Eric Allen


Research in our laboratory centers upon the use of environmentally-derived genome sequence information to explore the genetic potential, ecology, and evolution of environmental microbial populations. The nature of this work relies equally upon field-based collections, bioinformatics (genome assembly, annotation, and comparative analyses) and the tools of molecular ecology and genetics. Together, these approaches enable us to utilize environmental genome sequence data to understand natural microbial phenomena including environmental adaptation, evolutionary processes, lateral gene transfer events, biogeographical patterning, biogeochemical cycling, microbial interactions, and in situ metabolic activity.

Current investigations include exploring the genetic composition of microbial populations (Archaea & Bacteria) inhabiting hypersaline environments via cultivation- independent genomic approaches ("metagenomics"). Our primary study site for this project is a hypersaline lake system in NW Victoria, Australia (near the town of Sea Lake approx. 370 km NW of Melbourne). With over 1 billion bases (>1 Gbp) of environmental genome sequence data generated, near complete and complete genome sequences for resident microbial populations can be analyzed in the absence of cultivation requirements. Such a data set uniquely allows analysis of population structure (allelic variation) thus providing insight into natural mechanisms of genomic heterogeneity, diversification, and environmental selection. Additional projects are aiding in the analysis of various marine microbial metagenomic projects including the J. Craig Venter Institute's Global Ocean Sampling (GOS) expedition.

An omnipresent facet of the research in our laboratory is the use of genome sequence information (environmental or isolate-derived) to expand our understanding of microbial physiology and its relationship to environmental adapation and ecosystem function. Abiding by this paradigm, additional projects underway in our laboratory include:

  • Diversity and distribution of microbial "secondary lipid" biosynthesis
  • Ecology & evolution of microbial polyunsaturated fatty acid biosynthesis
  • Biological controls on Hg methylation in marine & estuarine sediments
  • Analysis of microbial & meiofaunal diversity at the Land/ Sea Interface
Eric Allen Graphic

Select Publications

  • Zeigler-Allen L, Allen EE, Badger J, McCrow JP, Paulson I, Elbourne LDH, Thiagrijan M, Nealson KH, Williamson SJ, Venter JC, Allen AE. (2012). Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME J in press.
  • Ugalde JA, Podell S, Narasingarao P, Allen EE. (2011). Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between Archaea and Bacteria. Biol Direct 6:52.
  • Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson J, Brocks JJ, Heidelberg, KB, Banfield JF, Allen EE. (2011). De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J Advanced Online Publication, 30 June 2011; doi:10.1038/ismej.2011.78.
  • Shulse CN, Allen EE. (2011). Widespread occurence of secondary lipid biosynthesis potential in microbial lineages. PLoS One 6:e20146.
  • Eloe EA, Fadrosh DW, Novotny M, Zeigler Allen L, Kim M, Lombardo M-J, Yee-Greenbaum J, Yooseph S, Allen EE, Lasken R, Williamson SJ, Bartlett DH. (2011). Going deeper: Metagenome of a hadopelagic microbial community. PLoS One 6:e20388.
  • Jones A, Monroe E, Podell S, Hess W, Klages S, Esquenazi E, Niessen S, Hoover H, Rothmann M, Lasken R, Yates III J, Reinhardt R, Kube M, Burkart M, Allen EE, Gerwick W, Gerwick L. (2011). Genomic insights into the physiology and ecology of the marine filamentous cyanbacterium Lyngbya majuscule. Proc Natl Acad Sci USA 108:8815-8820.
  • Shulse CN, Allen EE. (2011). Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment. Environ Microbiol 13:684-695.
  • Eloe EA, Shulse CN, Fadrosh DW, Williamson SJ, Allen EE, Bartlett DH. (2010). Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep ocean environment. Environ Microbiol Reports (first published online : 24 NOV 2010), DOI: 10.1111/j.1758-2229.2010.00223.
  • Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J. (2010). Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucl Acids Res 39:D546-551.
  • Han S, Narasingarao P, Obraztsova A, Gieskes J, Hartmann AC, Tebo BM, Allen EE, Deheyn DD. (2010). Mercury speciation in marine sediments under sulfate-limited conditions. Env Sci Technol 44:3752-3757.
  • Morin PA, Archer FI, Foote AD, Vilstrup J, Allen EE, Wade P, Durban J, Parsons K, Pitman R, Li L, Bouffard P, Abel Nielsen SC, Rasmussen M, Willerslev E, Gilbert MTP, Harkins T. (2010). Complete mitochondrial genome phylogeographic analysis of killer whales ( Orcinus orca) indicates multiple species. Genome Res 20:908-916.
  • Penn, K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, Foster B, Lapidus A, Podell S, Allen EE, Moore BS, Jensen PR. (2009). Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J 3:1193-1203.
  • Podell S, Gaasterland T, Allen EE. (2008). A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm. BMC Bioinformatics 9:419.
  • Robidart JC, Bench SR, Feldman RA, Novoradovsky A, Podell SB, Gaasterland T, Allen EE, Felbeck H. (2008). Metabolic versatility of the Riftia pachyptila endosymtiont revealed through metagenomics. Environ Microbiol 10:727-737.
  • Lo I, Denef V, VerBerkmoes NC, Shah M, Goltsman D, DiBartolo G, Tyson GW, Allen EE, Ram RJ, Detter C, Richardson P, Thelen MP, Hettich RL, Banfield JF. (2007). Strain-resolved community proteomics reveals that recombination shapes the genomes of acidophilic bacteria. Nature 446:537-541.
  • Allen EE, Tyson GW, Whitaker RJ, Detter JC, Richardson PM, Banfield JF. (2007). Genome dynamics in a natural archaeal population. Proc Natl Acad Sci USA 104:1883-1888.
  • Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF. (2006). Lineages of acidophilic archaea revealed by community genomic analysis. Science 314:1933-1935.
  • Banfield JF, Tyson GW, Allen EE, Whitaker RJ. (2005). The search for a molecular-level understanding of the processes that underpin the Earth's biogeochemical cycles. Rev Mineral Geochem 59:1-7.
  • Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF. (2005). Genome-directed isolation of the key nitrogen fixer, Leptospirillum ferrodiazotrophum sp. nov., from an acidophilic microbial community. Appl Environ Microbiol 71:6319-6324.
  • Allen EE, Banfield JF. (2005). Community genomics in microbial ecology and evolution. Nature Rev Microbiol 3:489-498.
  • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram R, Richardson P, Solovyev V, Rokhsar D, Banfield JF. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37-43.
  • Palenik B, Brahamsha B, Larimer FW, Land L, Hauser L, Chain P, Lamerdin J, Regala W, Allen EE, McCarren J, Paulsen I, Dufresne A, Partensky F, Webb EA, Waterbury J. (2003). The genome of a motile marine Synechococcus. Nature 424:1037-1042.
  • Allen EE, Bartlett DH. (2002). Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9. Microbiology 148:1903-1914.
  • Allen EE, Bartlett DH. (2002). Piezophiles: microbial adaptation to the deep-sea environment. In 'Extremophiles', UNESCO Encyclopedia for Life Support Systems. EOLSS Publishers, Oxford, UK.
  • Allen EE, Bartlett DH. (2000). FabF is required for piezoregulation of cis-vaccenic acid levels and piezophilic growth of the deep-sea bacterium, Photobacterium profundum strain SS9. J Bacteriol 182:1264-1271.
  • Allen EE, Facciotti D, Bartlett DH. (1999). Monounsaturated but not polyunsaturated fatty acids are required for growth of the deep-sea bacterium Photobacterium profundum SS9 at high pressure and low temperature. Appl. Environ Microbiol 65:1710-1720.


Eric Allen received his B.S. from the University of Oregon and his Ph.D. from the Scripps Institution of Oceanography at UC San Diego. He performed postdoctoral research at the University of California, Berkeley as an NSF Postdoctoral Fellow in Microbial Biology and joined the faculty of Biological Sciences and the Scripps Institution of Oceangraphy at UCSD in 2006.