Bucklin
Ann
Bucklin
Ann
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PreprintHabitat usage by the cryptic copepods Pseudocalanus moultoni and P. newmani on Georges Bank (Northwest Atlantic)( 2015-10-04) Bucklin, Ann ; McGillicuddy, Dennis J. ; Wiebe, Peter H. ; Davis, Cabell S.The cryptic copepod species, Pseudocalanus moultoni and P. newmani, co-occur on Georges Bank and in the Gulf of Maine (Northwest Atlantic); even recent studies have reported results and conclusions based on examination of the combined species. Species-specific PCR (SS-PCR) based on mitochondrial cytochrome oxidase I (COI) sequence divergence was used in this study to discriminate the species. Species-specific descriptions of habitat usage and predicted patterns of transport and retention on Georges Bank were made by mapping distributions and calculating abundances of each species from January to June, 1999 for four vertical strata (0-15 m, 15-40 m, 40-100 m, and 0-100 m) and five regions (Northern Flank, Bank Crest, Northeast Peak, Southern Flank, and Slope Water) identified on the basis of bathymetry and circulation. Patterns of distribution and abundance for the two species during January to June, 1999 were largely consistent with those described based on vertically integrating mapping and analysis for the same period in 1997 by McGillicuddy and Bucklin (2002). The region-specific and depth-stratified analyses allowed further discrimination in habitat usage by the species and confirmed the distinctive patterns for the two species. The observed differences between the species in abundances among the five regions and three depth strata over Georges Bank impact their transport trajectories. The concentration of P. moultoni in deep layers likely explains the higher rates of retention and lower rates of advective loss of this species from the Bank, compared to P. newmani, which may be more subject to wind-driven transport in the surface layer. Accurate identification and discrimination of even closely-related and cryptic species is needed to ensure full understanding and realistic predictions of changes in diversity of zooplankton and the functioning of pelagic ecosystems.
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DatasetCTD data from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from November to December 2011 (Salp_Antarctic project)(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, ) Bucklin, Ann ; Warren, Joseph D.Hydrographic data from 20 CTD casts in the Southern Ocean around the South Shetland Islands and Palmer Archipelago, Western Antarctic Peninsula in November 2011. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/559174
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DatasetAlongtrack data collected continuously by the ship's underway acquisition system from ARSV Laurence M. Gould cruise LMG1110 in the Southern Ocean in 2011(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, ) Bucklin, AnnThis alongtrack data set consists of a single file produced for each day of the LMG1110 cruise, from 11/2/2011 to 12/1/2011. The LMG alongtrack data acquisition systems continuously log data from a suite of instruments throughout the cruise. Data were obtained primarily by applying calibrations to raw data and decimating to whole point intervals. However, several fields are derived measurements from more than a single raw input. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/3636
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DatasetCTD data from MOCNESS tows taken in the Antarctic in 2011 from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from November to December 2011 (Salp_Antarctic project)(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, ) Bucklin, AnnCTD data from MOCNESS-1m tows in the Southern Ocean around the South Shetland Islands and Palmer Archipelago, Western Antarctic Peninsula in November 2011. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/488871
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DatasetCTD data collected during MOCNESS tows to Georges Bank and the Gulf of Maine on the US GLOBEC Georges Bank Broadscale and Process cruises, 1994-1999(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-01-30) Bollens, Steve M. ; Bucklin, Ann ; Garrahan, Peter ; Gifford, Dian J. ; Green, John ; Lough, Greg ; Miller, Charles B. ; Sibunka, John ; Taylor, Maureen ; Wiebe, Peter H.The MOCNESS is based on the Tucker Trawl principle (Tucker, 1951). The particular MOCNESS system from which these CTD data came is one of three net systems. The MOCNESS-10 (with 10 m2 nets)carries 6 nets of 3.0-mm circular mesh which are opened and closed sequentially by commands through conducting cable from the surface (Wiebe et al., 1976). In all three systems, "the underwater unit sends a data frame, comprised of temperature, depth, conductivity, net-frame angle, flow count, time, number of open net, and net opening/closing, to the deck unit in a compressed hexadecimal format every 2 seconds and from the deck unit to a microcomputer every 4 seconds... Temperature (to approximately 0.01 deg C) and conductivity are measured with SEABIRD sensors. Normally, a modified T.S.K.-flowmeter is used... Both the temperature and conductivity sensors and the flowmeter are mounted on top of the frame so that they face horizontally when the frame is at a towing angle of 45deg... Calculations of salinity (to approximately 0.01 o/oo S), potential temperature (theta), potential density (sigma), the oblique and vertical velocities of the net, and the approximate volume filtered by each net are made after each string of data has been received by the computer." (Wiebe et al., 1985) In addition, data were collected from four other sensors attached to the frame: the Transmissometer, the Fluorometer, the Downwelling light sensor, and the Oxygen sensor. A SeaBird underwater pump was also included in the sensor suite. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/2302
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DatasetSalp specimen log for genomic and transcriptomic study collected from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project)(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2018-02-23) Bucklin, Ann ; O'Neill, Rachel J. ; Payne, DianaThis dataset is a sample log of the Salpa thompsoni specimens used for genomic and transcriptomic analysis. Collections were from three cruises in the Southern Ocean. Collections were made in Summer of 2009 during a cruise of the Umitaka-Maru (UM-08-09) from off-shelf sites in the Indian Sector. During cruises of the ARSV Laurence M. Gould (LMG-1110) and R/V Polarstern (ANT-XXVII-2) samples were collected from on- and off-shelf regions of the Western Antarctic Peninsula Region and in Bransfield Strait during Spring and Summer 2011, respectively. Reported parameters include cruise id, region, season and area, location, number of samples collected, temperature, salinity, sampled depth range, and the depth of the water at the collection site. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/672600
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ArticleCOI metabarcoding of zooplankton species diversity for time-series monitoring of the NW Atlantic continental shelf(Frontiers Media, 2022-04-22) Bucklin, Ann ; Batta-Lona, Paola G. ; Questel, Jennifer M. ; Wiebe, Peter ; Richardson, David E. ; Copley, Nancy ; O'Brien, Todd D.Marine zooplankton are rapid-responders and useful indicators of environmental variability and climate change impacts on pelagic ecosystems on time scales ranging from seasons to years to decades. The systematic complexity and taxonomic diversity of the zooplankton assemblage has presented significant challenges for routine morphological (microscopic) identification of species in samples collected during ecosystem monitoring and fisheries management surveys. Metabarcoding using the mitochondrial Cytochrome Oxidase I (COI) gene region has shown promise for detecting and identifying species of some – but not all – taxonomic groups in samples of marine zooplankton. This study examined species diversity of zooplankton on the Northwest Atlantic Continental Shelf using 27 samples collected in 2002-2012 from the Gulf of Maine, Georges Bank, and Mid-Atlantic Bight during Ecosystem Monitoring (EcoMon) Surveys by the NOAA NMFS Northeast Fisheries Science Center. COI metabarcodes were identified using the MetaZooGene Barcode Atlas and Database (https://metazoogene.org/MZGdb) specific to the North Atlantic Ocean. A total of 181 species across 23 taxonomic groups were detected, including a number of sibling and cryptic species that were not discriminated by morphological taxonomic analysis of EcoMon samples. In all, 67 species of 15 taxonomic groups had ≥ 50 COI sequences; 23 species had >1,000 COI sequences. Comparative analysis of molecular and morphological data showed significant correlations between COI sequence numbers and microscopic counts for 5 of 6 taxonomic groups and for 5 of 7 species with >1,000 COI sequences for which both types of data were available. Multivariate statistical analysis showed clustering of samples within each region based on both COI sequence numbers and EcoMon counts, although differences among the three regions were not statistically significant. The results demonstrate the power and potential of COI metabarcoding for identification of species of metazoan zooplankton in the context of ecosystem monitoring.
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DatasetAntarctic salp genome and RNAseq transcriptome from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project)(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2018-02-23) Bucklin, Ann ; O'Neill, Rachel J. ; Payne, DianaA preliminary genome sequence and complete reference transcriptome have been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). The reference transcriptome contains 216,931 sequences; 41,210 (18%) were associated with predicted, hypothetical, or known proteins; 13,058 (6%) were mapped and annotated. Whole-transcriptome (RNA-seq) analysis of 39 samples collected during austral spring and summer 2011 in the WAP, and in summer 2009 in the Indian Sector revealed clustering of samples by regions, seasons, and areas (Bray-Curtis similarity). Spring versus summer samples showed significant differential expression of 77 genes associated with environmental stress response and 51 genes associated with sexual reproduction (paired t-tests, p<0.05). Gene Ontology (GO) term enrichment analysis identified 41 GO terms responsible for spring versus summer differences, including 156 genes associated with translation (i.e., protein synthesis). The genome sequence of 318,767,936 bp covers >50% of the estimated 602 MB (±173 MB) genome size for S. thompsoni, with >50% (16,823) of sequences showing significant homology to known proteins and ~38% (12,151) of the total protein predictions associated with Gene Ontology functional information. A total of 109,958 SNP variants and 9,782 indel predictions were generated, serving as a resource for future phylogenomic and population genomic studies. Salpa thompsoni exhibits rapid rates of evolution (>1.5 times that observed for vertebrates) typical of other urochordates examined. An initial survey of small RNAs revealed the presence of known, conserved miRNAs, as well as novel miRNA genes; unique piRNAs; and mature miRNA signatures for varying developmental stages. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/675040
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ArticleTwilight zone observation network: a distributed observation network for sustained, real-time interrogation of the ocean’s twilight zone(Marine Technology Society, 2021-05-01) Thorrold, Simon R. ; Adams, Allan ; Bucklin, Ann ; Buesseler, Ken O. ; Fischer, Godi ; Govindarajan, Annette F. ; Hoagland, Porter ; Di, Jin ; Lavery, Andone C. ; Llopez, Joel ; Madin, Laurence P. ; Omand, Melissa M. ; Renaud, Philip ; Sosik, Heidi M. ; Wiebe, Peter ; Yoerger, Dana R. ; Zhang, Weifeng G.The ocean's twilight zone (TZ) is a vast, globe-spanning region of the ocean. Home to myriad fishes and invertebrates, mid-water fishes alone may constitute 10 times more biomass than all current ocean wild-caught fisheries combined. Life in the TZ supports ocean food webs and plays a critical role in carbon capture and sequestration. Yet the ecological roles that mesopelagic animals play in the ocean remain enigmatic. This knowledge gap has stymied efforts to determine the effects that extraction of mesopelagic biomass by industrial fisheries, or alterations due to climate shifts, may have on ecosystem services provided by the open ocean. We propose to develop a scalable, distributed observation network to provide sustained interrogation of the TZ in the northwest Atlantic. The network will leverage a “tool-chest” of emerging and enabling technologies including autonomous, unmanned surface and underwater vehicles and swarms of low-cost “smart” floats. Connectivity among in-water assets will allow rapid assimilation of data streams to inform adaptive sampling efforts. The TZ observation network will demonstrate a bold new step towards the goal of continuously observing vast regions of the deep ocean, significantly improving TZ biomass estimates and understanding of the TZ's role in supporting ocean food webs and sequestering carbon.
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ArticleToward a global reference database of COI barcodes for marine zooplankton(Springer, 2021-05-04) Bucklin, Ann ; Peijnenburg, Katja T. C. A. ; Kosobokova, Ksenia N. ; O'Brien, Todd D. ; Blanco-Bercial, Leocadio ; Cornils, Astrid ; Falkenhaug, Tone ; Hopcroft, Russell R. ; Hosia, Aino ; Laakmann, Silke ; Li, Chaolun ; Martell, Luis ; Questel, Jennifer M. ; Wall-Palmer, Deborah ; Wang, Minxiao ; Wiebe, Peter ; Weydmann-Zwolicka, AgataCharacterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.
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Book chapterPopulation genomics of marine zooplankton( 2017-08-22) Bucklin, Ann ; DiVito, Kate ; Smolina, Irina ; Choquet, Marvin ; Questel, Jennifer M. ; Hoarau, Galice ; O’Neill, Rachel J.The exceptionally large population size and cosmopolitan biogeographic distribution that distinguish many – but not all – marine zooplankton species generate similarly exceptional patterns of population genetic and genomic diversity and structure. The phylogenetic diversity of zooplankton has slowed the application of population genomic approaches, due to lack of genomic resources for closelyrelated species and diversity of genomic architecture, including highly-replicated genomes of many crustaceans. Use of numerous genomic markers, especially single nucleotide polymorphisms (SNPs), is transforming our ability to analyze population genetics and connectivity of marine zooplankton, and providing new understanding and different answers than earlier analyses, which typically used mitochondrial DNA and microsatellite markers. Population genomic approaches have confirmed that, despite high dispersal potential, many zooplankton species exhibit genetic structuring among geographic populations, especially at large ocean-basin scales, and have revealed patterns and pathways of population connectivity that do not always track ocean circulation. Genomic and transcriptomic resources are critically needed to allow further examination of micro-evolution and local adaptation, including identification of genes that show evidence of selection. These new tools will also enable further examination of the significance of small-scale genetic heterogeneity of marine zooplankton, to discriminate genetic “noise” in large and patchy populations from local adaptation to environmental conditions and change.
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DatasetCTD data from the western Gulf of Maine collected on R/V Gulf Challenger (GC2002-4) from repeat visits to four locations from February to December 2002-2004 (REACH project)(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-05-28) Bucklin, Ann ; Manning, ChrisCTD data from the western Gulf of Maine collected on R/V Gulf Challenger (GC2002-4) from repeat visits to four locations from February to December 2002-2004 (REACH project). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/707014
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DatasetEvent logs from the U.S. GLOBEC Georges Bank project, from 10 vessels and 104 cruises in the Gulf of Maine and Georges Bank area from 1994-1999 (GB project)(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-02-18) Ashjian, Carin J. ; Bollens, Steve M. ; Bucklin, Ann ; Campbell, Robert ; Davis, Cabell S. ; Durbin, Edward ; Gallager, Scott ; Garrahan, Peter ; Gibson, James ; Gifford, Dian J. ; Green, John ; Greene, Charles H ; Hebert, Dave ; Horgan, Erich ; Houghton, Robert W ; Incze, Lewis ; Irish, Jim ; Ledwell, James R. ; Lentz, Steven J. ; Limeburner, Richard ; Lough, Greg ; Madin, Laurence P. ; Miller, Charles B. ; Mountain, David ; Oakey, Neil ; Schlitz, Ronald ; Sibunka, John ; Smith, Peter C. ; Taylor, Maureen ; Weller, Robert A. ; Wiebe, Peter H. ; Williams, Albert J. ; Wishner, Karen ; Lee, CraigEvent logs from the U.S. GLOBEC Georges Bank project, from 10 vessels and 104 cruises in the Gulf of Maine and Georges Bank area from 1994-1999. Event logs provide an overall summary of the sampling activities during a cruise. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/2321
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DatasetCTD data from the Gulf of Maine in 1998 from three cruises on the R/V Susan and Caitlyn - SC9801, SC9802, and SC9803 - in the Gulf of Maine and Georges Bank as part of the U.S. GLOBEC program (GB project)(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-10-28) Bub, Frank ; Bucklin, Ann ; Manning, James P.CTD data from the Gulf of Maine in 1998 from three cruises on the R/V Susan and Caitlyn - SC9801, SC9802, and SC9803 - in the Gulf of Maine and Georges Bank as part of the U.S. GLOBEC program. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/2419
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DatasetScientific sampling event log from ARSV Laurence M. Gould LMG1110 in the Southern Ocean from Nov. 2011 (Salp_Antarctic project)(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, ) Bucklin, AnnThe event log to record all instrument deployments during the cruise. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/3565
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ArticleTransition from stromatolite to thrombolite fabric: Potential role for reticulopodial protists in lake microbialites of a Proterozoic ecosystem analog(Frontiers Media, 2023-10-29) Bernhard, Joan M. ; Fisher, Luke A. ; Murphy, Quinne ; Sen, Leena ; Yeh, Heidi D. ; Louyakis, Artemis ; Gomaa, Fatma ; Reilly, Megan ; Batta-Lona, Paola G. ; Bucklin, Ann ; Le Roux, Veronique ; Visscher, Pieter T.Prior observations suggest that foraminiferan protists use their reticulopodia (anastomosing pseudopodia) to alter sediment fabric by disrupting laminations of subtidal marine stromatolites, erasing the layered structures in an experimental setting. Because microbialites and foraminifera are found in non-marine settings, we hypothesized that foraminifera living in lakes could also disrupt layered microbialite fabric. With this aim and using a variety of multidisciplinary approaches, we conducted field surveys and an experiment on microbialites from Green Lake (GL; Fayetteville, New York State, United States), which has been studied as a Proterozoic ecosystem analog. The lake is meromictic and alkaline, receiving calcium sulfate-rich water in the monimolimnion; it supports a well-developed carbonate platform that provides access to living and relict microbialites. The living microbialites grow from early spring to autumn, forming a laminated mat at their surface (top ~5 mm), but a clotted or massive structure exists at depth (> ~ 1 cm). We observed a morphotype of “naked” foraminiferan-like protist in samples from GL microbialites and sediments; thus, considered the possibility of freshwater foraminiferan impact on microbialite fabric. Results of an experiment that seeded the cultured freshwater foraminifer Haplomyxa saranae onto the GL microbialite surface indicates via micro-CT scanning and anisotropy analysis that the introduced foraminifer impacted uppermost microbialite layering (n = 3 cores); those cores with an added inhibitor lacked changes in anisotropy for two of those three cores. Thus, it remains plausible that the much smaller, relatively common, native free-form reticulate protist, which we identified as Chlamydomyxa labyrinthuloides, can disrupt microbialite fabrics on sub-millimeter scales. Our observations do not exclude contributions of other possible causal factors.