Recent (since starting at UT in 2015)


  • Baker BJ, Dick GJ. (2013) Omic approaches in microbial ecology; charting the unknown. Microbe 8, 353-359.
  • Baker BJ, Banfield JF (2003) Microbial communities in acid mine drainage. FEMS Microbial Ecol. 44, 1-14.


  • Miller CS, Baker BJ, Thomas BC, Singer S, Banfield JF (2011) EMIRGE: Reconstruction of full length ribosomal genes from microbial community short read sequencing dataGenome Biology 12, R44.
  • Dick GJ, Andersson, A, Baker BJ, Yelton P, Sheri SS, Thomas BC, Banfield JF. (2009) Community-wide analysis of microbial genome sequence signatures. Genome Biology 10:R85.


  • Li M, Toner BM, Baker BJ, Myneni S, Dick GJ. (2014) Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents. Nature Comm. 5, 3192.
  • Li M, Jain S, Baker BJ, Taylor C, Dick GJ. (2014) Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume. Environ. Microbiol. 16, 60-71.
  • BakerBJ, Taylor C, Jain S, Shiek CS, Bhasi A, Cavalcoli JD, Dick GJ (2013) Community transcriptomic assembly reveals microbes contribute to carbon and nitrogen cycling in the deep sea. ISME J. 7, 1962-1973.
  • Dick GJ, Anantharaman K, Baker BJ, Li M, Reed DC, Sheik CS. (2013) The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Frontiers in Microbiology. 4, 1-16.
  • Baker BJ, Lesniewski R, Dick GJ (2012) Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume. ISME J. 6, 2269-2279.

Acid Mine Drainage

  • Schönknecht G, Chen W-H, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Benning C, Carr K, Wilkerson C, Rensing SA, Gagneul D, Oesterhelt C, Lercher MJ, Weber APM. (2013) Gene Transfer from Bacteria and Archaea facilitated evolution of an extremophilic eukaryote. Science. 339, 1207-1210.
  • Fujishima K, Sugahara J, Miller CS, Baker BJ, Di Giulio M, Takesue K, Sato A, Tomita M, Banfield JF, Kanai A. (2011) A unique tRNA splicing endonuclease found in ultrasmall archaeon is a chimeric protein consisting of three domains. Nucleic Acids Res.39, 9695-9704.
  • Baker BJ, Comolli LR, Dick GJ, Hauser L., Land M, Hyatt, D, VerBerkmoes N, Hettich B, Banfield JF. (2010) Enigmatic, ultra-small uncultivated Archaea. Proc. Natl. Acad. Sci. 107, 8806-8811.
  • Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, Thomas BC, VerBerkmoes, NC, Hettich RL, Banfield, JF. (2010) Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Natl. Acad. Sci. 107, 2383-2390.
  • Goltsman, DSA, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Muller R, Dick GJ, Sun C, Wheeler K, Zemla A, Baker BJ, Hauser L, Land M, Shah M, Thelen MP, Hettich RL, Banfield JF (2009) Community genomics and proteomics of chemoautotrophic, iron-oxidizing  “Leptospirillum rubarum” and Leptospirillum ferrodiazotrophum populations in acid mine drainage. Appl. Environ. Microbiol. 75, 4599-4615.
  • Baker BJ, Tyson GW, Goosherst L, Banfield JF (2009) Insights into the diversity eukaryotes in acid mine drainage biofilm communities. Appl. Environ. Microbiol. 75, 2192-2199.
  • Comolli LR, Baker BJ, Downing KH, Siegerist CE, Banfield JF (2009) Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. ISME J. 3, 159-1671.
  •  Baker BJ, Tyson, GW, Webb RI, Flanagan J, Hugenholtz P, Banfield JF (2006) Lineages of acidophilic Archaea revealed by community genomic analysis. Science 314, 1933-1935.
  • 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.
  • Ram RJ, VerBerkmoes N, Thelen MP, Tyson GW, Baker BJ, Shah M, RC Blake II, Hettich R, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308, 1915-1920.
  • Baker BJ, Lutz MA, Dawson SC, Bond PL, Banfield JF (2004) Metabolically active eukaryotes in extremely acidic mine drainage. Appl. Environ. Microbiol. 70, 6264-6271.
  • Druschel GK*, Baker BJ*, Gihring TH, Banfield JF (2004) Acid mine drainage biogeochemistry at Iron Mountain, California. Geochem. Trans. 5, 13-32.   *contributed equally
  • Baker BJ, Hugenholtz, P, Dawson, SC, Banfield, JF (2003) Extremely acidophilic protists host Rickettsiales-lineage endosymbionts with an intervening sequence in their 16S rRNA genes. Appl Environ. Microbiol. 69, 5512-5518.

Deep Subsurface

  • Moser DP, Gihring TM, Brockman FJ, Fredrickson JK, Balkwill DL, Dollhopf ME, Sherwood Lollar B, Pratt LM, Boice E, Southam G, Wanger G, Baker BJ, Pfiffner SM, L-H Lin, Onstott TC. (2005) Desulfotomaculum spp. and Methanobacterium spp. a dominate 4-5 km deep fault. Appl. Environ. Microbiol. 71, 8773-8783.
  • Moser DP, Onstott TC, Fredrickson JK, Brockman FJ, Takai K, Balkwill DL, Drake, G, Pfiffner, S, White DC, Baker BJ, Pratt LM, Fong J, Lollar BS, Slater G, Phelps TJ, Spoelstra N, DeFlaun M, Southam G, Welty AT, Hoek J (2003) Evolution of microbial community structure and geochemistry in an ultradeep South African gold mine borehole. Geomicrobiology J. 20, 517-548.
  • Baker BJ, Moser DP, MacGregor BJ, Fishbain S, Wagner M, Fry N, Jackson B, Speolstra N, Loos S, Takai K, Fredrickson J, Balkwill D, Onstott TC, Wimpee CF, Stahl DA (2003) Related assemblages of sulfate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State. Environ. Microbiol. 5,267-277.
  •  Stahl DA, Fishbain S, Klein M, Baker BJ, Wagner M (2002) Origins and diversification of sulfate-respiring microorganisms. Antonie van Leeuwenhoek 81, 189-195.

Lake Michigan

  •  MacGregor BJ, Van Mooy B, Baker BJ, Mellon M, Moisander PH, Pearl HW, Zehr, J, Hollander, D, Stahl DA (2001) Microbiological, molecular biological and stable isotopic evidence for nitrogen fixation in the open waters of Lake Michigan. Environ. Microbiol. 3, 205-209.
  • MacGregor BJ, Moser DP, Baker BJ, Alm EW, Maurer M, Nealson KH, Stahl DA (2001) Seasonal and spatial variability in Lake Michigan sediment small-subunit rRNA concentrations. Appl Environ. Microbiol. 67, 3908-3922.

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