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Bernhard, J.M., Edgcomb, V.P., McIntyre-Wressnig, A., Summons, R.E., Visscher, P.T., Jeglinski, M. Benthic foraminifera in co-occurring extant microbialites: impact on sediment fabric. PNAS in press.

Burgaud, G., Woehlke, S., Redou, V., Orsi, W., Beaudoin, D., Barbier, G., Biddle, J.F., Edgcomb, V.P. Deciphering presence and activity of fungal communities in marine sediments using a model estuarine system. Aquatic Microbial Ecol in press.

Edgcomb, V.P., Bernhard JM. Heterotrophic protists in hypersaline microbial mats and deep hypersaline basin water columns. Special Issue “Extremophiles and Extreme Environments” Life in press. 

Orsi, W., Edgcomb, V.P., Christman, G.D., and Biddle, J.F. Gene expression in the deep biosphere. Nature in press.

Orsi, W., Biddle, J., and Edgcomb, V.P. 2013. Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces.  PLoS ONE 8(2): e56335.doi:10. 1371/journal.pone.0056335.

Edgcomb, V.P., R.E. Summons, J.M. Bernhard, D. Beaudoin, S. Pruss, A. Gillespie. 2013. Microbial diversity in oolitic sands of Highborne Cay, Bahamas. Geobiology doi: 10.1111/gbi.12029.

Filker, S., Stock, A., Breiner, H.W., Edgcomb, V.P., Orsi, W., Yakimov, M.M., and Stoeck, T. 2012. Environmental selection of protistan communities in hypersaline anoxic deep-sea basins, Eastern Mediterranean Sea. In press, MicrobiologyOpen.

Orsi, W. and Edgcomb, V.P. 2012, Microbial eukaryotes in marine oxygen minimum zones. In: Seckbach, J., Oren, A., and Stan-Lotter, H. (eds.), COLE Series: Polyextremophiles – Organisms Living Under Multiple Stress, Springer Verlag; in press.

Edgcomb, V.P. and Orsi, W. 2012, Microbial eukaryotes in hypersaline anoxic deep sea basins. In: Seckbach, J., Oren, A., and Stan-Lotter, H. (eds.), COLE Series: Polyextremophiles – Organisms Living Under Multiple Stress, Springer Verlag; in press.

Orsi, W., S. Charvet, J. Bernhard, and Edgcomb, V.P. 2012, Prevalence of partnerships between bacteria and ciliates in oxygen-depleted marine water columns. Frontiers in Extreme Microbiol.3:341. doi: 10.3389/fmicb.2012.00341. 

Bernhard, J.M., Casciotti, K.L., McIlvin, M.R., Beaudoin, D.J., Visscher, P.T., and Edgcomb, V.P.Potential importance of physiologically diverse benthic foraminifera in sedimentarty nitrate storage and respiration.JGR Biogeosciences 117, G03002, doi:10.1029/2012JG001949

Orsi, W., Y.C. Song, S. Hallam, and Edgcomb, V.P. 2012. Effect of oxygen minimum zone formation on communities of marine protists. ISME Journal, doi: 10.1038/ismej.2012.7

Beaudoin, D.J., J.M. Bernhard, and Edgcomb, V.P. 2012. A novel ciliate (Ciliophora: Hypotrichida) isolated from bathyal anoxic sediments. In press. In: A. Altenbach, J. Bernhard, and J. Seckbach (eds.) Anoxia: Paleontological Strategies and Evidence for Eukaryote Survival Springer-Verlag. 147-152.

Orsi, W., Edgcomb, V.P., Faria, J., Foissner, W., Fowle, W.H., Hohnmann, T., Suarez, P., Taylor, C., Taylor, G.T., Vd’acny, P., and Epstein, S.  2012. Class Cariatrichea, a novel ciliate taxon from the anoxic Cariaco Basin, Venezuela. In press, The International Journal of Systematic and Evolutionary Microbiology.

Bernhard, J.M., Edgcomb, V.P., Casciotti, K.L., McIlvin, M.R., and Beaudoin, D.J. 2011. Denitrification likely catalyzed by endobionts in an allogromiid foraminifer  ISME Journal 6(5):951-60.

Stock, A., Breiner, H.-W., Pachiadaki, M., Edgcomb, V.P., Filker, S., LaCono, V., Yakimov, M., Stoeck, T. 2011. Microbial eukaryote life in the new hypersaline deep-sea basin Thetis. Extremophiles 16(1):21-34.

Edgcomb, V.P., W. Orsi, H.-W. Breiner, M.M. Yakimov, and T. Stoeck. in press. Novel kinetoplastids associated with hypersaline anoxic lakes in the Eastern Mediterranean deep-sea. Deep Sea Research 58(10):1040-1048.

Edgcomb, V.P., Leadbetter, E.R., Bourland, W., Beaudoin, D., and Bernhard, J.M. 2011. Structured multiple endosymbiosis of bacteria and archaea in a ciliate from marine sediments: A survival mechanism in low oxygen, sulfidic sediments? Frontiers in Microbial Physiology and Metabolism 2: doi: 10.3389/fmicb.2011.00055.

Edgcomb, V.P., Orsi, W., Bunge, J., Jeon, S.-O., Christen, R.,  Leslin, C., Holder, M., Taylor, G.T., Suarez, P., Varela, R., and Epstein, S. 2011. Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs. Sanger insights into species richness. ISME J 5:1344-1356.

Edgcomb, V.P., Orsi, W., Taylor, G.T., Vdacny, P., Taylor, C.,  Suarez, P., and Epstein, S. 2011. Accessing marine protists from the anoxic Cariaco Basin. ISME J. 5:1237-1241.

Orsi, W., Edgcomb, V.P., Jeon, S.O., Leslin, C., Bunge, J., Taylor, G.T., Varela, R, and S. Epstein. 2011. Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization. ISME J 5:1357-1373.

Beaudoin, D.J., J.M. Bernhard, and Edgcomb, V.P. 2011. A novel ciliate (Ciliophora: Hypotrichida) isolated from bathyal anoxic sediments. In press. In: J. Seckbach (ed.) Anoxia: Paleontological Strategies and Evidence for Eukaryote Survival Springer-Verlag

Edgcomb, V.P., and Biddle, J. 2011.  Microbial eukaryotes in the marine subsurface? In: J. Seckbach (ed.) Anoxia: Paleontological Strategies and Evidence for Eukaryote Survival Springer-Verag

Edgcomb, V., and Stoeck, T. 2011. Massively parallel tag sequencing unveils the complexity of marine protistan communities in oxygen-depleted habitats. In: M. Harbers and G. Kahl (eds.) Tag-based Approaches for Next Generation Sequencing, Wiley-Blackwell-VCH, Weinheim.

Edgcomb, V.P., Beaudoin, D., Gast, R., Biddle, J., and Teske, A. 2010, Marine subsurface eukaryotes: the fungal majority. Environ. Microbiol. 13(1):172-183.

Edgcomb, V.P., Breglia, S.A., Yubuki, N., Beaudoin, D., Patterson, D.J., Leander, B.S., and Bernhard, J.M. 2010., Identity of epibiotic bacteria on symbiontid euglenozoans in O2-depleted marine sediments: evidence for symbiont and host co-evolution. ISME J.  5:231-243

Teske, A., Edgcomb, V., Rivers, A., Thompson, J.R., Gomez, A.D.V., Molyneaux, S.J., and Wirsen, C.O., 2009, Toward a molecular and physiological survey of the Jannasch lab Thermococcus and Pyrococcus culture collection, Extremophiles 13(1):151-167.

Stoeck, T.A., Behnke, A., Christen, R., Amaral-Zettler, L., Rodrigues-Mora, M.J., Chisterserdov, A., Orsi, W., and Edgcomb, V., 2009, Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities, BMC Biology 7:72 doi:10.1186/1741-7007-7-72.

Stoeck, T., and Edgcomb, V., 2009, Role of protists in microbial interactions with hydrocarbons, In: K. N. Timmis (ed.) Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds, Springer-Verlag.

Behnke, A., Engel, M, Edgcomb, V., and Stoeck, T., 2009, Studying the in situ role of protistan communities in hydrocarbon contaminated water samples via community profiling and CARD-FISH, In: K. N. Timmis (ed.) Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds,  Springer-Verlag.

Fernandez-Delgado, M., Garcia-Amado, M.A., Contreras, M., Edgcomb, V., Vitelli, J., Gueneau, P., and Suarez, P., 2009, Vibrio cholerae non-01, non-0139 associated with seawater and plankton fromn coastal marine areas of the Caribbean Sea, Journal of Environmental Health Research, 19(4):279-289.

Santelli, C.M., Bach, W., Edgcomb, V., and Edwards, K.J., 2009, The diversity and abundance of bacteria inhabiting seafloor lavas positively correlate with rock alteration, Environmental Microbiology, 11(1):86-98.

Yubuki, N., Edgcomb, V.P., Bernhard, J.M., and Leander, B.S., 2009, Cellular identity of a diverse group of deep sea, anoxic euglenozoans with epibiotic bacteria: Ultrastructure and molecular phylogeny of Calkinsia aureus from the Santa Barbara Basin (California, USA),  BMC Microbiology, 9:16.

Edgcomb, V., Orsi, W., Leslin, C., Epstein, S.S., Bunge, J., Jeon, S., Yakimov, M.M., Behnke, A., and Stoeck, T., 2009,  Protistan community patterns within the brine and halocline of deep hypersaline anoxic basins (DHABs) in the eastern Mediterranean Sea, Extremophiles 13(1):151-167.

Edgcomb, V.P., Molyneaux, S.J., Böer, S., Wirsen, C.O., Saito, M., Atkins, M., and A. Teske, 2007, Survival and growth of two heterotrophic hydrothermal vent archaea, Pyrococcus strain GB-D and Thermococcus fumicolans, under hydrothermal vent and subsurface stress factors, Extremophiles, 11(2):329-342.

Edgcomb, V.P., Bernhard, J.M., and Jeon, S., 2007, Deep-sea microbial eukaryotes in anoxic, microoxic, and sulfidic environments, In: J. Seckbach (ed.) Algae and Cyanobacteria in Extreme Environments. Series: Cellular Origin, Life in Extreme Habitats and Astrobiology, Vol. 11., Springer-Verlag.

Dufernez, F., Yernaux, C., Gerbod, D., Noël, C., Chauvenet , M., Wintjens, R., Edgcomb, V., Capron, M., Opperdoes, F., and Viscogliosi, E., 2006, The presence of four iron-containing superoxide dismutase isozymes in Trypanosomatidae: characterization and subcellular localization in Trypanosoma brucei, Free Radical Biology and Medicine, 40:210-225.

Lloyd, K.G., Molyneaux, S.J., Edgcomb, V.P., Wirsen, C.O., Atkins, M., and Teske, A.P.,  2005, Growth and Survival of the hyperthermophilic chemolithoautotrophic archaea Methanocaldococcus jannaschii and Archaeoglobus profundus under high temperature, high sulfide concentrations and low pH, Applied and Environmental Microbiology, 71:6383-6387.

Noel, C., Dufernez, F., Gerbod, D., Edgcomb, V., Delgado-Viscogliosi, P., Ho, L.-C., Singh, M., Wintjens, R., Sogin, M., Capron, M., Zenner, L., and Viscogliosi, E.,  2004, Molecular phylogenies of Blastocystis isolates from different hosts: implicataions for genetic diversity, speciation, and zoonosis,  Journal of Clinical Microbiology, 43(1):348-355.

Edgcomb, V.P., Molyneaux, S., Boer, S., Lloyd, K., Saito, M., Erickson, J., Atkins, M., Wirsen, C., and Teske, A., 2004, Sulfide Ameliorates metal toxicity for hydrothermal vent archaea, Applied and Environmental Microbiology, 70(4):2551-2555.

Kormas, K. Ar., Smith, D. C., Edgcomb, V., and Teske, A., 2003, Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176)., FEMS Micrbiology Letters, 45(2):115-125.

Noël, C., Peyronnet, C., Gerbod, D., Edgcomb, V.P., Delgado-Viscogliosi, P., Sogin, M.L., Capron, M., Viscogliosi, E., and Zenner, L., 2003, Phylogenetic analysis of Blastocystis isolates from different hosts based on the comparison of small-subunit rRNA gene sequences, Molecular and Biochemical Parasitology, 4063:1-5.

Gerbod,, D., Noel, C., Dolan, M.F., Edgcomb, V.P., Kitade, O., Noda, S., Dufernez, F., Ohkuma, M., Kudo, T., Capron, M., Sogin, M., and Viscogliosi, E., 2002,  Molecular phylogeny of parabasalids inferred from small subunit rRNA sequences, with emphasis on the Descovinidae and Calonymphidae (Trichomonadea), Molecular Phylogenetics and Evolution, 25(3):545-56.

Simpson, A.G.B., Roger, A.J., Silberman, J.D., Leipe, D., Edgcomb, V., Jermiin, L., Patterson, D.J., and Sogin, M.L., 2002, Evolutionary history of “early-diverging” eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia, Molecular Biology and Evolution, 19:1782-1791.

Edgcomb, V.P., Kysela, D.T., Teske, A., Gomez, A.D.V., and Sogin, M.L., 2002, Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment, PNAS, 99(11):7663-7668.

Edgcomb, V.P., Simpson, A.G.B., Amaral Zettler, L., Nerad, T.A., Patterson, D.J., and Sogin, M.L., 2002, Pelobionts are degenerate protists: Insights from molecules and morphology, Molecular Biology and Evolution, 19:978-982.

Teske, A., Hinrichs, K.-U., Edgcomb, V., Gomez, A.D.V., Kysela, D., Sogin, M.L., and Jannasch, H.W., 2002, Archaeal and bacterial population structure of hydrothermal sediments at the Guaymas Basin vent sites: evidence for anaerobic methanotrophy, Applied and Environmental Microbiology, 68(4):1994-2007.

Patterson, D., Sogin, M., Edgcomb, V., Amaral-Zettler,  L. and McArthur, A.,  2001, Web-based resources for promoting awareness of microbial biodiversity [Online].  Website:  http://mbl.edu/microscope

Gerbod, D., Edgcomb, V.P., Noël, C., Vanacova, S., Wintjens, R., Tachezy, J., Sogin, M.L., and Viscogliosi, E., 2001, Phylogenetic relationships of fumarase genes from trichomonad species,  Molecular Biology and Evolution 18(8):1574-1584.

Gerbod, D., Edgcomb, V.P., Noël, C., Zenner, L., Wintjens, R., Delgado-Viscogliosi, P., Holder, M.E., Sogin, M.L., and Viscogliosi, E., 2001, Phylogenetic identification of the trichomonad parasite of turkeys, Histomonas meleagridis (Smith) Tyzzer, inferred from small subunit rRNA sequence, Journal of Eukaryotic Microbiology, 48(4):498-504.

Walker, G., Simpson, A.G.B., Edgcomb, V.P., Sogin, M.L., and Patterson, D.J., 2001, Ultrastructural identities of Mastigamoeba punctachora, Mastigamoeba simplex, and Mastigella commutans and assessment of hypotheses of relatedness of the pelobionts (Protista), European Journal of Protistology, 37: 25-49.

Edgcomb, V.P., Roger, A., Kysela, D., Simpson, A.G.B., Silberman, J. and Sogin, M.L., 2001, New insights into the phylogeny of eukaryotes based on alpha and beta tubulin gene sequences: emphasis on the jakobid flagellates, Molecular Biology and Evolution, 18(4):514-522.

Gerbod, D., Edgcomb, V.P., Noël, C., Delgado-Viscogliosi, P., and Viscogliosi, E., 2000, Phylogenetic position of parabasalid symbionts from the termite Kalotermes flavicollis based on small subunit rRNA sequences, International Microbiology, 3:165-172.

Delgado-Viscogliosi, P., Viscogliosi, E., Gerbod, D., Kulda, J., Sogin, M.L., and Edgcomb, V.P., 2000, Molecular phylogeny of parabasalids based on small subunit rRNA sequences, with emphasis on the Trichomonadinae subfamily,  Journal of Eukaryotic Microbiology, 47(1):70-75.

Edgcomb, V.P., McDonald, J.H., Devereux, R., and Smith, D.W., 1999,  Estimation of bacterial cell numbers in humic-rich salt marsh sediments using probes to 16S rDNA, Applied and Environmental Microbiology, 65(4):1516-1523.

Viscogliosi, E., Edgcomb, V.P., Gerbod, D., Noël, C., and Delgado-Viscogliosi, P., 1999, Molecular evolution inferred from small subunit rRNA sequences: what does it tell us about phylogenetic relationships and taxonomy of the parabasalids? Parasite, 6:279-291.

Edgcomb, V.P., Viscogliosi, E., Simpson, A.G.B., Delgado-Viscogliosi, P., Roger, A.J. and Sogin, M.L.,1998, New Insights into the phylogeny of Trichomonads inferred from small subunit rRNA sequences, Protist, 149:359-366.

Edgcomb, V.P., McDonald, J.H., and Smith, D.W., 1996, Molecular analysis of spatial heterogeneity of sulfate-reducing bacteria in a Delaware salt marsh, Microbial & Comparative Genomics, 1(4):375.

MANUSCRIPTS SUBMITTED OR IN PREPARATION

Edgcomb, V.P., Orsi, W., Biddle, J.F. Fungi in the marine subsurface. In: Life in Extreme Environments, J. Kallmeyer ed., DeGruyter Publishing. Submitted.

Stock, A., Edgcomb, V.P., Orsi, W., Filker, S., Breiner, H.W., Yakimov, M.M., Stoeck, T. Evidence for isolated evolution of deep-sea ciliate communities through environmental selection and geological chronology. Submitted to BMC Microbiology. 

Edgcomb, V.P., Bernhard, J.M., Summons, R.E., Orsi, W., Beaudoin, D., Visscher, P. Eukaryotic diversity in microbialites of Highborne Cay, Bahamas and Shark Bay, Australia. Submitted ISME J.

ABSTRACTS (last 3 years)

Edgcomb, V., Bernhard, J.M., Visscher, P.T., and Summons, R.E. 2013. Eukaryotic communities of different microbialites in hypersaline Hamelin Pool, Shark Bay, W. Australia. 2013 ASLO Meeting, New Orleans, LA.

Salman, V., Edgcomb, V., Angert, E., Klein, F., Teske, A. Novel large sulfur-oxidizing bacteria in Sippewissett Salt Marsh. ASM 2013.

Summons, R.E., Gillespie, A.L., Schubotz, F., Welander, P.V., Pruss, S.B., Edgcomb, V.P., Bernhard, J.M., Beaudoin, D., Roberts, M., Beaupre, S., Sessions, A.L. 2013. The biogeochemistry of ooids and oolites. 2013 IMOG Meeting of the European Association of Organic Geochemists. 

Orsi, W., Biddle, J., Christman, G., Edgcomb, V. Active fungi in the marine subsurface amidst a eukaryotic rRNA paleome. AGU 2012.

Orsi, W., Edgcomb, V.P., Christmann, G., Biddle, J. Gene expression in the deep subsurface. C-DEBI All Hands Meeting, Ventura Beach, CA. 10/2012.

Bernhard, J.M., Visscher, P.T. and Summons, R.E. Eukaryotic communities of different microbialites in hypersaline Hamelin Pool, Shark Bay, Australia. Submitted for 2013 ASLO Ocean Sciences Meeting, New Orleans.

Bernhard, J.M., Edgcomb, V.P., Morrison, C., Orsi, W., Beaudoin, D.J. Halocline sediments of deep hypersaline anoxic basins appear to support protist populations. Submitted for 2013 ASLO Ocean Sciences Meeting, New Orleans.

Orsi, W., Biddle, J., Edgcomb, V.P., Active microbial eukaryotes amidst a marine subsurface paleome. 2012 International Society for Microbial Ecology (ISME) meeting in Copenhagen, Denmark 8/2012.

Orsi, W., Song, Y., Hawley, A., Torres-Beltran, M., Hallam, S., Edgcomb, V., Response of microbial eukaryotes to oxygen minimum zone formation. 2012 International Society for Microbial Ecology (ISME) meeting in Copenhagen, Denmark 8/2012.

Pachiadaki, M., Oikonomou, A., Orsi, W., Edgcomb, V., Taylor, C., Yakimov, M., and Stoeck, T. Assessing protistan grazing on marine prokaryotes in the mesopelagic realm of the Mediterranean Sea. 2012 International Society for Microbial Ecology (ISME) meeting in Copenhagen, Denmark 8/2012.

Orsi, W., Biddle, J., Edgcomb, V., Active microbial eukaryotes admidst a marine subsurface RNA paleome. Bioinformatics Workshop, Bremen, Germany, June, 2012.