Resources

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

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

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.

Extracting DNA

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

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