2nd Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics (BITMaB-2) Workshop

2nd Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics (BITMaB-2) Workshop

January 15-19, 2018

Texas A&M University-Corpus Christi
Harte Research Institute for Gulf of Mexico Studies
6300 Ocean Drive, Corpus Christi, Texas 78412 USA

All those interested in attending MUST submit the following workshop registration form: https://goo.gl/forms/RL5P6EAOzfQG16kq2 (EXTENDED application deadline November 20, 2017)

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.

Purpose: The BITMaB-2 workshop is 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 is no registration fee for BITMaB-2.

Objectives: There are two objectives of this workshop. 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 will focus on samples collected each morning during the workshop from relatively shallow sediments. This aspect of the workshop will be led by taxonomic experts and provide an opportunity for training students, at all levels. The anticipated outcome for this activity is to provide valuable experiences for many students and to produce as many potential reference samples competent for genome sequencing analysis as possible during the week. The taxonomy experience will take place in the facilities at the Harte Research Institute.

Confirmed taxonomic participants:

  • Maickel Armenteros (University of Havana, Cuba) – Nematoda
  • Noe Barrera (Texas A&M University-Corpus Christi) – Mollusca
  • Richard Heard (University of Southern Mississippi) – Isopoda, Amphipoda, Tanaidacea
  • Larry Hyde (Texas A&M University-Corpus Christi) – Polychaeta
    Rick Kalke (Texas A&M University-Corpus Christi) – Local macrofauna
  • Francesca Leasi (University of New Hampshire) – Meiofauna from environmental samples
  • Wonchoel Lee (Hanyang University, South Korea) – Copepoda
  • Fabio Moretzsohn (Texas A&M University-Corpus Christi) – Mollusca
  • Tiago Pereira (University of California Riverside) – Nematoda
  • Alessandro Prantoni (Federal University of Paraná) – Oligochaeta
  • Michael Reuscher (Texas A&M University-Corpus Christi) – Polychaeta
  • Adelaide Rhodes (University of Vermont) – Copepoda, Tanaidacea
  • Melissa Rohal (Texas A&M University-Corpus Christi) – Harpacticoida
  • Martin Sørensen (Natural History Museum of Denmark) – Kinorhyncha, Tardigrada, Gnathostomulida, Loricifera

The second objective of the workshop is 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 will take place every morning during the week. Students attending the workshop will emerge 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. This aspect of the proposal will be led by the UNH and UCR Genomics and Bioinformatics groups. The bioinformatics workshop will take place in the Harte auditorium. The bioinformatics portion will be led by Holly Bik, University of California-Riverside.

Outcomes: Participating students will (1) learn how to properly prepare benthic samples for morphological identification of invertebrates and DNA sequencing alike, (2) acquire taxonomic expertise about common invertebrate taxa of the Gulf of Mexico, (3) gain deeper understanding on the metagenomic sequencing approach to characterize the taxonomic composition of benthic samples, and (4) master the use of sophisticated bioinformatics tools needed for the analyses of genomic and metagenomic datasets.

Application and travel support: A limited number of BITMaB-2 travel stipends (covering airfare, accommodation, and subsistence) are available for workshop applicants – both US and international applicants are eligible to apply. Travel support will be provided through a combination of funding from a Gulf of Mexico Research Initiative (GOMRI) grant and National Science Foundation, Research Coordination Network (NSF-RCN) EukHiTS grant to Kelly Thomas and Holly Bik.

To apply for a travel stipend, please answer “yes” to the the relevant question on the workshop application form (see Google Form Link at top of this document).

Graduate and undergraduate students should also send a letter of support from their supervisory professor. The extended deadline for application is Monday, November 20, 2017. For any further questions, please email Michael Reuscher at michael.reuscher@tamucc.edu

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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.

 

THE 5-th DNA METABARCODING SPRING SCHOOL @ BIAŁOWIEŻA (POLAND)

DNA metabarcoding is a rapidly evolving method for assessing biodiversity from environmental DNA. It has a wide range of applications including biodiversity monitoring, animal diet assessment, or reconstruction of paleo communities among many others. This approach integrates several scientific areas and requires a broad range of skills beyond the classical ecological knowledge. It relies on molecular techniques such as PCR and next generation sequencing (NGS) and requires competence in bioinformatics and biostatistics to analyze sequencing data.

The DNA Metabarcoding Spring School is now in its 5-th edition and this year it is co-organized by the metabarcoding.org team and the Mammal Research Institute, Polish Academy of Sciences in Białowieża, Poland. The DNA Metabarcoding Spring School will be held 1 – 5 June 2015. Participants can register for the school (24 places) by sending an email to the following address : bialowieza2015@metabarcoding.org

The email must contain a brief curriculum vitae and a letter of motivation indicating how your research relates to DNA metabarcoding and what you are hoping to gain from the school. As part of the course program, each participant is required to give a 5 min-talk on his/her research and how it relates to DNA metabarcoding.

Registration deadline is 15 April 2015. There is no registration fee for the workshop. Participants will have to pay for accommodation, meals and travel. The cost for accommodation and meals for 6 days is estimated @ 1500 PLN ( 360€).

More detailed information, including tentative schedule, activities, and speakers can be found @ http://metabarcoding.org/spip.php?article70

Upcoming Ecometagenomics Symposium at the 2014 Joint British/French Ecological Society Meeting

We’ve just finalized details for an upcoming RCN-sponsored symposium at the Joint 2014 Annual Meeting of the British Ecological Society and Société Française d’Ecologie, to be held December 9-12, 2014 at the Grand Palais in Lille, France. Early bird registration is open until October 13th, so don’t delay if you’re interested in coming along!

Symposium Title: Accelerating ecology and biodiversity research via ecometagenomics: species, communities and environmental DNA.

Our confirmed list of speakers is as follows:

  • Pierre Taberlet, Centre National de la Recherche Scientifique Laboratoire d’Ecologie Alpine Grenoble – “Introduction to DNA metabarcoding” (Keynote)
  • Kristy Deiner, Eawag: Swiss Federal Institute of Aquatic Science and Technology – “Biomonitoring macroinvertebrates with environmental DNA”
  • Serita Frey, University of New Hampshire – “Fungal Biodiversity: Sustaining the Wood-Wide Web in Temperate Forests”
  • John Colbourne, University of Birmingham UK – “Genomes as Indicators of Environmental Health”
  • Dorota Porazinska, University of Colorado Boulder – “Highly endemic diversity patterns of soil microscopic taxa”

Symposium Description:  High-throughput sequencing technologies now offer tremendous opportunities to make major inroads into our understanding of global biodiversity, macroecology, species detection/biomonitoring and multi-level trophic interactions. For microbial eukaryotic taxa, we can now conduct en mass biodiversity assessment using taxonomic gene markers at a fraction of the time and cost required for traditional (morphological) approaches. Complimented by metagenomics, metatranscriptomics, metabarcoding of larger organismal communities and the analysis of “free” environmental DNA (eDNA), the possibilities of enhancing current approaches to biodiversity are vast. In addition, as databases of genes with functional descriptions expand and links between genotype and phenotype extend, metagenomic approaches become useful for linking functional diversity and 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. In order to make the most of emerging high-throughput sequencing approaches, we must draw on expertise from diverse disciplines, including microbial, molecular and contemporary ecology. The goal of this session is to catalyze cross-disciplinary discussions between the ecology and environmental sequencing communities and showcase the opportunities that currently exist for 21st Century ecologists. 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-based studies. This session would stimulate critical discussion related to the 2014 meeting theme of “Biodiversity and Ecosystem Services,” with interdisciplinary links to other international and EU-focused topics (Marine, Freshwater, and Agro-ecology). Since community-based molecular genetic analysis  represents an emerging ecological discipline, it is important to enhance linkages between the environmental DNA community and those focusing on contemporary ecological challenges, to facilitate high-throughput ecological research that will be relevant at the European scale.

This BES session proposal is timely: The understanding of patterns and mechanisms of biodiversity is among the central goals of ecology, yet patterns of the diversity of microscopic organisms continues to remain greatly uncharacterized and unexplored. Spatial patterns of species diversity are important because they generate knowledge for setting priorities for conservation, monitoring, and restoration programs that are strongly advocated in the European Union. Given that microscopic taxa are major components of detrital foodwebs and play key roles as decomposers, predators and parasites, the application of high-throughput sequencing is critical for expediting our understanding of species’ diversity and functional attributes.