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  • 1
    Publication Date: 2022-05-25
    Description: Author Posting. © National Shellfisheries Association, 2005. This article is posted here by permission of National Shellfisheries Association for personal use, not for redistribution. The definitive version was published in Journal of Shellfish Research 24 (2005): 719-731, doi:10.2983/0730-8000(2005)24[719:NSRRGC]2.0.CO;2.
    Description: Western Long Island Sound (LIS) lobsters collected by trawl surveys, lobstermen and coastal residents during 2000 to 2002 were identified histologically as infected with a parasome-containing amoeba. Primers to conserved SSU rRNA sequences of parasome-containing amoebae and their nonparasome-containing relatives were used to amplify overlapping SSU rRNA fragments of the presumptive parasite from gill, antenna, antennal gland and ventral nerve cord of infected lobsters. The consensus sequence constructed from these fragments had 98% or greater nucleotide sequence identity with SSU rRNA gene sequences of strains of Neoparamoeba pemaquidensis and associated with high confidence in distance- and parsimony-based phylogenetic analyses with strains of Neoparamoeba pemaquidensis and not members of the family Paramoebidae, e.g., Paramoeba eilhardi. Primers designed to SSU rRNA sequences of the lobster amoeba and other paramoebid/vexilliferid amoebae were used in a nested polymerase chain reaction (PCR) protocol to test DNA extracted from formalin-fixed paraffin-embedded tissues of lobsters collected during the 1999 die-off, when this amoeba initially was identified by light and electron microscopy and reported to be a paramoeba of the genera Paramoeba or Neoparamoeba (Mullen et al. 2004). All sequences amplified from 1999 lobsters, with the exception of one, had 98% to 99% identity to each other, and the 1999 PCR product consensus had 98% identity to Neoparamoeba pemaquidensis strains CCAP 1560/4 (AF371969.1) and 1560/5 (AF371970.1). Molecular characterization of the amoeba from western LIS lobsters by direct amplification circumvents a collective inability to culture the organism in vitro, provides insight into the molecular epidemiology of neoparamoebiasis in American lobster, and allows for PCR-based detection of infected lobsters for future research and diagnostics.
    Description: Funding for this work was provided by the Connecticut Department of Environmental Protection under Long Island Sound Research Fund Grant No. CWF 333-R to S. Frasca; and by the Connecticut Sea Grant College Program, Grants No. LR/LR-4 to R. Gast and No. LR/LR-5 to P. Gillevet and C. O’Kelly, through the US Department of Commerce, National Oceanic and Atmospheric Administration (NOAA), Award NA16RG1364.
    Keywords: Homarus americanus ; Lobster ; Molecular phylogeny ; Neoparamoeba pemaquidensis ; Paramoebiasis ; PCR ; Small-subunit rRNA
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 2
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e90815, doi:10.1371/journal.pone.0090815.
    Description: Recreational water quality, as measured by culturable fecal indicator bacteria (FIB), may be influenced by persistent populations of these bacteria in local sands or wrack, in addition to varied fecal inputs from human and/or animal sources. In this study, pyrosequencing was used to generate short sequence tags of the 16S hypervariable region ribosomal DNA from shallow water samples and from sand samples collected at the high tide line and at the intertidal water line at sites with and without FIB exceedance events. These data were used to examine the sand and water bacterial communities to assess the similarity between samples, and to determine the impact of water quality exceedance events on the community composition. Sequences belonging to a group of bacteria previously identified as alternative fecal indicators were also analyzed in relationship to water quality violation events. We found that sand and water samples hosted distinctly different overall bacterial communities, and there was greater similarity in the community composition between coastal water samples from two distant sites. The dissimilarity between high tide and intertidal sand bacterial communities, although more similar to each other than to water, corresponded to greater tidal range between the samples. Within the group of alternative fecal indicators greater similarity was observed within sand and water from the same site, likely reflecting the anthropogenic contribution at each beach. This study supports the growing evidence that community-based molecular tools can be leveraged to identify the sources and potential impact of fecal pollution in the environment, and furthermore suggests that a more diverse bacterial community in beach sand and water may reflect a less contaminated site and better water quality.
    Description: This work was supported by the National Science Foundation grant OCE-0430724, and the National Institute of Environmental Health Sciences grant P0ES012742 to the Woods Hole Center for Ocean and Human Health. E. Halliday was partially supported by WHOI Academic Programs and grants from the WHOI Ocean Ventures Fund and the WHOI Coastal Ocean Institute.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/msword
    Format: application/pdf
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  • 3
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2021. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Journal of Phycology, doi:10.1111/jpy.13135.
    Description: Gymnodinium gracile, described from the coasts of Denmark in 1881, is one of the first described unarmored dinoflagellates. Individuals which morphologically fit with the original description were isolated from the English Channel (North‐East Atlantic). The SSU rRNA gene sequences were identical to the sequences identified as Balechina pachydermata and Gymnodinium amphora from the Mediterranean Sea and Brazil. We propose the transfer of Gymnodinium gracile into the genus Balechina as B. gracilis comb. nov. These sequences constitute an independent lineage, clustering with numerous environmental sequences from polar to tropical waters. The widespread distribution, the high plasticity in size, shape and coloration and the difficulties in discerning the fine longitudinal striae have contributed to the description of numerous synonyms: Amphidinium vasculum, Balechina pachydermata (=Gymnodinium pachydermatum), Gymnodinium achromaticum, G. abbreviatum, G. amphora, G. dogielii, G. lohmannii (=G. roseum sensu Lohmann 1908), G. situla and Gyrodinium cuneatum (=G. gracile sensu Pouchet 1885).
    Description: F.G. was supported by the convention #2101893310 between CNRS INSU and the French Ministry of Ecology (MTES) for the implementation of the Monitoring Program of the European Marine Strategy Framework directive (MSFD) for pelagic habitats and the descriptor ‘biodiversity’. Samples were collected during the ECOPEL Manche 2018 spring and summer cruises (CNRS-LOG) onboard R/V "Antea" (IRD, Institut de Recherche pour le Développement) in the frame of the cited convention and the CPER ‘Hauts de France’ project MARCO supported by the French state, the ‘Hauts de France’ French Region and the European Regional Development Founds (ERDF).
    Keywords: Dinophyta ; naked Dinoflagellata ; Gymnodiniales ; new combination ; taxonomy ; molecular phylogenetics
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 4
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sutherland, K. M., Coe, A., Gast, R. J., Plummer, S., Suffridge, C. P., Diaz, J. M., Bowman, J. S., Wankel, S. D., & Hansel, C. M. Extracellular superoxide production by key microbes in the global ocean. Limnology and Oceanography, (2019), doi:10.1002/lno.11247.
    Description: Bacteria and eukaryotes produce the reactive oxygen species superoxide both within and outside the cell. Although superoxide is typically associated with the detrimental and sometimes fatal effects of oxidative stress, it has also been shown to be involved in a range of essential biochemical processes, including cell signaling, growth, differentiation, and defense. Light‐independent extracellular superoxide production has been shown to be widespread among many marine heterotrophs and phytoplankton, but the extent to which this trait is relevant to marine microbial physiology and ecology throughout the global ocean is unknown. Here, we investigate the dark extracellular superoxide production of five groups of organisms that are geographically widespread and represent some of the most abundant organisms in the global ocean. These include Prochlorococcus, Synechococcus, Pelagibacter, Phaeocystis, and Geminigera. Cell‐normalized net extracellular superoxide production rates ranged seven orders of magnitude, from undetectable to 14,830 amol cell−1 h−1, with the cyanobacterium Prochlorococcus being the lowest producer and the cryptophyte Geminigera being the most prolific producer. Extracellular superoxide production exhibited a strong inverse relationship with cell number, pointing to a potential role in cell signaling. We demonstrate that rapid, cell‐number–dependent changes in the net superoxide production rate by Synechococcus and Pelagibacter arose primarily from changes in gross production of extracellular superoxide, not decay. These results expand the relevance of dark extracellular superoxide production to key marine microbes of the global ocean, suggesting that superoxide production in marine waters is regulated by a diverse suite of marine organisms in both dark and sunlit waters.
    Description: The authors would like to acknowledge their funding sources including NASA NESSF NNX15AR62H (K.M.S.), NASA Exobiology grant NNX15AM04G to S.D.W. and C.M.H., NSF‐OCE grant 1355720 to C.M.H., NSF‐OPP 1641019 (J.S.B), and Simons Foundation SCOPE Award ID 329108 (Sallie W. Chisholm). The authors would also like to thank the Harvey lab (Skidaway Institute of Oceanography) for use of their flow cytometer in this study. We thank Stephen Giovannoni and Sallie Chisholm for providing bacteria strains and laboratory facilities. Additional thanks to Marianne Acker, Rogier Braakman, and Aldo Arellano for assistance in lab and helpful conversations.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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