Photo of Holly M. Simon, Ph.D.

Holly M. Simon Ph.D.

Projects in the lab cover a range of topics in microbial ecology, including the study of bacteria and archaea involved in carbon and nitrogen biogeochemical cycles, identification/monitoring of sentinels for environmental change, and remediation of environmental contaminants.


  • Ph.D., University of Wisconsin-Madison 1996


  • "Erratum" Environmental Microbiology  2001
  • "Comparative analysis of 16S rRNA and amoA Genes from archaea selected with organic and inorganic amendments in enrichment culture" Applied and Environmental Microbiology April 2012
  • "Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots" Applied and Environmental Microbiology August 2005
  • "Influence of tomato genotype on growth of inoculated and indigenous bacteria in the spermosphere" Applied and Environmental Microbiology  2001
  • "Comparison of Midgut Bacterial Diversity in Tropical Caterpillars (Lepidoptera" Environmental Entomology October 2011
  • "Restriction Cascade Exponential Amplification (RCEA) assay with an attomolar detection limit" Scientific Reports  2015
  • "Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem" Frontiers in Microbiology  2013
  • "Crenarchaeota colonize terrestrial plant roots" Environmental Microbiology  2000
  • "Importance of cis determinants and nitrogenase activity in regulated stability of the Klebsiella pneumoniae nitrogenase structural gene mRNA" Journal of Bacteriology June 1999
  • "Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River" Environmental Microbiology March 2011
  • "Real-time biosensor platform"   2010
  • "Effects of cryogenic preservation and storage on the molecular characteristics of microorganisms in sediments" Environmental Science & Technology September 24 2010
  • "Erratum" Environmental Microbiology  2001
  • "High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field" Harmful Algae September 2012
  • "Perturbation of nifT expression in Klebsiella pneumoniae has limited effect on nitrogen fixation" Journal of Bacteriology May 1996
  • "Seasonal changes in bacterial and archaeal gene expression patterns across salinity gradients in the Columbia River coastal margin" PLoS One  2010
  • "A new restriction endonuclease-based method for highly-specific detection of DNA targets from methicillin-resistant staphylococcus aureus" PLoS One May 15 2014
  • "Dark Carbon Fixation in the Columbia River's Estuarine Turbidity Maxima" Estuaries and Coasts September 2013
  • "Sensor array" Electroanalysis July 2009
  • "Cryogenic core collection and preservation of subsurface samples for biomolecular analysis" Groundwater Monitoring and Remediation March 2013
  • "Development of real-time assays for impedance-based detection of microbial double-stranded DNA targets" Biosensors May 15 2012
  • "Infrastructure for collaborative science and societal applications in the Columbia River estuary" Frontiers of Earth Science October 1 2015
  • "Assessment of anaerobic toluene biodegradation activity by bssA transcript/gene ratios" Applied and Environmental Microbiology  2013
  • "Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment" ISME Journal October 23 2015
  • "Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River" Frontiers in Microbiology  2015
  • "Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem" Frontiers in Microbiology  2014
  • "Use of continuous, real-time observations and model simulations to achieve autonomous, adaptive sampling of microbial processes with a robotic sampler" Limnology and Oceanography: Methods January 1 2016
  • "Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary" MicrobiologyOpen  2017
  • "Use of Highly Specific Molecular Markers Reveals Positive Correlation between Abundances of Mesodinium cf. major and Its Preferred Prey, Teleaulax amphioxeia, During Red Water Blooms in the Columbia River Estuary" Journal of Eukaryotic Microbiology  2017
  • "Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima" MicrobiologyOpen  2017

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