Nelson
James A.
Nelson
James A.
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ArticleBioTIME : a database of biodiversity time series for the Anthropocene(John Wiley & Sons, 2018-07-24) Dornelas, Maria ; Antao, Laura H. ; Moyes, Faye ; Bates, Amanda E. ; Magurran, Anne E. ; Adam, Dusan ; Akhmetzhanova, Asem A. ; Appeltans, Ward ; Arcos, Jose Manuel ; Arnold, Haley ; Ayyappan, Narayanan ; Badihi, Gal ; Baird, Andrew H. ; Barbosa, Miguel ; Barreto, Tiago Egydio ; Bässler, Claus ; Bellgrove, Alecia ; Belmaker, Jonathan ; Benedetti-Cecchi, Lisandro ; Bett, Brian J. ; Bjorkman, Anne D. ; Błazewicz, Magdalena ; Blowes, Shane A. ; Bloch, Christopher P. ; Bonebrake, Timothy C. ; Boyd, Susan ; Bradford, Matt ; Brooks, Andrew J. ; Brown, James H. ; Bruelheide, Helge ; Budy, Phaedra ; Carvalho, Fernando ; Castaneda-Moya, Edward ; Chen, Chaolun Allen ; Chamblee, John F. ; Chase, Tory J. ; Collier, Laura Siegwart ; Collinge, Sharon K. ; Condit, Richard ; Cooper, Elisabeth J. ; Cornelissen, Johannes H. C. ; Cotano, Unai ; Crow, Shannan Kyle ; Damasceno, Gabriella ; Davies, Claire H. ; Davis, Robert A. ; Day, Frank P. ; Degraer, Steven ; Doherty, Tim S. ; Dunn, Timothy E. ; Durigan, Giselda ; Duffy, J. Emmett ; Edelist, Dor ; Edgar, Graham J. ; Elahi, Robin ; Elmendorf, Sarah C. ; Enemar, Anders ; Ernest, S. K. Morgan ; Escribano, Ruben ; Estiarte, Marc ; Evans, Brian S. ; Fan, Tung-Yung ; Farah, Fabiano Turini ; Fernandes, Luiz Loureiro ; Farneda, Fabio Z. ; Fidelis, Alessandra ; Fitt, Robert ; Fosaa, Anna Maria ; Franco, Geraldo Antonio Daher Correa ; Frank, Grace E. ; Fraser, William R. ; García, Hernando ; Gatti, Roberto Cazzolla ; Givan, Or ; Gorgone-Barbosa, Elizabeth ; Gould, William A. ; Gries, Corinna ; Grossman, Gary D. ; Gutierrez, Julio R. ; Hale, Stephen ; Harmon, Mark E. ; Harte, John ; Haskins, Gary ; Henshaw, Donald L. ; Hermanutz, Luise ; Hidalgo, Pamela ; Higuchi, Pedro ; Hoey, Andrew S. ; Hoey, Gert Van ; Hofgaard, Annika ; Holeck, Kristen ; Hollister, Robert D. ; Holmes, Richard ; Hoogenboom, Mia ; Hsieh, Chih-hao ; Hubbell, Stephen P. ; Huettmann, Falk ; Huffard, Christine L. ; Hurlbert, Allen H. ; Ivanauskas, Natalia Macedo ; Janík, David ; Jandt, Ute ; Jazdzewska, Anna ; Johannessen, Tore ; Johnstone, Jill F. ; Jones, Julia ; Jones, Faith A. M. ; Kang, Jungwon ; Kartawijaya, Tasrif ; Keeley, Erin C. ; Kelt, Douglas A. ; Kinnear, Rebecca ; Klanderud, Kari ; Knutsen, Halvor ; Koenig, Christopher C. ; Kortz, Alessandra R. ; Kral, Kamil ; Kuhnz, Linda A. ; Kuo, Chao-Yang ; Kushner, David J. ; Laguionie-Marchais, Claire ; Lancaster, Lesley T. ; Lee, Cheol Min ; Lefcheck, Jonathan S. ; Levesque, Esther ; Lightfoot, David ; Lloret, Francisco ; Lloyd, John D. ; Lopez-Baucells, Adria ; Louzao, Maite ; Madin, Joshua S. ; Magnusson, Borgbor ; Malamud, Shahar ; Matthews, Iain ; McFarland, Kent P. ; McGill, Brian ; McKnight, Diane ; McLarney, William O. ; Meador, Jason ; Meserve, Peter L. ; Metcalfe, Daniel J. ; Meyer, Christoph F. J. ; Michelsen, Anders ; Milchakova, Nataliya ; Moens, Tom ; Moland, Even ; Moore, Jon ; Moreira, Carolina Mathias ; Muller, Jorg ; Murphy, Grace ; Myers-Smith, Isla H. ; Myster, Randall W. ; Naumov, Andrew ; Neat, Francis ; Nelson, James A. ; Nelson, Michael Paul ; Newton, Stephen F. ; Norden, Natalia ; Oliver, Jeffrey C. ; Olsen, Esben M. ; Onipchenko, Vladimir G. ; Pabis, Krzysztof ; Pabst, Robert J. ; Paquette, Alain ; Pardede, Sinta ; Paterson, David M. ; Pelissier, Raphael ; Penuelas, Josep ; Perez-Matus, Alejandro ; Pizarro, Oscar ; Pomati, Francesco ; Post, Eric ; Prins, Herbert H. T. ; Priscu, John C. ; Provoost, Pieter ; Prudic, Kathleen L. ; Pulliainen, Erkki ; Ramesh, B. B. ; Ramos, Olivia Mendivil ; Rassweiler, Andrew ; Rebelo, Jose Eduardo ; Reed, Daniel C. ; Reich, Peter B. ; Remillard, Suzanne M. ; Richardson, Anthony J. ; Richardson, J. Paul ; Rijn, Itai van ; Rocha, Ricardo ; Rivera-Monroy, Victor H. ; Rixen, Christian ; Robinson, Kevin P. ; Rodrigues, Ricardo Ribeiro ; Rossa-Feres, Denise de Cerqueira ; Rudstam, Lars ; Ruhl, Henry A. ; Ruz, Catalina S. ; Sampaio, Erica M. ; Rybicki, Nancy ; Rypel, Andrew ; Sal, Sofia ; Salgado, Beatriz ; Santos, Flavio A. M. ; Savassi-Coutinho, Ana Paula ; Scanga, Sara ; Schmidt, Jochen ; Schooley, Robert ; Setiawan, Fakhrizal ; Shao, Kwang-Tsao ; Shaver, Gaius R. ; Sherman, Sally ; Sherry, Thomas W. ; Sicinski, Jacek ; Sievers, Caya ; da Silva, Ana Carolina ; da Silva, Fernando Rodrigues ; Silveira, Fabio L. ; Slingsby, Jasper ; Smart, Tracey ; Snell, Sara J. ; Soudzilovskaia, Nadejda A. ; Souza, Gabriel B. G. ; Souza, Flaviana Maluf ; Souza, Vinícius Castro ; Stallings, Christopher D. ; Stanforth, Rowan ; Stanley, Emily H. ; Sterza, Jose Mauro ; Stevens, Maarten ; Stuart-Smith, Rick ; Suarez, Yzel Rondon ; Supp, Sarah ; Tamashiro, Jorge Yoshio ; Tarigan, Sukmaraharja ; Thiede, Gary P. ; Thorn, Simon ; Tolvanen, Anne ; Toniato, Maria Teresa Zugliani ; Totland, Orjan ; Twilley, Robert R. ; Vaitkus, Gediminas ; Valdivia, Nelson ; Vallejo, Martha Isabel ; Valone, Thomas J. ; Van Colen, Carl ; Vanaverbeke, Jan ; Venturoli, Fabio ; Verheye, Hans M. ; Vianna, Marcelo ; Vieira, Rui P. ; Vrska, Tomas ; Vu, Con Quang ; Vu, Lien Van ; Waide, Robert B. ; Waldock, Conor ; Watts, David ; Webb, Sara ; Wesołowski, Tomasz ; White, Ethan P. ; Widdicombe, Claire E. ; Wilgers, Wilgers ; Williams, Richard ; Williams, Stefan B. ; Williamson, Mark ; Willig, Michael R. ; Willis, Trevor J. ; Wipf, Sonja ; Woods, Kerry D. ; Woehler, Eric ; Zawada, Kyle ; Zettler, Michael L.The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community‐led open‐source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2). BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.
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ArticleEffects of preservation methods of muscle tissue from upper-trophic level reef fishes on stable isotope values (δ13C and δ15N)(PeerJ, 2015-03-26) Stallings, Christopher D. ; Nelson, James A. ; Rozar, Katherine L. ; Adams, Charles S. ; Wall, Kara R. ; Switzer, Theodore S. ; Winner, Brent L. ; Hollander, David J.Research that uses stable isotope analysis often involves a delay between sample collection in the field and laboratory processing, therefore requiring preservation to prevent or reduce tissue degradation and associated isotopic compositions. Although there is a growing literature describing the effects of various preservation techniques, the results are often contextual, unpredictable and vary among taxa, suggesting the need to treat each species individually. We conducted a controlled experiment to test the effects of four preservation methods of muscle tissue from four species of upper trophic-level reef fish collected from the eastern Gulf of Mexico (Red Grouper Epinephelus morio, Gag Mycteroperca microlepis, Scamp Mycteroperca phenax, and Red Snapper Lutjanus campechanus). We used a paired design to measure the effects on isotopic values for carbon and nitrogen after storage using ice, 95% ethanol, and sodium chloride (table salt), against that in a liquid nitrogen control. Mean offsets for both δ13C and δ15N values from controls were lowest for samples preserved on ice, intermediate for those preserved with salt, and highest with ethanol. Within species, both salt and ethanol significantly enriched the δ15N values in nearly all comparisons. Ethanol also had strong effects on the δ13C values in all three groupers. Conversely, for samples preserved on ice, we did not detect a significant offset in either isotopic ratio for any of the focal species. Previous studies have addressed preservation-induced offsets in isotope values using a mass balance correction that accounts for changes in the isotope value to that in the C/N ratio. We tested the application of standard mass balance corrections for isotope values that were significantly affected by the preservation methods and found generally poor agreement between corrected and control values. The poor performance by the correction may have been due to preferential loss of lighter isotopes and corresponding low levels of mass loss with a substantial change in the isotope value of the sample. Regardless of mechanism, it was evident that accounting for offsets caused by different preservation methods was not possible using the standard correction. Caution is warranted when interpreting the results from specimens stored in either ethanol or salt, especially when using those from multiple preservation techniques. We suggest the use of ice as the preferred preservation technique for muscle tissue when conducting stable isotope analysis as it is widely available, inexpensive, easy to transport and did not impart a significant offset in measured isotopic values. Our results provide additional evidence that preservation effects on stable isotope analysis can be highly contextual, thus requiring their effects to be measured and understood for each species and isotopic ratio of interest before addressing research questions.
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ArticleMicrobial associations with macrobiota in coastal ecosystems : patterns and implications for nitrogen cycling(John Wiley & Sons, 2016-05-02) Moulton, Orissa M. ; Altabet, Mark A. ; Beman, J. Michael ; Deegan, Linda A. ; Lloret, Javier ; Lyons, Meaghan K. ; Nelson, James A. ; Pfister, CatherineIn addition to their important effects on nitrogen (N) cycling via excretion and assimilation (by macrofauna and macroflora, respectively), many macrobiota also host or facilitate microbial taxa responsible for N transformations. Interest in this topic is expanding, especially as it applies to coastal marine systems where N is a limiting nutrient. Our understanding of the diversity of microbes associated with coastal marine macrofauna (invertebrate and vertebrate animals) and macrophytes (seaweeds and marine plants) is improving, and recent studies indicate that the collection of microbes living in direct association with macrobiota (the microbiome) may directly contribute to N cycling. Here, we review the roles that macrobiota play in coastal N cycling, review current knowledge of macrobial–microbial associations in terms of N processing, and suggest implications for coastal ecosystem function as animals are harvested and as foundational habitat is lost or degraded. Given the biodiversity of microbial associates of macrobiota, we advocate for more research into the functional consequences of these associations for the coastal N cycle.
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PreprintBiomass transfer subsidizes nitrogen to offshore food webs( 2013-03-17) Nelson, James A. ; Stallings, Christopher D. ; Landing, William M. ; Chanton, Jeffrey P.We evaluated the potential contribution of allochthonous biomass subsidies to the upper trophic levels of offshore food webs in the northeastern Gulf of Mexico (GOM). We made this evaluation considering nitrogen, an essential and often limiting nutrient in coastal ecosystems, to estimate the potential production of within-ecosystem biomass relative to the known import of biomass from an adjacent seagrass dominated ecosystem. When adjusted for trophic transfer efficiency, we found the biomass subsidy from a single species (pinfish, Lagodon rhomboides) from neashore seagrass habitat to the offshore GOM to be greater than the amount of nitrogen exported by a two major rivers and local submarine ground water discharge. Our calculations show that seagrass-derived biomass accounts for ~25% of the total potential production in the northeastern GOM. This estimate is in agreement with a previous study that found 18.5-25% of the biomass in a predatory reef fish was derived from seagrass biomass inputs. These results indicate that all of the sources we consider account for the majority of the nitrogen available to the food web in the northeastern GOM. Our approach could be adapted to other coupled ecosystems to determine the relative importance of biomass subsidies to coastal ocean food 48 webs.
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ArticleNot all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands(Oxford University Press, 2020-12-09) Bowen, Jennifer L. ; Giblin, Anne E. ; Murphy, Anna E. ; Bulseco, Ashley N. ; Deegan, Linda A. ; Johnson, David S. ; Nelson, James A. ; Mozdzer, Thomas J. ; Sullivan, Hillary L.Excess reactive nitrogen (N) flows from agricultural, suburban, and urban systems to coasts, where it causes eutrophication. Coastal wetlands take up some of this N, thereby ameliorating the impacts on nearshore waters. Although the consequences of N on coastal wetlands have been extensively studied, the effect of the specific form of N is not often considered. Both oxidized N forms (nitrate, NO3−) and reduced forms (ammonium, NH4+) can relieve nutrient limitation and increase primary production. However, unlike NH4+, NO3− can also be used as an electron acceptor for microbial respiration. We present results demonstrating that, in salt marshes, microbes use NO3− to support organic matter decomposition and primary production is less stimulated than when enriched with reduced N. Understanding how different forms of N mediate the balance between primary production and decomposition is essential for managing coastal wetlands as N enrichment and sea level rise continue to assail our coasts.