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Green-Saxena, A., Dekas, A. E., Dalleska, N. F., & Orphan, V. J. (2013). Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane. The ISME journal.

Dekas, A. E., Chadwick, G. L., Bowles, M. W., Joye, S. B., & Orphan, V. J. (2013). Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea. Environmental Microbiology.

Ussler III, W., Preston, C., Tavormina, P., Pargett, D., Jensen, S., Roman, B., Orphan,V, Scholin, C. (2013). Autonomous Application of Quantitative PCR in the Deep Sea: In Situ Surveys of Aerobic Methanotrophs Using the Deep-Sea Environmental Sample Processor. Environmental science & technology, 47(16), 9339-9346.

Bailey, J. V., Corsetti, F. A., Greene, S. E., Crosby, C. H., Liu, P., & Orphan, V. J. (2013). Filamentous sulfur bacteria preserved in modern and ancient phosphatic sediments: implications for the role of oxygen and bacteria in phosphogenesis. Geobiology.

Yang, Song, Janet B. Matsen, Michael Konopka, Abigail Green-Saxena, Justin Clubb, Martin Sadilek, Victoria J. Orphan, David Beck, and Marina G. Kalyuzhnaya. (2013) "Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. Metabolomics and 13C-labeling study." Frontiers in microbiology 4 .

Tocheva, E. I., Dekas, A. E., McGlynn, S. E., Morris, D., Orphan, V. J., & Jensen, G. J. (2013). Polyphosphate storage during sporulation in the Gram-negative bacterium Acetonema longum. Journal of bacteriology, 195(17), 3940-3946.

Green-Saxena, A et al. (2012) Active sulfur cycling by diverse mesophilic and thermophilic microorganisms in terrestrial mud volcanoes of Azerbaijan. Environ. Microbiol.

Tavormina, P et al. (in press) Abundance and distribution of diverse membrane-bound monooxygenase (Cu-MMO) genes within the Costa Rica oxygen minimum zone. Environ. Microbiol. Reports

McGlynn, S, E. S Boyd, J.W. Peters, V. J. Orphan (2012) Classifying metal dependence of uncharacterized nitrogenases. Frontiers in Microbiological Chemistry

Glass JB and Orphan VJ (2012) Trace metal requirements for microbial enzymes involved in the production and consumption of methane and nitrous oxide. Front. Microbio. 3:61. doi: 10.3389/ fmicb.2012.00061

Thurber, A.R, L.A. Levin, V. J. Orphan and J. J Marlow (2012) Archaea in metazoan diets: implications for food webs and biogeochemical cycling. ISME J.

Levin, L.A., V.J. Orphan, G.W. Rouse, A.E. Rathburn, W. Ussler III, G. Cook, S.K. Goffredi, E. M. Perez, A. Waren, B.M. Grupe, G. Chadwick, B Strickrott. (2012) A hydrothermal seep on the Costa Rica margin: middle ground in a continuum of reducing ecosystems. Proc. Royal. Soc. B. doi:10.1098/rspb.2012.0205

Harrison, B.K. and V.J. Orphan (2012) Method for assessing mineral composition dependent patterns in microbial diversity using magnetic and density separation. Geomicrobiology Journal. 29:435-449.

Orphan, VJ and Hoehler, TM (2011) MICROBIOLOGY: Hydrogen for dinner. Nature 476:154-155.

Orphan, V.J. (2011) Getting Cozy: hidden microbial interactions in nature. Environ. Microbiol. Reports 3: 16-18.

Newman, D.K, V.J. Orphan and A. Reysenbach (in press) "Molecular Biology's contribution to Geobiology".

Shapiro, OH; Hatzenpichler, R; Buckley, DH; Zinder, SH; Orphan, VJ (2011). Multicellular photo-magnetotactic bacteria. Environ. Microbiol. Reports 3: 233-238.

Bailey, J. V, V. Salman, G.W. Rouse, H.N. Schulz-Vogt, L.A. Levin and V.J. Orphan (2011) Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria. ISME J. doi:10.1038/ismej.2011.66

Dekas, AE and V.J. Orphan (2011) "Identification of diazotrophic microorganisms in marine sediments via fluorescence in situ hybridization coupled with secondary ion mass spectrometryIn: METHODS IN ENZYMOLOGY: RESEARCH ON NITRIFICATION AND RELATED PROCESSES. Ed. M. Klotz. 486: 281-305.

Tavormina, P.L., V.J. Orphan, Marina K, M. Jetten and M. Klotz (2011) A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gamma-proteobacterial methanotrophs. Environ. Microbiol. Reports. 3: 91-100.

Tavormina, P. L., W. Ussler III, S.M. Joye and V. J. Orphan (2010) Distributions of putative aerobic methanotrophs in diverse pelagic marine environments. ISME J. 4:700-710

Goffredi, S.K. and V.J. Orphan(2010) Bacterial community shifts in taxa and diversity in response to localized organic loading in the deep sea. Environ. Microbiol. [PDF]

Bailey, J.V., V.J. Orphan, S.M. Joye, F. A. Corsetti (2009) Chemotrophic microbial mats and their potential for preservation in the rock record. Astrobiology [PDF]

Bailey, J.V., T. Raub, N. Meckler, B. K. Harrison, T. Raub, A. Green, V.J. Orphan (2010) Pseudofossils in relict methane seep carbonates resemble endemic microbial consortia. Palaeogeography, Palaeoclimatology, Palaeoecology. 285:131-142. [PDF]

Dekas, A.D., R. S. Poretsky, and V.J. Orphan (2009) Deep-sea archaea fix and share nitrogen in methane-consuming microbial consortia. Science. 326: 422-426. [PDF] Perspective

Fike, D.A., N. Finke, G. Blake, J. Zha, T.M. Hoehler, V.J. Orphan (2009) The effect of sulfate concentration on (sub)millimeter-scale sulfide δ34S in hypersaline cyanobacterial mats over the diurnal cycle. Geochem. et Cosmochem. Acta. 73: 6187-6204. [PDF]

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

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): 1777â€"1791.[PDF]

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. [PDF]

Orphan, V.J. (2009) Methods for unveiling cryptic microbial partnerships in nature. Current Opinion Microbiology. 12:231â€"237. [PDF]
House, C.H., V.J. Orphan, K.A. Turk, B. Thomas, A. Pernthaler, J.M. Vrentas, S.B. Joye (2009) Extensive carbon isotopic heterogeneity among methane seep microbiota. Environ. Microbiol. 11(9), 2207â€"2215. [PDF]
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. [PDF]

Orphan, V.J., C.H. House, S.K. Goffredi (2008) Archaea, Methane, and Oases of the Deep. Nova Acta Leopoldina NF 96, Nr. 356:19-23.

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. [PDF]
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. [PDF]

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. [PDF] SupplementPatent

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. [PDF]

Tavormina, P. L., W. Ussler III, and V. J. Orphan (2008)Planktonic and Sediment-Associated Aerobic Methanotrophs in Two SeepSystems along the North American Margin. Appl. Environ. Microbiol. 74: 3985â€"3995.[PDF]
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. [PDF]Highlights

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. [PDF]

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. [PDF]

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. [PDF]

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. [PDF]
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. [PDF]

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.[PDF]

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. [PDF]

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. [PDF]

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. [PDF]

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. [PDF]

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. [PDF]

Orphan, V. J., D. Hafenbradl, 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. [PDF]

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. [PDF]