José R. de la Torre

My research program focuses on the ecology and evolution of microorganisms living in high temperature environments, particularly terrestrial hot springs. We are interested in how environmental conditions (chemistry, pH) and evolutionary history influence the composition and function of microbial communities in these extreme environments, with special attention to the contribution of these microorganisms to the Carbon and Nitrogen biogeochemical cycles.

Our work is at the exciting intersection of many disciplines including ecology, evolution, genomics, geobiology and geochemistry. We have ongoing research projects in Yellowstone National Park, California, Nevada and China, and have been working closely with researchers at the University of Washington, University of Nevada Las Vegas, Montana State University, Arizona State University, Northern Arisona University and UC Davis. Research projects in the lab are amenable to both undergraduate and graduate students.

Courses taught at San Francisco State University include Microbial Physiology, Molecular Techniques in Evolution & Ecology, Microbial Genomics.

• Fine stratification of microbial communities through a metagenomic profile of the photic zone.
  Haro-Moreno JM, Lopez-Perez M., de la Torre JR, Picazo A, Camacho A, Rodriguez-Valera F.
  Submitted (in review)

• Chemotaxonomic characterization of the thaumarchaeal lipidome.
  Elling FJ, Könneke M, Nicol GW, Stieglmeier M, Bayer B, Spieck E, de la Torre JR, Becker KW, Thomm M, Prosser JI, Herndl GJ, Schleper C, and Hinrichs KU.
  Environ Microbiol., (2017) 19(7):2681-2700.

• Candidatus Nitrosocaldaceae.
  Qin W, Jewell TNM, Russell VV, Hedlund BP, de la Torre JR, and Stahl DA.
  Bergey's Manual of Systematics of Archaea and Bacteria, (2017) 1-2.

• Candidatus Nitrosocaldales.
  Qin W, Jewell TNM, Russell VV, Hedlund BP, de la Torre JR, and Stahl DA.
  Bergey's Manual of Systematics of Archaea and Bacteria, (2017) 1-2.

• Candidatus Nitrosocaldus.
  Qin W, Jewell TNM, Russell VV, Hedlund BP, de la Torre JR, and Stahl DA.
  Bergey's Manual of Systematics of Archaea and Bacteria, (2017) 1-5.&

• Classroom Sound Can Be Used To Classify Teaching Practices in College Science Courses.
  Owens MT, et al.
  Proc Natl Acad Sci USA, (2017) 114(12):3085-3090.

• Distribution of ether lipids and composition of the archaeal community in terrestrial geothermal springs: impact of environmental variables.
  Xie W, Zhang CL, Wang J, Chen Y, Zhu Y, de la Torre JR, Dong H, Hartnett HE, Hedlund BP, and Klotz MG.
  Environ. Microbiol., (2015) 17(5):1600-14.

• Ammonia availability shapes the seasonal distribution and activity of archaeal and bacterial ammonia oxidizers in the Puget Sound Estuary.
  Urakawa H, Martens-Habbena W, Huguet C, de la Torre JR, Ingalls AE, Devol AH, and Stahl DA. (2014).
  Limnol. Oceanogr. (2014) 59(4):1321-1335.

• Competitive interactions influence the composition of a chemotrophic hydrothermal ecosystem.
  Hamilton TL, Koonce E, Howells A, Havig JR, Jewell T, de la Torre JR, Peters JW, and Boyd ES.
  Appl Environ Microbiol. (2014) 80:653-61.

• Physiology and diversity of ammonia-oxidizing archaea
  Stahl DA and de la Torre JR.
  Ann. Rev. Microbiol. (2012) 66:83-101.

• Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus.
  Pelve EA, Lindås AC, Martens-Habbena W, de la Torre JR, Stahl DA, Bernander R.
  Mol Microbiol., (2011) 82(3):555-66.

• Measuring nitrification, denitrification, and related biomarkers in terrestrial geothermal ecosystems.
  Dodsworth JA, Hungate B, de la Torre JR, Jiang H, Hedlund BP.
  Methods Enzymol., (2011) 486:171-203.

• The Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine Archaea.
  Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PSG, Chan PP, Golabgir-Anbarani A, Hemp J, Hügler M, Karr EA, Könneke M, Lang D, Lowe T, Martens-Habbena W, Sayavedra-Soto LA, Shin M, Sievert SM, Rosenzweig AC, Manning G, and Stahl DA.
  Proc. Natl. Acad. Sci. USA, (2010) 107(19):8818-23.

• Abundance of ammonia-oxidizing archaea and bacteria along an estuarine salinity gradient in relation to potential nitrification rates.
  Bernhard AE, Landry ZC, Blevins A, de la Torre JR, Giblin AE, and Stahl DA.
  Appl. Environ. Microbiol., (2010) 76(4):1285-9.

• Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria.
  Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR and Stahl DA.
  Nature, (2009) 461:976-9.

• Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol.
  de la Torre JR, Walker CB, Ingalls AE, Könneke M, and Stahl DA.
  Environ Microbiol. (2008) 10(3):810-8.

• Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm.
  Foesel BU, Gieseke A, Schwermer C, Stief P, Koch L, Cytryn E, de la Torre JR, van Rijn J, Minz D, Drake HL, and Schramm A.
  FEMS Microbiol Ecol. (2007) 63(2):192-204.

• Genomic analysis of the uncultivated marine crenarchaeon, Cenarchaeum symbiosum.
  Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe Y, Sugahara J, Preston C, de la Torre J, Richardson PM, and DeLong EF.
  Proc. Natl. Acad. Sci. USA. (2006) 103(48):18296-18301.

• Isolation of an autotrophic ammonia-oxidizing marine archaeon.
  Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, and Stahl DA.
  Nature (2005) 437: 543-6.

• Phylogenetic screening of ribosomal RNA gene-containing clones in Bacterial Artificial Chromosome (BAC) libraries from different depths in Monterey Bay.
  Suzuki MT, Preston CM, Béjà O, de la Torre JR, Steward GF, and DeLong EF.
  Environ. Microbiol. (2004) 48: 473-488.

• Proteorhodopsin genes are distributed among divergent marine bacterial taxa.
  de la Torre JR, Christianson LM, Béjà O, Suzuki MT, Karl DM, Heidelberg JF and DeLong EF.
  Proc. Natl. Acad. Sci. USA. (2003) 100: 12830-12835.

• Molecular characterization of cryptoendolithic communities from the McMurdo Dry Valleys, Antarctica.
  de la Torre JR, Goebel BM, Friedmann EI, and Pace NR. (2003).
  Appl. Environ. Microbiol., 69: 3858-3867.