Victoria Orphan, Ph.D.

Microbial community structure and function in deep subsurface habitats, deep sea marine sediments, oil and gas seeps


Our central aim is to develop enhanced, multidisciplinary laboratory approaches that can be transferred to the marine environment, enabling the quantification of variation in metabolic activities and associated cell-specific protein expression.

Victoria Orphan, Ph.D.

Research Description

One of the greatest roadblocks to understanding microbial interactions and nutrient flow in the environment is the lack of appropriate methodologies to quantitatively study these processes at a meaningful spatial scale. As part of MMI, we are actively engaging in the development and application of compatible fluorescence and stable isotope based methods for tracking the flow of carbon, nitrogen and sulfur within individual environmental microorganisms. When applied in concert with micro/mesocosms, substrate manipulation experiments, and geochemical analyses, we can begin to address fundamental ecological and biogeochemical processes from the prospective of individual cells in the environment. These methods provide a unique and critical perspective on microscale dynamics within ecosystems that is highly synergistic with other, predominately community based ‘omics approaches.

Research Impact

My team has focused on the development of two new ‘tools’ for tracking microbial interactions in the environment as well as continued refining of previously developed methods in the laboratory. Much of this work has been based on visualization techniques which enable direct analysis of general anabolic activity levels and transfer of substrates between physically associated microorganisms. Specifically these include optimization of analytical ion imaging techniques combined with stable isotope tracers (FISHnanoSIMS) for bacteria, archaea, microeukaryotes and viruses and single cell fluorescence detection of transcriptionally active environmental microorganisms (BONCAT).

Specific deliverables from this project include:

  1. Optimize assays to visualize cells that are actively synthesizing proteins in lab cultures and environmental samples
  2. Characterize de novo protein synthesis in microbial communities in laboratory cultures and field experiments
  3. Examine the influence of nutrient stress, energy limitation, and microbial spatial associations on gene and protein expression and the resulting isotopic signatures
  4. Develop stable isotope experiments combined with high resolution nanoSIMS imaging to trace the metabolic links between environmental viruses and their autotrophic hosts and the impact of viral infection on host activity and growth


related links

Marine Microbiology Initiative Science California Institute of Technology, Division of Geology and Planetary Sciences Back


Postdoctoral: NASA AMES RESEARCH CENTER      2002-2004
National Research Council Associate 

Ph.D. Ecology, Evolution, and Marine Biology 

Bachelor’s Aquatic Biology



Editor, Environmental Microbiology 2012-present
Young investigator award: International Society of Microbial Ecology (ISME) 2012
Presidential Early Career Award in Science and Engineering (PECASE) 2011
GAST Lectureship, European Association of Geochemisty 2011
DOE Early Career Research Award 2010
Gordon and Betty Moore Foundation Young Investigator 2005                                           National Research Council Fellowship, NASA Ames Research Center 2001                  


Five most relevant:
1. 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.

2. 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.

3. Beal, E.J., C.H. House, V.J. Orphan (2009) Manganese and Iron Dependent Marine Methane Oxidation: Novel microbial sinks for methane.  Science. 325:184-187.

4. 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

5. 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.

Ten additional publications:
1. Tavormina, PT, W. Ussler III, J. A. Steele, S. A. Connon, M. G. Klotz and V. J. Orphan (2013) Abundance and distribution of diverse membrane-bound monooxygenase (Cu- MMO) genes within the Costa Rica oxygen minimum zone Environ. Microbiol. DOI: 10.1111/1758-2229.12025.

2. Thurber, AR.; Levin, L A.; Orphan, V. J., Marlow, J (2012) Archaea in metazoan diets: implications for food webs and biogeochemical cycling. ISME J. 6: 1602-1612

3. Green-Saxena, A.; Feyzullayev, A.; Hubert, C. R. J.; et al. (2012) Active sulfur cycling by diverse mesophilic and thermophilic microorganisms in terrestrial mud volcanoes of Azerbaijan. Environ. Microbiol. 14: 3271-3286

4. Levin, L. A., V. J. Orphan, G. W. Rouse, A. E. Rathburn, W. Ussler, G. S. 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. of the Royal Society B:  Biological Sciences,  279, 1738, 2580

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

6. Bailey, J. V. Aalman, G. W. Rouse, H. N. Shultz-Vogt, L.A. Levin, V. J. Orphan (2011) Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria ISME J. 5: 1926–1935

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

8. 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), 2207–2215.

9. 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. 12: 344-363.

10. 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.


Affiliated Investigators