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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Wrap-up post – “Ecometagenomics” Symposium at BES/SFE meeting

Thanks to everyone who attended our Symposium at the Joint British/French Ecological Society Meeting last week in Lille, France –  “Accelerating ecology and biodiversity research via ecometagenomics: species, communities and environmental DNA”. A collection of Tweets from this session is now available here on Storify.

We had a great turnout for the meeting session, followed by a hugely successful wine & cheese social sponsored in conjunction with the BES Plants, Soils, and Ecosystems Special Interest Group. And of course we managed to find plenty of holiday cheer walking around the streets of Lille!

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Simon, Dorota, Holly and Serita (left to right), on their way to the wine & cheese social!

 

ESA 2014 – Workshop materials posted

Thanks to everyone for coming out to our workshop at the ESA 2014 annual meeting, entitled “Environmental sequencing approaches and computational tools for ecologists”. We had a great group of participants who helped facilitate some very productive discussions!

Our workshop materials have now been posted online:

  • QIIME demonstration and discussion (PDF slides – Dorota Porazinska and Zhenjiang Xu, University of Colorado, Boulder) Topics covered:
    • Demonstration with default vs. modified parameters in software workflows (covering the different options possible, and how to modify them for different datasets and questions)
    • Explanation of how files are generated, what the software outputs look like, and how users can make use of the different files
    • Discussion will include data visualization tools for data analysis and exploration

RCN EukHiTS 2014 Annual Meeting to be held in conjunction with ESA in Sacramento, CA

The RCN EukHiTS annual catalysis meeting venue has just been announced; this year’s event will be held in conjunction with the Ecological Society of America’s 2014 Annual Meeting to be held in Sacramento, California, August 10-15, 2014. The main events will consist of a hands-on workshop and a special session that includes talks and discussion (times and abstracts listed below).

Workshops #9884: “Environmental sequencing approaches and computational tools for ecologists”
Sunday, August 10, 2014
8:00 AM – 5:00 PM

Description: This workshop will bring together an interdisciplinary pool of researchers to discuss current approaches, challenges, and future directions for environmental sequencing studies (-omic studies of bacteria, archaea and microbial eukaryotes). The workshop program will introduce ecologists to common data types and scientific workflows currently employed for the analysis of high-throughput sequencing data (e.g. Illumina/454). Participants will be given overview presentations and hands-on demonstrations for a number of different approaches, including rRNA marker gene analysis, shotgun metagenomics, and metatranscriptomics. This workshop will introduce participants to computational biology tools and software pipelines which can be harnessed for DNA/RNA-based “ecometagenomic” studies. In addition, we aim to solicit feedback from workshop participants, fostering discussions on how to establish better links between traditional ecological research and new, high-throughput sequencing approaches.

Special Sessions #9883:”Ecometagenomics”
Monday, August 11, 2014
10:15 AM – 11:30 AM

Description: The goal of this session is to catalyze cross-disciplinary discussions between the ecology and environmental sequencing communities.  High-throughput sequencing technologies now offer tremendous opportunities to make major inroads into our understanding of global biodiversity and biogeographic patterns. However, in order to make the most of emerging high-throughput sequencing approaches, we must move towards a “systems ecology” mindset, drawing expertise from diverse disciplines. For microbial eukaryotic taxa in particular, we can now conduct en mass biodiversity assessment using traditional loci (rRNA genes) at a fraction of the time and cost required for traditional (morphological) approaches. In addition, as databases of genes with functional descriptions expand, metagenomic approaches become useful for elucidating ecosystem function. Despite this promise, current bottlenecks and roadblocks lie in the development of useful distributed tools, links between molecules and morphology/ecology, and common data standards to allow global comparisons across individual studies. This session will begin with an overview of environmental sequencing approaches, introducing participants to the methods, data types and current advantages and limitations of DNA/RNA-based studies. The session is intended to be highly interactive, including brief talks, moderated discussion points, and solicitation of questions and feedback from audience members. This session would stimulate critical discussion related to the 2014 meeting theme of “Its all ecology.” DNA/RNA-based studies represent an emerging ecological discipline, and as such, it is imperative that the growing community of microbial ecologists begins to build strong links to the traditional ecological research that forms the center point of the ESA meetings.

Another ESA session linked to RCN EukHiTS is oral session OOS10: Ecological Genomics as an Emerging Field: Opportunities for Non-model Organisms (organized by Melis Akman, UC Davis)