Abundance and biomass of ciliates from inverted microscope counts from samples taken on R/V Atlantic Explorer cruises AE1102, AE1118, AE1206, AE1219 in the Sargasso Sea, Bermuda Atlantic Time-Series Station in 2011-2012 (Trophic BATS project)

Website: https://www.bco-dmo.org/dataset/4018
Data Type: Cruise Results
Version: 1
Version Date: 2013-08-22

Project
» Plankton Community Composition and Trophic Interactions as Modifiers of Carbon Export in the Sargasso Sea (Trophic BATS)

Program
» Ocean Carbon and Biogeochemistry (OCB)
ContributorsAffiliationRole
Neuer, SusanneArizona State University (ASU)Principal Investigator, Contact
De Martini, FrancescaArizona State University (ASU)Student
Rauch, ShannonWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
Abundance and biomass of ciliates from inverted microscope counts from samples taken on R/V Atlantic Explorer cruises AE1102, AE1118, AE1206, AE1219 in the Sargasso Sea, Bermuda Atlantic Time-Series Station in 2011-2012.


Coverage

Spatial Extent: N:33.48 E:-64.17 S:30.83 W:-64.83
Temporal Extent: 2011-02-23 - 2012-07-31

Dataset Description

Abundance (cells per L) and biomass (ng C per L) of ciliates from samples collected during four cruises in the Sargasso Sea during spring and summer 2011-2012.

Plot of total_biomass vs. depth. (Generated by BCO-DMO.) Click the image to view a larger version.


Methods & Sampling

Water Column Sampling:
Water column sampling was performed on four cruises during the spring and the summer of 2011 and 2012 at the Bermuda Atlantic Time-series Study station (31’40°N 64’10°W, BATS) and in the mesoscale eddies found in the surrounding area of the Sargasso Sea. For each cruise, 2 stations were sampled, usually in the center of a mesoscale eddy and at BATS. The edge of the eddy was sample two times, as well. To be able to get a better reproducibility of data, each experiment was replicated.

For each experiment, seawater samples were collected pre-dawn (on deck 2:30-4:00, local time) at four different depths within the euphotic zone (20m, 50m, 80m and the Deep Chlorophyll Maximum, DCM). Twenty-one 10L Niskin bottles were attached to a rosette with conductivity, temperature, depth sensors (CTD), and an in vivo fluorometer. This sensor allowed for recording in real time of chlorophyll fluorescence and the DCM for each station. The water that was collected from the 10L Niskin bottles was sampled for abundance and biomass of the plankton community.

Microscopy Analyses:
Inverted microscopy was used to determine abundance and biomass of planktonic ciliates. Seawater was collected into 200ml amber glass bottles which had previously been supplied with 2.5% of Lugol’s dye (v/v). Samples were stored in the dark and at room temperature onboard ship and in the laboratory at ASU. 100 ml of sample were settled onto settling chambers for 48hr according to the Utermöhl method (Utermöhl, 1931). A Nikon Elipse TE300 inverted microscope was used at 40x magnification to count the entire slide and all the ciliates found were measured and classified based on the classification system introduced by Agatha (2004) and Agatha & Struder-Kypke (2007). Ciliates were classified into 4 standard shapes: prolate spheroid, sphere, cone, cone + half sphere.

Biomass calculations were done for each category of organism counted. Biovolume for each group was determined based on size and shape of the organism by approximating the closest geometric shape (Hillebrand et al. 1999) and then converted into units of carbon based on the carbon to volume ratio (Menden-Deuer and Lessard 2000). To determine the carbon biomass of the ciliates, carbon to volume conversion factors were used, as in Putt and Stoecker (1989). The 95% confidence intervals were calculated according to Lund et al. (1958).


Data Processing Description

BCO-DMO Processing Notes:
- Moved cruise_id, location_description, station, and cast into columns.
- Replaced blanks with 'nd' to indicate 'no data'.
- Removed 'm' from the depth column.
- Replaced "Tot#/L" with "Total_num_per_liter" in the taxon column.
- Added lat and lon for each station & cast from the metadata form.


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Data Files

File
ciliates_abund_biomass.csv
(Comma Separated Values (.csv), 30.39 KB)
MD5:05534b9f6326f6ee2a02ae645a460b49
Primary data file for dataset ID 4018

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Related Publications

Agatha S. (2004). A Cladistic Approach for the Classification of Oligotrichid Ciliates (Ciliophora: Spirotricha). Acta protozoologica, 43(3), 201–217. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854820/
Methods
Agatha, S., & Strüder-Kypke, M. C. (2007). Phylogeny of the order Choreotrichida (Ciliophora, Spirotricha, Oligotrichea) as inferred from morphology, ultrastructure, ontogenesis, and SSrRNA gene sequences. European Journal of Protistology, 43(1), 37–63. doi:10.1016/j.ejop.2006.10.001
Methods
Amacher, J., Neuer, S., Anderson, I., & Massana, R. (2009). Molecular approach to determine contributions of the protist community to particle flux. Deep Sea Research Part I: Oceanographic Research Papers, 56(12), 2206–2215. doi:10.1016/j.dsr.2009.08.007
General
Hillebrand, H., Dürselen, C.-D., Kirschtel, D., Pollingher, U., & Zohary, T. (1999). Biovolume calculation for pelagic and benthic microalgae. Journal of Phycology, 35(2), 403–424. doi:10.1046/j.1529-8817.1999.3520403.x
Methods
Lund, J. W. G., Kipling, C., & Le Cren, E. D. (1958). The inverted microscope method of estimating algal numbers and the statistical basis of estimations by counting. Hydrobiologia, 11(2), 143–170. doi:10.1007/bf00007865 https://doi.org/10.1007/BF00007865
Methods
Menden-Deuer, S., & Lessard, E. J. (2000). Carbon to volume relationships for dinoflagellates, diatoms, and other protist plankton. Limnology and Oceanography, 45(3), 569–579. doi:10.4319/lo.2000.45.3.0569
Methods
Neuer, S., & Cowles, T. (1994). Protist herbivory in the Oregon upwelling system. Marine Ecology Progress Series, 113, 147–162. doi:10.3354/meps113147
General
Putt, M., & Stoecker, D. K. (1989). An experimentally determined carbon : volume ratio for marine “oligotrichous” ciliates from estuarine and coastal waters. Limnology and Oceanography, 34(6), 1097–1103. doi:10.4319/lo.1989.34.6.1097
Methods

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Parameters

ParameterDescriptionUnits
cruise_idOfficial cruise identifier e.g. AE1102 = R/V Atlantic Explorer cruise number 1102. dimensionless
castCast number. dimensionless
stationStation number. dimensionless
location_descriptionDescription of sampling location. dimensionless
latLatitude. Positive values = North. decimal degrees
lonLongitude. Positive values = East. decimal degrees
depthSample depth. meters
total_biomassTotal biomass (ng C/L) at the particular cast and depth. nanograms C per Liter
taxonName of the taxonomic group. dimensionless
abundanceAbundance of planktonic ciliates (cells/L). cells per Liter
abund_upper_95pcnt_CIUpper 95% confidence interval for abundance. cells per Liter
abund_lower_95pcnt_CILower 95% confidence interval for abundance. cells per Liter
biomassBiomass (ng C/L) of planktonic ciliates. nanograms C per Liter


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Instruments

Dataset-specific Instrument Name
Niskin bottle
Generic Instrument Name
Niskin bottle
Dataset-specific Description
Samples were collected using 10-Liter Niskin bottles attached to a CTD rosette.
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
Inverted Microscope
Generic Instrument Name
Inverted Microscope
Dataset-specific Description
Ciliate abundance and biomass was determined using bright-field inverted microscopy (Amacher et al. 2009; Neuer and Cowles 1994). A Nikon Elipse TE300 inverted microscope was used at 40x magnification to count the entire slide.
Generic Instrument Description
An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana). Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives. The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications.


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Deployments

AE1102

Website
Platform
R/V Atlantic Explorer
Start Date
2011-02-23
End Date
2011-03-07
Description
This cruise was the first in a series of four cruises planned to study the trophic interactions and particle export during the winter season in the Sargasso Sea. The researchers focused on several sampling locations including an anticyclonic eddy, slope waters of the eddy, and repeated visits to the Bermuda Atlantic Time Series (BATS) study site.  The research focus for the cruise included phytoplankton production, microzooplankton grazing, mesozooplankton grazing and particle export.  This process cruise was designed to quantify stocks and rate processes in the Sargasso Sea food web. Work entailed CTD casts, over the stern deployment of in situ primary production arrays and surface tethered sediment traps. Until 26 November 2012 this cruise was identified by BIOS and R2R as AE-X1101. On 26 November 2012, the cruise ID was corrected to AE1102. Original cruise data are available from the NSF R2R data catalog

AE1118

Website
Platform
R/V Atlantic Explorer
Start Date
2011-07-22
End Date
2011-08-04
Description
AE1118 was a process cruise aboard the R/V Atlantic Explorer to quantify stocks and rate processes in the Sargasso Sea food web. This was the second in a series of cruises for the Trophic BATS project. On each cruise, sampling was conducted at three stations: the center and edge of a mesoscale eddy and at one station outside of the eddy. Core CTD casts to ~2000 meters and pre-dawn 'Productivity' CTD casts were made at each station. Original cruise data are available from the NSF R2R data catalog.

AE1206

Website
Platform
R/V Atlantic Explorer
Start Date
2012-03-14
End Date
2012-03-23
Description
AE1206 was the third in a series of four cruises for the Trophic BATS project. On each cruise, sampling was conducted at three stations: the center and edge of a mesoscale eddy and at one station outside of the eddy. Core CTD casts to ~2000 meters and pre-dawn 'Productivity' CTD casts were made at each station. Cruise information and original data are available from the NSF R2R data catalog.

AE1219

Website
Platform
R/V Atlantic Explorer
Start Date
2012-07-19
End Date
2012-07-31
Description
AE1219 was the final cruise in a series of four for the Trophic BATS project. On each cruise, sampling was conducted at three stations: the center and edge of a mesoscale eddy and at one station outside of the eddy. Core CTD casts to ~2000 meters and pre-dawn 'Productivity' CTD casts were made at each station. Cruise information and original data are available from the NSF R2R data catalog.


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Project Information

Plankton Community Composition and Trophic Interactions as Modifiers of Carbon Export in the Sargasso Sea (Trophic BATS)

Coverage: Sargasso Sea, BATS site


Fluxes of particulate carbon from the surface ocean are greatly influenced by the size, taxonomic composition and trophic interactions of the resident planktonic community. Large and/or heavily-ballasted phytoplankton such as diatoms and coccolithophores are key contributors to carbon export due to their high sinking rates and direct routes of export through large zooplankton. The potential contributions of small, unballasted phytoplankton, through aggregation and/or trophic re-packaging, have been recognized more recently. This recognition comes as direct observations in the field show unexpected trends. In the Sargasso Sea, for example, shallow carbon export has increased in the last decade but the corresponding shift in phytoplankton community composition during this time has not been towards larger cells like diatoms. Instead, the abundance of the picoplanktonic cyanobacterium, Synechococccus, has increased significantly. The trophic pathways that link the increased abundance of Synechococcus to carbon export have not been characterized. These observations helped to frame the overarching research question, "How do plankton size, community composition and trophic interactions modify carbon export from the euphotic zone". Since small phytoplankton are responsible for the majority of primary production in oligotrophic subtropical gyres, the trophic interactions that include them must be characterized in order to achieve a mechanistic understanding of the function of the biological pump in the oligotrophic regions of the ocean.

This requires a complete characterization of the major organisms and their rates of production and consumption. Accordingly, the research objectives are: 1) to characterize (qualitatively and quantitatively) trophic interactions between major plankton groups in the euphotic zone and rates of, and contributors to, carbon export and 2) to develop a constrained food web model, based on these data, that will allow us to better understand current and predict near-future patterns in export production in the Sargasso Sea.

The investigators will use a combination of field-based process studies and food web modeling to quantify rates of carbon exchange between key components of the ecosystem at the Bermuda Atlantic Time-series Study (BATS) site. Measurements will include a novel DNA-based approach to characterizing and quantifying planktonic contributors to carbon export. The well-documented seasonal variability at BATS and the occurrence of mesoscale eddies will be used as a natural laboratory in which to study ecosystems of different structure. This study is unique in that it aims to characterize multiple food web interactions and carbon export simultaneously and over similar time and space scales. A key strength of the proposed research is also the tight connection and feedback between the data collection and modeling components.

Characterizing the complex interactions between the biological community and export production is critical for predicting changes in phytoplankton species dominance, trophic relationships and export production that might occur under scenarios of climate-related changes in ocean circulation and mixing. The results from this research may also contribute to understanding of the biological mechanisms that drive current regional to basin scale variability in carbon export in oligotrophic gyres.



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Program Information

Ocean Carbon and Biogeochemistry (OCB)


Coverage: Global


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.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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