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107. Elbon CE, Stewart FJ, Glass JB. 2024. Novel Alphaproteobacteria transcribe genes for nitric oxide transformation at high levels in a marine oxygen-deficient zone. Applied and Environmental Microbiology. E-published ahead of print.


106. Clements CS, Pratte ZA, Stewart FJ, Hay ME. 2024. Removal of detritivore sea cucumbers from reefs increases coral disease. Nature Communications. 15:1338. Open Access Copy. Georgia Tech Press release.


105. Graciette AGC, Hoopes LA, Clauss T, Stewart FJ, Pratte ZA. 2023. The microbiome of African penguins (Spheniscus demersus) under managed care resembles that of wild marine mammals and birds. Scientific Reports. 13:16679. Open Access Copy.

104. Bertagnolli AD, Maritan AJ, Tumolo BB, Fritz SF, Oakland HC, Mohr EJ, Poole GC, Alberston LK, Stewart FJ. 2023. Net-spinning caddisflies create denitrifier-enriched niches in the stream microbiome. ISME Communications. 3:111. Open Access Copy.


103. Pratte ZA, Stewart FJ, Kellogg CA. 2023. Functional gene composition and metabolic potential of deep-sea coral-associated microbial communities. Coral Reefs. Open Access Copy.


102. Anstett J, Plominsky AM, DeLong EF, Kiesser A, Jürgens K, Morgan-Lang C, Stepanauskas R, Stewart FJ, Ulloa O, Woyke T, Maelstrom R, Hallam SJ. 2023. A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters. Scientific Data. 10:332. Open Access Copy.


101. Muratore D, Bertagnolli AD, Bristow LA, Thamdrup B, Weitz JS, Stewart FJ. 2023. Microbial and viral genome and proteome nitrogen demand varies across multiple spatial scales within a marine oxygen minimum zone. mSystems. 8:e01095-22. Open Access Copy.


100. Shaffer… Earth Microbiome Project 500 (EMP500) Consortium. 2022. Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity. Nature Microbiology. 7:2128–2150. Open Access Copy.

99. Henríquez-Castillo CA, Munoz Plominsky A, Ramirez S, Bertagnolli A, Stewart F, Ulloa O. 2022. MetaOmics unveils the contribution of Alteromonas bacteria to carbon cycling in marine Oxygen Minimum Zones. Frontiers in Marine Science. Open Access Copy.

98. Beatty DS, Clements CS, Valayil JM, Jarvis SY, Ritchie KB, Stewart FJ, Hay ME. 2022. Variance of coral anti-pathogen defense in response to transplantation between coral- and macroalgal-dominated reefs. Coral Reefs. Open Access Copy.

97. Fremin… Global Phage Small Open Reading Frame Consortium, et al. 2022. Thousands of small, novel genes predicted in global phage genomes. Cell Reports. Open Access Copy.

96. Clavere Graciette AG, McWhirt ME, Hoopes LA, Bassos-Hull K, Wilkinson KA, Stewart FJ, Pratte ZA. 2022. Microbiome differences between wild and aquarium whitespotted eagle rays (Aetobatus narinari). Animal Microbiome. 4:34. Open Access Copy.


95. Steinsdóttir HGR, Ramírez EG, Mhatre S, Schauberger C, Bertagnolli AD, Pratte ZA, Stewart FJ, Thamdrup B, Bristol LA. 2022. Anaerobic methane oxidation in a coastal oxygen minimum zone: spatial and temporal dynamics. Environmental Microbiology. 24:2361-2379. Open Access Copy.

94. Pratte ZA, Perry C, Dove ADM, Hoopes LA, Ritchie KB, Hueter RE, Fisher C, Newton A, Stewart FJ. 2022. Microbiome structure in large pelagic sharks with distinct feeding ecologies. Animal Microbiome. 4:17. Open Access Copy.

93. Jurgensen SK, Roux S, Schwenck SM, Stewart FJ, Sullivan MB, Brum JR. 2022. Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state. The ISME Journal. 16:972-982. Open Access Copy.

92. Perry CT, Pratte ZA, Clavere-Graciette A, Ritchie KB, Hueter RE, Newton AL, Fischer GC, Dinsdale EA, Doane MP, Wilkinson KA, Bassos-Hull K, Lyons K, Dove ADM, Hoopes LA, Stewart FJ. 2021. Elasmobranch microbiomes: emerging patterns and implications for host health and ecology. Animal Microbiome. 3:61. Open Access Copy.

91. Glass JB, Ranjan P, Kretz CB, Nunn BL, Johnson AM, Xu M, McManus J, Stewart FJ. 2021. Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments. Environmental Microbiology Reports. 23:4646-4660.

90. Rondel F, Hosseini R, Sahoo B, Knyazev S, Mandric I, Stewart F, Mandoiu II, Prozov Y, Zelikovsky A. 2021. Pipeline for analyzing activity of metabolic pathways in planktonic communities using metatranscriptomic data. Journal of Computational Biology. 28:842-855..

89. Caughman AM, Pratte ZA, Patin NV, Stewart FJ. 2021. Coral microbiome changes over the day-night cycle. Coral Reefs. 40 921-935.

88. Patin NV, Dietrich ZA, Stancil A, Quinan M, Beckler JS, Hall ER, Culter J, Smith CG, Taillefert M, Stewart FJ. 2021. Gulf of Mexico blue hole harbors high levels of novel microbial lineages. The ISME Journal. 15:2206-2232.

87. Rogener MK, Hunter KS, Rabalais NN, Roberts BJ, Bracco A, Stewart FJ, Joye SB. 2021. Pelagic denitrification and methane oxidation in oxygen-depleted waters of the Louisiana Shelf. Biogeochemistry.  154: 231-254.

86. Ruiz-Pérez CA, Bertagnolli AD, Tsementzi D, Woyke T, Stewart FJ, Konstantinidis KT. 2021. Description of Candidatus Mesopelagibacter cooxidans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones. Systematic and Applied Microbiology. 44: 126185.


85. Abdelrahman SM, Patin NV, Hanora AM, Aboseidah AA, Desoky SM, Desoky SG, Stewart FJ, Lopanik NB. 2021. The natural product potential of Red Sea nudibranch microbiomes. PeerJ. 9e:19525. Open Access Copy.

84. Clements CS Burns AS, Stewart FJ, Hay ME. 2020. Parasite-host ecology: the limited impacts of an intimate enemy on host microbiomes. Animal Microbiome. 2:42. Open Access Copy.


83. Bertagnolli AD, Konstantinidis KT, Stewart FJ. 2020. Non-denitrifier nitrous oxide reductases dominate marine biomes. Environmental Microbiology Reports. 12: 681-692.


82. Nayfach… IMG/M Data Consortium, et al. 2020. A Genomic Catalogue of Earth’s Microbiomes. Nature Biotechnology.  Open Access Copy.


81. Hotopp JD, Baltrus D, Bruno V, Dennehy J, Gill S, Maresca J, Matthijnssens, Newton I, Putonti C, Rasko D, Roux S, Stajich J, Stedman K, Stewart F, Thrash JC. 2020. Best practices for successfully writing and publishing a genome announcement in Microbial Resource Announcements. Microbial Resource Announcements. 9: e00763-20.


80. Szeinbaum N, Nunn BL, Cavazos AR, Crowe SA, Stewart FJ, DiChristina TJ, Reinhard CT, Glass JB. 2020. Novel insights into the taxonomic diversity and molecular mechanisms of bacterial Mn(III) reduction. Environmental Microbiology Reports. 12:583-593. Link to bioRxiv version.


79. Patin NV, Brown E, Chebli G, Garfield C, Kubanek J, Stewart FJ. 2020. Microbial and chemical dynamics of a toxic dinoflagellate bloom. PeerJ. 8:e9493.  Open Access Copy.


78. Murray AE et al. (63 authors). 2020. A roadmap for naming uncultivated microorganisms. Nature Microbiology. 5:987-994. Open Access Copy.


77. Clements CS, Burns AS, Stewart FJ, Hay ME. 2020. Seaweed-coral competition in the field: effects on coral growth, photosynthesis, and microbiomes require direct contact. Proceedings of the Royal Society B: Biological Sciences. 287:20200366.


76. Kitzinger K, Marchant HK, Bristow LA, Herbold CW, Padilla CC, Kidane AT, Littmann S, Daims H, Pjevac P, Stewart FJ, Wagner M, Kuypers MMM. 2020. Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean.  Nature Communications. 11:767. Open Access Copy.


75. Bray MS, Wu J, Padilla CC, Stewart FJ, Fowle DA, Henny C, Simister RL, Thompson KJ, Crowe SA, Glass JB. 2020. Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes. Environmental Microbiology Reports.  12:49-57. Abstract.


74. Canfield DE, Kraft B, Löscher C, Boyle RA, Thamdrup B, Stewart FJ. 2019. The regulation of oxygen to low concentrations in marine oxygen-minimum zones. Journal of Marine Research.  77:297-324. PDF


73. Beatty DS, Valayil JM, Clements CS, Ritchie KB, Stewart FJ, Hay ME. 2019. Variable effects of local management on coral defenses against a thermally-regulated bleaching pathogen. Science Advances. 5:eaay1048. Open Access Copy.


72. Beinart RA, Luo C, Konstantinidis KT, Stewart FJ, Girguis PR. 2019. The bacterial symbionts of closely related hydrothermal vent snails with distinct geochemical habitats show broad similarity in chemoautotrophic gene content. Frontiers in Microbiology. 10:1818.  Open Access Copy.


71. Thamdrup B, Steinsdóttir HGR, Bertagnolli AD, Patin NV, Padilla CC, García-Robledo E, Bristow LA, Stewart FJ. 2019. Anaerobic methane oxidation is an important sink for methane in the ocean’s largest oxygen minimum zone. Limnology & Oceanography. 64:2569-2585.


70. Lau E, Frame CH, Nolan IV EJ, Stewart FJ, Dillard ZW, Lukich DP, Mihalik NE, Yauch KE, Kinker MA, Waychoff SL. 2019. Diversity and relative abundance of nitrifying microorganisms in the offshore Namibian hypoxic zone. PLoS ONE.14:e0217136.  Open Access Copy.


69. Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CR, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Mark Welch DB, Martiny JBH, Moran MA, Orphan V, Reay D, Remais JV, Rich V, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster N. 2019. Scientists’ Warning to Humanity: microorganisms and climate change. Nature Reviews Microbiology. 17:569-586. Open Access Copy.


68. Patin NV, Locklear S, Stewart FJ, Lopanik NB. 2019. Symbiont frequency predicts microbiome composition in a model bryozoan-bacterial symbiosis. Aquatic Microbial Ecology.  83:1-13.

67. Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, Könneke M, Littmann S, Mooshammer M, Niggemann J, Petrov S, Richter A, Stewart FJ, Wagner M, Kuypers MMM, Bristow LA. 2019. Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment. Nature Microbiology.  4:234-243. Open Access Copy.  News Article.


66. Parris DJ, Morgan MM, Stewart FJ.  2019.  Feeding rapidly alters microbiome composition and gene transcription in the clownfish gut. Applied and Environmental Microbiology. 83:e02479-18.  doi:10.1128/AEM.02479-18.


65. Pratte ZA, Patin NV, McWhirt ME, Caughman AM, Parris DJ, Stewart FJ. 2018. Association with a sea anemone alters the skin microbiome of clownfish. Coral Reefs, 37:1119-1125.  Abstract.  News Article.  YouTube video.


64. Burns AS, Padilla CC, Pratte ZA, Gilde K, Regensburger M, Hall E, Dove ADM, Stewart FJ. 2018. Broad phylogenetic diversity associated with nitrogen loss through sulfur oxidation in a large public marine aquarium.  Applied and Environmental Microbiology. 84: e01250-18. doi:10.1128/AEM.01250-18. Link to News Article.


63. Bertagnolli AD, Stewart FJ. 2018. Microbial niches in marine oxygen minimum zones. Nature Reviews Microbiology.  16:723-729.  Abstract.


62. Fareed S, Sarode N, Stewart FJ, Malik A, Laghale E, Khizer S, Yan F, Pratte Z, Lewis J Immergluck I. 2018. Applying fecal microbiota transplantation (FMT) to treat recurrent Clostridium difficile infections (rCDI) in children. PeerJ. 6:e4663.  Open Access Copy.


61. Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, Bourbonnais A, Altabet MA, Woyke T, Ulloa O, Konstantinidis KK, Thamdrup B, Stewart FJ. 2018. Genomic evidence for the use of alternative nitrogen substrates by anammox bacteria. The ISME Journal. 12:2706-2722. View only version.


60. Patin NV, Pratte ZA, Regensburger M, Hall E, Gilde K, Dove ADM, Stewart FJ. 2018. Microbiome dynamics in a large artificial seawater aquarium. Applied and Environmental Microbiology. 84:e00179-18.  Open Access Copy.  News Article.  Science Matters Podcast.


59. Pratte ZA, Besson M, Hollman RD, Stewart FJ. 2018. The gills of reef fish support a distinct microbiome influenced by host-specific factors.  Applied and Environmental Microbiology. 84:e00063-18.  DOI: 10.1128/AEM.00063-18.


58. Beatty DS, Clements CS, Stewart FJ, Hay ME. 2018. Inter-generational effects of macroalgal reef dominance on coral: major declines in survival of coral larvae but subtle changes in microbiomes. Marine Ecology Progress Series. 589:97-114. Open Access Copy.


57. Sharp KH, Pratte ZA, Kerwin AH, Rotjan RD, Stewart FJ. 2017. Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata. Microbiome. 5:120.  Open Access Copy.


56. Pratte ZA Longo GO, Burns AS, Hay ME, Stewart FJ. 2017. Contact with turf algae alters the coral microbiome: contact versus systemic impacts.  Coral Reefs. 37:1-13.  doi:10.1007/s00338-017-1615-4


55. Bertagnolli AD, Padilla CC, Glass JB, Thamdrup B, Stewart FJ. 2017. Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column. Environmental Microbiology. 19:4392-4416.  DOI: 10.1111/1462-2920.13879


54. Hay ME, Beatty DS, Stewart FJ. 2017. Chemical ecology: the language of microbiomes.  In: Exploring the Chemistry of Microbiomes.  National Academies Proceedings Series.


53. Garcia-Robledo E, Padilla CC, Aldunate M, Paulmier A, Gregori G, Stewart FJ, Ulloa O, Revsbech NP. 2017. Cryptic oxygen cycling in anoxic marine zones. Proceedings of the National Academy of Sciences of the USA. 114:8319-8324. doi: 10.1073/pnas.1619844114


52. Vik DR, Roux S, Brum JR, Bolduc B, Emerson JB, Padilla CC, Stewart FJ, Sullivan MB. 2017. Putative Archaeal viruses from the mesopelagic ocean. PeerJ. 5:e3428. Open Access Copy.

51. Bray MS, Wu J, Reed BC, Kretz CB, Stewart FJ, DiChristina TJ, Brandes JA, Fowle DA, Crowe SA, Glass JB. 2017.  Shifting microbial communities sustain multi-year iron reduction and methanogenesis in ferruginous sediment communities.  Geobiology. 15:678-689.  DOI: 10.1111/gbi.12239


50. Padilla CC, Bertagnolli AD, Bristow LA, Sarode N, Glass JB, Thamdrup B, Stewart FJ. 2017. Metagenomic binning recovers a transcriptionally active Gammaproteobacterium linking methanotrophy to partial denitrification in an anoxic oxygen minimum zone. Frontiers in Marine Science.  4:23. Open Access Copy.


49. Parris DJ, Brooker RM, Morgan MA, Dixson DL, Stewart FJ. 2016. Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement.  PeerJ. 4:e2412  Open Access Copy


48. Tsementzi D, Wu J, Deutsch S, Nath N, Rodriguez-R LM, Burns AS, Ranjan P, Sarode N, Malmstrom RR, Padilla CC, Stone BK, Bristow LA, Larsen M, Glass JB, Thamdrup B, Woyke T, Konstantinidis KT, Stewart FJ. 2016. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature. 536:179-183. doi:10.1038/nature19068  A view only version is available here.  News Article.


47. Seston SL, Beinart R, Sarode N, Shockey AC, Ranjan P, Ganesh S, Girguis PR, Stewart FJ. 2016. Metatranscriptional response of chemoautotrophic Ifremeria nautilei endosymbionts to differing sulfur regimes. Frontiers in Microbiology. 7:1074. Open Access Copy.


46. Larsen M, Lehner P, Borisov SM, Klimant I, Fischer J, Stewart FJ, Canfield DE, Glud RN. 2016. In situ quantification of ultra-low O2 concentrations in oxygen minimum zones. Limnology & Oceanography Methods. 14:784-800. doi:10.1002/lom3.10126


45. Beckler JS, Kiriazis N, Rabouille C, Stewart FJ, Taillefert M. 2016. Importance of microbial iron reduction in deep sediments of river-dominated continental margins.  Marine Chemistry. 178:22-34. Abstract.


44. Padilla CC, Bristow LA, Sarode N, Garcia-Robledo E, Gomez Ramirez E, Benson CR, Bourbonnais A, Altabet MA, Girguis PR, Thamdrup B, Stewart FJ. 2016. NC10 bacteria in marine oxygen minimum zones. The ISME Journal. 10:2067-2071. Open Access Copy.


43. Glass JB, Kretz CB, Ganesh S, Ranjan P, Seston SL, Buck KN, Landing WL, Morton PL, Moffett JW, Giovannoni SJ, Vergin KL, Stewart FJ. 2015. Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones. Frontiers in Microbiology. 6:998. Open Access copy.


42. Bristow LA, Sarode N, Cartee J, Caro-Quintero A, Thamdrup B, Stewart FJ. 2015. Biogeochemical and metagenomic analysis of nitrite accumulation in the Gulf of Mexico hypoxic zone. Limnology & Oceanography. 60:1733-1750. Open Access Copy.


41. Padilla CC, Ganesh S, Gantt S, Huhman A, Parris DJ, Sarode N, Stewart FJ. 2015. Standard filtration practices may significantly distort planktonic microbial diversity estimates. Frontiers in Microbiology. 6:547. Open Access Copy.


40. Duret MT, Pachiadaki MG, Stewart FJ, Sarode N, Christaki U, Monchy S, Edgcomb VP. 2015. Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone. FEMS Microbiology Ecology. 91. fiv037. Open Access Copy.


39. Ganesh S, Bristow LA, Larsen M, Sarode N, Thamdrup B, Stewart FJ. 2015. Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone. The ISME Journal. 9:2682-2696. Open Access Copy.


38. Sarode N, Parris DJ, Ganesh S, Seston SL, Stewart FJ. 2015. Generation and analysis of microbial metatranscriptomes. Manual of Environmental Microbiology, Fourth Edition.


37. Parris DJ, Ganesh S, Edgcomb VP, DeLong EF, Stewart FJ. 2014. Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile. Frontiers in Microbiology. 5:543. Open Access Copy.


36. Dalsgaard T, Stewart FJ, Thamdrup B, De Brabandere L, Revsbech NP, Ulloa O, Canfield DE, DeLong EF. 2014. Oxygen at nanomolar levels reversibly suppresses process rates and gene expression of anammox and denitrification in the oxygen minimum zone off northern Chile. mBio, 5(6), e01966-14. Open Access Copy. 


35. Dmytrenko O, Russel SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton ILG, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. 2014. The genome of the intracellular bacterium of the coastal bivalve Solemya velum: A blueprint for thriving in and out of symbiosis. BMC Genomics. 15:924. Open Access Copy.


34. Lee FJ, Rusch D, Stewart FJ, Mattila HR, Newton ILG. Saccharide breakdown and fermentation by the honey bee gut microbiome. Environmental Microbiology. 17:796-815.
Abstract PDF


33. Lin Y, Cradick TJ, Brown MT, Deshmukh H, Ranjan P, Sarode N, Wile BM, Vertino PM, Stewart FJ, Bao G. 2014. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Research. 42:7473-7485. Open Access Copy. 

32. Stewart FJ, Ulloa O. 2014. Microbial metagenomics of oxygen minimum zones. Marco D (ed.) Metagenomics of the Microbial Nitrogen Cycle: Current innovations and future trends. Horizon Scientific Press. Book access


31. Ganesh S, Parris DJ, DeLong EF, Stewart FJ. 2014. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. The ISME Journal. 8:187-211. Open Access Copy. 


30. Stewart FJ. 2013. Where the genes flow. Nature Geoscience. 6:688-690. Abstract.


29. Stewart FJ. 2013. Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton. Methods in Enzymology. 531:187-218. Abstract.


28. Cavanaugh, CM, McKiness ZP, Newton ILG, Stewart FJ. 2013. Marine chemosynthetic symbioses. In: Rosenberg et al. (eds). The Prokaryotes. 1:579-607. Springer-Verlag, New York. Book Access


27. Sanders JG, Beinart RA, Stewart FJ, DeLong EF, Girguis PR. 2013. Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts. The ISME Journal. 7:1556-1567. Open Access


26. Dimond JL, Kerwin AH, Rotjan R, Sharp K, Stewart FJ, Thornhill DJ. 2013. A simple temperature-based model predicts the upper latitudinal limit of the temperate coral Astrangia poculata. Coral Reefs. 32:401-409. Abstract.


25. Ulloa O, Canfield DE, DeLong EF, Letelier RM, Stewart FJ. 2012. Perspective: Microbial oceanography of anoxic oxygen minimum zones. Proceedings of the National Academy of Sciences of the USA. 109:15996-16003. Open Access Copy


24. 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. 7:e37118. Open Access Copy


23. 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. 93:1659-1673. Abstract


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


21. Stewart FJ, 2011. Dissimilatory sulfur cycling in oxygen minimum zones: an emerging metagenomics perspective. Biochemical Society Transactions. 39:1859-11863.
PubMed PDF


20. Stewart FJ, Dmytrenko O, DeLong EF, Cavanaugh CM. 2011. Metatranscriptomic analysis of sulfur oxidation genes in the endosymbiont of Solemya velum. Frontiers in Microbiology. 2:134. Open Access Copy.


19. 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. Book Access


18. 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. Open Access Copy


17. 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. Abstract. PDF. Perspectives Article PDF.


16. Stewart FJ, Ottesen EA, DeLong EF. 2010. Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. The ISME Journal. 4:896-907. Open Access CopyProtocol


15. Roeselers G, Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson P, Barry K, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. 2010. Complete genome sequence of Candidatus Ruthia magnifica. Standards in Genomics Sciences. 3:163-173. Open Access Copy.


14. Stewart FJ, Baik AHY, Cavanaugh CM. 2009. Genetic subdivision of chemosynthetic endosymbionts of Solemya velumalong the southern New England coast. Applied and Environmental Microbiology. 75:6005-6007. Open Access Copy.


13. 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. AbstractPDF


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


11. 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 Res. Pt II. 55:2059-2067. Abstract. PDF


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


9. 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. AbstractPDF


8. 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. Abstract. PDF


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


6. 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. Springer, New York.
Book Access PDF


5. 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. 6:735-813. Open Access CopyPDF


4. Stewart FJ, Cavanaugh CM. 2005. Symbiosis of thioautotrophic bacteria with Riftia pachyptila. In: Overmann, J. (ed.). Molecular Basis of Symbiosis. Prog. Mol. Subcell. Biol. vol-41. Springer Berlin Heidelberg. p.197-225.
Book Access. PDF


3. Stewart FJ, Newton ILG, Cavanaugh CM. 2005. Chemosynthetic endosymbioses: adaptations to oxic-anoxic interfaces. Trends in Microbiology. 13:439-448. Abstract.  PDF


2. 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 Unites States. 33:38-41. Open Access Copy.


1. Stewart FJ, Fritsen CH. 2004. Bacteria-algae relationships in Antarctic sea ice. Antarctic Science. 16:143-156. AbstractPDF

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