Table of Contents

• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Parameters
• Deployments
• Project Information
• Funding

Accession numbers with links to GenBank sequences of labyrinthulomycete 18S rRNA genes from sediment and water column samples collected around Long Island, NY.

Collado Mercado et al, 2010 ABSTRACT: Labyrinthulomycetes (Labyrinthulea) are ubiquitous marine osmoheterotrophic protists that appear to be important in decomposition of both allochthonous and autochthonous organic matter. We used a cultivation-independent method based on the labyrinthulomycete-specific primer LABY-Y to PCR amplify, clone, and sequence 68 nearly full-length 18S rDNA amplicons from 4 sediment and 3 seawater samples collected in estuarine habitats around Long Island, New York, USA. Phylogenetic analyses revealed that all 68 amplicons belonged to the Labyrinthulea. Only 15 of the 68 amplicons belonged to the thraustochytrid phylogenetic group (Thraustochytriidae). None of these 15 were similar to cultivated strains, and 11 formed a novel group. The remaining 53 amplicons belonged either to the labyrinthulid phylogenetic group (Labyrinthulidae) or to other families of Labyrinthulea that have not yet been described. Of these amplicons, 37 were closely related to previously cultivated Aplanochytrium spp. and Oblongichytrium spp. Members of these 2 genera were also cultivated from 1 of the sediment samples. The 16 other amplicons were not closely related to cultivated strains, and 15 belonged to 5 groups of apparently novel labyrinthulomycetes. Most of the novel groups of amplicons also contained environmental sequences from surveys of protist diversity using universal 18S rDNA primers. Because the primer LABY-Y is biased against several groups of labyrinthulomycetes, particularly among the thraustochytrids, these results may underestimate the undiscovered diversity of labyrinthulomycetes.

Approximate sampling positions (latitude and longitude) were determined from navigational maps.

See:
Collado Mercado, E., J. C. Radway, and J. L. Collier. 2010. Novel uncultivated labyrinthulomycetes revealed by 18S rDNA sequences from seawater and sediment samples. Aquatic Microbial Ecology 58: 215-228. [pdf]

Sequence accession numbers deposited in GenBank are indicated in the data file via hyperlinks.

The following description is an excerpt from the NSF award abstract:
The Labyrinthulomycetes (labyrinthulids, thraustochytrids, and aplanochytrids) are ubiquitous, diverse, and abundant marine protists. They are thought to live mainly as saprobes, obtaining their nutrition from non-living particulate organic matter (POM) of algal, higher plant, or animal origin. Thus, while Labyrinthulomycetes are not "fungi" in a taxonomic sense, they may function as "fungi" in an ecological sense, playing similar roles in the decomposition of POM. Because of their high content of essential polyunsaturated fatty acids (PUFAs), Labyrinthulomycetes may also play a role in the nutrition of marine metazoans by improving the food quality of detritus ("trophic upgrading"). However, evidence of their role decomposing marine POM is somewhat circumstantial, and thus does not support quantitative conclusions about their function or importance. The long-term goal of this project is to gather the evidence about Labyrinthulomycete abundance and diversity that will be needed to better understand their role in marine ecosystems.

This project aims to develop molecular genetic methods based on the polymerase chain reaction (PCR) to investigate the diversity and abundance of Labyrinthulomycetes. The existing Labyrinthulomycete-specific PCR primers for 18S ribosomal DNA (rDNA) cannot recognize a potentially important component of Labyrinthulomycete diversity (some groups of thraustochytrids). The investigators will develop new 18S rDNA primers that will allow better estimation of the diversity of the Labyrinthulomycetes, and then use these primers to gather 18S rDNA sequence data from a variety of habitats. The resulting sequence data will diversity of these organisms to be quantified in the field relative to the representatives currently in culture. These primers (or others designed in the course of the project) will be used to develop quantitative real-time PCR assays to determine the abundance of Labyrinthulomycetes (and subgroups of Labyrinthulomycetes) in environmental samples. Methods will also be developed to cultivate novel Labyrinthulomycetes detected in local sediments during the preliminary sequencing efforts.