Upcoming RCN Events: BES 2017 and OSM 2018

We are excited to announce two upcoming RCN EukHiTS events taking place during international scientific conferences in 2017-2018.

A limited number of travel stipends will be available for participants to attend these events. Preference will be given attendees traveling from US institutions, due to NSF funding restrictions. Please complete this Google Form if you plan on attending either of these events and would like to apply for a travel stipend (e.g. if you will be submitting an abstract to the OSM 2018 session or attending the BES workshop and also presenting a talk/poster). Researchers of all career stages are encouraged to apply, in particular females and underrepresented minorities.

Lunchtime Workshop at the British Ecological Society 2017 Annual Meeting**

1:45PM-2:45Pm, Wednesday December 13, 2017
ICC Ghent, Belgium

**Full meeting registration and attendance is required for RCN travel support

Workshop Flyer: https://www.dropbox.com/s/ppppowjd1ie1trf/BES-eDNA-workshop-advert.pdf?dl=0

Who is there and how do we know? Navigating the Complexities of Taxonomy assignments during eDNA Metabarcoding Studies.

Moderators: Holly Bik (University of California, Riverside), Simon Creer (Bangor University, UK) & John Colbourne (University of Birmingham, UK)

In contrast to traditional ecological studies, high-throughput sequencing approaches (eDNA metabarcoding and other –Omics workflows) are commonly carried out without any direct link between morphological and molecular data. Thus, one of the most challenging aspects of eDNA studies is the process of matching unknown nucleotides with a known taxonomic assignment (family, genus, or species ID). This workshop will clarify the use of databases and taxonomy assignment steps in eDNA metabarcoding studies. What tools and resources can (and should) be used for particular environments and target organisms? If an appropriate tool/database does not exist, how do you go about constructing your own local resource? The first part of the workshop will offer a lecture-based introduction to eDNA workflows, with an emphasis on common marker genes (16S/18S rRNA, ITS, COI, matK, etc.) and the tools/databases available for preparing standardized files for downstream ecological analysis (OTU tables analyzed in QIIME, mothur, OBITools, etc.). Next, small topic-focused groups will convene in a breakout session, to exchange ideas surrounding the use of both traditional and non-traditional metabarcoding markers; participants will be encouraged to share tools/scripts in a centrally accessible Dropbox folder. The workshop will conclude with a final reporting session by breakout group leaders and a wrap-up discussion to identify opportunities for moving forward. Workshop outputs will be used to prepare a review paper or community resource article focused on eDNA marker genes and current challenges with taxonomy assignments, and all participants will be invited to contribute as co-authors.

2018 Ocean Sciences Meeting (February 11-16, 2018 in Portland, Oregon)

Marine Microbial Eukaryotes: Environmental ‘Omics and Molecular Ecology Approaches

Session Organizers: Holly Bik (University of California, Riverside), Sarah Hardy (University of Alaska, Fairbanks)

Microbial eukaryotes (organisms <1mm, such as phytoplankton, meiofauna, fungi, protists, and eggs/larval stages of larger species) are abundant and ubiquitous in both pelagic and benthic habitats, performing key functions such as nutrient cycling and sediment stability in marine ecosystems. Yet, their unexplored diversity represents one of the major challenges in biology and currently limits our capacity to understand, mitigate and remediate the consequences of environmental change. Environmental ‘Omics tools are being increasingly used to address major gaps in our knowledge of diverse microbial eukaryote taxa. The modern molecular toolkit includes environmental rRNA surveys, metagenomics, metatranscriptomics, and targeted genome sequencing, and such deep sequencing approaches are now being used to test biological hypotheses for many taxa across marine habitats. Participants will be called upon to highlight the promise and challenge of using molecular approaches across the Eukaryotic Tree of Life, focusing on applications in diverse disciplines such as benthic ecology, biological oceanography, and computer science. We aim to catalyze cross-disciplinary interactions, facilitating discussions on how the ocean sciences can adapt to continued, rapid advances in sequencing technologies and bioinformatics. This session will be sponsored by NSF RCN EukHiTS (https://eukhits.wordpress.com), providing travel awards for selected students and early-career participants with submitted abstracts.


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).


2017-01-09 16.40.45-1.jpg

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!

2017-01-12 07.39.10 (1).jpg