Publications
2023
Mara, P., Zhou, Y., Teske, A., Morono, Y., #Beaudoin, D., Edgcomb, V.P. 2023. Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation. The ISME Journal, doi: 10.1038/s41396-023-01492-z.
Wang, M., Mara, P., Burgaud, G. Edgcomb V., Long, X., Zheng, Y., Yang, H., Ma, Y., Cai, L., Li, W. 2023. Metatranscriptomics and metabarcoding reveal spatiotemporal shifts in fungal commubutues abd their activities in Chinese coastal waters. Molecular Ecology, doi:10.1111/mec.16905.
Lizarralde, D. and shipboard scientists Expedition 385. 2023. Carbon release due to sill intrusion into sediments measured through scientific drilling. Geology 51(4):329-333, doi:10.1130/G50665.1..
Geller-McGrath, D., Mara, P., Edgcomb, V.P., Taylor, G., Pachiadaki, M. 2023. Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently-stratified Cariaco Basin water column. Nature Communications 14:656, doi:10.1038/s41467-023-36026-w.
2022
Powers, C., Gomaa, F., Billings, E., Utter, D.R., Beaudoin, D.J., Edgcomb, V.P., Hansel, C.M., Wankel, S.D., Filipsson, H.L., Zhang, Y., Bernhard, J.M. 2022. Highly adaptive mitochondrial and peroxisomal metabolisms in chemocline foraminifera. Frontiers
in Marine Science, 9:1010319, doi:10.3389/fmars.2022.1010319
Mara, P., Nelson, R.K., Reddy, C., Teske, A., Edgcomb, V. 2022. Sterane and hopane biomarkers capture microbial transformations of complex hydrocarbons in young hydrothermal Guaymas Basin sediments. Comm. Earth and Environment 3, 250, doi: 10.1038/s43247-022-00582-8.
Zhou, Y.-L., Mara, P., Cui, G.-J., Edgcomb, V.P. 2022. Ecogenomics reveals novel viral communities in the deepest ocean trench on Earth. Communications Biology 5, 1055, doi: 10.1038/s42003-022-04027-y.
Edgcomb, V.P., Teske, A.P., Mara, P. 2022. Microbial hydrocarbon degradation in Guaymas Basin - Exploring the roles and potential interactions of fungi and sulfate-reducing bacteria. Frontiers in Extreme Microbiology, doi: 10.3389/fmicb.2022.831828.
Pachiadaki, M., Edgcomb, V. 2022. Marine Extreme Habitats. In: Stal LJ, Cretoiu MS (eds) The Marine Microbiome. The Microbiomes of Humans, Animals, Plants, and the Environment, vol 3. Springer, Cham. doi:10.1007/978-3-030-90383-1_14.
Sehein, T., Gast, R., Pachiadaki, M., Guillou, L., Edgcomb, V.P. 2022. Seasonal shifts in non-bloom-forming dinoflagellates correlate with modifications of parasitic Group II Syndiniales populations. Environmental Microbiology, doi:10.1111/1462-2920.25977.
Zhou, Y.-L., Mara, P., Cui, G.-J., Edgcomb,
V.P., Wang, Y. 2022. Microbiomes in the Challenger Deep slope and bottom-axis sediments. Nature Communications 13:1515, doi:10.1038/s41467-022-29144-4.
Gomaa, F., Li, Z.H., Beaudoin, D.J., Alzan, H., Girguis, P.R., Docampo, R., Edgcomb,
V.P. 2022. CRISPR/Cas9-induced disruption of Bodo saltans paraflagellar rod-2 gene reveals its importance for cell survival. Journal of Environmental Microbiology
doi:10.1111/1462-2920.15918.
Suter, E.A., Pachiadaki, M., Taylor, G.T., Edgcomb, V.P. 2022, Eukaryotic parasites are integral to a productive microbial food web in oxygen-depleted waters. Frontiers in Microbiology, Aquatic Microbiology, doi:10.3389/fmicb.2021.764605.
Rotterová, J., Edgcomb, V.P., Čepička, I., Beinart, R. 2022. Anaerobic ciliates as a model group for studying symbiosis in anoxic environments and the evolution of life in anoxia. J. Eukaryotic Microbiology, doi: 10.1111/jeu.12912.
2021
Keeler, E., Burgaud, G., Teske, A., Beaudoin, D., Mehiri, M., Dayras, M., Cassand, J., Edgcomb, V. 2021. Deep-sea hydrothermal vent sediments reveal diverse fungi with antibacterial activities. FEMS Microbiology
Ecology 97, doi:10.1093/femsec/fiab103.
Weber, F., Zaliznyak, T., Edgcomb, V., Taylor, G. 2021. Using stable isotope probing and Raman microspectroscopy to measure growth rates of heterotrophic bacteria. Applied and Environmental Microbiology 87:e01460-21. https://doi.org/10.1128/EM.02460-21.
Wee, S.Y., Edgcomb, V.P., Beaudoin, D., Yvon-Lewis, S. Sylvan, J.B. 2021. Microbial abundance and diversity in subsurface lower oceanic crust at Atlantis Bank, Southwest Indian Ridge. AEM 87(22):e0151921, doi:10.1128/AEM.01519-21.
Quemener, M., Dayras, M., Frotte, N., Debaets, S., Lemeur, C., Barbier, G., Edgcomb, V., Mehiri, M., Burgaud, 2021. G. Highlighting the biotechnological potential of deep oceanic crust fungi through the prism of their antimicrobial activity. Marine
Drugs 19(8): 441, doi.org/10.3390/md19080411.
Ramirez, G., Mara, P., Sehein, T., Wegener, G., Chambers, C., Joye, S., Peterson, R., Philippe, A. Burgaud, G., Edgcomb, V., Teske, A. 2021. Environmental factors shaping bacterial, archaeal, and fungal community structure in hydrothermal sediments of Guaymas Basin, Gulf of California. PloS ONE, doi:10.1371/journal.pone.0256321.
Gomaa, F., Utter, D.R., Powers, C., Beaudoin, D.J., Edgcomb, V.P., Filipsson, H.L., Hansel, C.M., Wankel, S.D., Zhang, Y., Bernhard, J.M. 2021. Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments. Science Advances 7(22), doi: 10.1126/sciadv.abf1586
Hu, S.K., Herrera, E.L., Smith, A.R., Pachiadaki, M.G., Edgcomb, V.P., Sylva, S.P., Chan, E.W., Seewald, J.S., German, C.R., Huber, J.A. 2021. Protist grazing impacts microbial communities and carbon cycling at deep-sea hydrothermal vents. Submitted PNAS, BioRxiv: 10.1101/2021.02.08.430233
Mara, P., Edgcomb, V.P., Beaudoin, D., Martinsen, C., Lovely, C., Belcher, B., Cox, R., Curran, M., Farnan, C., Giannini, P., Lott, S., Paquette, K., Pinckney, A., Schafer, N., Sehein, T.R., Surgeon-Rogers, T.-M, Rogers, D.R. 2021. Comparison of oyster aquaculture methods and their potential to enhance microbial nitrogen removal from coastal ecosystems. Frontiers in Marine Science, doi:10.3389/fmars.2021.633314.
Ingels, J., Vanreusel, A., Pape, E., Pasotti, F., Arbizu, P.M., Macheriotou, L, Sorensen, M.V., Edgcomb,
V.P., Sharma, J., Sanchez, N., Homoky, W.B., Leduc, D., Gooday, A.J., Pawlowski, J., Dolan, J., Schratzberger, M., Gollner, S., Schoenle, A., Arndt, H., Woulds, C., Seppilli, D. 2021. Ecological variables for deep-ocean monitoring must include microbiota and meiofauna for effective conservation. Nature
Ecology and Evolution, doi: 10.1038/s41559-019-1091-z.
2020
Li, J., Mara, P., Schubotz, F., Sylvan, J.B., Burgaud, G., Klein, F., Beaudoin, D., Wee, S.-Y., Dick, H., Lott, S., Cox, R., Meyer, L.A.E., Quemener, M., Blackman, D.K., Edgcomb, V.P.2020. Recycling and metabolic flexibility dictate life in the lower oceanic crust. Nature, https://nature.com/articles/s41586-020-2075-5, doi:10.1038/s41586-020-2075-5
Mara, P., Vik, D., Pachiadaki, M.G., Suter, E.A., Taylor, G.T., Sullivan, M., Poulos, B., Edgcomb, V.P. Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline. The ISME J, doi:10.1038/s41396-020-00739-3.
Flegontova, O., Flegontova, P., Edgcomb, V., Lukes, J., Horak, A. 2020. Environmental determnants of the dstribution of planktonic diplonemds and kinetoplastids in the oceans. Environmental Microbiology, doi: doi: 10.1111/1462-2920.15190.
Suter, E., Pachiadaki, M.G., Montes, E., Edgcomb, V., Scranton, M., Taylor, C., Taylor, G. 2020. Diverse nitrogen cycling pathways across a marine oxygen gradient indicate nitrogen loss coupled to chemoautotrophic activity. Environmental Microbiology, doi:10.1111/1462-2920.15187.
Quemener, M., Mara, P., Schubotz, F., Beaudoin, D., Li, W., Pachiadaki, M., Sehein, T., Sylvan, J., Barbier, G., Edgcomb, V., Burgaud, G. 2020. Meta-omics highlights the diversity, activity and adaptations of fungi in deep oceanic crust. Environmental Microbiology, doi:10.1111/1462-2920.15181.
Ingels, J., Vanreusel, A., Pape, E., Pasotti, F., Arbizu, P.M., Macheriotou, L, Sorensen, M.V., Edgcomb,
V.P., Sharma, J., Sanchez, N., Homoky, W.B., Leduc, D., Gooday, A.J., Pawlowski, J., Dolan, J., Schratzberger, M., Gollner, S., Schoenle, A., Arndt, H., Woulds, C., Seppilli, D. 2020. Ecological variables for deep-ocean monitoring must include microbiota and meiofauna for effective conservation. Nature
Ecology and Evolution. in press.
Faull, L.M., Mara, P., Taylor, G.T., Edgcomb, V.P. 2020. Imprint of trace dissolved oxygen on prokaryoplankton community structure in an oxygen minimum zone. Frontiers in Marine Science.
doi:10.3389/fmars.2020.00360.
Rotterova, J., Salomaki, E., Panek, T., Bourland, W., Zihala, D., Taborsky, P., Edgcomb, V.P., Beinart, R.A., Kolisko, M., Cepicka, I. 2020. Genomics of new ciliate lineages provides insight into the evolution of obligate anaerobiosis. Current Biology 30:2037-2050.
Scranton, M.I., Taylor, G.T., Thunell, R.C., Muller-Karger, F.E., Astor, Y., Swart, P., Edgcomb, V.P.,
Pachiadaki, M.G. 2020. Anomalous d13C in POC at the chemoautotrophy maximum in the Cariaco Basin. 125:2 J. Geophys. Res. Biogeosciences, doi: 10.1029/2019JG005276.
2019
Dick, H.J.B., MacLeod, C.J., Blum, P., Abe, N., Blackman, D.K., Bowles, J.A., Cheadle, M.J., Cho, K., Ciążela, J., Deans, J.R., Edgcomb, V.P., Ferrando, C., France, L., Ghosh, B., Ildefonse, B., John, B., Kendrick, M.A., Koepke, J., Leong, J.A.M., Liu, C., Ma, Q., Morishita, T., Morris, A., Natland, J.H., Nozaka, T., Pluemper, O., Sanfilippo, A., Sylvan, J.B., Tivey, M.A., Tribuzio, R., Viegas, G, 2019. Dynamic accretion beneath a slow spreading ridge segment: IODP Hole 1473A and the Atlantis Bank Oceanic Core Complex. J. Geophysical Res. Solid Earth doi:10.1029/2018JBO16858.
Edgcomb, V.P. 2019. Symbiotic magnetic motility. News and Views, Nature Microbiology 4:1066-1067.
Drahomíra Faktorová, R. Ellen R. Nisbet, José A. Fernández Robledo, Elena Casacuberta, Lisa Sudek, Andrew E. Allen, Manuel Ares Jr., Cristina Aresté, Cecilia Balestreri, Adrian C. Barbrook, Patrick Beardslee, Sara Bender, David S. Booth, François-Yves Bouget, Chris Bowler, Susana A. Breglia, Anita Broellochs, Colin Brownlee, Gertraud Burger, Heriberto Cerutti, Rachele Cesaroni, Miguel A. Chiurillo, Thomas Clemente, Duncan B.Coles, Jackie L. Collier, Liz Cooney, Kathryn Coyne, Roberto Docampo, Christopher L.Dupont, Virginia Edgcomb, Elin Einarsson, Pía A. Elustondo, Fernan Federici, VeronicaFreire-Beneitez, Nastasia J. Freyria, Kodai Fukuda, Paulo A. García, Peter R. Girguis, Fatma Gomaa, Sebastian Gornik, Jian Guo, Vladimír Hampl, Yutaka Hanawa, Esteban R.Haro-Contreras, Elisabeth Hehenberger, Andrea Highfield, Yoshihisa Hirakawa, AmandaHopes, Christopher J. Howe, Ian Hu, Jorge Ibañez, Nicholas A.T. Irwin, Yuu Ishii, Natalia Ewa Janowicz, Adam C. Jones, Ambar Kachale, Konomi Fujimura-Kamada, BinnypreetKaur, Jonathan Z. Kaye, Eleanna Kazana, Patrick J. Keeling, Nicole King, Lawrence A.Klobutcher, Noelia Lander, Imen Lassadi, Zhuhong Li, Senjie Lin, Jean-Claude Lozano, Fulei Luan, Shinichiro Maruyama, Tamara Matute, Cristina Miceli, Jun Minagawa, MarkMoosburner, Sebastián R. Najle, Deepak Nanjappa, Isabel C. Nimmo, Luke Noble, Anna M.G. Novák Vanclová, Mariusz Nowacki, Isaac Nuñez, Arnab Pain, Angela Piersanti, Sandra Pucciarelli, Jan Pyrih, Joshua S. Rest, Mariana Rius, Deborah Robertson, AldaneRuaud, Iñaki Ruiz-Trillo, Monika A. Sigg, Pamela A. Silver, Claudio H. Slamovits, EstienneSwart, G. Jason Smith, Brittany Sprecher, Rowena Stern, Tobias von der Haar, LevTsypin, Aaron Turkewitz, Jernej Turnšek, Matus Valach, Valérie Vergé, Peter von Dassow, Anastasios Tsaousis, Ross F. Waller, Lu Wang, Xiaoxue Wen, Glen Wheeler, April Woods, Huan Zhang, Thomas Mock, Alexandra Z. Worden, Julius Lukeš. Genetic tool development in marine protists: Emerging model organisms for experimental cell biology. bioRxix 718239; doi: https://doi.org/10.1101/718239.s, and in review Nature Methods.
Schwaha, T., Bernhard, J.M., Edgcomb, V.P., Todaro, M.A. 2019. Aethozooides uraniae, a new deep-sea genus and species of solitary bryozoan from the Mediterranean Sea, with a revision of the Aethozoidae. Marine Biodiversity, doi:10.1007/s12526-019-00948-w.
Dick, H.J.B., MacLeod, C.J., Blum, P., Abe, N., Blackman, D.K., Bowles, J.A., Cheadle, M.J., Cho, K., Ciazela, J., Deans, J.R., Edgcomb, V.P., Ferrando, C., France, L., Ghosh, B., Ildefonse, B., John, B., Kendrick, M.A., Koepke, J., Leong, J.A.M., Liu, C., Ma, Q., Morishita, T., Morris, A., Natland, J.H., Nozaka, T., Pluemper, O., Sanfilippo, A., Sylvan, J.B., Tivey, M.A., Tribuzio, R., Viegas, G. 2019. Dynamic accretion beneath a slow spreading ridge segment: IODP Hole 1473A and the Atlantis Bank Oceanic Core Complex, J Geophysical Research - Solid Earth, in press.
Torres-Beltran, M., Mueller, A., Scofield, M., Pachiadaki, M., Taylor, C., Tyshchenko, K., Michiels, C., Lam, P., Ulloa, O., Jurgens, K., Hyun, J-H., Edgcomb, V.P., Crowe, S.A., Hallam, S.J. 2019. Sampling and processing methods impact microbial community structure and potential activity in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Frontiers in Marine Science, Marine Biogeochemistry, doi: 10.3389/fmars.2019.00132.
Gladfelter, A., Quandt, A., Yarden, O., Ianiri, G., Jones, A., Cunliffe, M., Kagami, M., Burgaud, G., Stajich, J., Horn, E., Amend, A. ,Picard, K., Raghukumar, S., Walker, A., Gutierrez, M.H., Vargas-Muniz, J., Riquelme, M., Edgcomb, V., Heitman, J. 2019. Fungi in the marine environment: open questions and unsolved problems. In press, mBio.
2018
Gaboyer, F., Burgaud, G., Edgcomb, V. 2018. The deep subseaflloor and biosignatures, In: B. Cavalezzi and F. Westall eds, Biosignatures for Astrobiology, Springer, NY.
Taylor, G.T., Suter E.A., Pachiadaki, M.G., Astor, Y., Edgcomb, V.P., Scranton, M.I. 2018. Temporal shifts in dominant sulfur-oxidizing chemoautotrophic populations across the Cariaco Basin’s redoxcline. Deep-Sea Res. Part II. DOI: 10.1016/j.dsr2.2017.11.016.
Beinart, R., Rotterová, J., Čepička, I., Gast, R.J., Edgcomb,
V.P. 2018. The genome of an endosymbiotic methanogen is very similar to those of its free-living relatives, Environmental Microbiology DOI: 10.1111/1462-2920.14279.
Waller, R.F., Cleves, P.A., Rubio-Brotons, M., Woods, A., Bender, S.J., Edgcomb,
V., Gann, E.R., Jones, A.C., Teytelman, L., von Dassow, P., Wilhelm, S.W., Collier, J.L. 2018. Strength in numbers: collaborative science for new experimental model systems. bioRxiv doi: https://doi.org/10.1101/308304. in press PLoS Biology.
Torres-Beltran, M., Sehein, T., Pachiadaki, M., Hallam, S., Edgcomb, V. 2018. Protistan parasites along oxygen gradients in a seasonally anoxic fjord: a network approach to assessing potential host-parasite interactions. Deep
Sea Research II doi: 10.1016/j.dsr2.2017.12.026.
2017
Suter, E.A., Pachiadaki, M. (co-first authors), Edgcomb, V.P., Astor, Y., Taylor, G.T. 2017. Free-living chemoautotrophic and particle-attached heterotrophic prokaryotes dominate microbial assemblages along a pelagic redox gradient. Env Microbiol. doi: 10.1111/1462-2920.13997.
Beinart, R., Beaudoin, D.J., Bernhard, J.M., Edgcomb, V.P. 2017. Insights into the metabolic functioning of a multi-partner ciliate symbiosis from oxygen-depleted sediments. Molecular Ecology doi: 10.1111/mec.14465.
Taylor, G.T., Suter, E.A., Pachiadaki, M.G., Astor, Y., Edgcomb, V.P., Scranton, M.I. 2017. Temporal shifts in dominant sulfur-oxidizing chemoautotrophic populations across the Cariaco Basin’s redoxcline. Deep Sea
Research II doi: doi:10.1016/j.dsr2.2017.11.016
Beinart, R.A., Beaudoin, D., Bernhard, J.M., Edgcomb, V.P. Insights into the metabolic functioning of a multi-partner ciliate symbiosis from oxygen-depleted sediments. Molecular Ecology doi: 10.1111/mec.14465.
Gomaa, F., Garcia, P.A., Delaney, J., Girguis, P.R., Buie, C.R., Edgcomb, V.P. 2017. Toward establishing model organisms for marine protists: successful transfection protocols for Parabodo caudatus. In press, Environmental Microbiology.
Berney, C., Ciuprina, A., Bender, S., Brodie, J., Edgcomb, V.P., Kim, E., et al. 2017. UniEuk: time to speak a common language in protistology! in press, J. Euk.Micro.
Medina, L.E., Taylor, C.G., Pachiadaki, M.G., Henríquez-Castillo, C., Ulloa, O., Edgcomb, V.P. 2017. A review of protist grazing below the photic zone emphasizing studies of oxygen-depleted water columns and recent applications of in situ approaches. In press, Frontiers in Marine Science.
2016
Pachiadaki, M.G., Redou, V., Beaudoin, D., Burgaud, G., Edgcomb, V.P. 2016. Fungal and prokaryotic activities in the marine subsurface biosphere at Peru Margin and Canterbury Basin inferred from RNA-based analyses and microscopy. Frontiers in Extreme Microbiol. doi: 10.3389/fmicb.2016.00846.
Cobban, A., Edgcomb V.P., Burgaud, G., Repeta D., Leadbetter E.R. 2016. Revisiting the pink-red pigmented basidiomycete mirror yeast of the phyllosphere Microbiology Open. DOI: 10.1002/mbo3.374.
Edgcomb, V.P. 2016. Marine protist associations and environmental impacts across trophic levels in the twilight zone and below. Curr. Opinions Microbiology 31:169-175.
Edgcomb, V.P., Pachiadaki, M.P., Kormas, K.Ar., Paraskevi, M., Bernhard, J.M., Leadbetter, E.R. 2016. Microbial activities in sediments below haloclines of thalassohaline and athalassohaline deep-sea brine lakes. The ISME J. 1-15. doi: 10.1038/ismej.2016.58.
2015
Bernhard, J.M., Morrison, C.R., Pape, E., Beaudoin, D.J., Todaro, M.A., Pachiadaki, M.G., Kormas, K.Ar., Edgcomb, V.P. 2015. Metazoans of redoxline sediments in Mediterranean deep-sea hypersaline anoxic bains. BMC Biology 13:105, doi: 10.1186/s12915-015-0213-6.
Panek, T., Taborsky, P., Pachiadaki, M.G., Hroudova, M., Vlcek, C., Edgcomb, V.P., Cepicka, I. 2015. Combined culture-based and culture-independent approaches provide insights into diversity of jakobids, an extremely plesiomorphic eukaryotic lineage. Frontiers in Microbiology 6:1288.
Duret, M.T., Pachiadaki, M.G., Stewart, F.J., Sarode, N., Christaki, U., Monchy, S., Srivastava, A., Edgcomb, V.P. 2015. Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone. FEMS Microbiol Ecol 91, doi: 10.1093/femsec/fiv037.
Kormas, K.A., Pachiadaki, M., Karayanni, H., Leadbetter, E.R., Bernhard, J.M., Edgcomb, V.P. 2015. Inter-comparison of the potentially active prokaryotic communities in the halocline sediments of Mediterranean deep-sea hypersaline basins, doi: 10.1007/s00792-015-0770-1, Extremophiles.
Rocke, E., Pachiadaki, M.G., Cobban, A., Kujawinski, E.B., Edgcomb, V.P. 2015. Protist community grazing in deep ocean waters. PLoS ONE, doi: 10.1371/journal.pone.0124505.
Taylor, C.D., Edgcomb, V.P., Doherty, K.W., Engstrom, I., Shanahan, T., Pachiadaki, M.G., Molyneaux, S.J., and Honjo, S. 2015. Fixation filter, device for the rapid in situ preservation of particulate samples. Deep Sea Research I, 96:69-79.
Gong, J., Shi, F., Ma, B., Dong, J., Pachiadaki, M., Zhang, X., Edgcomb, V.P. 2015. Depth shapes alpha- and beta-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems. Environmental Microbiology
2014
Parris, D.J., Ganesh, S., Edgcomb V., DeLong, E.F., Stewart, F.J. 2014. Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile. Frontiers in Microbiol, Aquatic Microbiology, doi: 10.3389/fmicb.2014.00543.
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. 2014. Benthic protists and fungi of Mediterranean deep hypersaline anoxic basin redoxcline sediments. Frontiers in Extreme Microbiology, doi: 10.3389/fmicb.2014.00605.
Redou, V., Ciobanu, M.C., Pachiadaki, M.G., Edgcomb, V., Alain, K., Barbier, G., and Burgaud G. 2015. In-depth analyses of deep subsurface sediments using 454-pyrosequencing reveals a reservoir of buried fungal communities. FEMS Microbiol Ecol, doi:10.1111/1574-6941.12447.
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. Oceanography 27(3):10-16, doi: 10.5670/oceanog.2014.78.
Pachiadaki, M., Taylor, C., Oikomomou, A., Yakimov, M., Stoeck, T., Edgcomb, V.P. 2014. In situ grazing experiments apply new technology to gain insights into deep sea food webs. Deep Sea Res II, doi:10.1016/j.dsr2.2014.10.019.
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. Deep Sea Res II, doi: 10.1016/j.dsr2.2014.10.020.
Edgcomb, V.P., Pachiadaki, M. 2014. Ciliates along oxyclines of permanently stratified marine water columns. J. Euk. Microbiol. 61:434-445.
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.