2Nd Benthic Invertebrate Taxonomy, Metagenomics and Bioinformatics (Bitmab-2) Workshop 2018
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2nd Benthic Invertebrate Taxonomy, Metagenomics and Bioinformatics (BITMaB-2) Workshop 2018 Final Report for the Gulf of Mexico Alliance, Gulf of Mexico Research Initiative (GoMRI) project 16-052 Hosted by the Harte Research Institute for Gulf of Mexico Studies Texas A&M University - Corpus Christi Corpus Christi, Texas January 15-19, 2018 Acknowledgements The BITMaB-2 workshop was part of the Gulf of Mexico Research Initiative (GoMRI) research project “Genomic Responses to the Deepwater Horizon Event and Development of High- Throughput Biological Assays for Oil Spills”. The workshop was organized by W. Kelley Thomas (Principal Investigator, University of New Hampshire), Holly M. Bik (co-Principal Investigator, University of California, Riverside), Paul A. Montagna (co-Principal Investigator, Texas A&M University – Corpus Christi), Francesca Leasi (University of New Hampshire), Krystalynne Morris (University of New Hampshire), and Michael G. Reuscher (Texas A&M University - Corpus Christi). Paul A. Montagna and Francesca Leasi reviewed this report and provided valuable feedback. Data from this project are publicly available at the Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), doi: R5.x272.000:0001 and R5.x272.000:0002. i Cover photo credit The parasitic isopod Probopyrus pandalicola Packard, 1879 with attached dwarf male, collected during the workshop. Photo taken by Michael G. Reuscher. Suggested Citation Reuscher, M.G. 2018. 2nd Benthic Invertebrate Taxonomy, Metagenomics and Bioinformatics (BITMaB-2) Workshop 2018. Final Report for the Gulf of Mexico Alliance, Gulf of Mexico Research Initiative (GoMRI) project 16-052. Harte Research Institute for Gulf of Mexico Studies, Corpus Christi, TX, 23 pp. Contact Michael G. Reuscher Harte Research Institute for Gulf of Mexico Studies Texas A&M University - Corpus Christi 6300 Ocean Drive, Unit 5869 Corpus Christi, Texas 78412-5869 United States of America Office: (361) 825-2037 Email: [email protected] ii Table of Contents Background ..................................................................................................................................... 1 Sampling ......................................................................................................................................... 4 Lab Work ........................................................................................................................................ 8 Taxonomic Seminars .................................................................................................................... 12 Bioinformatics Seminars ............................................................................................................... 13 Outcome and Outlook ................................................................................................................... 15 iii Background The second Benthic Invertebrate Taxonomy, Metagenomics, and Bioinformatics (BITMaB-2) workshop was hosted at the Harte Research Institute for Gulf of Mexico Studies on the campus of Texas A&M University – Corpus Christi between January 15 and 19, 2018. The workshop was part of the Gulf of Mexico Research Initiative (GoMRI) research project “Genomic Responses to the Deepwater Horizon Event and Development of High-Throughput Biological Assays for Oil Spills”. The scientific goal of the project is to develop methodologies and infrastructure for the use of genetic markers to characterize the taxonomic composition of benthic communities via metagenomics. The benefit of this approach is that benthic assessment studies and monitoring efforts will produce quicker results at lower costs than the labor-intensive morphological identification of individual benthic specimens. This is particularly important when immediate scientific results are required for informed decisions about environmental, legal, and/or financial issues following oil spills, as it has been the case in the aftermath of the Deepwater Horizon disaster. However, the lack of genetic sequences for many benthic meiofauna and macrofauna taxa is currently a major limitation of metagenomics techniques, which means that taxonomic resolution of metagenomics analyses are currently poor. Thus, one of the main goals of the workshop was to alleviate this problem by enhancing a reference library of genetic sequences from positively identified marine benthic organisms. For this purpose, nine national and international taxonomic specialists were invited to the workshop, in addition to the taxonomic specialists on the workshop organizing committee (Table 1). These taxonomists identified benthic meiofauna and macrofauna organisms from samples obtained during the workshop and previously collected ethanol preserved specimens to the lowest taxonomic level possible. All identified specimens were then preserved in either absolute ethanol or frozen in -80˚C for genetic sequencing at the Smithsonian Institution National Museum of Natural History. Eight of the nine invited taxonomic experts extended their visits to the Harte Research Institute the week prior to the workshop (January 8-12). During this week, they were able to focus on sample collection, identification, and preservation of benthic organisms for DNA sequencing. 1 Table 1. List of workshop participants. Organizing committee Workshop participants (continued) Name Institution Name Institution W. Kelley Thomas (PI) University of New Hampshire Will Ballentine Dauphin Island Sea Lab Holly M. Bik (Co-PI) University of California, Riverside Lauren Ballou Texas A&M University at Galveston Paul A. Montagna (Co-PI) Texas A&M University-Corpus Christi Titilope Bukunmi-Omidiran Texas Southern University Francesca Leasi University of New Hampshire Francesco Cicala CICESE Krystalynne Morris University of New Hampshire Brooke Denney Texas A&M University-Corpus Christi Michael G. Reuscher Texas A&M University-Corpus Christi Jennifer Dreyer Virginia Institute of Marine Science Invited Scientists Erin Easton University of Texas Rio Grande Valley Name Institution Hannah Ehrmann Texas A&M University-Corpus Christi Richard Heard University of Southern Mississippi Doug Faircloth University of Texas Rio Grande Valley Alberto de Jesús Navarrete ECOSUR-Chetumal Rachel Hale University of Southampton Wonchoel Lee Hanyang University Ashley Hamilton Texas A&M University-Corpus Christi Fabio Moretzsohn Texas A&M University-Corpus Christi Mary Colleen Hannon Texas A&M University at Galveston Tiago Pereira University of California, Riverside Amanda Heidt Moss Landing Marine Laboratories Alessandro Prantoni Federal University of Paraná Maria Herranz Matesanz University of British Columbia Adelaide Rhodes University of Vermont I-Shuo Huang Texas A&M University-Corpus Christi Melissa Rohal Texas A&M University-Corpus Christi Erin Kiskaddon Dauphin Island Sea Lab Martin V. Sørensen Natural History Museum of Denmark Jennifer Le Scripps Institution of Oceanography Bioinformatics team Jessica Lunt Smithsonian Marine Station 2 Name Institution Adam Martens Environment and Climate Change Canada Taruna Schuelke University of California, Riverside Michael McGee Louisiana State University Joseph Sevigny University of New Hampshire Marta Miatta Memorial University of Newfoundland Devin Thomas University of New Hampshire Andre Giovani Morales-Núñez University of Maryland Eastern Shore Field work and lab technicians Lilian A. Palomino Alvarez UNAM, UMDI-Sisal Name Institution Phillip Randsø Natural History Museum of Denmark Noe Barrera Texas A&M University-Corpus Christi Patrick Rayle Louisiana State University Ag Center Larry Hyde Texas A&M University-Corpus Christi Michelle Stephens Smithsonian Marine Station Rick Kalke Texas A&M University-Corpus Christi Diana Marlen Ugalde Garcia UNAM, UMDI-Sisal Elani Morgan Texas A&M University-Corpus Christi Katie Vaccaro-Garska University of West Florida Terry Palmer Texas A&M University-Corpus Christi Niels Van Steenkiste University of British Columbia Jamie Smith Texas A&M University-Corpus Christi Nichelle Van Tassel University of West Florida Workshop participants Rebecca Varney University of Alabama Name Institution Colleen Walsh Louisiana State University Ag Center Nestor Ardila ECOMAR Rachel Weisend Texas A&M University-Corpus Christi Amy Baco-Taylor Florida State University Tom Wilding Scottish Association for Marine Science This additional week was added to increase the workshop productivity towards the scientific goals of the project. The second major objective of the BITMaB-2 workshop was training students, staff researchers, and faculty in techniques pertinent to the methodology involved in the metagenomics analyses of benthic communities. The workshop offered insights into sample processing techniques, taxonomy and identification of marine meiofauna and macrofauna organisms, proper preservation and micrography techniques, background information on metagenomics and next-generation- sequencing, and bioinformatics tools used for DNA sequence analyses. Forty workshop participants from a pool of more than 100 national and international applicants attended. The participants consisted of two undergraduate students, 17 graduate students, five postdoctoral researchers, nine staff scientists, and three faculty. Four invitees did not attend. Overall, 60 scientists attended at the BITMaB workshop, including the aforementioned organizing committee, invited taxonomists and invited participants, as well as a team of bioinformatics specialists and a field work crew (Fig.