Stewart FJ, Dalsgaard T, Thamdrup B, Revsbech NP, Ulloa O, Canfield DE, and DeLong EF. Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton. PLoS ONE. In press.

Bryant JA, Stewart FJ, Eppley JM, and DeLong EF. 2012. Microbial community phylogenetic and trait diversity decline steeply with depth in a marine oxygen minimum zone. Ecology. In press.

Stewart FJ, Ulloa O, DeLong EF. 2012. Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environmental Microbiology. 14:23-40. pdf copy

Stewart FJ, 2011. Dissimilatory sulfur cycling in oxygen minimum zones: an emerging metagenomics perspective. Biochem. Soc. Trans. 39: 1859-63. pdf copy

Stewart FJ, Dmytrenko O, DeLong EF, Cavanaugh CM. 2011. Metatranscriptomic analysis of sulfur oxidation genes in the endosymbiont of Solemya velum. Front. Microbiol. 2:134. pdf copy

Stewart FJ, Cavanaugh CM. Pyrosequencing analysis of endosymbiont diversity.  2011. In: de Bruijn FJ (ed.). Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats.  Wiley-Blackwell. In press.

Stewart FJ, Sharma AK, Bryant JA, Eppley JM, DeLong EF. 2011. Community transcriptomics reveals universal patterns of protein sequence conservation in microbial communities. Genome Biology. 12:R26. link to Open Access copy

Canfield DE, Stewart FJ, Thamdrup B, De Brabandere L, Dalsgaard T, DeLong EF, Revsbech NP, Ulloa O. 2010. A cryptic sulfur cycle in oxygen-minimum zone waters off the Chilean Coast. Science. 330: 1375-1378. link to copy, pdf of Perspectives Article (A. Teske)

Stewart FJ, Ottesen EA, DeLong EF. 2010. Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J. 4: 896-907. pdf copy, protocol

Stewart FJ, Baik AHY, Cavanaugh CM. 2009. Genetic subdivision of chemosynthetic endosymbionts of Solemya velum along the southern New England coast. Applied and Environmental Microbiology. 75:6005-6007. pdf copy

Stewart FJ, Cavanaugh CM. 2009. Pyrosequencing analysis of endosymbiont population structure: co-occurrence of divergent symbiont lineages in a single vesicomyid host clam. Environmental Microbiology. 11:2136-2147. pdf copy

Stewart FJ, Young CR, Cavanaugh CM. 2009. Evidence for homologous recombination in intracellular chemosynthetic clam symbionts. Molecular Biology and Evolution. 26: 1391-1404. pdf copy

Fritsen CH, Memmott JC, Stewart FJ.  2008. Inter-annual sea ice dynamics and micro-algal biomass in winter pack ice: Marguerite Bay, Antarctica.  Deep-Sea Research Part II. 55:2059-2067. pdf copy

Stewart FJ, Young CR, Cavanaugh CM. 2008. Lateral symbiont acquisition in a maternally transmitted chemosynthetic clam endosymbiosis. Molecular Biology and Evolution. 25:673-687. pdf copy

Stewart FJ, Cavanaugh CM. 2007. Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in Bacteria. Journal of Molecular Evolution. 65:44-67. pdf copy

Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Detter JC, Wu D, Eisen JA, Cavanaugh CM. 2007. The Calyptogena magnifica chemoautotrophic symbiont genome. Science. 315:998-1000. pdf copy

Stewart FJ, Cavanaugh CM. 2006. Bacterial endosymbioses in Solemya (Mollusca, Bivalvia): model systems for studies of symbiont-host adaptation. Antoine van Leeuwenhoek. 90:343-360. pdf copy

Cavanaugh CM, McKiness ZP, Newton ILG, Stewart FJ. 2006. Marine chemosynthetic symbioses.  In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds.). The Prokaryotes. Third Edition. A Handbook on the Biology of Bacteria:Symbiotic Associations, Biotechnology, Applied Microbiology. Springer, New York. pdf copy

Mix LJ, Armstrong JC, Mandell AM, Mosier AC, Raymond J, Raymond SN, Stewart FJ, von Braun K, Zhaxybayeva O (eds.). 2006. The Astrobiology Primer: An outline of general knowledge.  Astrobiology. 6(5):735-813. pdf copy

Stewart FJ, Cavanaugh CM. 2005. Symbiosis of thioautotrophic bacteria with Riftia pachyptila. In: Overmann, J. (ed.). Molecular Basis of Symbiosis. Springer-Verlag, Berlin. p.197-225. pdf copy

Stewart FJ, Newton ILG, Cavanaugh CM. 2005. Chemosynthetic endosymbioses: adaptations to oxic-anoxic interfaces. Trends in Microbiology. 13(9): 439-448. pdf copy

Stewart FJ, Fritsen CH, Garrison DL. 2005. Bacteria-algae associations in the sea ice and upper water column of the Ross Sea in late austral summer.  Antarctic Journal of the United States. 33: 38-41. pdf copy

Stewart FJ, Fritsen CH. 2004. Bacteria-algae relationships in Antarctica sea ice. Antarctic Science. 16(2): 143-156. pdf copy

Stewart FJ. 2000. Bacteria and bacteria-phototroph associations in ice habitats of the Ross Sea and the McMurdo Dry Valleys, Antarctica. undergraduate thesis. Middlebury College.

In collaboration w/ Bristow LA (lead author), Altabet MA, Ulloa O, and DeLong EF. Enriched nitrate and depleted nitrite isotopic signatures in the OMZ off Northern Chile. (tentative title)