http://lod.bco-dmo.org/id/dataset/681997
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-02-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Data from: Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It’s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices.
2017-02-10
publication
2017-02-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2017-02-14
publication
http://dx.doi.org/10.1575/1912/bco-dmo.682247
Dr Erica Goetze
University of Hawaii at Manoa
principalInvestigator
Dr Matthew Iacchei
University of Hawaii at Manoa
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
documentDigital
Cite this dataset as: Goetze, Erica and Iacchei, Matthew (2017) Data from: Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It’s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Dataset version 2017-02-10 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.682247 [access date]
Temporal genetic patterns in P. xiphias and H. longicornis - Mitochondrial data, station ALOHA Dataset Description: <p>This dataset&nbsp;consists of mitochondrial sequence data and specimen information for two species of copepods, <em>Haloptilus longicornis</em> and <em>Pleuromamma xiphias</em>, collected at an open ocean time series site in the North Pacific Subtropical Gyre (station ALOHA, 22.45N, 158W) during 11 of the routine Hawai'i Ocean Time-series (HOT) research cruises from September of 2012 to October of 2013 (HOT-246 to HOT-256).&nbsp;Data for <em>Haloptilus longicornis</em> include&nbsp;a 546 base-pair fragment of mitochondrial cytochrome <em>c </em>oxidase subunit II for each of 483 individuals (mean of 44 animals per cruise). Data for <em>Pleuromamma xiphias</em> include&nbsp;a 551 base-pair fragment of mitochondrial cytochrome <em>c </em>oxidase subunit I for each of 510 individuals (mean of 46 animals per cruise). Information is also provided on the HOT cruise number, date, and specific tow from which each individual was collected. Life stage and sex of each animal are also noted when identifiable</p><p>These data are associated with the forthcoming publication:<br />Iacchei, M.<u>,</u> E. Butcher, E. Portner, Goetze, E. (in press) It’s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices.&nbsp; <em>Limnology and Oceanography &nbsp;</em></p><p>The unique haplotypes in these data are also available under NCBI accession numbers KY560470 - KY560514 [<em>Haloptilus longicornis</em>], KY560515 - KY560565&nbsp;[<em>Pleuromamma xiphias</em>].</p><p>The following files have been included in this dataset (note that the sequence IDs in these files differ from the NCBI sequence IDs):<br />HOT-HALO.fasta: A fasta-formatted text file containing sequences for a portion of the mitochondrial cytochrome <em>c</em> oxidase subunit II gene (COII; 546 bp) for 483 <em>Haloptilus longicornis</em> individuals collected at Station ALOHA.</p><p>HOT-PLXI.fasta: A fasta-formatted text file containing sequences for a portion of the mitochondrial cytochrome <em>c</em> oxidase subunit I gene (COI; 551 bp) for 510 <em>Pleuromamma xiphias</em> individuals collected at Station ALOHA.</p><p>HALO.csv and PLXI.csv: Converted to csv from an Excel file consisting of one worksheet for <em>Haloptilus longicornis </em>and one worksheet for <em>Pleuromamma xiphias. </em>In each worksheet, column headings designate:<br />sample_id: the sample ID number associated with the original organism collected, DNA extraction, and PCR amplification.<br />sequence_id: the sample ID number associated with sequences analysed for the project.<br />genus: Genus of the collected organism.<br />species: Species of the collected organism.<br />cruise: The cruise number for the Hawai'i Ocean Time Series (HOT) cruise on which the specimen was collected.<br />tow: The net tow number on which the specimen was collected.<br />collection_date: The date on which the specimen was collected, formatted as yyyy-mm-dd.<br />stage_sex: The life stage (Copepodite or Adult) of the individual, and the sex (Copepodite, Female, Male).<br />stage: The life stage (Copepodite or Adult) of the individual. Column added by BCO-DMO&nbsp;from the original stage_sex column for ease of use.<br />sex: The sex (Copepodite, Female, or Male) of the individual.&nbsp;Column added by BCO-DMO&nbsp;from the original stage_sex column for ease of use.<br />mtCO*_sequence: The mtDNA sequence (COII for <em>Haloptilus longicornis; </em>COI for <em>Pleuromamma xiphias</em>) associated with that individual. This sequence matches the sequence associated with the Sequence ID number in the respective fasta file.</p> Acquisition Description: <p><strong>Collection:&nbsp;</strong>Bulk zooplankton were collected at an open ocean time series site in the North Pacific Subtropical Gyre (station ALOHA, 22.45N, 158W) during 11 of the routine Hawai'i Ocean Time-series (HOT) research cruises at approximately monthly intervals from September of 2012 to October of 2013 (HOT-246 to HOT-256). Mesozooplankton were collected using a 1 m<sup>2</sup>, 200 um-mesh ring net towed obliquely from a mean maximum depth of 155 m (SD = 31 m) to the sea surface. Zooplankton for this study were collected from three nighttime tows completed between the hours of 2200-0200 on consecutive nights for each sampling period so that all collections for a single cruise were collected within three days of one another. Following net retrieval, bulk plankton were quantitatively split using a Folsom plankton splitter, and 1/4 of the material was preserved in 95% non-denatured ethyl alcohol (EtOH) and stored at -20C. From these bulk collections, 50 <em>Haloptilus longicornis</em> and 50 <em>Pleuromamma xiphias </em>individuals were sorted from each net tow for use in this study.</p><p><strong>mtDNA Sequence Generation:</strong><em>&nbsp;</em>For both <em>H. longicornis </em>and <em>P. xiphias,</em> DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit (Qiagen, Inc., Valencia, CA). For <em>H. longicornis</em>, a 546 base-pair fragment of the mitochondrial cytochrome <em>c</em> oxidase subunit II (mtCOII) gene was amplified by polymerase chain reaction (PCR) with species-specific primers COII_F6 and COII_R9. For <em>P. xiphias, </em>a 551 base-pair fragment of the mitochondrial cytochrome <em>c</em> oxidase subunit I (mtCOI) was amplified by PCR using species-specific primers PLXI_VH and PLXI_VL. Specific information on primer sequences, PCR reaction mixes, thermal cycler conditions, and PCR purification is provided in the manuscript associated with this submission. Purified PCR products were sequenced on an ABI 3730XL capillary sequencer (Applied Biosystems, Foster City, CA). Sequences were aligned, edited and trimmed using Geneious 7.0.6 (Biomatters, Ltd., Auckland, New Zealand). Unique haplotypes were identified using the Haplotype Collapser and Converter in FaBox 1.35 (<a href="http://users-birc.au.dk/biopv/php/fabox/" target="_blank">http://users-birc.au.dk/biopv/php/fabox/</a>), and deposited with their respective protein translations in GenBank under accession numbers: KY560470 - KY560565. An mtDNA sequence for each individual specimen is deposited in this BCO-DMO submission as part of one of two fasta files. Each fasta file contains the mtDNA sequence fragments from all individuals from a single species aligned together.</p><p>Methodology is further described in the paper itself:<br />Iacchei, M.<u>,</u> E. Butcher, E. Portner, Goetze, E. (in press) It’s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices.&nbsp; <em>Limnology and Oceanography</em></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1260164 Award URL: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1260164&HistoricalAwards=false
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1338959 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1338959
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1029478 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1029478
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1522572 Award URL: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1522572
onGoing
Dr Erica Goetze
University of Hawaii at Manoa
808-956-7156
Department of Oceanography, University of Hawaii at Manoa 1000 Pope Road
Honolulu
HI
96822
United States
egoetze@hawaii.edu
pointOfContact
Dr Matthew Iacchei
University of Hawaii at Manoa
HI
USA
iacchei@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 10 February 2017
Unknown
file_link
brief_desc
mesh ring net
Folsom Plankton Splitter
theme
None, User defined
file_link
brief description
featureType
BCO-DMO Standard Parameters
Ring Net
PCR Thermal Cycler
Folsom Plankton Splitter
instrument
BCO-DMO Standard Instruments
HOT_cruises
service
Deployment Activity
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Ocean Carbon and Biogeochemistry
http://us-ocb.org/
Ocean Carbon and Biogeochemistry
The Ocean Carbon and Biogeochemistry (OCB) program focuses on the ocean's role as a component of the global Earth system, bringing together research in geochemistry, ocean physics, and ecology that inform on and advance our understanding of ocean biogeochemistry. The overall program goals are to promote, plan, and coordinate collaborative, multidisciplinary research opportunities within the U.S. research community and with international partners. Important OCB-related activities currently include: the Ocean Carbon and Climate Change (OCCC) and the North American Carbon Program (NACP); U.S. contributions to IMBER, SOLAS, CARBOOCEAN; and numerous U.S. single-investigator and medium-size research projects funded by U.S. federal agencies including NASA, NOAA, and NSF.The scientific mission of OCB is to study the evolving role of the ocean in the global carbon cycle, in the face of environmental variability and change through studies of marine biogeochemical cycles and associated ecosystems.The overarching OCB science themes include improved understanding and prediction of: 1) oceanic uptake and release of atmospheric CO2 and other greenhouse gases and 2) environmental sensitivities of biogeochemical cycles, marine ecosystems, and interactions between the two.The OCB Research Priorities (updated January 2012) include: ocean acidification; terrestrial/coastal carbon fluxes and exchanges; climate sensitivities of and change in ecosystem structure and associated impacts on biogeochemical cycles; mesopelagic ecological and biogeochemical interactions; benthic-pelagic feedbacks on biogeochemical cycles; ocean carbon uptake and storage; and expanding low-oxygen conditions in the coastal and open oceans.
OCB
largerWorkCitation
program
U.S. Joint Global Ocean Flux Study
http://usjgofs.whoi.edu/
U.S. Joint Global Ocean Flux Study
The United States Joint Global Ocean Flux Study was a national component of international JGOFS and an integral part of global climate change research.The U.S. launched the Joint Global Ocean Flux Study (JGOFS) in the late 1980s to study the ocean carbon cycle. An ambitious goal was set to understand the controls on the concentrations and fluxes of carbon and associated nutrients in the ocean. A new field of ocean biogeochemistry emerged with an emphasis on quality measurements of carbon system parameters and interdisciplinary field studies of the biological, chemical and physical process which control the ocean carbon cycle. As we studied ocean biogeochemistry, we learned that our simple views of carbon uptake and transport were severely limited, and a new "wave" of ocean science was born. U.S. JGOFS has been supported primarily by the U.S. National Science Foundation in collaboration with the National Oceanic and Atmospheric Administration, the National Aeronautics and Space Administration, the Department of Energy and the Office of Naval Research. U.S. JGOFS, ended in 2005 with the conclusion of the Synthesis and Modeling Project (SMP).
U.S. JGOFS
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program
Ocean Time-series Sites
http://www.bco-dmo.org/program/562656
Ocean Time-series Sites
Program description text taken from Chapter 1: Introduction from the Global Intercomparability in a Changing Ocean: An International Time-Series Methods Workshop report published following the workshop held November 28-30, 2012 at the Bermuda Institute of Ocean Sciences. The full report is available from the workshop Web site hosted by US OCB: http://www.whoi.edu/website/TS-workshop/homeDecades of research have demonstrated that the ocean varies across a range of time scales, with anthropogenic forcing contributing an added layer of complexity. In a growing effort to distinguish between natural and human-induced earth system variability, sustained ocean time-series measurements have taken on a renewed importance. Shipboard biogeochemical time-series represent one of the most valuable tools scientists have to characterize and quantify ocean carbon fluxes and biogeochemical processes and their links to changing climate (Karl, 2010; Chavez et al., 2011; Church et al., 2013). They provide the oceanographic community with the long, temporally resolved datasets needed to characterize ocean climate, biogeochemistry, and ecosystem change.The temporal scale of shifts in marine ecosystem variations in response to climate change are on the order of several decades. The long-term, consistent and comprehensive monitoring programs conducted by time-series sites are essential to understand large-scale atmosphere-ocean interactions that occur on interannual to decadal time scales. Ocean time-series represent one of the most valuable tools scientists have to characterize and quantify ocean carbon fluxes and biogeochemical processes and their links to changing climate.Launched in the late 1980s, the US JGOFS (Joint Global Ocean Flux Study; http://usjgofs.whoi.edu) research program initiated two time-series measurement programs at Hawaii and Bermuda (HOT and BATS, respectively) to measure key oceanographic measurements in oligotrophic waters. Begun in 1995 as part of the US JGOFS Synthesis and Modeling Project, the CARIACO Ocean Time-Series (formerly known as the CArbon Retention In A Colored Ocean) Program has studied the relationship between surface primary production, physical forcing variables like the wind, and the settling flux of particulate carbon in the Cariaco Basin.The objective of these time-series effort is to provide well-sampled seasonal resolution of biogeochemical variability at a limited number of ocean observatories, provide support and background measurements for process-oriented research, as well as test and validate observations for biogeochemical models. Since their creation, the BATS, CARIACO and HOT time-series site data have been available for use by a large community of researchers. Data from those three US funded, ship-based, time-series sites can be accessed at each site directly or by selecting the site name from the Projects section below.
Ocean Time-series
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program
Hawaii Ocean Time-series (HOT): Sustaining ocean ecosystem and climate observations in the North Pacific Subtropical Gyre
http://hahana.soest.hawaii.edu/hot/hot_jgofs.html
Hawaii Ocean Time-series (HOT): Sustaining ocean ecosystem and climate observations in the North Pacific Subtropical Gyre
Systematic, long-term observations are essential for evaluating natural variability of Earth’s climate and ecosystems and their responses to anthropogenic disturbances. Since October 1988, the Hawaii Ocean Time-series (HOT) program has investigated temporal dynamics in biology, physics, and chemistry at Stn. ALOHA (22°45' N, 158°W), a deep ocean field site in the oligotrophic North Pacific Subtropical Gyre (NPSG). HOT conducts near monthly ship-based sampling and makes continuous observations from moored instruments to document and study NPSG climate and ecosystem variability over semi-diurnal to decadal time scales. HOT was founded to understand the processes controlling the time-varying fluxes of carbon and associated biogenic elements in the ocean and to document changes in the physical structure of the water column. To achieve these broad objectives, the program has several specific goals:Quantify time-varying (seasonal to decadal) changes in reservoirs and fluxes of carbon (C) and associated bioelements (nitrogen, oxygen, phosphorus, and silicon).Identify processes controlling air-sea C exchange, rates of C transformation through the planktonic food web, and fluxes of C into the ocean’s interior.Develop a climatology of hydrographic and biogeochemical dynamics from which to form a multi-decadal baseline from which to decipher natural and anthropogenic influences on the NPSG ecosystem. Provide scientific and logistical support to ancillary programs that benefit from the temporal context, interdisciplinary science, and regular access to the open sea afforded by HOT program occupation of Sta. ALOHA, including projects implementing, testing, and validating new methodologies, models, and transformative ocean sampling technologies.Over the past 24+ years, time-series research at Station ALOHA has provided an unprecedented view of temporal variability in NPSG climate and ecosystem processes. Foremost among HOT accomplishments are an increased understanding of the sensitivity of bioelemental cycling to large scale ocean-climate interactions, improved quantification of reservoirs and time varying fluxes of carbon, identification of the importance of the hydrological cycle and its influence on upper ocean biogeochemistry, and the creation of long-term data sets from which the oceanic response to anthropogenic perturbation of elemental cycles may be gauged. A defining characteristic of the NPSG is the perennially oligotrophic nature of the upper ocean waters. This biogeochemically reactive layer of the ocean is where air-sea exchange of climate reactive gases occurs, solar radiation fuels rapid biological transformation of nutrient elements, and diverse assemblages of planktonic organisms comprise the majority of living biomass and sustain productivity. The prevailing Ekman convergence and weak seasonality in surface light flux, combined with relatively mild subtropical weather and persistent stratification, result in a nutrient depleted upper ocean habitat. The resulting dearth of bioessential nutrients limits plankton standing stocks and maintains a deep (175 m) euphotic zone. Despite the oligotrophic state of the NPSG, estimates of net organic matter production at Sta. ALOHA are estimated to range ~1.4 and 4.2 mol C m2 yr1. Such respectable rates of productivity have highlighted the need to identify processes supplying growth limiting nutrients to the upper ocean. Over the lifetime of HOT numerous ancillary science projects have leveraged HOT science and infrastructure to examine possible sources of nutrients supporting plankton productivity. Both physical (mixing, upwelling) and biotic (N2 fixation, vertical migration) processes supply nutrients to the upper ocean in this region, and HOT has been instrumental in demonstrating that these processes are sensitive to variability in ocean climate.Station ALOHA - site selection and infrastructureStation ALOHA is a deep water (~4800 m) location approximately 100 km north of the Hawaiian Island of Oahu. Thus, the region is far enough from land to be free of coastal ocean dynamics and terrestrial inputs, but close enough to a major port (Honolulu) to make relatively short duration (<5 d) near-monthly cruises logistically and financially feasible. Sampling at this site occurs within a 10 km radius around the center of the station. On each HOT cruise, we begin each cruise with a stop at a coastal station south of the island of Oahu, approximately 10 km off Kahe Point (21' 20.6'N, 158' 16.4'W) in 1500 m of water. Station Kahe (termed Station 1 in our database) is used to test equipment and train new personnel before departing for Station ALOHA. Since August 2004, Station ALOHA has also been home to a surface mooring outfitted for meteorological and upper ocean measurements; this mooring, named WHOTS (also termed Station 50), is a collaborative project between Woods Hole Oceanographic Institution and HOT. WHOTS provides long-term, high-quality air-sea fluxes as a coordinated part of HOT, contributing to the program’s goals of observing heat, fresh water and chemical fluxes. In 2011, the ALOHA Cabled Observatory (ACO) became operational. This instrumented fiber optic cabled observatory provides power and communications to the seabed (4728 m). The ACO currently configured with an array of thermistors, current meters, conductivity sensors, 2 hydrophones, and a video camera.HOT Sampling StrategyHOT relies on the UNOLS research vessel Kilo Moana operated by the University of Hawaii for most of our near-monthly sampling expeditions. The exact timing of HOT cruises is dictated by the vessel schedule, but to date, our sampling record is not heavily aliased by month, season, or year. When at Station ALOHA, HOT relies on a variety of sampling strategies to capture the dynamic range of time-variable physical and biogeochemical dynamics inherent to the NPSG ecosystem, including high resolution conductivity-temperature-depth (CTD) profiles; biogeochemical analyses of discrete water samples; in situ vertically profiling bio-optical instrumentation; surface tethered, free-drifting arrays for determinations of primary production and particle fluxes; bottom-moored, deep ocean (2800 m, 4000 m) sediment traps; and oblique plankton net tows. The suite of core measurements conducted by HOT has remained largely unchanged over the program’s lifetime. On each HOT cruise, samples are collected from the surface ocean to near the sea bed (~4800 m), with the most intensive sampling occurring in the upper 1000 m (typically 13-15 CTD hydrocasts to 1000 m and 2 casts to ~4800 m). HOT utilizes a “burst” vertical profiling strategy where physical and biogeochemical properties are measured at 3-h intervals over a 36-h period, covering 3 semidiurnal tidal cycles and 1 inertial period (~31 h). This approach captures energetic high-frequency variability in ocean dynamics due to internal tides around Sta. ALOHA. Scientific Background and FindingsCentral to the mission of the HOT program is continued quantification of ocean carbon inventories and fluxes, with a focus on describing changes in the sizes of these pools and fluxes over time. HOT routinely quantifies the vertical distributions of the major components of the ocean carbon cycle: dissolved inorganic carbon (DIC), pH, total alkalinity, dissolved organic carbon (DOC), and particulate carbon (PC). The HOT dataset constitutes one the longest running records from which to gauge the oceanic response to continued anthropogenic changes to the global carbon cycle. The 24+ year record of ocean carbon measurements at Station ALOHA document that the partial pressure of CO2 (pCO2) in the mixed layer is increasing at a rate (1.92 ± 0.13 microatm yr-1), slightly greater than the trend observed in the atmosphere (1.71 ± 0.03 microatm yr1). Moreover, mixed layer concentrations of salinity-normalized DIC are increasing at 1.03 ± 0.07 micromol kg1 yr1 (Winn et al., 1998; Dore et al., 2009). These long-term changes in upper ocean carbon inventories have been accompanied by progressive decreases in seawater pH (-0.0018 ± 0.0001 yr1) and declines in aragonite and calcite saturation states (Dore et al., 2009). Although the penetration of anthropogenic CO2 is evidenced by long-term decreases in seawater pH throughout the upper 600 m, the rate of acidification at Sta. ALOHA varies with depth. For example, in the upper mesopelagic waters (~160-310 m) pH is decreasing at nearly twice the rate observed in the surface waters (Dore et al., 2009). Such depth-dependent differences in acidification derive from a combination of regional differences in the time-varying climate signatures imprinted on the ventilation history of the waters, mixing, and changes in biological activity associated with different water masses. Superimposed on these progressive long-term trends in the seawater carbonate system are seasonal- to decadal-scale variations in climate and biogeochemical dynamics that ultimately influence CO2 inventories, fluxes, and trends. Changes in temperature, evaporation-precipitation, and mixing all impart complex, time-varying signatures on the ocean carbon cycle. For example, interactions among low-frequency climate oscillations such as those linked to the El-Niño Southern Oscillation (ENSO), Pacific Decadal Oscillation (PDO), and North Pacific Gyre Oscillation (NPGO) influence the frequency, intensity, and tracks of winter storms in the NPSG (Lukas, 2001), which in turn modifies physical forcing (wind and air-sea heat/water fluxes) and upper ocean response (stratification, currents and mixing). Such dynamics have important, often non-linear, influences on ocean carbon uptake and biogeochemistry. Time-series measurements at HOT have also highlighted complex relationships between ecosystem dynamics and climate-driven physical forcing. Historically, the abundances and distributions of the resident plankton community of the NPSG were thought to be relatively stable in both space and time. However, HOT program measurements have identified remarkable temporal (and spatial) heterogeneity in biogeochemical processes and planktonic community structure over seasonal to interannual time scales. In many cases, climate-forced fluctuations in plankton population dynamics resonate from the base of the picoplankton food web to higher trophic levels (Karl, 1999; Karl et al., 2001; Sheridan and Landry, 2004; Corno et al., 2007; Bidigare et al., 2009). However, we currently lack a complete mechanistic understanding of the processes underlying variability in NPSG biogeochemistry. With continued lengthening of the time series record, HOT measurements have become increasingly useful for identifying low-frequency, interannual- to decadal-scale signals in ocean climate and biogeochemistry. Upper ocean physical dynamics, nutrient availability, plankton productivity, biomass and community structure, and material export at Sta. ALOHA have all been shown to be sensitive to regional- to basin- scale climate oscillations of the Pacific (Karl et al., 1995; Karl, 1999; Dore et al., 2002; Corno et al., 2007; Bidigare et al., 2009). One of the most notable examples coincided with major phase shifts in the ENSO, PDO, and NPGO indices in 1997-1998. Fluctuations in mixing and hydrological forcing accompanying these transitions had important consequences for ocean biogeochemistry and plankton ecology, including changing upper ocean nutrients, concentrations of DIC, and ultimately influencing organic matter export (Dore et al., 2003; Corno et al., 2007; Bidigare et al., 2009). Moreover, these dynamics preceded a shift in plankton community composition, as reflected through nearly 40% increases in concentrations of 19-butanoyoxyfucoxanthin (19-but), 19-hexoyloxyfucoxanthin (19-hex), and fucoxanthin pigment biomarkers used as proxies for pelagophytes, prymnesiophytes, and diatoms, respectively (Bidigare et al., 2009). Similarly, mesozooplankton biomass increased nearly 50% during this period, suggesting sensitivity of trophodynamic coupling to interannual to subdecadal scale variations in ocean climate. HOT also provides some of the only decadal-scale measurements of in situ primary production necessary for assessing seasonal to secular scale change. Since 1988, depth integrated (0-125 m) inventories of both chlorophyll a and 14C-based estimates of primary production at Sta. ALOHA and BATS have increased significantly (Corno et al., 2007; Saba et al., 2010). However, these long-term trends are punctuated by considerable interannual variability, much of which occurs in the mid- to lower regions of the euphotic zone (>45 m depth), below depths of detection by Earth-orbiting satellites. The emerging data emphasize the value of in situ measurements for validating remote and autonomous detection of plankton biomass and productivity and demonstrate that detection of potential secular-scale changes in productivity against the backdrop of significant interannual and decadal fluctuations demands a sustained sampling effort. Careful long-term measurements at Stn. ALOHA also highlight a well-resolved, though relatively weak, seasonal climatology in upper ocean primary productivity. Measurements of 14C-primary production document a ~3-fold increase during the summer months (Karl et al., 2012) that coincides with increases in plankton biomass (Landry et al., 2001; Sheridan and Landry, 2004). Moreover, phytoplankton blooms, often large enough to be detected by ocean color satellites, are a recurrent summertime feature of these waters (White et al., 2007; Dore et al., 2008; Fong et al., 2008). Analyses of ~13-years (1992-2004) of particulate C, N, P, and biogenic Si fluxes collected from bottom-moored deep-ocean (2800 m and 4000 m) sediment traps provide clues to processes underlying these seasonal changes. Unlike the gradual summertime increase in sinking particle flux observed in the upper ocean (150 m) traps, the deep sea particle flux record depicts a sharply defined summer maximum that accounts for ~20% of the annual POC flux to the deep sea, and appears driven by rapidly sinking diatom biomass (Karl et al., 2012). Analyses of the 15N isotopic signatures associated with sinking particles at Sta. ALOHA, together with genetic analyses of N2 fixing microorganisms, implicates upper ocean N2 fixation as a major control on the magnitude and efficiency of the biological carbon pump in this ecosystem (Dore et al., 2002; Church et al., 2009; Karl et al., 2012).Motivating QuestionsScience results from HOT continue to raise new, important questions about linkages between ocean climate and biogeochemistry that remain at the core of contemporary oceanography. Answers have begun to emerge from the existing suite of core program measurements; however, sustained sampling is needed to improve our understanding of contemporary ecosystem behavior and our ability to make informed projections of future changes to this ecosystem. HOT continues to focus on providing answers to some of the questions below:How sensitive are rates of primary production and organic matter export to short- and long-term climate variability?What processes regulate nutrient supply to the upper ocean and how sensitive are these processes to climate forcing? What processes control the magnitude of air-sea carbon exchange and over what time scales do these processes vary?Is the strength of the NPSG CO2 sink changing in time?To what extent does advection (including eddies) contribute to the mixed layer salinity budget over annual to decadal time scales and what are the implications for upper ocean biogeochemistry?How do variations in plankton community structure influence productivity and material export? What processes trigger the formation and demise of phytoplankton blooms in a persistently stratified ocean ecosystem?References
HOT
largerWorkCitation
project
Basin-scale genetics of marine zooplankton
http://www.bco-dmo.org/project/537991
Basin-scale genetics of marine zooplankton
Description from NSF award abstract:Marine zooplankton show strong ecological responses to climate change, but little is known about their capacity for evolutionary response. Many authors have assumed that the evolutionary potential of zooplankton is limited. However, recent studies provide circumstantial evidence for the idea that selection is a dominant evolutionary force acting on these species, and that genetic isolation can be achieved at regional spatial scales in pelagic habitats. This RAPID project will take advantage of a unique opportunity for basin-scale transect sampling through participation in the Atlantic Meridional Transect (AMT) cruise in 2014. The cruise will traverse more than 90 degrees of latitude in the Atlantic Ocean and include boreal-temperate, subtropical and tropical waters. Zooplankton samples will be collected along the transect, and mitochondrial and microsatellite markers will be used to identify the geographic location of strong genetic breaks within three copepod species. Bayesian and coalescent analytical techniques will test if these regions act as dispersal barriers. The physiological condition of animals collected in distinct ocean habitats will be assessed by measurements of egg production (at sea) as well as body size (condition index), dry weight, and carbon and nitrogen content. The PI will test the prediction that ocean regions that serve as dispersal barriers for marine holoplankton are areas of poor-quality habitat for the target species, and that this is a dominant mechanism driving population genetic structure in oceanic zooplankton.Note: This project is funded by an NSF RAPID award. This RAPID grant supported the shiptime costs, and all the sampling reported in the AMT24 zooplankton ecology cruise report (PDF).Online science outreach blog at: https://atlanticplankton.wordpress.com
Plankton Population Genetics
largerWorkCitation
project
Does habitat specialization drive population genetic structure of oceanic zooplankton?
http://www.bco-dmo.org/project/539717
Does habitat specialization drive population genetic structure of oceanic zooplankton?
Description from NSF award abstract:This research will test whether habitat depth specialization is a primary trait driving large-scale population genetic structure in open ocean zooplankton species. Very little is known about population connectivity in marine zooplankton. Although zooplankton were long thought to be high-gene-flow systems with little genetic differentiation among populations, recent observations have challenged this view. In fact, zooplankton species may be genetically subdivided at macrogeographic, regional, or even smaller spatial scales. Recent studies also indicate that subtle, species-specific ecological factors play an important role in controlling gene flow among plankton populations. The investigator hypothesizes that depth-related habitat, including diel vertical migration (DVM) behavior, plays a critical role in controlling dispersal of plankton among ocean regions, through interactions with ocean circulation and bathymetry. This study will compare the population genetic structures of eight planktonic copepods that utilize different depth-related habitats, in order to test key predictions of genetic structure based on the interaction of organismal depth with the oceanographic environment. The objectives of the research are to:1) Develop novel nuclear markers that can be used to resolve genetic structure and estimate gene flow among copepod populations,2) Characterize the spatial patterns of gene flow among populations in distinct ocean regions of the Atlantic, Pacific, and Indian Oceans for eight target species using a multilocus approach, and3) Test the central hypothesis that depth-related habitat will significantly impact the extent of genetic structure both across and within ocean basins, the magnitude and direction of gene flow among populations, and in the timing of major slitting events within species.Drawing on genomic resources (cDNA libraries) recently developed by the PI, five (or more) polymorphic nuclear markers will be developed for each species. These new markers will be used, in combination with the mitochondrial gene cytochrome oxidase I, to characterize the population genetic structure of each species throughout its global distribution using graph theoretic and coalescent analytical techniques. Gene flow among populations and the timing of major splitting events will be estimated under a coalescent model (IMa), and empirical support for the hypothesis of depth-related trends in population structure will be assessed using graph theoretic congruence tests. Because the depth specialization and diel vertical migration behaviors of the target species are representative of distinct zooplankton species groups, the results of this study will have broad implications for understanding and predicting the genetic structure of these important grazers in pelagic ecosystems.Publications produced with support from this award include:Burridge, A., Goetze, E., Raes, N., Huisman, J., Peijnenburg, K. T. C. A. (in revision) Global biogeography and evolution of Cuvierina pteropods. BMC Evolutionary Biology.Andrews, K. R., Norton, E. L., Fernandez-Silva, I., Portner†, E. Goetze, E. (in press) Multilocus evidence for globally-distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod. Molecular Ecology.Halbert , K. M. K., Goetze, E., Carlon, D. B. (2013) High cryptic diversity across the global range of the migratory planktonic copepods Pleuromamma piseki and P. gracilis. PLOS One 8(10): e77011. doi:10.1371/journal.pone.0077011Norton , E. L., Goetze, E. (2013) Equatorial dispersal barriers and limited connectivity among oceans in a planktonic copepod. Limnology and Oceanography 58: 1581-1596.Peijnenburg, K. T. C. A., Goetze, E. (2013) High evolutionary potential of marine zooplankton. Ecology & Evolution 3(8): 2765-2781. doi: 10.1002/ece3.644 (both authors contributed equally).Fernandez-Silva, I., Whitney, J., Wainwright, B., Andrews, K. R., Ylitalo-Ward, H., Bowen, B. W., Toonen, R. J., Goetze, E., Karl, S. A. (2013) Microsatellites for Next-Generation Ecologists: A Post-Sequencing Bioinformatics Pipeline. PLOS One 8(2): e55990. doi:10.1371/journal.pone.0055990Bron, J. E., Frisch, D., Goetze, E., Johnson, S. C., Lee, C. E., Wyngaard, G. A. (2011) Observing Copepods through a Genomic Lens. Frontiers in Zoology 8: 22.Goetze, E. (2011) Population differentiation in the open sea: Insights from the pelagic copepod Pleuromamma xiphias. Integrative and Comparative Biology 51: 580-597. Master’s theses supported under this award include:Emily L. Norton. Empirical and biophysical modeling studies of dispersal barriers for marine plankton. (2013). University of Hawaii at Manoa.K. M. K. Halbert. Genetic isolation in the open sea: Cryptic diversity in the Pleuromamma piseki - P. gracilis species complex. (2013). University of Hawaii at Manoa.
Plankton_PopStructure
largerWorkCitation
project
eng; USA
oceans
-158
-158
22.75
22.75
2012-09-01
2013-10-31
From projects that focused on the following 3 locations: 1. North Pacific Subtropical Gyre; 22 deg 45 min N, 158 deg W 2. Atlantic Ocean, 46 N - 46 S 3. Global Ocean
0
BCO-DMO catalogue of parameters from Data from: Iacchei, M., E. Butcher, E. Portner, Goetze, E. (in press) It’s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices.
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/682016.rdf
Name: file_link
Units: unitless
Description: Link to data file containing sequence information.
http://lod.bco-dmo.org/id/dataset-parameter/682017.rdf
Name: description
Units: unitless
Description: Description of data in file.
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Parameters for this dataset
physicalMeasurement
file_link
file_link
PI-supplied Description: Link to data file containing sequence information.; General Description: Link to file (such as a data file or document).
http://lod.bco-dmo.org/id/dataset-parameter/682016.rdf
unitless
description
brief description
PI-supplied Description: Description of data in file.; General Description: brief description, open ended, specific to the data set in which it appears
http://lod.bco-dmo.org/id/dataset-parameter/682017.rdf
unitless
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://dx.doi.org/10.1575/1912/bco-dmo.682247
download
onLine
dataset
<p><strong>Collection:&nbsp;</strong>Bulk zooplankton were collected at an open ocean time series site in the North Pacific Subtropical Gyre (station ALOHA, 22.45N, 158W) during 11 of the routine Hawai'i Ocean Time-series (HOT) research cruises at approximately monthly intervals from September of 2012 to October of 2013 (HOT-246 to HOT-256). Mesozooplankton were collected using a 1 m<sup>2</sup>, 200 um-mesh ring net towed obliquely from a mean maximum depth of 155 m (SD = 31 m) to the sea surface. Zooplankton for this study were collected from three nighttime tows completed between the hours of 2200-0200 on consecutive nights for each sampling period so that all collections for a single cruise were collected within three days of one another. Following net retrieval, bulk plankton were quantitatively split using a Folsom plankton splitter, and 1/4 of the material was preserved in 95% non-denatured ethyl alcohol (EtOH) and stored at -20C. From these bulk collections, 50 <em>Haloptilus longicornis</em> and 50 <em>Pleuromamma xiphias </em>individuals were sorted from each net tow for use in this study.</p><p><strong>mtDNA Sequence Generation:</strong><em>&nbsp;</em>For both <em>H. longicornis </em>and <em>P. xiphias,</em> DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit (Qiagen, Inc., Valencia, CA). For <em>H. longicornis</em>, a 546 base-pair fragment of the mitochondrial cytochrome <em>c</em> oxidase subunit II (mtCOII) gene was amplified by polymerase chain reaction (PCR) with species-specific primers COII_F6 and COII_R9. For <em>P. xiphias, </em>a 551 base-pair fragment of the mitochondrial cytochrome <em>c</em> oxidase subunit I (mtCOI) was amplified by PCR using species-specific primers PLXI_VH and PLXI_VL. Specific information on primer sequences, PCR reaction mixes, thermal cycler conditions, and PCR purification is provided in the manuscript associated with this submission. Purified PCR products were sequenced on an ABI 3730XL capillary sequencer (Applied Biosystems, Foster City, CA). Sequences were aligned, edited and trimmed using Geneious 7.0.6 (Biomatters, Ltd., Auckland, New Zealand). Unique haplotypes were identified using the Haplotype Collapser and Converter in FaBox 1.35 (<a href="http://users-birc.au.dk/biopv/php/fabox/" target="_blank">http://users-birc.au.dk/biopv/php/fabox/</a>), and deposited with their respective protein translations in GenBank under accession numbers: KY560470 - KY560565. An mtDNA sequence for each individual specimen is deposited in this BCO-DMO submission as part of one of two fasta files. Each fasta file contains the mtDNA sequence fragments from all individuals from a single species aligned together.</p><p>Methodology is further described in the paper itself:<br />Iacchei, M.<u>,</u> E. Butcher, E. Portner, Goetze, E. (in press) It’s about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices.&nbsp; <em>Limnology and Oceanography</em></p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing:<br />- re-formatted the date column to yyyy-mm-dd;<br />- created separate columns for stage and sex;<br />- generated csv files from the Excel file submitted.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
mesh ring net
mesh ring net
PI Supplied Instrument Name: mesh ring net PI Supplied Instrument Description:Mesozooplankton were collected using a 1 m2, 200 um-mesh ring net towed obliquely from a mean maximum depth of 155 m (SD = 31 m) to the sea surface. Instrument Name: Ring Net Instrument Short Name:Ring Net Instrument Description: A Ring Net is a generic plankton net, made by attaching a net of any mesh size to a metal ring of any diameter. There are 1 meter, .75 meter, .25 meter and .5 meter nets that are used regularly. The most common zooplankton ring net is 1 meter in diameter and of mesh size .333mm, also known as a 'meter net' (see Meter Net). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/
PI Supplied Instrument Name: PI Supplied Instrument Description:Specific information on primer sequences, PCR reaction mixes, thermal cycler conditions, and PCR purification is provided in the manuscript associated with this submission. Instrument Name: PCR Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then rises and lowers the temperature of the block in discrete, pre-programmed steps.(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Folsom Plankton Splitter
Folsom Plankton Splitter
PI Supplied Instrument Name: Folsom Plankton Splitter PI Supplied Instrument Description:Following net retrieval, bulk plankton were quantitatively split using a Folsom plankton splitter. Instrument Name: Folsom Plankton Splitter Instrument Short Name:Folsom Splitter Instrument Description: A Folsom Plankton Splitter is used for sub-sampling of plankton and ichthyoplankton samples.
Deployment: HOT_cruises
HOT_cruises
Unknown Platform
HOT_cruises
Dr Matthew J. Church
University of Hawaii
http://hahana.soest.hawaii.edu/hot/
Report describing HOT_cruises
Unknown Platform