Friday, April 17, 2015

Niche partitioning in diatoms

Life on Earth is diverse and abundant, and there's no need to look any farther than the ocean's surface for proof. There are over 200,000 species of phytoplankton alone, and all of those species of microscopic marine plants that form the base of the marine food web need the same basic resources to grow--light and nutrients. This diversity of phytoplankton has puzzled researchers for a long time. The many different species coexist in this relatively stable environment, competing for the same resources but no species seems to out-compete others.

A study by a team of researchers from the Woods Hole Oceanographic Institution (WHOI), University of Rhode Island (URI), and Columbia University, reveals how diatom species - one of the several major types of marine phytoplankton - use resources in different ways to coexist in the same community. The colleagues used a novel approach combining new molecular and analytic tools to investigate how similar species utilize resources differently - known as niche partitioning - in Narragansett Bay, R.I.  In conjunction with the sequencing analysis, the research team developed a new bioinformatic approach that uses data from nutrient amendment experiments to help interpret signals from the environment.

Here, we use quantitative metatranscriptome analyses to examine pathways of nitrogen (N) and phosphorus (P) metabolism in diatoms that co-occur regularly in an estuary on the east coast of the United States (Narragansett Bay).

Using these data the researchers e.g. observed two species of chain-forming diatoms--Skeletonema spp. and Thalassiosira rotula--coexisting in the same subset of water, but doing fundamentally different things with available nutrients, specifically nitrogen and phosphorus. Skeletonema is the more dominant species of the two and has specialized on inorganic nitrogen sources, like nitrate and nitrite. The less dominant species, Thalassiosira, is bringing in nitrogen from organic sources, such as amino acids.

We have long suspected that even closely related phytoplankton must have ways of distinguishing their needs from that of their neighbors, for example using different forms phosphorus or nitrogen, but this has been hard to track in the environment, as most approaches are not species-specific...Part of the challenge is that you would need to track species-specific patterns in resource utilization to compare one diatom to another.

The annotation of RNA sequences via "pattern matching" was facilitated by the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP), which has sequenced the genetic material of more than 300 marine species. In this study, a new database that is part of the MMETSP was leveraged to identify species-specific signals. In addition the team developed a way to normalize those signals to be able to compare quantitatively between species.


  1. Quote: "There are over 200,000 species of phytoplankton alone."

    I am interested to know where this number comes from

    There are currently >220,000 species for all marine organisms in WoRMS and 45,000 species incl, freshwater in AlgaeBase, incl. Pro- and Eukaryota.

    Nicolas Bailly
    FishBase, SeaLifeBase, Catalogue of Life, WoRMS

  2. The colleagues reference two publications for that number:
    Sournia A, Chrdtiennot-Dinet M-J, Ricard M (1991) Marine phytoplankton: How manyspecies in the world ocean? J Plankton Res 13(5):1093–1099.
    Tett P, Barton E (1995) Why are there about 5000 species of phytoplankton in the sea? J Plankton Res 17(8):1693–1704.

  3. Thanks Dirk.
    Well the publication of Alain is certainly outdated, although I must admit he knows the domain quite well with the 3 vols of his atlas of marine phytoplankton.
    I don't know the other paper.
    Will check the two.

  4. Just checked the second: 5,000 species.
    Citations and abstract of the second: 474-504 genera and 3444–4375 species.

    Did the author mixed up WoRMS with Phytoplankton?


  5. Just exchanged with authors. There was a mistake. The estimation of 200,000 is about diatoms, both benthic and planktonic, and the reference is:
    Mann, D.G. & Droop, S.J.M. 1996. 3. Biodiversity, biogeography and conservation of diatoms. In: Biogeography of Freshwater Algae, J. Kristiansen (ed.), Hydrobiologia 336: 19-32, Kluwer Academic Publishers.


  6. Thanks a lot for the clarification, Nicolas.