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Publications

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2014

Parris, D.J., Ganesh, S., Edgcomb V., DeLong, E.F., Stewart, F.J. Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile. In Press, Frontiers in Microbiol, Aquatic Microbiology.

Bernhard, J.M., Kormas, K.A., Pachiadaki, M.G., Rocke, E., Beaudoin, D.J., Morrison, C., Visscher, P.T., Cobban, A., Starczak, V.R., and Edgcomb, V.P. Benthic protists and fungi of Mediterranean deep hypersaline anoxic basin redoxcline sediments. In press, Frontiers in Extreme Microbiology. 

Redou, V., Ciobanu, M.C., Pachiadaki, M.G., Edgcomb, V., Alain, K., Barbier, G., and Burgaud G. In-depth analyses of deep subsurface sediments using 454-pyrosequencing reveals a reservoir of buried fungal communities. In press, FEMS Microbiol Ecol.

Taylor, C.D., Edgcomb, V.P., Doherty, K.W., Engstrom, I., Shanahan, T., Pachiadaki, M.G., Molyneaux, S.J., and Honjo, S. Fixation filter, device for the rapid in situ preservation of particulate samples. In press, DSR II.

Pachiadaki, M.G., Yakimov, M.M., Leadbetter, E., Edgcomb, V.P. 2014. Unveiling microbial activities along the halocline of Thetis, a deep hypersaline anoxic basin in the Eastern Mediterranean Sea. The ISME J. doi:10.1038/ismej.2014.100.

Stoeck, T., Filker, S., Edgcomb, V., Orsi, W., Yakimov, M.M., Pachiadaki, M., Breiner, H.-W., LaCono, V., and Stock, A. 2014. Living at the limits: Evidence for microbial eukaryotes thriving under pressure in deep anoxic, hypersaline habitats. Advances in Ecology vol. 2014, Article ID 532687, doi:10.1155/2014/532687.

Honjo, S., Eglinton, T.I., Taylor, C.D., Edgcomb, V., Iglesias-Rodrigues, D.M., Krishfield, R.A., van Mooy, B., Repeta, D.J., Sievert, S.M., Ulmer, K.M., and members of the GBF Scientific Steering Committee. 2014. A biogeochemical flux observatory initiative to understand the ocean’s role in global cycling of bioactive carbon. In press. Oceanography

Pachiadaki, M., Taylor, C., Oikomomou, A., Yakimov, M., Stoeck, T., Edgcomb, V.P. 2014. Grazing studies conducted in situ reveal protist turnover of bacterial biomass in the deep E. Mediterranean Sea. In press, Deep Sea Res II.

Edgcomb, V.P., Taylor, C., Pachiadaki, M., Engstrom, I., Yakimov, M. 2014. Comparison of Niskin vs. in situ approaches for analysis of gene expression in deep Mediterranean Sea water samples. In press, Deep Sea Res II.

Edgcomb, V.P., Pachiadaki, M. 2014. Ciliates along oxyclines of permanently stratified marine water columns. J. Euk. Microbiol. 61:434-445.

Stoeck, T., Filker, S., Edgcomb, V., Orsi, W., Yakimov, M.M., Pachiadaki, M., Breiner, H.-W., LaCono, V., Stock, A. 2014. Living at the limits: Evidence for microbial eukaryotes thriving under pressure in deep anoxic, hypersaline habitats. In press, Advances in Ecology.

Beaudoin, D.J., Carmichael, C.A., Nelson, R.K., Reddy, C.M., Teske, A., Edgcomb, V.P. 2014. Impact of protists on a hydrocarbon degrading bacterial community from deep-sea Gulf of Mexico sediments. Deep-Sea Research II, doi:10.1016/j.dsr2.2014.01.007. 

2013

Heger, T.J., Edgcomb, V.P., Kim, E., Lukes, J., Leander, B.S., Yubuki, N. 2013. Field Protistology: Cornerstone for understanding the diversity, ecology, and evolution of microbial eukaryotes. In press, J. Euk. Microbiol.

Grabenstatter, J., Mehay, S., McIntyre-Wressnig, A., Giner, J.-L., Edgcomb, V.P., Beaudoin, D., Bernhard, J., Summons, R.E. 2013. Identification of 24-n-propylidenecholesterol in a member of the Foraminifera. Organic Geochemistry 63:145-151.

Edgcomb, V.P., Bernhard, J.M., Summons, R.E., Orsi, W., Beaudoin, D., Visscher, P. 2013. Active eukaryotes in microbialites of Highborne Cay, Bahamas and Shark Bay, Australia. ISME Journal, doi: 10.1038/ismej.2013.130.

Stock, A., Edgcomb, V.P., Orsi, W., Filker, S., Breiner, H.W., Yakimov, M.M., Stoeck, T. 2013. Evidence for isolated evolution of deep-sea ciliate communities through environmental selection and geological chronology. BMC Microbiology 13:150 doi:10.1186/1471-2180-13-150. 

Edgcomb, V.P., Orsi, W., Biddle, J.F. 2013. Fungi in the marine subsurface. In: Life in Extreme Environments, J. Kallmeyer ed., DeGruyter Publishing. In press.

Burgaud, G., Woehlke, S., Redou, V., Orsi, W., Beaudoin, D., Barbier, G., Biddle, J.F., Edgcomb, V.P. 2013, Deciphering presence and activity of fungal communities in marine sediments using a model estuarine system. Aquatic Microbial Ecol 70:45-62.

Bernhard, J.M., Edgcomb, V.P., McIntyre-Wressnig, A., Summons, R.E., Visscher, P.T., Jeglinski, M. 2013, Insights into foraminiferal influences on microfabrics of microbialites at Highborne Cay, Bahamas. PNAS doi:10.1073/pnas.1221721110.

Orsi, W., Edgcomb, V.P., Christman, G.D., and Biddle, J.F. 2013, Gene expression in the deep biosphere. Nature doi:10.1038/nature12230.

Orsi, W. and Edgcomb, V.P. 2013, Microbial eukaryotes in marine oxygen minimum zones. In: Seckbach, J., Oren, A., and Stan-Lotter, H. (eds.), COLE Series: Polyextremophiles – Life Under Multiple Forms of Stress, Cellular Origin, Life in Extreme Habitats and Astrobiology, Vol. 27, Springer Verlag, 634pp.

Edgcomb, V.P. and Orsi, W. 2013, Microbial eukaryotes in hypersaline anoxic deep sea basins. In: Seckbach, J., Oren, A., and Stan-Lotter, H. (eds.), COLE Series: Polyextremophiles – Life Under Multiple Forms of Stress, Cellular Origin, Life in Extreme Habitats and Astrobiology, Vol. 27, Springer Verlag, 634pp.

Edgcomb, V.P., Bernhard JM. 2013, Heterotrophic protists in hypersaline microbial mats and deep hypersaline basin water columns. Special Issue “Extremophiles and Extreme Environments” Life doi:10.3390/life3020346. 

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.

2012
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. MicrobiologyOpen 2(1):54-63.

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. 2012, Potential importance of physiologically diverse benthic foraminifera in sedimentary 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 Cariacotrichea, a novel ciliate taxon from the anoxic Cariaco Basin, Venezuela. The International Journal of Systematic and Evolutionary Microbiology doi:10.1099/ijs.0.034710-0.

2011
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, A. Stock, S. Filker, M.M. Yakimov, and T. Stoeck. 2011, Novel kinetoplastids associated with hypersaline anoxic lakes in the Eastern Mediterranean deep-sea. Deep-Sea Research I 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.

Edgcomb, V.P., and Biddle, J. 2011, Microbial eukaryotes in the marine subsurface? In: A. Altenbach, J. Bernhard, and J. Seckbach (eds.) Anoxia: Paleontological Strategies and Evidence for Eukaryote Survival Springer-Verlag 479-491.

Edgcomb, V.P., 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.

Dilegge, S.K., Edgcomb, V.P., and Leadbetter, E.R. 2011, Presence of the oral bacterium Capnocytophaga canimorsus in the tooth plaque of canines. Vet. Microbiol. 149(3-4):437-45.

2010
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

2009
Teske, A., Edgcomb, V.P., 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 from 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.

2007
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.

2006 and Prior
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.



Last updated: December 16, 2014



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