Picoplankton & Bacteria
Picoplankton and Bacteria Abundance (CalCOFI Cruise)
cce-lter_picoplankton-bacteriaCCE-LTERv2026.09.05ingested
- years
- 2004–2023
- observations
- 60,802
- sampling events
- 16,011
- stations
- 64
- variables
- 4
- depth
- 1–270 m
Overview
Picophytoplankton (Prochlorococcus, Synechococcus, picoeukaryotes) and heterotrophic bacteria abundances analyzed by flow cytometry (FCM) from CCE-CalCOFI Augmented cruises in the California Current System, 2004-2023 (ongoing). Seawater collected from Niskin bottles at 3-8 depths per station; cells fixed shipboard with paraformaldehyde, stained with a DNA-specific dye, and enumerated on an Altra flow cytometer with dual argon-ion lasers.
Open with the provider
- Q06 license — proposed
Access
Every endpoint this dataset can be reached through, grouped by how you would use it. Every URL is in the release record and answered when the release was cut.
Explore
Apps that read this dataset from the release. A row marked “this dataset” opens with it already selected.
https://calcofi.io/explore/?datasets=cce-lter_picoplankton-bacteria
https://app.calcofi.io/station/?dataset=cce-lter_picoplankton-bacteria
https://app.calcofi.io/hex/?datasets=cce-lter_picoplankton-bacteria
https://app.calcofi.io/cruise/?datasets=cce-lter_picoplankton-bacteria
Query
SQL against the release itself, in the browser — nothing to install and nothing downloaded until a query asks for it. __TBL:obs__ resolves to the pinned release’s parquet.
-- cce-lter_picoplankton-bacteria in the CalCOFI release v2026.09.05
SELECT *
FROM __TBL:obs__
WHERE dataset_key = 'cce-lter_picoplankton-bacteria'
LIMIT 100;https://calcofi.io/db-query/?sql=--+cce-lter_picoplankton-bacteria+in+the+CalCOFI+release+v2026.09.05%0ASELECT+%2A%0AFROM+__TBL%3Aobs__%0AWHERE+dataset_key+%3D+%27cce-lter_picoplankton-bacteria%27%0ALIMIT+100%3B#sql-shell--shell
Code
The same release, from a script.
con <- calcofi4r::cc_get_db()
calcofi4r::cc_cite("cce-lter_picoplankton-bacteria")con = calcofi4py.cc_get_db()
calcofi4py.cite("cce-lter_picoplankton-bacteria")SELECT * FROM read_parquet('https://storage.googleapis.com/calcofi-db/ducklake-staging/tables/obs/dataset_key=cce-lter_picoplankton-bacteria/bfff0b257acfaa17b604403e/data_0.parquet') LIMIT 100;Get the data
Every way to have the bytes, by source. Nothing here asks you to register first.
Files from the release (Parquet)
The frozen objects this release is made of. A partition holds only this dataset’s rows; a shared table holds every dataset’s, so filter on dataset_key.
https://storage.googleapis.com/calcofi-db/ducklake-staging/tables/obs/dataset_key=cce-lter_picoplankton-bacteria/bfff0b257acfaa17b604403e/data_0.parquet
CF netCDF
One self-describing file, for a tool that reads netCDF.
how far this file is CF
Fully CF: each row is an independent observation with its own time and position, which is a CF point collection. Rows are at the OCCURRENCE grain (event x taxon x life stage x depth), not the event grain, so a sample with many taxa contributes many points.
https://storage.calcofi.io/calcofi-files-public/netcdf/cce-lter_picoplankton-bacteria/v2026.09.04/cce-lter_picoplankton-bacteria.nc
ERDDAP (erddap.calcofi.io)
One ERDDAP dataset per grain, each with its own data formats and its own pages. Subset in the browser or query it from a script.
- observations
- one row per measurement, joined to the event it was taken on
- sampling events
- one row per cast, tow or transect — when, where and how it was sampled
From the provider
The dataset as its provider publishes it, before CalCOFI ingested it.
https://oceaninformatics.ucsd.edu/datazoo/catalogs/ccelter/datasets/159
Metadata records
Records about the data, in the standards each portal harvests.
https://erddap.calcofi.io/erddap/metadata/iso19115/xml/cce-lter_picoplankton-bacteria_iso19115.xml
https://erddap.calcofi.io/erddap/metadata/fgdc/xml/cce-lter_picoplankton-bacteria_fgdc.xml
https://calcofi.io/datasets/cce-lter_picoplankton-bacteria.jsonld
https://calcofi.io/datasets/cce-lter_picoplankton-bacteria.json
https://calcofi.io/data.json
https://calcofi.io/stac/#/collections/cce-lter_picoplankton-bacteria/collection.json
Archives & portals
Where this dataset is registered outside calcofi.io, by the identifier each portal knows it as.
https://erddap.calcofi.io/erddap/info/cce-lter_picoplankton-bacteria/index.html
https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-cce&identifier=159
https://doi.org/10.5281/zenodo.22281994
https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-cce&identifier=159
Everything here is open — nothing on calcofi.io asks you to register first. If this dataset ends up in something you build or publish, register your use so it can be credited and linked back; to hear when a release changes it, stay informed. Questions: data@calcofi.io.
Cite
Landry, M. (2004-2023). Picoplankton and Bacteria Abundance (CalCOFI Cruise). CCE LTER.BibTeX
@misc{cce-lter_picoplankton-bacteria,
title = {Picoplankton and Bacteria Abundance (CalCOFI Cruise)},
howpublished = {Landry, M. (2004-2023). Picoplankton and Bacteria Abundance (CalCOFI Cruise). CCE LTER.},
year = {2004}
}…and the release it came from
CalCOFI (2026). CalCOFI Integrated Database, release v2026.09.05 [Data set]. Scripps Institution of Oceanography, NOAA Fisheries, and California Department of Fish and Wildlife. https://calcofi.io/db-schema/?v=v2026.09.05BibTeX
@misc{calcofi_release_v2026_09_05,
title = {CalCOFI Integrated Database, release v2026.09.05},
author = {CalCOFI},
year = {2026},
publisher = {Scripps Institution of Oceanography, NOAA Fisheries, and California Department of Fish and Wildlife},
url = {https://calcofi.io/db-schema/?v=v2026.09.05}
}