The Baselines Initiative is a grass-roots effort to bring together 16S rRNA datasets that will be useful for assessing future change. This means that they must either come from multi-year sampling efforts at the same location, such as the Bermuda Atlantic Time-series Study in the North Atlantic (Western Sargasso Sea), or repeat sampling at a high spatial resolution (such as data sets from the Bay of Bengal). Three types of data are currently available, the Baselines Foundational Set, which holds near full-length Sanger 16S rRNA gene sequences, Baselines 16S V1-V2 Illumina-amplicons and Baselines 16S V1-V2 454-amplicons. If you would like us to add pointers to a dataset that meets these goals please contact firstname.lastname@example.org. We can also host pointers to 18S rRNA datasets. Look for release 1 on 15 October 2016.
What are picophytoplankton?
This is a diverse group of photosynthetic microbes which is composed of multiple different taxa within the eukaryotic ToL. They are grouped purely on the basis of cell size – pico being used to refer to cells less than 2 microns in diameter. Evolutionarily taxa composing this size fraction can be very different. Amongst the more commonly found marine taxa are genera within the Prasinophytes (in the eukaryotic Supergroup Archaeplastida) and the Prymnesiophytes (in the eukaryotic Supergroup Chromalveolata) as well as organisms such as Pelagomonas, a Stramenopile (also Chromalveolata). There are several excellent reviews on these organisms – for a comprehensive review from our lab please see e.g. Worden & Not in Microbial Ecology of the Oceans (ed. Kirchman, Wiley 2008).
Cultures are easily available for several lineages and genomes are available for several prasinophytes that can be purchased from a number of different culture collections.
Genomic resources for picophytoplankton
Micromonas RCC299 genome browser at JGI
Micromonas CCMP1545 genome browse at JGI
For a more detailed overview of these and other picophytoplankton genome projects go here
Updated chloroplast genome assembly and gene models for Micromonas commoda associated with Cuvelier et al. in review
Micromonas commoda CP genome assembly
Micromonas commoda CP gene model coordinates
Micromonas commoda CP protein sequences
Micromonas commoda CP gene sequences
Proteomic resources for picophytoplankton
Micromonas pusilla CCMP1545 Genomic Database for Proteomics LC-MS/MS Analysis (data files associated with Waltman et al. 2016)
Micromonas commoda RCC299 Genomic Database for Proteomics LC-MS/MS Analysis (data files associated with van Baren et al. 2016)
Getting started with picophytoplankton
(especially prasinophytes in the order Mamiellales)
Order strains (in the U.S.) from the Provasoli-Guillard National Center for Culture of Marine Phytoplankton
- Micromonas RCC299, the strain sequenced for the genome project as rendered axenic and deposited by Worden lab (CCMP2709)
- Micromonas pusilla CCMP1545, the strain sequenced for the genome project (CCMP1545)
- Many other Mamiellales (Micromonas, Ostreococcous, Bathycoccus) as well as Pelagophytes and other taxa are available at the CCMP
- The Roscoff Culture Collection also has a good selection of picophytoplankton cultures
Prepare culture media in artificial seawater (appropriate for Micromonas RCC299 and some other strains) using this protocol
View general culturing information and growth curves here. View fluorescent and LED light spectra here.
Extract from cultures – with minimized shearing (i.e. appropriate for large insert libraries, or controlled shearing) using this protocol
Extract from large scale marine metagenomic samples – with minimized shearing using this protocol
Extract for environmental qPCR/single gene studies using a modification of the Qiagen DNeasy kit protocol
Internal Lab BLAST Server and Genome Browser
To blast internal datasets (password needed) go here. For descriptions of the sequences, download this spreadsheet.
To blast publicly available relevant predicted proteomesI go here. For descriptions of the sequences, download this spreadsheet.
Micromonas Genome Browser