|Carpenter, Edward J.
|San Francisco State University (SFSU)
|Principal Investigator, Contact
|San Francisco State University (SFSU)
|Gegg, Stephen R.
|Woods Hole Oceanographic Institution (WHOI BCO-DMO)
|BCO-DMO Data Manager
Microphytoplankton station counts for the ANACONDAS cruises
Phytoplankton by species in cells/ml
Sampled 2-6 liters from Niskin bottle attached to CTD rosette. Filtered through 20 micrometer mesh, to concentrate down to 40 ml, and fixed with acid lugol’s solution. Counted taxa on 1-ml Sedgwick rafter cell via light microscopy at 200x.
(See Processing Notes for Individual Deployments)
|ANACONDAS Cruise Id and Year of Cruise (ANYY_YYYY)
|ANACONDAS Sample Id (Sample Id = CruiseIdxxxxx)
|ANACONDAS Station Id
|ANACONDAS Event Id (Event Id = Station Id.Event Id at station)
|Event Date (GMT)
|Event Time (GMT)
|Event Latitude (South is negative)
|Event Longitude (West is negative)
|Dataset-specific Instrument Name
|Generic Instrument Name
|Generic 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.
|Dataset-specific Instrument Name
CTD SBE 911plus
|Generic Instrument Name
CTD Sea-Bird SBE 911plus
|Generic Instrument Description
The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics
ANACONDAS: Amazon iNfluence on the Atlantic: CarbOn export from Nitrogen fixation by DiAtom SymbiosesROCA: River Ocean Continuum of the Amazon WHOI cruise planning synopsis Original data are available from the NSF R2R data catalog Cruise Track over Salinity Climatology (Image from Dr. Ajit Subramaniam)
Notes from original spreadsheet for: AT21-04 These are the phytoplankton counts from the Atlantis in july 2012, we sampled at each station and underway Station counts were 2 liter samples from the CTD at the surface and usually an additional depth (generally the chlorophyll max) All samples were filtered through 20 µm mesh to concentrate down to about 50 ml, and fixed with Acid lugol's solution Most samples were further concentrated in a centerfuge for 10 minutes at 2000 RPM (15 ml down to 1 ml) Concentrate was placed in a Sedgewick Rafter counting chamber, and counted under 320x magnification Collected by RED, AJK Counted by EJC, AJK Data Entry by AJK Data corrrection by MTM BCO-DMO Processing Notes - Generated from original file: "At21-04 Microphytoplankton station counts.xlsx" contributed by Andrew Kalmbach - Cruise "Id_Year" added to data (i.e. "AN12_2012") - Event Date/Time GMT added from event logs - Event Lat/lon added from event logs - Parameters modified to conform to BCO-DMO parameter naming conventions - "nd" (Not Detected) inserted into blank cells
ANACONDAS: Amazon iNfluence on the Atlantic: CarbOn export from Nitrogen fixation by DiAtom SymbiosesROCA: River Ocean Continuum of the Amazon WHOI cruise planning synopsis Cruise information and original data are available from the NSF R2R data catalog. Cruise Track over Salinity Climatology (Image from Dr. Ajit Subramaniam)
Notes from original spreadsheet for: KN197-8 These are the cell counts collected from the biomass casts during the knorr KN-197 cruise AJK went through the notebooks, and re-entered the counts that contained errors Errors removed included merged counts (data from 2 or more samples combined) Added cell counts that were not entered (AN1000071 and AN100206) Changed station numbers to reflect the dates Some of the event/AN numbers may be inaccurate - I don't have the original event log - I will uptadate as soon as I get a hold of it AN numbers/cast numbers with question marks were not on the original data sheet, and may be wrong For questions, email me at Andrew.Kalmbach@gmail.com, or Dr. Edward Carpenter at email@example.com Red numbers have been added or removed from the original spreadsheet BCO-DMO Processing Notes - Generated from original file: "Kn197-8 Microphytoplankton station counts.xlsx" contributed by Andrew Kalmbach - Cruise "Id_Year" added to data (i.e. "AN10_2010") - Event Date/Time GMT added from event logs - Event Lat/lon added from event logs - Parameters modified to conform to BCO-DMO parameter naming conventions - "nd" (Not Detected) inserted into blank cells
ANACONDAS: Amazon iNfluence on the Atlantic: CarbOn export from Nitrogen fixation by DiAtom SymbiosesROCA: River Ocean Continuum of the Amazon Original data are available from the NSF R2R data catalog Cruise Track over Salinity Climatology (Image from Dr. Ajit Subramaniam)
Notes from original spreadsheet for: MV1110 Station cell counts from the September 2011 ANACONDAS cruise Counts are 2 liters from CTD cast, filtered and washed through 10 um filters Cells were fixed with acidified lugol's solution in 50 ml vials Samples were counted through a 32X objective on a sedgewick rafter hemocytometer Sampled by IB and AJK Counted by EJC and AJK Data Entry by AJK Corrected by MTM BCO-DMO Processing Notes - Generated from original file: "Mv1110 Microphytoplankton station counts.xlsx" contributed by Andrew Kalmbach - Cruise "Id_Year" added to data (i.e. "AN11_2011") - Event Date/Time GMT added from event logs - Event Lat/lon added from event logs - Parameters modified to conform to BCO-DMO parameter naming conventions - "nd" (Not Detected) inserted into blank cells
ANACONDAS is an IMBER endorsed project.
View list of all IMBER endorsed projects
View the ANACONDAS project GCMD DIF record
The ANACONDAS project was funded as part of the US National Science Foundation (NSF) Emerging Topics in Biogeochemical Cycles (ETBC) program (Directorate for Geosciences, NSF 07 -049, September 19, 2007) explicitly intended to support emerging areas of interdisciplinary research. The ETBC program aimed to foster transformational advances in the quantitative or mechanistic understanding of biogeochemical cycles that integrated physical-chemical-biological processes over the range of temporal and/or spatial scales in Earth's environments. The program especially sought proposals that addressed emerging topics in biogeochemical cycles, the water cycle or their coupling, across the interfaces of atmosphere, land, and oceans.
The ANACONDAS investigators hypothesize that large tropical river plumes with low N: P ratios provide an ideal niche for diatom-diazotroph assemblages (DDAs). They suggest that the ability of these organisms to fix N2 within the surface ocean is responsible for significant C export in the Amazon River plume. Their previous observations in the Amazon River plume helped reveal that blooms comprised of the endosymbiotic N2-fixing cyanobacterium Richelia and its diatom hosts (e.g. Hemiaulus) were a significant source of new production and carbon export. The previous work focused largely on the sensitivity of DDAs to external forcing from dust and riverine inputs, so the ecology of these organisms and the fate of their new production were largely unstudied. It is now known that DDAs are responsible for a significant amount of CO2 drawdown in the Amazon River plume, and floating sediment traps at 200 m measured 4x higher mass fluxes beneath the plume than outside the plume. This led the researchers to hypothesize that this greater export is due either to aggregation and sinking of DDAs themselves or to grazing of DDAs by zooplankton.
In this study the researchers will undertake a suite of field, satellite and modeling studies aimed at understanding the ecology and tracing the fate of C and N fixed by DDAs and other phytoplankton living in the plume. By examining C and silicate (Si) export from offshore surface waters, through the upper oceanic food web, the mesopelagic, and down to the deep sea floor, they will quantify the impact of the Amazon River on biological processes that control C sequestration and the implications of these regional processes on C, N and Si budgets. The study will go beyond previous research because they will quantify 1) the distribution, nutrient demands, and activity of DDAs in the context of phytoplankton species succession, 2) the sensitivity of the CO2 drawdown to the mix of phytoplankton, 3) the grazing and aggregation processes contributing to the sinking flux, 4) the composition of this flux, and 5) the proportion of this material that reaches the seafloor. This effort truly represents a measure of C sequestration and pump efficiency. Ecological modeling will be used to place observational results from field studies and satellites into the context of the larger Atlantic basin with tropical climate variability on interannual and longer time scales.
Three cruises were carried out during the ANACONDAS project:
AN10/KN197-08 - R/V KNORR - May/June 2010 - Cruise Track over Salinity Climatology (Image: Yager, et al, 2007)
AN11/MV1110 - R/V MELVILLE - September/October 2011 - Cruise Track over Salinity Climatology (Image: Yager, et al, 2007)
AN12/AT21-04 - R/V ATLANTIS - July/2012 - Cruise Track over Salinity Climatology (Image: Yager, et al, 2007)
The ANACONDAS project builds on observations made by MANTRA/PIRANA in 2001 and 2003 (RV Knorr and Seward Johnson I cruises to the same region) to address specifically 1) how carbon cycling and sequestration in the western tropical North Atlantic (WTNA) is influenced by the Amazon River through its impact on pelagic ecosystem dynamics and 2) the sensitivity of this ecosystem to anthropogenic climate change. PIRANA revealed the importance of both riverine and atmospheric inputs for driving the high productivity of the WTNA through N2-fixation, and demonstrated the significance of the region to basin-wide biogeochemistry and C cycling. ANACONDAS will now focus on what drives phytoplankton community succession through the plume, light and nutrient requirements, factors limiting productivity, and the fate of production. These components are critical to understand the role of the plume in the regional C cycle, and to predict its response to climate variability and change.
The NSF-funded ANACONDAS project will also serve as a platform for additional measurements supported by the Gordon and Betty Moore Foundation's Marine Microbiology Initiative. ROCA (River-Ocean Continuum of the Amazon) brings additional focus on marine microbial community structure and activities, along with high-resolution measurements of organic matter along the river-ocean continuum.
ANACONDAS: Amazon iNfluence on the Atlantic: CarbOn export from Nitrogen fixation by DiAtom Symbioses
ROCA: River Ocean Continuum of the Amazon
The project is funded by NSF-OCE-0934095 and NSF-OCE-0934036: Collaborative Research: ETBC: Amazon iNfluence on the Atlantic: CarbOn export from Nitrogen fixation by DiAtom Symbioses and by the Gordon and Betty Moore Foundation through GBMF-MMI-2293: River Ocean Continuum of the Amazon.
Water Column Characterization (hydrographic sampling with CTD/Rosette):
Nutrient (NO2, NO2+NO3, PO4, SiO4) concentrations
Chlorophyll a and pigments concentrations
Inorganic carbon (discrete DIC, ALK, underway pCO2)
Organic carbon, nitrogen, phosphorus
Phytoplankton and Diazotroph Abundance (using rosette and also small nets to collect)
Carbon and Nitrogen Fixation by plankton
Kinetic and Physiological Measurements of phytoplankton
Stable Isotopic Measurements of particulate material
Microbial community structure and gene expression
Organic carbon and biomarker characterization
MOCNESS tows for zooplankton
Zooplankton collection for abundance and biomass
Zooplankton grazing and POC flux measurements
Multicorer for deep sea sediment analyses
Solid phase analysis
Pore water chemistry
Isotopic composition (Pb, Th, C)
Other instrumentation over the side:
The in-water light field will be characterized with a free-falling 14 channel spectroradiometer
Two "Carbon Explorers" - autonomous Sounding Oceanographic Lagrangian Observer profilers
Sediment Trap Studies (using 48h deployments of floating Particle Interceptor Traps; PITs)
Surface water pumps - directly bring large volumes of surface water to the deck of the ship for processing.
ADCP 75 kHz
Bathymetry System 12 kHz
Bathymetry System 3.5 kHz
Deionized Water System
Uncontaminated Seawater System
CTD/Water Sampling: 911+ Rosette 24-position, 10-liter bottle Rosette with dual T/C sensors
Biospherical underwater PAR (1000m depth limit)
SBE43 oxygen sensor
Wet Labs C*Star transmissometer (660nm wavelength)
Wet Labs ECO-AFL fluorometer
Dissolved Oxygen Titration System (Portable modified Winkler titration system)
The BCO-DMO database includes data from IMBER endorsed projects lead by US funded investigators. There is no dedicated US IMBER project or data management office. Those functions are provided by US-OCB and BCO-DMO respectively.
The information in this program description pertains to the Internationally coordinated IMBER research program. The projects contributing data to the BCO-DMO database are those funded by US NSF only. The full IMBER data catalog is hosted at the Global Change Master Directory (GCMD).
IMBER Data Portal: The IMBER project has chosen to create a metadata portal hosted by the NASA's Global Change Master Directory (GCMD). The GCMD IMBER data catalog provides an overview of all IMBER endorsed and related projects and links to datasets, and can be found at URL http://gcmd.nasa.gov/portals/imber/.
IMBER research will seek to identify the mechanisms by which marine life influences marine biogeochemical cycles, and how these, in turn, influence marine ecosystems. Central to the IMBER goal is the development of a predictive understanding of how marine biogeochemical cycles and ecosystems respond to complex forcings, such as large-scale climatic variations, changing physical dynamics, carbon cycle chemistry and nutrient fluxes, and the impacts of marine harvesting. Changes in marine biogeochemical cycles and ecosystems due to global change will also have consequences for the broader Earth System. An even greater challenge will be drawing together the natural and social science communities to study some of the key impacts and feedbacks between the marine and human systems.
To address the IMBER goal, four scientific themes, each including several issues, have been identified for the IMBER project: Theme 1 - Interactions between Biogeochemical Cycles and Marine Food Webs; Theme 2 - Sensitivity to Global Change: How will key marine biogeochemical cycles, ecosystems and their interactions, respond to global change?; Theme 3 - Feedback to the Earth System: What are the roles of the ocean biogeochemistry and ecosystems in regulating climate?; and Theme 4 - Responses of Society: What are the relationships between marine biogeochemical cycles, ecosystems, and the human system?
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.
The original call for proposals for Emerging Topics in Biogeochemical Cycles (ETBC) was issued in September 2007 by the US NSF Directorate for Geosciences (NSF 07-049).
The Geosciences Directorate (GEO) is substantially augmenting our past funding sources to explicitly support emerging areas of interdisciplinary research. We seek to foster transformational advances in our quantitative or mechanistic understanding of biogeochemical cycles that integrate physical-chemical-biological processes over the range of temporal and/or spatial scales in Earthâ€™s environments. We encourage submission of proposals that address emerging topics in biogeochemical cycles, the water cycle or their coupling, across the interfaces of atmosphere, land, and oceans. Proposals must cross the disciplinary boundaries of two or more divisions in Geosciences (e.g. ATM, EAR, OCE) or of at least one division in Geosciences and a division in another NSF directorate.
Although funding programmatic disciplines continues to provide a robust and adaptable framework to build our understanding of the geosciences and the earth as a system, there are classes of emerging and challenging problems that require integration of concepts and observations across diverse fields. Our goal is to enhance such integration. Successful proposals need to develop intellectual excitement in the participating disciplinary communities. Also encouraged are proposals that have broader educational, diversity, societal, or infrastructure impacts that capitalize on this interdisciplinary opportunity.
A Gordon and Betty Moore Foundation Program.
Forging a new paradigm in marine microbial ecology:
Microbes in the ocean produce half of the oxygen on the planet and remove vast amounts of carbon dioxide, a greenhouse gas, from the atmosphere. Yet, we have known surprisingly little about these microscopic organisms. As we discover answers to some long-standing puzzles about the roles that marine microorganisms play in supporting the ocean’s food webs and driving global elemental cycles, we realized that we still need to learn much more about what these organisms do and how they do it—including how they evolved and contribute to our ocean's health and productivity.
The Marine Microbiology Initiative seeks to gain a comprehensive understanding of marine microbial communities, including their diversity, functions and behaviors; their ecological roles; and their origins and evolution. Our focus has been to enable researchers to uncover the principles that govern the interactions among microbes and that govern microbially mediated nutrient flow in the sea. To address these opportunities, we support leaders in the field through investigator awards, multidisciplinary team research projects, and efforts to create resources of broad use to the research community. We also support development of new instrumentation, tools, technologies and genetic approaches.
Through the efforts of many scientists from around the world, the initiative has been catalyzing new science through advances in methods and technology, and to reduce interdisciplinary barriers slowing progress. With our support, researchers are quantifying nutrient pools in the ocean, deciphering the genetic and biochemical bases of microbial metabolism, and understanding how microbes interact with one another. The initiative has five grant portfolios:
Individual investigator awards for current and emerging leaders in the field.
Multidisciplinary projects that support collaboration across disciplines.
New instrumentation, tools and technology that enable scientists to ask new questions in ways previously not possible.
Community resource efforts that fund the creation and sharing of data and the development of tools, methods and infrastructure of widespread utility.
Projects that advance genetic tools to enable development of experimental model systems in marine microbial ecology.
We also bring together scientists to discuss timely subjects and to facilitate scientific exchange.
Our path to marine microbial ecology was a confluence of new technology that could accelerate science and an opportunity to support a field that was not well funded relative to potential impact. Around the time we began this work in 2004, the life sciences were entering a new era of DNA sequencing and genomics, expanding possibilities for scientific research – including the nascent field of marine microbial ecology. Through conversations with pioneers inside and outside the field, an opportunity was identified: to apply these new sequencing tools to advance knowledge of marine microbial communities and reveal how they support and influence ocean systems.
After many years of success, we will wind down this effort and close the initiative in 2021. We will have invested more than $250 million over 17 years to deepen understanding of the diversity, ecological activities and evolution of marine microbial communities. Thanks to the work of hundreds of scientists and others involved with the initiative, the goals have been achieved and the field has been profoundly enriched; it is now positioned to address new scientific questions using innovative technologies and methods.