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Harvard Forest Symposium Abstract 2018

  • Title: Seeing the Invisible: Application of long-read sequencing technology for identifying and assembling genomes from Harvard Forest soil organisms
  • Primary Author: Jacob Barnett (University of Massachusetts - Amherst )
  • Additional Authors: Jeffrey Blanchard (University of Massachusetts - Amherst )
  • Abstract:

    Soil organisms are vital to the functioning of a forest ecosystem, yet a basic picture of the invisible organisms that populate the soil remains unclear. We have started to sharpen the focus of that picture by applying Pacific Bioscience (PacBio) long-read sequencing technology to soil biota.

    Identifying microbes and their potential ecological roles through a “metagenomic” approach requires assembling many short pieces of DNA together into longer, biologically meaningful “contigs” - much like arranging a bunch of disconnected sentences into a novel. Through the use of PacBio technology, we have increased the length of each sequence piece of DNA, or read, by an order of magnitude. We now have reads that are thousands, rather than hundreds, of nucleotides long - expanding our ability to put together biologically meaningful “novels.”

    Long-read sequencing has also improved our “marker-based” approach to identifying bacteria, using the 16S ribosomal gene. Previous approaches were only able to sequence a short region of this gene, but with PacBio we have been able to sequence the entire 1500 nucleotide gene. This improves our ability to identify organisms down to the species level - a sharper picture that gives us more insight into the ecological role of these microbes.

    Soil communities are teeming with immense biological diversity that current methods can only partially capture. Our development of new long-read sequencing approaches will improve our ability to “see” the inhabitants of these invisible yet essential ecosystems. With an enhanced sense of this biodiversity, we will gain insight into how soil organisms have responded to long-term warming at the Harvard Forest plots.

  • Research Category: Biodiversity Studies; Soil Carbon and Nitrogen Dynamics