2017 Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics (BITMaB) Workshop

RCN EukHits kicked off 2017 with a successful workshop focusing on the intersection of morphological taxonomy and high-throughput sequencing. The first annual Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics (BITMaB) Workshop was held January 9-13, 2017 at the Harte Research Institute for Gulf of Mexico Studies at Texas A&M University in Corpus Christi, Texas. We had ~50 participants in attendance, representing a range of career stages (undergraduates to Tenured Professors) and taxonomic expertise spanning a wide range of microbial eukaryote groups (nematodes, polychaetes, gastrotrichs, flatworms, molluscs, and other “minor” phyla).

 

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Workshop Background: Morphological identification of benthic meiofauna and macrofauna samples is labor intensive, time consuming, and costly.  A more efficient method, using DNA markers from metagenomic sequencing of sediment samples to characterize benthic communities, is being developed. For this purpose, a reference library for whole genomes of widely distributed infauna species of the Gulf of Mexico is currently being populated.  While still in its infancy, we are anticipating that this new methodology will become a standard procedure for ecological surveys and environmental monitoring procedures.

Workshop Purpose: The BITMaB workshop is was designed to train graduate students and researchers in the full spectrum involved in this new cutting edge methodology, including sample preparation, taxonomy of common benthic meiofauna and macrofauna taxa of the Gulf of Mexico, metagenomics, and bioinformatics.

There are two objectives of the ongoing BITMaB workshops. First, we intend to produce meio-and macrofaunal specimens from which we will generate draft genomes in support of the development of the eukaryotic genomes reference databases.  We strive to include as many unique families/phyla represented in the GoM as possible.  A complication for many groups is that fresh material will be required to find and identify individual specimens.  As such this workshop focused on samples collected each morning during the workshop from relatively shallow sediments. This aspect of this first workshop was led by taxonomic experts and provided an opportunity for training students, at all levels.  Workshop participants gained valuable experience in morphological identifications of diverse eukaryotic groups.  

Taxonomic participants included:

  • Alberto De Jesus Naverrete – Nematoda
  • Rick Hochberg (Lowell, MA) — Gastrotricha, Rotifera
  • Julian Smith III (Winthrop, NC) – Platyhelminthes
  • Martin Sørensen (Denmark) – Kinorhyncha, Tardigrada, Gnathostomulida, Loricifera
  • Anja Schulz (TAMU-Galveston) – Polychaeta, Sipuncula
  • Michael Reuscher (TAMUCC) – Polychaeta
  • Jon Norenburg (SI) – Nemertea, soft-bodied mollusks
  • Melissa Rohal (TAMUCC) – Harpacticoida
  • Francesca Leasi (SI, UNH) – Environmental samples, general taxonomy of meiofauna

The second objective of the workshop was to provide training in core bioinformatics analysis.  These skills are critical to the effective use of genomic data for analyzing community structure and function.  The bioinformatics workshop took place every morning during the week.  Students emerged with core skills in UNIX (BASH), simple scripting tools and analyzing metagenomics data using open source bioinformatics programs, such as PhyloSift, iPython workflows, and data visualization software.  The bioinformatics workshop was be led by the University of New Hampshire (RCN PI Kelley Thomas) and the University of California, Riverside (RCN PI Holly Bik).

We will be running a second BITMaB workshop in January 2018 – stay tuned for further announcements and a call to participate!

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