planktonic and biofloc-associated Dehalococcoides and Applied and Environmental Microbiology (IF=3.823) 74 (21): 6709-6719.
  39. Rahm, BG, and RE Richardson. (2008) Dehalococcoides’ gene transcripts as quantitative bioindicators of PCE, TCE and cDCE dehalorespiration rates. Environmental Science & Technology (IF=5.393). 42 (14): 5099-5105.
  40. Rahm, BG, and RE Richardson. (2008) Correlation of Respiratory Gene Expression Levels and Pseudo-Steady State PCE Respiration Rates in Dehalococcoides ethenogenes. Environmental Science & Technology (IF=5.393). 42 (2): 416-421.
  41. Morris, RM, JM Fung, BG Rahm, S Zhang, DL Freedman, SH Zinder, and RE Richardson. (2007) Comparative Proteomics of Dehalococcoides Reveals Strain-Specific Peptides Associated with Activity. Applied and Environmental Microbiology (IF=3.823) 73(1): 320-326.
  42. Morris, RM, S Sowell, D Barofsky, SH Zinder, and RE Richardson. (2006) Transcription and mass-spectroscopic proteomic studies of electron transport oxidoreductases in Dehalococcoides ethenogenes. Environmental Microbiology (IF=5.932). 8 (9), 1499–1509.
  43. Rahm, BG, RM Morris, and Richardson, RE. (2006) Temporal Expression of Respiratory Genes in an Enrichment Culture Containing Dehalococcoides ethenogenes. Applied and Environmental Microbiology (IF=3.823) 72(8): 5486–5491.
  44. Freeborn, RA, VK Bhupathiraju, S Chauhan, KA West, BG Rahm, RE Richardson, and L Alvarez-Cohen. (2005) Phylogenetic Analysis of TCE-Dechlorinating Consortia Enriched on a Variety of Electron Donors. Applied and Environmental Microbiology (IF=3.823) 39, 8358-8368.
  45. Richardson, RE, CA James, VK Bhupathiraju, and L Alvarez-Cohen. (2002) Microbial Rebound in Soils Following Steam Exposure. Biodegradation (IF=2.446). 13: 285-295.
  46. Richardson, RE, VK Bhupathiraju, DL Song, T Goulet, and L Alvarez-Cohen. (2002) Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques. Applied and Environmental Microbiology (IF=3.823) 36(12): 2652-2662.