Resources

Baselines

The Baselines Initiative brings 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 cjchoi@mbari.org. We can also host pointers to 18S rRNA datasets. Note that GenBank session numbers will not be active until the end of October 2016.

Baselines Foundational Set: Download the FASTA file and corresponding accession table for the Baselines Foundational Set. This contains 6,177 near-full length 16S rRNA gene sequences that have also been deposited at GenBank under the accessions KX932494 to KX938325.

Baselines Release 1 (R1) 16S Illumina Amplicons: Download the zipped quality controlled amplicon files for Baselines Release 1 16S amplicon data (paired-end Illumina V1-V2). These data are also available at BioProject PRJNA345162, PRJNA345164, and PRJNA345177.

Baselines Release 1 (R1) 16S 454 Amplicons: Eastern North Pacific 454 data is available at BioProject PRJNA258669 and Sargasso Sea BATS 454 data is available at http://data.imicrobe.us/project/view/101.

Metadata for all Baselines R1 samples including Baselines Foundational Set: Download the excel sheet containing available metadata for these samples and numbers of plastid and cyanobacterial sequences based on phyloassigner analysis.

Bacterial-focused V1-V2 16S analysis tool: Download the phyloassigner package and associated 16S rRNA gene alignment plus tree file for the pipeline used in Vergin et al. ISME J 2013 Vol 7:1322–1332 also used in preliminary steps of Sudek et al. Environmental Microbiology 2015 Vol 17:3692-3707 and Choi, Bachy et al. submitted.

Plastid-focused V1-V2 16S analysis tool: Download the plastid-focused phyloassigner package containing the 16S rRNA gene alignment and treefile used to analyze Baselines Release 1 amplicon data for Choi, Bachy et al. submitted.

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.

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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