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.

 

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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.