A very important paper for any interested in microbial ecology: importance of rare taxa

Got pointed to this paper by automated Google Scholar searches that I have for many of the authors of the paper: Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity in mBio by Ashley Shade, Stuart E. Jones, J. Gregory Caporaso, Jo Handelsman, Rob Knight, Noah Fierer, and Jack A. Gilbert.

In the paper (which is, thankfully, fully Open Access) the authors use new informatics methods to look at what they call (conditionally rare taxa [CRT]).  They report:

We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. This observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.

This is very interesting.  Having participated in a workshop that led to a report on “The Rare Biosphere” I think for many reasons we need much more work on rare microbes and whether and how they may be important.  Kudos to the authors for tackling this issue. (Note – the full text of the paper is available in PDF but the HTML version does not seem to be working right now).

4 thoughts on “A very important paper for any interested in microbial ecology: importance of rare taxa

  1. As long as we cannot identify the organisms we are dealing with, and many well-known microorganisms remain unsequenced or – worse- wrongly sequenced, we have to acknowledge that “the rare biosphere” can be largely composed of extracellular DNA, chimeras, etc, not real organisms. How can we assess the ecology of sequences? I know I am very critical, but one sequence does not always equals one organism

    1. Not 100% sure what you are saying here. But a few comments

      1. In our report on the Rare Biosphere we spent a lot of time discussion the compexities of determining if it is even real or an artifact of some kind.

      2. We concluded and I think rightly, that it is a very interesting topic and that it is worth pursuing in more detail and that DNA methods are one of the only ways to address it.

      3. I think the new paper is quite interesting, even if there are limitations.

  2. Just read the AAM’s “Rare Biosphere rapport”. It states clearly: “We need to know whether the rare biosphere is real not an artifact of the methods we use to analyze microbial communities” (Recommendations, pg. 27). I could not agree more.

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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.