http://lod.bco-dmo.org/id/dataset/852569
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
2021-05-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Phytoplankton growth and grazing from flow cytometry in the eastern Indian Ocean
2021-05-28
publication
2021-05-28
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-06-03
publication
https://doi.org/10.26008/1912/bco-dmo.852569.1
Michael R. Landry
University of California-San Diego Scripps
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
Cite this dataset as: Landry, M. R. (2021) Phytoplankton growth and grazing from flow cytometry in the eastern Indian Ocean. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-05-28 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.852569.1 [access date]
Phytoplankton growth and grazing from flow cytometry in the eastern Indian Ocean Dataset Description: Methods and Sampling: <p>We sampled 21 stations, most on a south-to-north transect from 39.5 to 11.5°S along longitude 110°E, west of Australia. Stations were occupied on successive days, with sampling done on a consistent daily schedule, followed by late-night transit between stations. Mean light extinction coefficients determined from morning CTD hydrocasts were used to compute sampling depths corresponding to the transmission characteristics of light-calibrated shipboard incubators. Experimental water was collected on the evening (~21:00 local) hydrocasts at depths corresponding to 75.6, 31.7, 18.0, 7.6, 2.6 and 1.3% Io.</p>
<p>For each depth, we prepared a two-treatment dilution experiment (Landry et al. 2008, 2011), with one polycarbonate bottle (2.7 L) containing unfiltered seawater (100%) and the second (diluted) bottle consisting of ~33% whole seawater with filtered water from the same depth. Seawater was filtered directly from the Niskin bottles using a peristaltic pump, silicone tubing and an in-line 0.2-µm Suporcap filter capsule that had previously been acid washed. Each bottle was subsampled for flow cytometry (FCM) analysis (2 mL) for initial microbial concentrations, and the bottles were placed in their respective light boxes for 24 h, cooled with constant high flow from the ship’s running seawater line. The incubators were covered to protect from deck lighting during nighttime operations and received full solar lighting during the daytime.</p>
<p>Picoplankton FCM samples were preserved with 1% paraformaldehyde and frozen at –80°C. Thawed samples were stained with Hoechst 34580 (1 µg mL-1) and analyzed at a flow rate of 30 µL min-1 with a Beckman-Coulter CytoFLEX-S instrument with 4 lasers (Selph, in review). Side scatter, forward angle light scatter (FALS) and fluorescence signals were collected using laser excitation (EX)/emission (EM) filters of EX375/EM450±45 for Hoechst-stained DNA, EX488/EM690±50 for chlorophyll, and EX561/EM585±42 for phycoerythrin. Listmode files (FCS 3.0) were analyzed with FlowJo software (v.10.6.1) for abundances of <em>Prochlorococcus</em> (PRO), <em>Synechococcus</em> (SYN), photosynthetic (pico-)eukaryotes (EUK) and heterotrophic bacteria (HBact).</p>
<p>We determined rate profiles for phytoplankton growth (µ, d-1) and microzooplankton grazing (m, d-1) from each pair of dilution experiment bottles and for each FCM population according to the following equations:</p>
<p>m = (kd - k)/(1 - D)<br />
and<br />
µ = k + m,</p>
<p>where kd and k are the measured net rates of change between initial and final concentrations in the diluted and undiluted treatments, respectively, and D is the portion of unfiltered water in the dilution treatment (Landry et al., 2008; Selph et al., 2011).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851558 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851558
completed
Michael R. Landry
University of California-San Diego Scripps
858-534-4702
9500 Gilman Drive Mail Code: 0227
La Jolla
CA
92093-0227
USA
mlandry@ucsd.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise
Station
Date
Lat
Long
CTD
pcnt_Io
Depth
Temp
Abun_Pro
Grow_Pro
Graz_Pro
Abun_Syn
Grow_Syn
Graz_Syn
Abun_Euk
Grow_Euk
Graz_Euk
Abun_Hbact
Grow_HBact
Graz_HBact
CTD hydrocasts
Beckman-Coulter CytoFLEX-S Flow Cytometer
Niskin bottles
theme
None, User defined
Cruise identfier
station
date
latitude
longitude
cast
irradiance level set for incubation experiments
depth
water temperature at measurement depth
abundance
growth
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
CTD - profiler
Flow Cytometer
Niskin bottle
instrument
BCO-DMO Standard Instruments
IN2019_V03
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.
Second International Indian Ocean Expedition
https://web.whoi.edu/iioe2/
Second International Indian Ocean Expedition
Description from the program website:
The Second International Indian Ocean Expedition (IIOE-2) is a major global scientific program which will engage the international scientific community in collaborative oceanographic and atmospheric research from coastal environments to the deep sea over the period 2015-2020, revealing new information on the Indian Ocean (i.e. its currents, its influence upon the climate, its marine ecosystems) which is fundamental for future sustainable development and expansion of the Indian Ocean's blue economy. A large number of scientists from research institutions from around the Indian Ocean and beyond are planning their involvement in IIOE-2 in accordance with the overarching six scientific themes of the program. Already some large collaborative research projects are under development, and it is anticipated that by the time these projects are underway, many more will be in planning or about to commence as the scope and global engagement in IIOE-2 grows.
Focused research on the Indian Ocean has a number of benefits for all nations. The Indian Ocean is complex and drives the region's climate including extreme events (e.g. cyclones, droughts, severe rains, waves and storm surges). It is the source of important socio-economic resources (e.g. fisheries, oil and gas exploration/extraction, eco-tourism, and food and energy security) and is the background and focus of many of the region's human populations around its margins. Research and observations supported through IIOE-2 will result in an improved understanding of the ocean's physical and biological oceanography, and related air-ocean climate interactions (both in the short-term and long-term). The IIOE-2's program will complement and harmonise with other regional programs underway and collectively the outcomes of IIOE-2 will be of huge benefit to individual and regional sustainable development as the information is a critical component of improved decision making in areas such as maritime services and safety, environmental management, climate monitoring and prediction, food and energy security.
IIOE-2 activities will also include a significant focus on building the capacity of all nations around the Indian Ocean to understand and apply observational data or research outputs for their own socio-economic requirements and decisions. IIOE-2 capacity building programs will therefore be focused on the translation of the science and information outputs for societal benefit and training of relevant individuals from surrounding nations in these areas.
A Steering Committee was established to support U.S. participation in IIOE-2. More information is available on their website at https://web.whoi.edu/iioe2/.
IIOE-2
largerWorkCitation
program
Collaborative Research: Mesoscale variability in nitrogen sources and food-web dynamics supporting larval southern bluefin tuna in the eastern Indian Ocean
https://osprey.bco-dmo.org/project/819488
Collaborative Research: Mesoscale variability in nitrogen sources and food-web dynamics supporting larval southern bluefin tuna in the eastern Indian Ocean
<p><em>NSF Award Abstract:</em><br />
The small area between NW Australia and Indonesia in the eastern Indian Ocean (IO) is the only known spawning ground of Southern Bluefin Tuna (SBT), a critically endangered top marine predator. Adult SBT migrate thousands of miles each year from high latitude feeding areas to lay their eggs in these tropical waters, where food concentrations on average are below levels that can support optimal feeding and growth of their larvae. Many critical aspects of this habitat are poorly known, such as the main source of nitrogen nutrient that sustains system productivity, how the planktonic food web operates to produce the unusual types of zooplankton prey that tuna larvae prefer, and how environmental differences in habitat quality associated with ocean fronts and eddies might be utilized by adult spawning tuna to give their larvae a greater chance for rapid growth and survival success. This project investigates these questions on a 38-day expedition in early 2021, during the peak time of SBT spawning. This project is a US contribution to the 2nd International Indian Ocean Expedition (IIOE-2) that advances understanding of biogeochemical and ecological dynamics in the poorly studied eastern IO. This is the first detailed study of nitrogen and carbon cycling in the region linking Pacific and IO waters. The shared dietary preferences of SBT larvae with those of other large tuna and billfish species may also make the insights gained broadly applicable to understanding larval recruitment issues for top consumers in other marine ecosystems. New information from the study will enhance international management efforts for SBT. The shared larval dietary preferences of large tuna and billfish species may also extend the insights gained broadly to many other marine top consumers, including Atlantic bluefin tuna that spawn in US waters of the Gulf of Mexico. The end-to-end study approach, highlights connections among physical environmental variability, biogeochemistry, and plankton food webs leading to charismatic and economically valuable fish production, is the theme for developing educational tools and modules through the "scientists-in-the-schools" program of the Center for Ocean-Atmospheric Prediction Studies at Florida State University, through a program for enhancing STEM learning pathways for underrepresented students in Hawaii, and through public outreach products for display at the Birch Aquarium in San Diego. The study also aims to support an immersive field experience to introduce talented high school students to marine research, with the goal of developing a sustainable marine-related educational program for underrepresented students in rural northwestern Florida.</p>
<p>Southern Bluefin Tuna (SBT) migrate long distances from high-latitude feeding grounds to spawn exclusively in a small oligotrophic area of the tropical eastern Indian Ocean (IO) that is rich in mesoscale structures, driven by complex currents and seasonally reversing monsoonal winds. To survive, SBT larvae must feed and grow rapidly under environmental conditions that challenge conventional understanding of food-web structure and functional relationships in poor open-ocean systems. The preferred prey of SBT larvae, cladocerans and Corycaeidae copepods, are poorly studied and have widely different implications for trophic transfer efficiencies to larvae. Differences in nitrogen sources - N fixation vs deep nitrate of Pacific origin - to sustain new production in the region also has implications for conditions that may select for prey types (notably cladocerans) that enhance transfer efficiency and growth rates of SBT larvae. The relative importance of these N sources for the IO ecosystem may affect SBT resiliency to projected increased ocean stratification. This research expedition investigates how mesoscale variability in new production, food-web structure and trophic fluxes affects feeding and growth conditions for SBT larvae. Sampling across mesoscale features tests hypothesized relationships linking variability in SBT larval feeding and prey preferences (gut contents), growth rates (otolith analyses) and trophic positions (TP) to the environmental conditions of waters selected by adult spawners. Trophic Positions of larvae and their prey are determined using Compound-Specific Isotope Analyses of Amino Acids (CSIA-AA). Lagrangian experiments investigate underlying process rates and relationships through measurements of water-column 14C productivity, N2 fixation, 15NO3- uptake and nitrification; community biomass and composition (flow cytometry, pigments, microscopy, in situ imaging, genetic analyses); and trophic fluxes through micro- and mesozooplankton grazing, remineralization and export. Biogeochemical and food web elements of the study are linked by CSIA-AA (N source, TP), 15N-constrained budgets and modeling. The project elements comprise an end-to-end coupled biogeochemistry-trophic study as has not been done previously for any pelagic ecosystem.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
BLOOFINZ-IO
largerWorkCitation
project
eng; USA
oceans
110
111.4
-39.5
-11.5
2019-05-11
2019-06-08
Eastern Indian Ocean, Indonesian Throughflow area, and the Gulf of Mexico
0
BCO-DMO catalogue of parameters from Phytoplankton growth and grazing from flow cytometry in the eastern Indian Ocean
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/852793.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/852794.rdf
Name: Station
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/852795.rdf
Name: Date
Units: unitless
Description: <p>Sampling date (local); format: YYYY-MM-DD</p>
http://lod.bco-dmo.org/id/dataset-parameter/852796.rdf
Name: Lat
Units: degrees North
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/852797.rdf
Name: Long
Units: degrees East
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/852798.rdf
Name: CTD
Units: unitless
Description: <p>CTD cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/852799.rdf
Name: pcnt_Io
Units: percent
Description: <p>Light depth (% of incident PAR)</p>
http://lod.bco-dmo.org/id/dataset-parameter/852800.rdf
Name: Depth
Units: meters (m)
Description: <p>Depth of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/852801.rdf
Name: Temp
Units: degrees Celsius
Description: <p>Temperature at collection depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/852802.rdf
Name: Abun_Pro
Units: cells per milliliter (cells/mL)
Description: <p>Abundance of Prochlorococcus</p>
http://lod.bco-dmo.org/id/dataset-parameter/852803.rdf
Name: Grow_Pro
Units: per day (d-1)
Description: <p>Growth of Prochlorococcus</p>
http://lod.bco-dmo.org/id/dataset-parameter/852804.rdf
Name: Graz_Pro
Units: per day (d-1)
Description: <p>Grazing mortality of Prochlorococcus</p>
http://lod.bco-dmo.org/id/dataset-parameter/852805.rdf
Name: Abun_Syn
Units: cells per milliliter (cells/mL)
Description: <p>Abundance of Synechococcus</p>
http://lod.bco-dmo.org/id/dataset-parameter/852806.rdf
Name: Grow_Syn
Units: per day (d-1)
Description: <p>Growth of Synechococcus</p>
http://lod.bco-dmo.org/id/dataset-parameter/852807.rdf
Name: Graz_Syn
Units: per day (d-1)
Description: <p>Grazing mortality of Synechococcus</p>
http://lod.bco-dmo.org/id/dataset-parameter/852808.rdf
Name: Abun_Euk
Units: cells per milliliter (cells/mL)
Description: <p>Abundance of (pico-)eukaryotes</p>
http://lod.bco-dmo.org/id/dataset-parameter/852809.rdf
Name: Grow_Euk
Units: per day (d-1)
Description: <p>Growth of (pico-)eukaryotes</p>
http://lod.bco-dmo.org/id/dataset-parameter/852810.rdf
Name: Graz_Euk
Units: per day (d-1)
Description: <p>Grazing mortality of (pico-)eukaryotes</p>
http://lod.bco-dmo.org/id/dataset-parameter/852811.rdf
Name: Abun_Hbact
Units: cells per milliliter (cells/mL)
Description: <p>Abundance of heterotrophic bacteria</p>
http://lod.bco-dmo.org/id/dataset-parameter/852812.rdf
Name: Grow_HBact
Units: per day (d-1)
Description: <p>Growth of heterotrophic bacteria</p>
http://lod.bco-dmo.org/id/dataset-parameter/852813.rdf
Name: Graz_HBact
Units: per day (d-1)
Description: <p>Grazing mortality of heterotrophic bacteria</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
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
15960
https://darchive.mblwhoilibrary.org/bitstream/1912/27187/1/dataset-852569_phyto-growth-grazing-fcm-in2019__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.852569.1
download
onLine
dataset
<p>We sampled 21 stations, most on a south-to-north transect from 39.5 to 11.5°S along longitude 110°E, west of Australia. Stations were occupied on successive days, with sampling done on a consistent daily schedule, followed by late-night transit between stations. Mean light extinction coefficients determined from morning CTD hydrocasts were used to compute sampling depths corresponding to the transmission characteristics of light-calibrated shipboard incubators. Experimental water was collected on the evening (~21:00 local) hydrocasts at depths corresponding to 75.6, 31.7, 18.0, 7.6, 2.6 and 1.3% Io.</p>
<p>For each depth, we prepared a two-treatment dilution experiment (Landry et al. 2008, 2011), with one polycarbonate bottle (2.7 L) containing unfiltered seawater (100%) and the second (diluted) bottle consisting of ~33% whole seawater with filtered water from the same depth. Seawater was filtered directly from the Niskin bottles using a peristaltic pump, silicone tubing and an in-line 0.2-µm Suporcap filter capsule that had previously been acid washed. Each bottle was subsampled for flow cytometry (FCM) analysis (2 mL) for initial microbial concentrations, and the bottles were placed in their respective light boxes for 24 h, cooled with constant high flow from the ship’s running seawater line. The incubators were covered to protect from deck lighting during nighttime operations and received full solar lighting during the daytime.</p>
<p>Picoplankton FCM samples were preserved with 1% paraformaldehyde and frozen at –80°C. Thawed samples were stained with Hoechst 34580 (1 µg mL-1) and analyzed at a flow rate of 30 µL min-1 with a Beckman-Coulter CytoFLEX-S instrument with 4 lasers (Selph, in review). Side scatter, forward angle light scatter (FALS) and fluorescence signals were collected using laser excitation (EX)/emission (EM) filters of EX375/EM450±45 for Hoechst-stained DNA, EX488/EM690±50 for chlorophyll, and EX561/EM585±42 for phycoerythrin. Listmode files (FCS 3.0) were analyzed with FlowJo software (v.10.6.1) for abundances of <em>Prochlorococcus</em> (PRO), <em>Synechococcus</em> (SYN), photosynthetic (pico-)eukaryotes (EUK) and heterotrophic bacteria (HBact).</p>
<p>We determined rate profiles for phytoplankton growth (µ, d-1) and microzooplankton grazing (m, d-1) from each pair of dilution experiment bottles and for each FCM population according to the following equations:</p>
<p>m = (kd - k)/(1 - D)<br />
and<br />
µ = k + m,</p>
<p>where kd and k are the measured net rates of change between initial and final concentrations in the diluted and undiluted treatments, respectively, and D is the portion of unfiltered water in the dilution treatment (Landry et al., 2008; Selph et al., 2011).</p>
Specified by the Principal Investigator(s)
<p>Data were processed using&nbsp;FlowJo software (v.10.6.1).</p>
<p><strong>BCO-DMO Processing:</strong><br />
- renamed fields to comply with BCO-DMO naming conventions;<br />
- changed years of '2017' to '2019';<br />
- converted date to YYYY-MM-DD format;<br />
- converted latitude values to negative (to indicate South direction).</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
CTD hydrocasts
CTD hydrocasts
PI Supplied Instrument Name: CTD hydrocasts Instrument Name: CTD - profiler Instrument Short Name: Instrument Description: The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.
This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Beckman-Coulter CytoFLEX-S Flow Cytometer
Beckman-Coulter CytoFLEX-S Flow Cytometer
PI Supplied Instrument Name: Beckman-Coulter CytoFLEX-S Flow Cytometer Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Niskin bottles
Niskin bottles
PI Supplied Instrument Name: Niskin bottles Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: IN2019_V03
IN2019_V03
R/V Investigator
Community Standard Description
International Council for the Exploration of the Sea
R/V Investigator
vessel
R/V Investigator
Community Standard Description
International Council for the Exploration of the Sea
R/V Investigator
vessel