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.

 

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

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

Methods in Ecological Genomics Analysis workshops (MEGA 2015)

Ecological genomics is the new and extremely powerful way to address old-standing ecological and evolutionary questions. We endeavor to teach the methods that we have developed specifically for working with non-model organisms to students with limited or no genomics or bioinformatics experience. Two back-to-back workshops will take place at the Mote Tropical Research Laboratory, using reef-building corals as subjects for specific research projects. The projects are designed to yield novel publishable results, and we encourage students to continue collaborating on these projects after the course has ended. Students making significant contributions to data analysis and manuscript preparation will be offered authorship (see previous publications stemming from our workshops at Mote).

Click on these links to see syllabi and costs (costs include accommodation but not board):

Instructor-in-chief: Mikhail V. Matz (google scholar page)

Applications now open for the summer 2015 “Bioinformatics & Biodiversity” Undergraduate Workshop

Following on from a highly successful event last year, we’re very excited to announce the second annual “Bioinformatics & Biodiversity” Undergraduate Workshop at the University of New Hampshire, scheduled for July 27-30, 2015 in Durham, NH. Click here to download a PDF flyer – we encourage you to post and share this opportunity!

2015_workshop_flyer

Microscopic eukaryotes (meiofauna e.g. nematode worms, copepods, protists, fungi, etc.) are some of the most abundant animals on Earth, but species within these groups are often overlooked by the general public and even many biologists. This NSF-sponsored workshop will explore the field of environmental DNA sequencing, including collection and analysis of data. Students will learn how high-throughput approaches (rRNA gene surveys, metagenomics) are being used to investigate the biodiversity of microbial eukaryotes and deepen our knowledge of ecosystem function. The workshop program will be a combination of lectures and practical exercises, where students will learn about traditional taxonomic approaches and also gain experience using the command line and bioinformatics tools to analyze environmental DNA datasets.

We welcome applications from undergraduates currently enrolled in any higher-educational institution in the USA.  All applicants are expected to have taken, at minimum, an introductory college-level course in Biology. Successful applicants will receive a stipend to cover all costs including travel.

To apply, e-mail the following materials to eukhits@gmail.com by Monday April 13, 2015:

  • Curriculum Vitae (including contact details for references)
  • Statement of interest (indicating biology courses taken and how attending the workshop would benefit your long-term career goals; maximum length 1 page)
  • Reference letters are recommended but not required

Frequently Asked Questions

Q. Can international/overseas students apply for this workshop? 

A.  No, unfortunately workshop application is restricted to students currently enrolled at US-based institutes (which includes international students attending US colleges). For future workshops we may extend the application process to students enrolled at overseas institutes (this will depend on the conditions of our funding). Thanks for your interest, and keep an eye on on the RCN website for future opportunities.

Q. For the CV (including references), exactly how many and what kind of references are preferred? 

A. One letter of recommendation can accompany the application (written by a professor or research supervisor) – this is optional, but may significantly increase the strength of your application. On your CV you can also list contact information for any additional professional references (up to three references); for example, you may want to list references relating to any relevant work experience or research projects.

 

NSF Dimensions of Biodiversity Funding Opportunity

[reposting an email from the American Society for Microbiology]

The National Science Foundation (NSF) has requested that ASM bring to the attention of interested members the following funding opportunity:

Dimensions of Biodiversity FY 2015
URL: http://www.nsf.gov/pubs/2015/nsf15533/nsf15533.htm 
Full Proposal Deadline: April 9, 2015 (due by 5 p.m. proposer’s local time)

Synopsis of Program:

Despite centuries of discovery, most of our planet’s biodiversity remains unknown. The scale of the unknown diversity on Earth is especially troubling given the rapid and permanent loss of biodiversity across the globe. The goal of the Dimensions of Biodiversity campaign is to transform, by 2020, how we describe and understand the scope and role of life on Earth.

This campaign promotes novel integrative approaches to fill the most substantial gaps in our understanding of the diversity of life on Earth. It takes a broad view of biodiversity, and focuses on the intersection of genetic, phylogenetic, and functional dimensions of biodiversity. Successful proposals must integrate these three dimensions to understand interactions and feedbacks among them. While this focus complements several core programs in BIO and GEO, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, in novel ways, to understand their synergistic roles in critical ecological and evolutionary processes.

Award Information:      

  • Anticipated Type of Award: Standard Grant or Continuing Grant
  • Estimated Number of Awards: 8 to 12
  • Anticipated Funding Amount: $16,000,000 to $22,000,000

More Information:  

Matthew D. Kane, BIO/DEB: (703) 292-7186, Dimensions@nsf.gov

Sincerely,
Ronald M. Atlas, Ph.D.
Chair, Public and Scientific Affairs Board