Table of Contents

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

Particles were collected on the monthly sampling cruises affiliated with the Bermuda Atlantic Time-series Study (BATS) in fall 2017 (AE1718) and spring 2018 (AE1809) using surface-tethered Particle Interceptor Traps deployed at 150 m, 200 m, and 300 m depths for 72 h (Table 1). To collect particles with minimal alteration to their structure, traps containing a polycarbonate jar with 100 mL of 12% polyacrylamide gel were deployed at each depth. Seawater was collected from the surface, deep chlorophyll maximum (DCM) or 20 m above the mixed layer depth (MLD), and at every trap deployment depth using 12 L Niskin bottles mounted on a CTD rosette.

8 particles were categorized and manually picked based on their morphology using characteristics described in the literature (phytodetrital aggregates or fecal aggregates), washed three times using ultrapure nuclease-free distilled water (Invitrogen), and pooled in Eppendorf LoBind tubes stored at -80C. For DNA analysis of the microbial community in the ambient seawater, 2 L from each sampling depth was filtered onto GF/F and stored in Eppendorf LoBind tubes at -80C.

DNA from the pooled particles and GF/F were extracted using a DNeasy Blood and Tissue extraction kit, and bacterial and eukaryotic paired-end V4 amplicon sequences were acquired via an Illumina MiSeq platform.

Problem report: 
As a result of low DNA yield, five samples of pooled aggregates failed PCR amplification attempts using eukaryotic (18S, V4) primers: fall 200m and 300m phytodetrital aggregates, fall 200m fecal aggregates, spring 300m phytodetrital aggregates, and spring 300m fecal aggregates.

Supplemental file "16S_Control-Blanks_Species_Raw.csv" contains the taxa excluded from downstream analyses.

Bioinformatic analyses were performed using QIIME2 v2019.1. PhiX reads and chimeric sequences were removed and remaining reads were assembled, demultiplexed, and trimmed to salvage reads with a median quality score above 25 using DADA2 within the QIIME2 pipeline.

BCO-DMO data manager processing notes:
* After correspondence with the submitter, the final format of this dataset was combined into one table with added columns for sample name, and transformed to have abundances for the samples in an additional "abundance" column instead of an abundance column per sample.
* Data originally submitted in excel sheets was combined into one data table.  The originally named Sheet "16S_Control-Blanks_Species_Raw" with the description "Taxa excluded from downstream analyses" was not combined into the dataset and was instead served as an independent data table in the supplemental files section.

NSF abstract:

Marine phytoplankton are microscopic algae that live in the sunlit zone of the ocean. They play an important role in the uptake of carbon dioxide from the atmosphere through photosynthesis, similar to what plants do on land, and are the basis of the marine food web. However, instead of storing this organic carbon in leaf tissue and roots, marine phytoplankton are grazed by planktonic animals, or die and subsequently sink out of the sunlit zone in the form of aggregates, also called "Marine Snow". These particles not only export the organic carbon contained in their cells to the deep ocean, but also serve as food for animals and bacteria that live in the deep. A considerable portion of these phytoplankton are extremely small, among the tiniest of all organisms known. These extremely small cells have not been thought to play an important role in the formation and sinking of marine snow; however, recent findings challenge this view. This project will investigate how the smallest of these phytoplankton contribute to the rain of sinking particles from the sunlit surface to the deep ocean. This research is important because, in some of the largest expanses of the open oceans, these minute cells dominate the phytoplankton community, and larger plankton organisms are very sparse. The project, through a combination of work in the laboratory and at a field station, will shed light on how these tiny phytoplankton cells make aggregates, which ultimately enable them to sink as "Marine Snow". The project also provides unique opportunities for undergraduate students at Arizona State University, a land-locked public university, to gain experience in working with marine research. The project will serve to educate one PhD student, one MS student in an accelerated BS-MS program, and 8-10 undergraduate students/semester in a unique, inquiry based learning effort termed Microbial EducatioN Training and OutReach (MENTOR). The undergraduate students will also participate in Arizona State University (ASU)'s School of Life Sciences, Undergraduate Research Program (SOLUR), which seeks to increase the participation of minorities in science. They will also contribute towards developing web and classroom materials, based on this project, which will then be distributed through a partnership with the award-winning ASU-sponsored Ask A Biologist K-12 web site.

The oceanic "biological carbon pump", the photosynthetically mediated transformation of dissolved inorganic carbon into particulate and dissolved organic carbon and its subsequent export to deep water, functions as a significant driver of atmospheric carbon uptake by the oceans. The traditional view of the biological carbon pump in the ocean is that of sinking of large aggregates (marine snow) or fecal pellets, which are made up of large, mineral ballasted cells of phytoplankton. However, recent evidence, stemming from in situ investigations of particulate matter, trap studies and modelling studies, have shown that micron-sized phytoplankton such as picocyanobacteria as well as picoeukaryotes can contribute significantly to the sinking of particulate matter. The specific mechanisms behind the sinking of these micrometer sized cells remain elusive as the cells are too small to sink on their own, and mesozooplankton is likely unable to ingest single cells. Intriguingly, recent research by the investigators has shown that the ubiquitous picocyanobacteria Synechococcus are able to form aggregates and sink at velocities comparable to those of marine snow. They found that the matrix of the Synechococcus aggregates was made of Transparent Exopolymeric Particles (TEP), and that TEP production was enhanced under nutrient limited culture conditions. Interaction with clays and presence of heterotrophic bacteria also enhanced aggregation and sinking velocity. This study aims to further investigate aggregation of other common picoplankton in the laboratory and aggregation occurring in natural settings at an oligotrophic open ocean site, the Bermuda Atlantic Time-series Site (BATS). Ultimately, this project will increase and refine our understanding of the role of the smallest phytoplankton in aggregation and sinking - information vital to understanding carbon cycling processes in the oceans.