Publications – James Barry

Webb, Thomas J., Barry, James P., McClain, Craig R., (2017). Abundance-occupancy relationships in deep sea wood fall communities. Ecography : . http://dx.doi.org/10.1111/ecog.02618
McClain, C. R., Barry, J. P., Eernisse, D., Horton, T., Judge, J., Kakui, K., Mah, C., Waren, A., (2016). Multiple processes generate productivity–diversity relationships in experimental wood-fall communities. Ecology, 97: 885-898. http://dx.doi.org/10.1890/15-1669.1
Judge, J., Barry, J. P., (2016). Macroinvertebrate community assembly on deep-sea wood falls in Monterey Bay is strongly influenced by wood type. Ecology, 97: 3031-3043. http://dx.doi.org/10.1002/ecy.1546
Gaylord, B., Kroeker, K. J., Sunday, J. M., Anderson, K. M., Barry, J. P., Brown, N. E., Connell, S. D., Dupont, S., Fabricius, K. E., Hall-Spencer, J. M., Klinger, T., Milazzo, M., Munday, P. L., Russell, B. D., Sanford, E., Schreiber, S. J., Thiyagarajan, V., Vaughan, M. L. H., Widdicombe, S., Harley, C. D. G., (2015). Ocean acidification through the lens of ecological theory. Ecology, 96: 3-15. http://dx.doi.org/10.1890/14-0802.1
Taylor, J.R., DeVogelaere, A.P., Burton, E.J., Frey, O., Lundsten, L., Kuhnz, L.A., Whaling, P.J., Lovera, C., Buck, K.R., Barry, J.P., (2014). Deep-sea faunal communities associated with a lost intermodal shipping container in the Monterey Bay National Marine Sanctuary, CA. Marine Pollution Bulletin, 83: 92-106. http://dx.doi.org/10.1016/j.marpolbul.2014.04.014
Taylor, J.R., Lovera, C., Whaling, P.J., Buck, K.R., Pane, E.F., Barry, J.P., (2014). Physiological effects of environmental acidification in the deep-sea urchin Strongylocentrotus fragilis. Biogeosciences, 11: 1413-1423.
McClain, C.R., Barry, J., (2014). Beta-diversity on deep-sea wood falls reflects gradients in energy availability. Biology Letters, 10: . http://dx.doi.org/10.1098/rsbl.2014.0129
Gattuso, J.-P., Kirkwood, W., Barry, J.P., Cox, E., Gazeau, F., Hansson, L., Hendricks, I., Kline, D.I., Mahacek, P., Martin, S., McElhany, P., Peltzer, E.T., Reeve, J., Roberts, D., Saderne, V., Tait, K., Widdicombe, S., Brewer, P.G., (2014). Free-ocean CO2 enrichment (FOCE) systems: Present status and future developments. Biogeosciences, 11: 4057-4075. http://dx.doi.org/10.5194/bg-11-4057-2014
Barry, J.P., Lovera, C., Buck, K.R., Peltzer, E.T., Taylor, J.R., Walz, P., Whaling, P.J., Brewer, P.G., (2014). Use of a Free Ocean CO2 Enrichment (FOCE) system to evaluate the effects of ocean acidification on the foraging behavior of deep-sea urchin. Environmental Science & Technology, 48: 9890-9897. http://dx.doi.org/10.1021/es501603r
Tang, Q., Chen, C.-T.A., Yu, K., Dai, M., Zhao, M., Ke, C., Wong, G.T.F., Chai, F., Wei, G., Zhou, L., Chen, L., Song, J., Barry, J.P., Wu, Y., Gao, K., (2013). The effects of ocean acidification on marine organisms and ecosystem. Chinese Science Bulletin, 58: 1307-1314.
Sedlacek, L., Thistle, D., Fernandez-Leborans, G., Carman, K.R., Barry, J.P., (2013). First report of ciliate (Protozoa) epibionts on deep-sea harpacticoid copepods. Deep Sea Research II, 92: 165-171. http://dx.doi.org/10.1016/j.dsr2.2013.01.033
Shane, F.F., Headley, K., Walz, P., Kecy, C., Matsumoto, G.I., Herlien, R.A., Peltzer, E.T., Scholfield, J., Salamy, K.A., Maughan, T., O'Reilly, T.C., Lovera, C., Kirkwood, W.J., Barry, J., Brewer, P.G., (2013). xFOCE: An open source, multi-disciplinary resource for in-situ ocean acidification research. Proceedings of Marine Technology Society/Institute of Electrical and Electronics Engineers Oceans 2013 : .
Kecy, C.D., Peltzer, E.T., Walz, P.M., Headley, K., Herlien, R.A., Maughan, T., Matsumoto, G.I., O'Reilly, T.C., Salamy, K.A., Shane, F., Lovera, C., Scholfield, J., Kirkwood, W., Barry, J.P., Brewer, P.G., (2013). Open source instrumentation nodes for the greater oceanographic community. Proceedings of Marine Technology Society/Institute for Electrical and Electronics Engineers Oceans 2013 : .
Buck, K.R., Barry, J.P., Hallam, S.J., (2013). Thioploca spp. sheaths as niches for bacterial and protistan assemblages. Marine Ecology, 35: 395-400. http://dx.doi.org/10.1111/maec.12076
Curtis, B.A., Tanifuji, G., Burki, F., Gruber, A., Irimia, M., Maruyama, S., Arias, M.C., Ball, S.G., Gile, G.H., Hirakawa, Y., Hopkins, J.F., Kuo, A., Rensing, S.A., Schmutz, J., Symeonidi, A., Elias, M., Eveleigh, J.M., Herman, E.K., Klute, M.J., Nakayama, T., Obornik, M., Reyes-Prieto, A., Armbrust, E.V., Aves, S.J., Beiko, R.G., Coutinho, P., Dacks, J.B., Durnford, D.G., Fast, N.M., Green, B.R., Grisdale, C.J., Hempel, F., Henrissat, B., Höppner, M.P., Ishida, K.-I., Kim, E., Kořený, L., Kroth, P.G., Liu, Y., Malik, S.-B., Maier, U.G., McRose, D., Mock, T., Neilson, J.A.D., Onodera, N.T., Poole, A.M., Pritham, E.J., Richards, T.A., Rocap, G., Roy, S.W., Sarai, C., Schaack, S., Shirato, S., Slamovits, C.H., Spencer, D.F., Suzuki, S., Worden, A.Z., Zauner, S., Barry, K., Bell, C., Bharti, A.K., Crow, J.A., Grimwood, J., Kramer, R., Lindquist, E., Lucas, S., Salamov, A., McFadden, G.I., Lane, C.E., Keeling, P.J., Gray, M.W., Grigoriev, I.V., Archibald, J.M., (2012). Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature, 492: 59-65. http://dx.doi.org/10.1038/nature11681
Levin, L.A., Gambi, M.C., Barry, J.P., Genin, A., Thrush, S., (2011). The Dayton legacy: baselines, benchmarks, climate, disturbance, and proof. Marine Ecology, 32: 261-265. http://dx.doi.org/10.1111/j.1439-0485.2011.00473.x
Fleeger, J.W., Johnson, D.S., Carman, K.R., Weisenhorn, P.B., Gabriele, A., Thistle, D., Barry, J.P., (2010). The response of nematodes to deep-sea CO2 sequestration: A quantile regression approach. Deep-Sea Research Part I, 57: 696-707. http://dx.doi.org/10.1016/j.dsr.2010.03.003
Sedlacek, L., Thistle, D., Carman, K.R., Fleeger, J.W., Barry, J.P., (2009). Effects of carbon dioxide on deep-sea harpacticoids revisited. Deep-Sea Research Part I, 56: 1018-1025. http://dx.doi.org/10.1016/j.dsr.2009.01.004
Thistle, D., Sedlacek, L., Carman, K.R., Fleeger, J.W., Barry, J.P., (2007). Emergence in the deep-sea: Evidence from harpacticoid copepods. Deep-Sea Research Part I, 54: 1008-1014. http://dx.doi.org/10.1016/j.dsr.2007.03.002
Levin, L.A., Barry, J.P., Felbeck, H., Smith, C.R., Young, C.R., (2007). Advances in vent, seep, whale-, and wood-fall biology. Marine Ecology, 28: 1-2. http://dx.doi.org/10.1111/j.1439-0485.2007.00153.x
Caldeira, K, Archer, D., Barry, J.P., Bellerby, R., Brewer, P.G., Cao, L., Dickson, A.G., Doney, S.C., Elderfield, H., Fabry, V., Freely, R.A., Gattuso, J.P., Hoegh-Guldberg, O., Haugan, P.M., Kleypas, J.A., Langdon, C., Orr, J.C., Ridgwell, A., Sabine, C.L., Seibel, B.A., Turley, C., Watson, A., Zeebe, R., (2007). Comment on "Modern-age buildup of CO2 and its effects on seawater acidity and salinity". Geophysical Research Letters, 34: . http://dx.doi.org/10.1029/2006GL027288
Barry, J.P., Whaling, P.J., Kochevar, R.K., (2007). Growth, production, and mortality of the chemosynthetic vesicomyid bivalve, Calyptogena kilmeri, from cold seeps off central California. Marine Ecology, 28: 169-182. http://dx.doi.org/10.1111/j.1439-0485.2007.00119.x
Kogan, I., Paull, C.K., Kuhnz, L., Burton, E.J., Von Thun, S., Greene, H.G., Barry, J., (2006). ATOC/Pioneer Seamount cable after 8 years on the seafloor: Observations and environmental impact. Continental Shelf Research, 26: 771-787. http://dx.doi.org/10.1016/j.csr.2006.01.010
Fleeger, J.W., Carman, K.R., Weisenhorn, P.B., Sofranko, H., Marshall, T., Thistle, D., Barry, J., (2006). Simulated sequestration of anthropogenic carbon dioxide at a deep-sea site: Effects on nematode abundance and biovolume. Deep-Sea Research Part I, 53: 1135-1147. http://dx.doi.org/10.1016/j.dsr.2006.05.007
Paull, C.K., Ussler III, W. , Greene, H.G., Barry, J., Keaten, R., (2005). Bioerosion by chemosynthetic biological communities on holocene submarine slide scars. Geo-Marine Letters, 25: 11-19. http://dx.doi.org/10.1007/s00367-004-0184-z
Drazen, J.C., Bird, L.E., Barry, J.P., (2005). Development of a hyperbaric trap-respirometer for the capture and maintenance of live deep-sea organisms. Limnology and Oceanography: Methods, 3: 488-498.
Orange, D.L., J. Yun, N. Maher, J.P. Barry, H.G. Greene, (2002). Tracking California seafloor seeps with bathymetry, backscatter and ROVs. Continental Shelf Research, 22: 2273–2290. http://dx.doi.org/10.1016/S0278-4343(02)00054-7
Eastman, J.T., J.P. Barry, (2002). Underwater video observation of the Antarctic toothfish, Dissostichus mawsoni (Perciformes: Nototheniidae) in the Ross Sea, Antarctica. Polar Biology, 25: 391–395.
Torres, M.E., J.P. Barry, D.A. Hubbard, E. Suess, (2001). Reconstructing the history of fluid flow at cold seep sites from Ba/Ca ratios in vesicomyid clam shells. Limnology and Oceanography, 46: 1701–1708.
Johnson, Kenneth S., Paull, Charles K., Barry, James P., Chavez, Francisco P., (2001). A decadal record of underflows from a coastal river into the deep sea. Geology, 29: 1019-1022. http://dx.doi.org/10.1130/0091-7613(2001)029<1019:Adrouf>2.0.Co;2
Bernhard, Joan M., Buck, Kurt R., Barry, James P., (2001). Monterey Bay cold-seep biota: Assemblages, abundance, and ultrastructure of living foraminifera. Deep Sea Research Part I: Oceanographic Research Papers, 48: 2233-2249. http://dx.doi.org/10.1016/S0967-0637(01)00017-6
Peek, Andrew S., Gaut, Brandon S., Feldman, Robert A., Barry, James P., Kochevar, Randall E., Lutz, Richard A., Vrijenhoek, Robert C., (2000). Neutral and nonneutral mitochondrial genetic variation in deep sea clams from the family Vesicomyidae. Journal of Molecular Evolution, 50: 141-153.
DiTullio, G.R., Grebmeier, J., Arrigo, K.R., Lizotte, M.P., Robinson, D.H., Leventer, A., Barry, James P., VanWoert, M., Dunbar, R.B., (2000). Rapid and early export of Phaeocystis antarctica blooms in the Ross Sea, Antarctica. Nature, 404: 595-598. http://dx.doi.org/10.1038/35007061
Buck, Kurt R., Barry, James P., Simpson, Alastair G.B., (2000). Monterey Bay cold seep biota: Euglenozoa with chemoautotrophic bacterial epibionts. European Journal of Phycology, 36: 117-126.
Barry, James P., Maher, Norman, (2000). Observation of the prickly shark, Echinorhinus cookei, from the oxygen minimum zone in Santa Barbara Basin, California. California Fish and Game, 86: 213-215.
Tamburri, Mario N., Barry, James P., (1999). Adaptations for scavenging by three diverse bathyla species, Eptatretus stouti, Neptunea amianta and Orchomene obtusus. Deep-Sea Research I, 46: 2079-2093. http://dx.doi.org/10.1016/S0967-0637(99)00044-8
Tamburri, Mario N., Barry, James P., (1999). Corrigendum to "Adaptations for scavenging by three diverse bathyla species Eptatretus stouti, Neptunea amianta and Orchomene obtusus" [Deep-Sea Research 46 (1999) 2079-2093]. Deep Sea Research Part I: Oceanographic Research Papers, 47: 755.
Sagarin, Raphael D., Barry, James P., Gilman, Sarah E., Baxter, Charles H., (1999). Climate-related change in an intertidal community over short and long time scales. Ecological monographs, 69: 465-490. http://dx.doi.org/10.1890/0012-9615(1999)069[0465:Crciai]2.0.Co;2
Pennington, J. Timothy, Tamburri, Mario N., Barry, James P., (1999). Development, temperature tolerance, and settlement preference of embryos and larvae of the articulate brachiopod Laqueus californianus. Biological Bulletin, 196: 245-256. http://dx.doi.org/10.2307/1542949
Orange, Daniel L., Greene, H. Gary, Reed, Donald L., Martin, Jonathan B., McHugh, Cecilia M., Ryan, William B.F., Maher, Norman, Stakes, Debra S., Barry, James P., (1999). Widespread fluid expulsion on a translational continental margin: Mud volcanoes, fault zones, headless canyons, and organic-rich substrate in Monterey Bay, California. Geological Society of America Bulletin, 111: 992-1009. http://dx.doi.org/10.1130/0016-7606(1999)111<0992:Wfeoat>2.3.Co;2
Barry, James P., Kochevar, Randall E., (1999). Calyptogena diagonalis, a new vesicomyid bivalve from subduction zone cold seeps in the eastern north Pacific. Veliger, 42: 117-123.
Ahmad, Azeem, Barry, James P. , Nelson, Douglas C. , (1999). Phylogenetic affinity of a wide, vacuolate, nitrate-accumulating Beggiatoa sp. from Monterey Canyon, California, with Thioploca spp.. Applied and Environmental Microbiology, 65: 270-277.
Lisin, S.E., Hannan, E.E., Kochevar, Randall E., Harrold, Christopher, Barry, James P., (1997). Temporal variation in gametogenic cycles of vesicomyid clams. Invertebrate Reproduction and Development, 31: 307-318. http://dx.doi.org/10.1080/07924259.1997.9672590
Barry, J.P., Kochevar, R.E. , Baxter, C.H. , (1997). The influence of pore-water chemistry and physiology on the distribution of vesicomyid clams at cold seeps in Monterey Bay: Implications for patterns of chemosynthetic community organization. Limnology and Oceanography, 42: 318-328.
Barry, J.P., Kochevar, R.E. , Baxter, C.H. , Harrold, C., (1997). Calyptogena packardana, a new species of vesicomyid bivalve from cold seeps in Monterey Bay, California. Veliger, 40: 341-349.
Orange, Daniel L., Barry, J., Maher, N., Stakes, D., Paduan, Jenny, Greene, H. G., Martin, J. B., McAdoo, B., Yun, J., Anonymou, (1996). ROV observations of fluid expulsion in Monterey Bay, California [Monograph] American Association of Petroleum Geologists 1996 annual convention. : .
Orange, Daniel L., Barry, J., Maher, N., Greene, H. G., Martin, J. B., McAdoo, B., Yun, J., Anonymou, (1996). ROV studies of fluid expulsion along a transpressional continental margin (Monterey Bay, California) [Monograph] 1996 ocean sciences meeting. : .
McHatton, Sarah C., James P. Barry, Holger W. Jannasch, Douglas C. Nelson, (1996). High nitrate concentrations in vacuolate, autotrophic marine Beggiatoa spp.. Applied and Environmental Microbiology, 62: 954-958.
Barry, James P., Gary Greene, H., Orange, Daniel L., Baxter, Charles H., Robison, Bruce H., Kochevar, Randall E., Nybakken, James W., R, Donald L., McHugh, Cecilia M., (1996). Biologic and geologic characteristics of cold seeps in Monterey Bay, California. Deep Sea Research Part I: Oceanographic Research Papers, 43: 1739-1762. https://doi.org/10.1016/S0967-0637(96)00075-1
Barry, James P., Charles H. Baxter, R.D. Sagarin, S.E. Gilman, (1995). Climate-related long-term faunal changes in a California rocky intertidal community. Science, 267: 672-675. http://dx.doi.org/10.1126/science.267.5198.672
Stoker, Carol R., Barry, James, Barch, Donald R., Hine III, Butler P., (1994). Use of telepresence and virtual reality in undersea exploration: 1993 Antarctic telepresence experiment. Technologies in Environmental Applications : 37-44.
Greene, H. G., Yoklavich, M. M., Barry, J. P., Orange, D. L., Sullivan, D. E., Cailliet, G. M., Anonymou, (1994). Geology and related benthic habitats of Monterey Canyon, Central California [Monograph] 1994 ocean sciences meeting. : .
McFeters, Gordon A., Barry, James P., Howington, James P., (1993). Distribution of enteric bacteria in Antarctic seawater surrounding a sewage outfall. Water Research, 27: 645-650.