Beal, E. J.; C.H. House, V.J. Orphan. (2009) Manganese- and Iron-Dependent Marine Methane Oxidation. Science 325, 184.

Orphan, V.J., K.A. Turk, A. Green, C.H. House (2009) Patterns of 15N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS Environ. Microbiol. 11(7): 1777–1791.

Orphan, V.J. and C.H. House. (2009) Geobiological investigations using secondary ion mass spectrometry (SIMS): microanalysis of extant and paleo-microbial processes. Geobiology. 7(3): 360-372.

Orphan, V.J. (2009) Methods for unveiling cryptic microbial partnerships in nature. Current Opinion Microbiology. 12:231–237

Fike, D.A. N Finke, J. Zha, G. Blake, T. M. Hoehler, V. J. Orphan. (in press) The effect of sulfate concentration on (sub)millimeter-scale sulfide δ34S in hypersaline cyanobacterial mats over the diurnal cycle. Geochem. et Cosmochem Acta.

House, C.H., V.J. Orphan, K.A. Turk, B. Thomas, A. Pernthaler, J.M. Vrentas, S.B. Joye (In Press) Extensive carbon isotopic heterogeneity among methane seep microbiota. Environ. Microbiol. doi:10.1111/j.1462-2920.2009.01934.x

Goffredi, S.K. and V.J. Orphan. Bacterial community shifts in taxa and diversity in response to localized organic loading in the deep sea. Environ. Microbiol. In Review.

Harrison, B., H. Zhang, W. Berelson, V.J. Orphan (2009) Variations in archaeal and bacterial diversity associated with the sulfate-methane transition zone in continental margin sediments (Santa Barbara Basin, CA). Appl. Environ. Microbio. 75: 1487-1499

Orphan, V.J., L.L. Jahnke, T. Embaye, K.A. Turk, A. Pernthaler, R.E. Summons, D.J. Des Marais (2008) Characterization and spatial distribution of methanogens and methanogenic biosignatures in hypersaline microbial mats of Baja California. Geobiology 6:376-393

Fike, D. A., C. L. Gammon, W. Ziebis, V. J. Orphan (2008) Micron-scale mapping of sulfur cycling across the oxycline of a cyanobacterial mat: A paired nanoSIMS and CARD-FISH approach.  ISME Journal 2: 749-759.

Pernthaler, A., A. E. Dekas, C. Titus Brown, S. K. Goffredi, T. Embaye, and V. J. Orphan (2008) Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics.  Proc. Natl. Acad. Sci. 105: 7052-7057.

Jahnke, L., V. J. Orphan, T. Embaye, K. Turk, M. Kubo, R. Summons, and D. Des Marais (2008) Lipid Biomarker and phylogentic analyses to reveal archaeal biodiversity and distribution in hypersaline microbial mat and underlying sediment. GeoBiology 6:394-410.

Tavormina, P. L., W. Ussler III, and V. J. Orphan (2008) Diversity and stratification of aerobic methylotrophs in methane seeps along the North American continental margin. Appl. Environ. Microbiol. 74: 3985–3995.

Goffredi S.K., R. Wilpiszeski, R. W. Lee, and V. J. Orphan (2008) Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale fall in Monterey Canyon (CA). ISME Journal. 2: 204-220

Moran, J., E. Beal, J. M. Vrentas, V. J. Orphan, K. H. Freeman, and C. H. House (2007) Methyl sulfides as intermediates in the anaerobic oxidation of methane. Environ. Microbiol. 10: 162-173.

Treude, T, V. J. Orphan, K. Knittel, J. Gieske, C. H. House, and A. Boetius (2007) Consumption of methane and CO2 by methanotrophic microbial mats from gas seeps of the anoxic Black Sea. Appl. Environ. Microbiol. 73: 2271-2283.

Naehr, T.M., P. Eichhubl, V. J. Orphan, M. Hovland, C. K. Paull, W. Ussler, T. D. Lorenson, and H. G. Greene (2007) Authigenic carbonate formation at hydrocarbon seeps in continental margin sediments: A comparative study. Deep Sea Research II 54:1268-1291.

Goffredi S.K., Orphan V.J. Rouse G.W., Jahnke L., Embaye T., Turk K., Lee R. and Vrijenhoek R.C. (2005) Evolutionary innovation: A bone-eating marine symbiosis. Environ. Microbiol. 7: 1369-78.

Orphan, V. J., W. Ussler III, T. Naehr, K.-U. Hinrichs, C.H. House and C.K. Paull.  (2004) Geological, geochemical, and microbiological heterogeneity of seafloor methane vents in the Eel River Basin, offshore California.  Chem. Geol. 205: 265-289.

Goffredi, S.K., A. Warén, V.J., Orphan, C.L. Van Dover, R.C. Vrijenhoek (2004) Novel forms of structural integration between microbes and a hydrothermal vent gastropod from the Indian Ocean. Appl. Environ. Microbiol. 70: 3082-3090.

Orphan, V. J., J. Boles, S. K. Goffredi, and E. F. Delong (2003) Geochemical influence on community structure and microbial processes in high temperature oil reservoirs. Geomicrobiology Journal, 20: 295-311.

Girguis, P.R., V.J., Orphan, S.J. Hallam, and E.F. Delong (2003) Growth and methane oxidation rates of anaerobic methanotrophic Archaea in a continuous -flow bioreactor. Appl. Environ. Microbiol. 69: 5472-5482.

Orphan, V. J., C.H. House, K.-U. Hinrichs, K.D. McKeegan, and E.F. Delong (2002) Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc. Natl. Acad. Sci. U.S.A., 99(11): 7663-7668.

Orphan, V. J., C.H. House, K.-U. Hinrichs, K.D. McKeegan, and E.F. Delong (2001) Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293: 484-487.

Orphan, V. J., K.-U. Hinrichs, W. Ussler III, C.K. Paull, L.T. Taylor, S. Sylva, J.M. Hayes, and E.F. Delong (2001) Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl. Environ. Microbiol., 67: 1922-1934.

Orphan, V. J., D. Haffenbradl, L. T. Taylor, and E. F. Delong (2000) Culture-dependent and culture-independent characterization of microbial assemblages associated with high temperature petroleum reservoirs.  Appl. Environ. Microbiol., 66: 700-711.

K.-U. Hinrichs, R.R. Summons, V.J. Orphan, S. Sylva, and J.M. Hayes (2000) Molecular and isotopic analysis of anaerobic methane-oxidizing communities in marine sediments. Org. Geochem. 31: 1685-1701.