Images of particles collected in sediment traps for quantitative analysis from multiple platforms from 2016-2017

Data Type: Cruise Results
Version: 1
Version Date: 2018-11-07

» Collaborative Research: EAGER: Particle-specific DNA sequencing to directly observe ecological mechanisms of the biological pump (EAGER DNA BioPump)
Durkin, ColleenMoss Landing Marine Laboratories (MLML)Principal Investigator
Estapa, Margaret L.Skidmore CollegeCo-Principal Investigator
Omand, MelissaUniversity of Rhode Island (URI-GSO)Co-Principal Investigator
Biddle, MathewWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Spatial Extent: N:39.94 E:-70.8119 S:21.52 W:-151.779
Temporal Extent: 2016-06-13 - 2017-11-07

Dataset Description

Samples were collected at the New England shelf break aboard the R/V Endeavor on 3-7 November 2017 (EN572) and 13-18 June 2016 (EN581) and on a transit between Honolulu, Hawaii and Portland, Oregon aboard the R/V Falkor between 24 January-20 February, 2017 (FK170124).  Sediment trap collector tubes were deployed on various platform designs, including a neutrally-buoyant sediment trap (NBST), a surface tethered sediment trap (STST), and a Wire Walker (WW) trap.   The location, time, duration, depth, and collection types from each trap deployment are listed in Trap Deployment Log.

Acquisition Description

The NBST carried 4 collection tubes with a diameter of 12 cm (Valdes and Price 2000). The STST included 5 frames (KC Denmark) clipped onto a surface-tethered, free drifting array line at increasing depths and each frame carried 4, 7 cm diameter collection tubes. The WW trap consisted of one, 4-tube trap frame (KC Denmark) tethered by a bungee below the profiling component of the WW array.  To prepare tubes for deployment, seawater was collected from a depth of 150 m using a CTD rosette and pumped through a 1 μm filter cartridge. Trap tubes were filled with filtered water overlying a jar containing a polyacrylamide gel layer (Durkin et al. 2015). Trap platforms were deployed for between 1 day and 3.5 days (see Trap Deployment Log).  Identically prepared tubes were incubated in parallel onboard the ship to serve as process blanks.

Upon recovery, collection tubes were allowed to settle for at least 1 hour before the overlying water was siphoned off.  Jars containing polyacrylamide gel were removed from trap tubes and the remaining overlying water was carefully pipetted off the gel.  Gels were stored at 4 degrees C and imaged within the following 2 days before being stored at -80 degrees C. 

Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16) with either a Luminera Infinity 2 (FK170124) or an Allied Vision Technologies StingRay (EN572 and EN581) camera attachment.  Particles collected in gel layers during EN572 and EN581 were imaged under brightfield illumination.  Particles collected in gel layers during FK170124 were imaged under both brightfield and oblique illumination, producing two separate sets of images for each sample.  EN572 gel layers were imaged with a transparent grid to assist in tracking gel location during imaging. The grid was not used when imaging samples collected during subsequent cruises because the pronounced grid lines complicated image analysis. All gel layers were imaged at 4 increasing magnifications, though the combination of magnifications varied by cruise: at 7x, 20x, 40x, and 115x for EN572 samples, at 7x, 20x, 40x, and 80x for EN581 samples, and at 7x, 20x, 50x, and 115x for FK170124 samples. At magnifications greater than 7x, multiple focal planes within a field of view were imaged to capture particles embedded in different depths of the gel layer.  The number of focal planes imaged was consistent across all fields of view for a given magnification but varied across cruises due to variation in gel thickness and particle types present. To determine whether measured particle properties changed if gel layers are frozen, samples collected during FK170124 were thawed after being stored for approximately 1 year at -80  degrees C and imaged again under both brightfield and oblique illumination.

Processing Description

Infinity Capture for Mac

BCO-DMO Processing Notes:

  • images have been zipped into packages.

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Related Publications

Durkin, C. A., Estapa, M. L., & Buesseler, K. O. (2015). Observations of carbon export by small sinking particles in the upper mesopelagic. Marine Chemistry, 175, 72–81. doi:10.1016/j.marchem.2015.02.011

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Parameters for this dataset have not yet been identified

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Dataset-specific Instrument Name
Luminera Infinity 2 microscope camera
Generic Instrument Name
Dataset-specific Description
Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16) with either a Luminera Infinity 2 (FK170124) or an Allied Vision Technologies StingRay (EN572 and EN581) camera attachment.
Generic Instrument Description
All types of photographic equipment including stills, video, film and digital systems.

Dataset-specific Instrument Name
Olympus SZX16 Stereomicroscope
Generic Instrument Name
Dataset-specific Description
Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16)
Generic Instrument Description
Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope".

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R/V Falkor
Start Date
End Date
Station 1: 01/28/2017 17:45 to 02/02/2017 05:43 (GMT) Station2: 02/05/2017 16:06 to 02/08/2017 17:20 (GMT) Station3_dep1:  02/12/2017 04:23 to 02/13/2017 16:42 (GMT) Station3_dep2:  02/13/2017 17:48 to 02/14/2017 18:46 (GMT)


R/V Endeavor


R/V Endeavor

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Project Information

Collaborative Research: EAGER: Particle-specific DNA sequencing to directly observe ecological mechanisms of the biological pump (EAGER DNA BioPump)

Coverage: Eastern Pacific

Text from the NSF award abstract: Carbon is fixed into organic matter by phytoplankton growing in the surface ocean, and is naturally sequestered in the ocean interior when particles and organisms sink: a process called the "biological pump." Because of its recognized influence on the global carbon cycle, ocean scientists have studied the biological pump for decades. However, we still do not have a sufficient understanding of the underlying processes to accurately quantify and predict carbon cycling. Much of this uncertainty stems from an inability to directly link specific plankton in the surface ocean with the types of particles sinking out of the surface ocean. To address this missing link in biological pump research, this work will directly observe how plankton are transported out of the surface ocean using novel, particle-specific observational approaches embedded within an interdisciplinary field program that will finely resolve upper ocean plankton groups and the resulting amount of sinking carbon across space and in time. The genetic identity of organisms within different types of sinking particles will be determined by sequencing the genetic contents of individually collected particles. This new application of a molecular method will definitively link surface plankton with sinking particles at five locations across the Pacific Ocean. This work has the potential to transform our understanding of the biological pump by identifying previously unknown links between surface ecosystems and sinking carbon particles. Because this work is embedded within an interdisciplinary field program, including biogeochemical modelers and remote sensing scientists, these data will feed directly into new models of the biological pump, improving our ability to quantify and predict carbon uptake by the ocean. This project will train 1 graduate student and at least 2 undergraduate researchers. Findings will be communicated to the non-scientific public through blogs, videos, and the public communication channels of participating institutions. Accurate prediction of the global carbon cycle requires an understanding of the specific processes that link surface plankton communities and sinking particulate carbon flux (export) out of the surface ocean, but current methodological paradigms in biological pump research do not directly observe these processes. This project will comprehensively determine who is exported from the surface ocean and how using new, particle-resolving optical and molecular techniques embedded within a sampling scheme that characterizes export events at high time and space resolution. The investigation suggests that different plankton types in the surface waters are transported out of the surface ocean by distinct export pathways, and that an understanding of these connections is critical knowledge for global carbon cycle modeling. If successful, this work has the potential to transform our conceptual understanding of the biological pump by directly identifying mechanisms that link surface plankton with particle export, without relying on bulk sampling schemes and large-scale correlation analysis. Particle export environments will be studied at five open ocean locations during a cruise from Hawaii to Seattle in January-February 2017. The surface plankton communities will be characterized by a combination of satellite observations, sensors attached to a free-drifting, continuously profiling WireWalker, an in situ holographic camera, microscopy, and by sequencing 18S and 16S rRNA gene fragments. Exported particles will simultaneously be captured by various specialized sediment traps and their characteristics will be directly related to their sources in the surface community by identifying the genetic contents of individual particle types. Individual particles will be isolated from gel layers and the 16S and 18S rRNA gene fragments will be amplified and sequenced. This work would, for the first time, combine molecular approaches with particle-specific observations to enable simultaneous identification of both which organisms are exported and the processes responsible for their export.

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Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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