Microscopy and Image Analysis Facility Publications

Publications

Apprill, A., McNally, S., Parsons, R. and Weber, L. (2015) “Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton.” AME Vol. 75, No. 2. Online publication date: June 04, 2015

Angly, F., Felts, B., Breitbart, M., Salamon, P., Edwards, R., Carlson, C., Chan, A., Haynes, M., Kelley, S., Liu, H., et al. (2006). "The marine viromes of four oceanic regions." PLoS Biology 4, e368.

Bodnar, A.G. and Coffman, J.A. (2016) "Maintenance of somatic regenerative capacity with age in short- and long-lived species of sea urchins." Aging Cell. doi: 10.1111/acel.12487. http://onlinelibrary.wiley.com/doi/10.1111/acel.12487/full

Carlson, C.A., Giovannoni, S.J., Hansell, D.A., Goldberg, S.J., Parsons, R., Otero, M.P., Vergin, K., and Wheeler, B.R. (2002). "Effect of nutrient amendments on bacterioplankton production, community structure, and DOC utilization in the northwestern Sargasso Sea." Aquatic Microbial Ecology 30, 19-36.

Carlson, C.A., Giovannoni, S.J., Hansell, D.A., Goldberg, S.J., Parsons, R., and Vergin, K. (2004). "Interactions between DOC, microbial processes, and community structure in the mesopelagic zone of the northwestern Sargasso Sea." Limnology and Oceanography 49, 1073- 1083.

Carlson, C.A., Morris, R., Parsons, R., Giovannoni, S.J., and Vergin, K. (2009). "Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea." ISME Journal 3, 283-295.

Casey, J.R., Lomas, M.W., Mandecki, J., and Walker, D.E. (2007). "Prochlorococcus contributes to new production in the Sargasso Sea deep chlorophyll maximum." Geophys Res Lett 34.

Du, C., Anderson, A., Lortie, M., Parsons, R., and Bodnar, A. (2013). "Oxidative Damage and Cellular Defense Mechanisms in Sea Urchin Models of Aging." Free Radical Biology and Medicine 63, 254-263.

Goldsmith, D.B., Parsons, R.J., Beyene, D., Salamon, P., and Breitbart, M. (2015). "Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea." PeerJ 3, e997.

James, A, Carlson, C., Passow, U, Brzezinski, M, Parsons, RJ and Trapani, JN. (2017) “Elevated bacterioplankton removal of organic carbon.” PLoS ONE 12(3:e0173145

Jones, R., Johnson, R., Noyes, T., and Parsons, R. (2012). “Spatial and temporal patterns of coral black band disease in relation to a major sewage outfall in Bermuda.” Mar Ecol Prog Ser 462: 79-92.

Jones, R., Parsons, R., Watkinson, E., and Kendall, D. (2010). “Sewage contamination of a densely populated coral ‘atoll’ (Bermuda).” Environ. Monit. Assess. 179 (104): 309-324.

Liu, S., Parsons, R., Opalk, K., Bates, N., Giovannoni, S., Bolanos, L.M., Kujawinksi, E.B., Longnecker, K., Lu Y., Halewood, E., and Carlson, C.A. (2020) “Different carboxy-rich alicyclic molecules proxy compounds select distinct bacterioplankton for oxidation of dissolved organic matter in the mesopelagic Sargasso Sea.” Limnology and Oceanography 1-22 doi:10.1002/lno.11405

Lomas, M.W., and Bates, N.R. (2004). "Potential controls on interannual partitioning of organic carbon during the winter/spring phytoplankton bloom at the Bermuda Atlantic Time- series Study (BATS) site." Deep-Sea Research Part I-Oceanographic Research Papers 51, 1619-1636.

Lomas, M.W., Steinberg, D.K., Dickey, T., Carlson, C.A., Nelson, N.B., Condon, R.H., and Bates, N.R. (2010). "Increased ocean carbon export in the Sargasso Sea linked to climate variability is countered by its enhanced mesopelagic attenuation." Biogeosci 7, 57-70.

Marston, M.F., Taylor, S., Sme, N, Parsons, R.J., Noyes, T.J.E. and Martiney J.B.H. (2013). “Marine cyanophages exhibit local and regional biogeography.” Environmental Microbiology 15 (5):1452-1463.

McCaughey, C., and Bodnar, A. (2012). "Investigating the sea urchin immune system: Implications for disease resistance and aging." Journal of Young Investigator 23, 25-33.

McDonald, N., Achterberg, E.P., Carlson, C.A., Gledhill, M., Liu, S. Matheson-Barker, J.R., Nelson, N.B., Parsons, R.J. (2019). The role of heterotrophic bacteria and Archaea in the transformation of lignin in the open ocean. Frontiers in Marine Science 6(743) https://doi.org/10.3389/fmars.2019.00743

McNally, S.P., Parsons, R.J., Santoro, A.E., and Apprill, A. (2017). Multifaceted impacts of the stony coral Porites astreoides on picoplankton abundance and community composition. Limnology and Oceanography 62, 217-234.

Nelson, C.E., and Carlson, C.A. (2012). "Tracking differential incorporation of dissolved organic carbon types among diverse lineages of Sargasso Sea bacterioplankton." Environmental Microbiology 14, 1500-1516.

Nelson, C.E., Carlson, C.A., Ewart, C.S., and Halewood, E.R. (2014). "Community differentiation and population enrichment of Sargasso Sea bacterioplankton in the euphotic zone of a mesoscale mode-water eddy." Environ Microbiol 16, 871-887.

Nelson, N.B., Carlson, C.A., and Steinberg, D.K. (2004). "Production of chromophoric dissolved organic matter by Sargasso Sea microbes." Marine Chemistry 89, 273-287.

Parsons, R.J., Breitbart, M., Lomas, M.W., and Carlson, C.A. (2011). "Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea." ISME J 6, 273-284.

Parsons, R.J., Nelson, C.E., Carlson, C.A., Denman, C.C., Andersson, A.J., Kledzik, A.L., Vergin, K.L., McNally, S.P., Treusch, A.H., and Giovannoni, S.J. (2014). "Marine bacterioplankton community turnover within seasonally hypoxic waters of a sub-tropical sound: Devil's Hole, Bermuda." Environmental Microbiology, n/a-n/a.

Pause-Tucker, K., Parsons, R., Symonds, E.M., and Breitbart, M. (2011). "Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean." ISME Journal 5, 822- 830.

Pocklington, P., and Coates, K.A. (2010) "Three new species of polychaete (Annelida: Polychaeta) from Bermuda." Proceedings of the Biological Society of Washington 123: 220- 233.

Reinardy, H.C., Emerson, C.E., Manley, J.M., and Bodnar, A.G. (2015). "Tissue Regeneration and Biomineralization in Sea Urchins: Role of Notch Signaling and Presence of Stem Cell Markers." PloS ONE 10, e0133860.

Saw, J.H.W., Nunoura, T., Hirai, M., Takaki, Y., Parsons, R., Michelsen, M., Longnecker, K., Kujawinski, E.B., Stepanauskas, R., Landry, Z., Carlson, C.A., and Giovannoni, S.J. (2019) Pangenomics reveal diversification of enzyme families and nich specialization in globally abundant SAR202 bacteria. bioRxiv. https://doi.org/10.1128/mBio.02975-19

Steinberg, D.K., Nelson, N.B., Carlson, C.A., and Prusak, A.C. (2004). "Production of chromophoric dissolved organic matter (CDOM) in the open ocean by zooplankton and the colonial cyanobacterium Trichodesmium spp." Marine Ecology Progress Series 267, 45-56. Treusch, A.H., Demir-Hilton, E., Vergin, K.L., Worden, A.Z., Carlson, C.A., Donatz, M.G., Burton, R.M., and Giovannoni, S.J. (2012). "Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids." ISME Journal 6, 481-492.

Treusch, A.H., Vergin, K.L., Finlay, L.A., Donatz, M.G., Burton, R.M., Carlson, C.A., and Giovannoni, S.J. (2009). "Seasonality and vertical structure of microbial communities in an ocean gyre." ISME J 3, 1148-1163.

Venter, J.C., K. Remington, J. Heidelberg, A.L. Halpern, S. Levy, J.A. Eisen, I. Paulsen, K.E. Nelson, D.E. Fouts, W. Nelson, D. Rusch, A.H. Knap, M.W. Lomas, K. Nealson, O. White, J. Peterson, H.O. Smith, J. Hoffman, R. Parsons, C. Pfannkoch and Y. Rogers. (2004). “Environmental whole genome shotgun sequencing: The Sargasso Sea.” Science 304:66-74

Zhang, T., Diaz, J.M., Brighi, C., Parsons, R.J., McNally, S., Apprill, A., and Hansel, C.M. (2016). Dark Production of Extracellular Superoxide by the Coral Porites astreoides and Representative Symbionts. Frontiers in Marine Science 3, 232.

Conference Proceedings

Bodnar, A., Lortie, M., Parsons, R. and Coffman, J. (2015) “Tissue homeostasis, regeneration and negligible senescence: insight from sea urchins.” Presented at the Comparative Biology of Tissue Repair, Regeneration and Aging Symposium, June 2015. Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory

Bodnar, A. (2015) “Sea urchins as models for aging, tissue regeneration and resistance to cancer.” Presented at the Gloucester Marine Genomics Institute Science Forum, September 2015

Denman, C.C., Parsons, R.J., Andersson, A.J., Nelson, C.E., Treusch, A.H., Carlson, C.A. et al. (2010) “Microbial Community Abundance and Structure in Seasonally Stratified Waters: Observations from Devil’s Hole, Harrington Sound, Bermuda.” (Poster) 16th American Society of Limnology and Oceanography Ocean Sciences Meeting, Portland OR

Emerson, C.E., Reinardy, H.C., Manley, J.M. and Bodnar, A.G. (2016) “Sea urchins as a model for tissue regeneration: role of Notch signaling and presence of stem cell markers.” Presented at the Keystone Symposia: Molecular and Cellular Basis of Growth and Regeneration, Breckenridge, CO, February 2016

James, A, Carlson, C., Passow, U, Brzezinski, M, Parsons, RJ and Trapani, JN. the Role of DOC in Vertical Export. (Oral) February 21-26, 2016 22nd American Society of Limnology and Oceanography Ocean Sciences Meeting., New Orleans, Louisiana. Loram, J., Du., C., Anderson, A., Lortie, M., Parsons, R. and Bodnar, A. (2013) “Cellular mechanisms of negligible senescence in sea urchins.” Presented at Congress of Invertebrate Reproduction and Development, Detroit, MI.

Lortie, M., Du, C., Parsons, R., Coffman, J. and Bodnar, A. (2014) “Tissue homeostasis, regeneration and negligible senescence: insight from the sea urchin.” Presented at Molecular Genetics of Aging, Cold Spring Harbor Laboratory Meeting, September 2014

Lortie, M., Du., C., Parsons, R., Coffman, J. and Bodnar, A. “Tissue homeostasis, regeneration and negligible senescence: insight from the sea urchin.” Presented at the Developmental Biology of the Sea Urchin Conference. The Marine Biological Laboratory, Woods Hole, MA. April 2014

Matheson, J, Johnson, RJ, Bates, NR and Parsons, RJ. Elucidating the Relationship Between Phytoplankton and Primary Production in the Sargasso Sea Using New Observations of Nanoplankton and Picoplankton. (Poster) February 21-26, 2016 22nd American Society of Limnology and Oceanography Ocean Sciences Meeting., New Orleans, Louisiana.

McLeod, K, Desmarais, M, Carlson, C, and Johnson, R. and Parsons, R. “Distribution of the microbial lineages within the oxygen minimum zone of the mesopelagic Sargasso Sea and the relative contribution of chemoautotrophs.” (Poster) Symposium on Microbial Ecology, Montreal, Canada.

McNally, SP, Parsons, RJ, Santoro, AE and Apprill, A. “Multifaceted Impacts of the Stoney Coral Porites Astreoides on Picoplankton Abundance and Community Composition.” (Poster) June 19- 25, Coral Reef Symposium, Honolulu, Hawaii.

McNally, S., Parsons, R. J., Apprill, A. (2014) “Porites Astreoides corals influence reef water bacterioplankton communities.” (Poster) February 2014. 20th American Society of Limnology and Oceanography Ocean Sciences Meeting, Honolulu, HI.

Mescioglu, E., McDonald, N. and Parsons, R. (2015) “The microbial degradation of lignin and the subsequent production of marine dissolved organic matter in the Sargasso Sea.” (Poster) February 22-27, 2015 21st American Society of Limnology and Oceanography Ocean Sciences Meeting, Granada, Spain.

Parsons, R, McLeod, K, Carlson, C, and Johnson, R. “Distribution of the microbial lineages within the oxygen minimum zone of the mesopelagic Sargasso Sea and the relative contribution of chemoautotrophs.” (Poster) August 21-26, 2016 Symposium on Microbia Ecology, Montreal, Canada.

Parsons, R.J., Breitbart, M., Lomas, M.W., and Carlson, C.A. (2010) “Time-series study reveals regular temporal and vertical variability of viral abundance in the subtropical North Atlantic”. (Poster) International Society for Microbial Ecology Meeting, Seattle, WA.

Reinardy, H.C., Emerson, C.E., Manley, J.M. and Bodnar, A.G. (2015) “Tissue regeneration and biomineralization in sea urchins: role of Notch signaling and presence of stem cell markers.” Presented at the Comparative Biology of Tissue Repair, Regeneration and Aging Symposium, June 2015. Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory

Schuler, G, Parsons, RJ and Johnson, RJ. Bacterioplankton Populations within the Oxygen Minimum Zone of the Sargasso Sea. (Oral) February 21-26, 2016 22nd American Society of Limnology and Oceanography Ocean Sciences Meeting., New Orleans, Louisiana.

Schuler G, and Parsons R. “Bacterioplankton Populations within the Oxygen Minimum Zone of the Sargasso Sea.” (Poster) November 6-7, 2015 Alleghany Branch of the American Society for Microbiologists; Greensburg, PA

Shepard, A.K., Jones, R.J., Parsons, R.J., and C.A., C. (2008) “Microbial Abundance of the Inshore Waters of Bermuda and Coral Reef Ecosystems: Monitoring for Sewage Outfall Impacts.” (Poster)14th American Society of Limnology and Oceanography Ocean Sciences Meeting, Orlando, FL.

Stevens, S, Johnson, RJ, Bates, NR and Parsons, RJ. Physical and Biogeochemical Factors Affecting Deep Oxygen Minimum Zone Variability at the Bermuda Atlantic Time-series Study Site. (Poster) February 21-26, 2016 22nd American Society of Limnology and Oceanography Ocean Sciences Meeting., New Orleans, Louisiana.