Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Processing Description
  • Problem Description
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

SEM = Scanning Electron Microscopy
EBSD = Electron Backscatter Diffraction
CTF = Channel Text File

These data support the results publication Smart et al. (in review):
Smart, S.M., S. E. Fawcett, H. Stowell & A. Pérez-Huerta. (n.d.) Changes in Shell and Crystal Structure from Life to Sediments: an EBSD Characterization of Subantarctic Planktic Foraminifera. Geochemistry, Geophysics, Geosystems.  In review.

Additional funding description:
In addition to NSF award OCE-2205603, this dataset was supported by South African National Research Foundation (Grants 111090 and 120714); University of Cape Town's URC Postdoctoral Fellowship.

Living specimens were collected using a plankton net towed at 40-60 m depth, and preserved in a pH-buffered, 5–10% formalin-seawater solution kept at 4°C. Foraminifera shells were separated using a combination of wet-sieving, NaCl density separation and dry picking under a microscope. For more details, see Smart et al. (2020). Core-top specimens were picked from the 0-1 cm sediment interval after sieving and rinsing with tap water. Most living and subfossil specimens were sonicated in high-purity ethanol, oxidatively cleaned and rinsed in MilliQ before epoxy mounting. Others were left uncleaned. Cleaning treatment is indicated in dataset file "foram_ebsd_supplemental_metadata.csv" and Supplemental Table S1 of the companion publication to this dataset (Smart et al., in review). Once fully dry, shells were mounted in EpoThin 2 epoxy, cured, and cross-sectioned using SiC grit-papers and Alumina polish with progressively smaller particle sizes. Shortly before EBSD analysis, sample mounts were coated with ~4-5 nm gold. For details, see Smart et al. (in review).

Here we provide the original AZtec crystal orientation files (in .ctf format) as well as the corrected and minimally processed data (as both .ctf files and .txt files). During data collection, the software automatically compares the collected EBSD patterns with calcite in the American Mineralogist crystal structure database to find the best fit (i.e., crystal orientation). Data files in .ctf format can be loaded into any standard EBSD software (e.g., EDAX OIM Analysis; https://www.edax.com/products/ebsd/oim-analysis) or using the free, open-source MTEX toolbox using MATLAB (https://mtex-toolbox.github.io/) as done in Smart et al. (in review).  See Hiscocks, J. (2021) "Getting Started with MTEX for EBSD analysis Rev6" for further guidance on loading .ctf files.

Our data correction and processing steps include:

1) Applying a 180° rotation to the Z axis (i.e., around the sample normal) to correct for a difference in reference frame between the data collection software (AZtec) and the analysis software we used (MTEX). This is the same correction we use for our own analysis in Smart et al. (in review).

2) Converting from the spatial reference frame to the Euler reference frame. This step aligns the map axes with the crystal axes (i.e., the Euler rotation axes) so that the X axis of the map corresponds to the X axis of rotation in the Euler angle system. Euler angles for a specific EBSD data-point are the minimum rotations around the X-Y-Z axes needed for the map frame to match that pixel's crystallographic frame.

3) Basic quality control: We removed any data with a mean angular deviation (MAD) >2.5° as well as any grains smaller than 2 pixels with MAD>1°. Note that we define a grain (domain of similar orientation) using a threshold of 5°. Areas containing epoxy (i.e., not within the calcite shell) were also excluded. We did not apply any algorithms for de-noising, smoothing or indexing of non-indexed pixels. 

We also provide supplemental metadata (foram_ebsd_supplemental_metadata.csv), which contains additional metadata for each .ctf map file (species, collection type, site, chamber mapped), and summary statistics on crystal orientation observed in our specimens (e.g., abundance of different crystal twinning relationships).

Data Files:

EBSDdatafiles_corr.zip = Contains the corrected .Channel Text Files (.ctf) crystal orientation data files.

*  Each corrected .ctf file was concatenated into one table and imported into the BCO-DMO data system. The combined table appears as Data File: 964206_v1_foram_ebsd_crystal_orientation.csv (along with other download format options).

* Experiment and collection metadata (Specimen, Type, Species, Chamber, Site, lat, lon, depth,cruise_id,DateTime_Start_GMT,DateTime_End_GMT) was added to the combined table (joined on corrected ctf filename) from supplemental file foram_ebsd_supplemental_metadata.csv

* Missing Data Identifiers:
In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.

* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores.  Can not start with a number]

* Lat and Lon in the combined table was rounded to five decimal places.

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Supplemental files:

EBSDdatafiles_orig.zip = All the original (uncorrected) crystal orientation .ctf files were packaged into this zip file. See more information in the file description and Data Processing sections.

EBSDdatafiles_corr_txt.zip = All the corrected .txt data files were packaged into this zip file. Same data as the corrected .ctf data files, files differ in formatting. See more information in the file description and Data Processing sections.

foram_ebsd_supplemental_metadata.csv
* A table corresponding to Table S1 in the pending publication Smart et al. (in review) TableS1_Summary-statistics.xlsx was revised and resubmitted to BCO-DMO with additional collection metadata, including date,start and end times, depth, lat, lon etc. The revised file "foram_EBSD-supplemental-metadata_SScompleted_UTF-8.csv" was imported into the BCO-DMO data system, columns for datetime with timezone were added, and file column names were adjusted to match BCO-DMO naming conventions. The attached to this dataset as supplemental file foram_ebsd_supplemental_metadata.csv.
* negative (-) prefixed to latitude values to indicate degrees South (format: Decimal Degrees where South and West are negative). The location of this dataset is Sub-Antarctic south of South Africa.
* Column Data Filename updated to be "Orig_Filename" (corresponding to file within EBSDdatafiles_orig.zip) and a second column "Corrected_Filename" (corresponding to the file within EBSDdatafiles_corr.zip)

NSF abstract:
This project dives into the microscopic world of planktic foraminifera, tiny shelled zooplankton that inhabit oceans across the globe. As foraminifera build their shells, they incorporate tiny amounts or organic matter and, with it, information about their surroundings and ecology. When their shells sink and gather on the seafloor, they add to an ever-growing archive of Earth history. Exactly how well the organic matter and its original signals are preserved in shells during sinking and early burial is a key uncertainty for its use in reconstructing past climate. To address this, the PI will use ultra-high resolution crystal and chemical mapping to compare shells before and after this crucial transition to the fossil record. Understanding the feedbacks that have regulated Earth’s climate in the past is an essential part of our future response and preparedness as a nation to face the challenges of a warming planet, and is thus well aligned with NSF directives. Furthermore, by characterizing the biomineral structures of modern shells, this work will assist with monitoring ocean acidification, which can compromise fisheries, tourism and the natural buffering of coastal communities from storms (e.g., by coral reefs). As a female scientist and immigrant from a developing country, the PI is dedicated to encouraging other young women and underrepresented groups to pursue a career in science. By partnering with a local Alabama middle school that serves underrepresented students, she hopes to inspire those who might not otherwise consider science as a career path, to take STEM subjects in high school. In this way, students will be better equipped to take on the challenge of climate change, and be made aware of the need for their talents in building a more sustainable future. The nitrogen (N) isotope composition (δ15N) of organic matter within the shell walls of planktic foraminifera is emerging as a promising new tool for tracking the amount and partitioning of nitrogen, an essential nutrient for life, in the ocean. The number of foraminifera-bound δ15N records has grown rapidly in recent years, yielding tantalizing insights into the interplay between ocean fertility, oxygen concentrations and atmospheric greenhouse gas levels. Yet, fundamental questions remain about the mechanism of N incorporation into calcite, taxonomic differences in N uptake, and the preservation potential of the organic matter to which N is bound, particularly in the earliest stages of sinking and burial. The utility of bulk geochemical analyses (which require combining hundreds of shells) in answering these questions is limited by inherent issues of scale. Hence, the PI proposes to use electron backscatter diffraction (EBSD) and nanoscale secondary ion mass spectrometry (NanoSIMS) on individual shells from living (tow-caught) and dead (seafloor sediment) assemblages to evaluate changes in the biomineral structure, organic matter distribution and relative N content of foraminifera shells from life in the surface ocean to burial on the seafloor. The PI expects her investigation will also provide insight into the role of organic matter in the formation (i.e., biomineralization) and behavior (e.g., susceptibility to breakage/dissolution, mineral-fluid exchange) of biogenic calcite, a geologically important material of interest to a broad range of scientists. Thus while her specific motivation for this work is the N isotope paleo-proxy, the implications extend beyond N to other systems of organic matter and associated tracers (e.g., δ34S, I/Ca, Na/Ca), and to fundamental research areas like habitability and the co-evolution of life and planet. Already, the paleo-δ15N proxy is yielding high-impact results concerning the often-complex feedbacks between the marine biosphere and climate. Thus, by seeking to inform these interpretations, the proposed work has the potential to help predict the unintended consequences of a rapidly warming and acidifying ocean. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.