Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

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).

Image Acquisition:
For more information on sediment trap deployment and image acquisition, see the related dataset "Geltrap micrographs" (https://www.bco-dmo.org/dataset/749412). In brief, 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. Trap tubes were filled with filtered water overlying a jar containing a polyacrylamide gel layer (Durkin et al. 2015). 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. 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

Determination of Particle Flux:
Particles in gel images were quantified with an image processing protocol created using functions available in python’s Sci-Kit Image. Particles present in each micrograph were detected through a series of image transformation steps that maximize the detection of entire particle areas while minimizing the detection of imaging noise. The background was removed, a brightness threshold was applied, and an edge-detection kernel transformation was used to identify the in-focus particles. Duplicate particles detected in multiple focal planes were removed and the remaining particles were counted and measured.

Particles were categorized into 9 different sinking particle classes. Identities were assigned by manually identifying particle images. Aggregates were defined as loosely packed detritus with irregular edges. Dense detritus was defined as densely packed amorphous material, often brown or golden in color. Large, loose pellets were similar to dense detritus but were also elongated like a fecal pellet. Long fecal pellets were defined as long, thin, cylindrical fecal pellets with a smooth edge, such as the chitin-encased pellets produced by euphausiids. Short fecal pellets were also smooth-edged pellets but with an oval or ellipsoid shape, such as those produced by larvaceans. Mini pellets were defined as small (usually <100 micrometer ESD), spheres such as those produced by rhizarians and microzooplankton (Gowing & Silver, 1985). A small number of individual organisms considered to be passively sinking were also detected, including Rhizarians, primarily Phaeodaria, and various phytoplankton, usually diatoms. Pteropods, copepods, amphipods, foraminifera, and other zooplankton that probably swam into the gel and human-produced fibers were also detected but not considered passive flux and not included in the categories of sinking particles. Unidentifiable objects were also detected and were likely caused by out-of-focus particles, shadows, smudges, or noise detected by the image processing steps that are sensitive to the particular thresholds used.

Only identifiable, sinking particle classes from the dataset were considered in calculations of sinking flux. For each imaging magnification, particles were grouped by their equivalent spherical diameter (ESD) into logarithmically-scaled size bins. To calculate number fluxes at each magnification, the number of particles counted in each size bin was divided by the total imaged surface area of the gel and the trap collection time. Uncertainty of the number flux was estimated by applying these same calculations to the counting uncertainty (square root of the number of particles counted, ie. Poisson distribution).

The carbon flux by each particle type was determined by modeling particle volumes, calculating the carbon per unit volume, and multiplying the carbon per particle by the measured particle number fluxes in each size category.

BCO-DMO Processing:
- Adjusted field/parameter names to comply with BCO-DMO naming conventions;
- Concatenated data from separate files into one dataset;
- Rounded "_flux" and "_uncertainty" columns to 3 decimal places,
- Added a conventional header with dataset name, PI names, version date.

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.