SCGC Workshop 2019

Fourth Microbial Single Cell Genomics Workshop

September 22-26, 2019
Spruce Point Inn, Boothbay Harbor, Maine

Application deadline has passed for the workshop. If you would like us to consider an exception, please contact Workshop Coordinator, Brian Thompson.

Organizing Committee:

Ramunas Stepanauskas (chair), Bigelow Laboratory for Ocean Sciences
Tanja Woyke, DOE Joint Genome Institue
Michael Wagner, University of Vienna
Beth Orcutt (vice-chair), Bigelow Laboratory for Ocean Sciences
David Emerson, Bigelow Laboratory for Ocean Sciences
Nicole Poulton, Bigelow Laboratory for Ocean Sciences

Workshop Coordinator:

Brian Thompson, Bigelow Laboratory for Ocean Sciences


Sunday, September 22

6:00-8:00 PMWelcome reception & registration

Monday, September 23. Focus: Single cell genomics in fundamental studies of microorganisms

8:15 AMWelcome and logistics: Ramunas Stepanauskas and Brian Thompson
8:30 AMKEYNOTE: Eugene Koonin (National Institutes of Health) Discovery of novel defense systems and viruses in genomic and metagenomic data
9:30 AMPatrick Wincker (Genoscope) TBD
10:10 AMCoffee Break
10:40 AMGerhard Herndl (University of Vienna) Microbes in the dark ocean: phylogenetic versus functional diversity
11:20 AMPaul Berube (Massachusetts Institute of Technology) Leveraging single cell genomics to explore cyanobacterial ecology and evolution
12:00 PMLunch break
1:30 PMPoster lightning-talks (1 minute per poster)
1:50 PMPoster session 1 (coffee available)
4:00 PMThomas Hackl (Massachusetts Institute of Technology) Integrative elements abundant in marine vesicles shape Prochlorococcus' genomic plasticity
4:20 PMMaria Pachiadaki (Woods Hole Oceanographic Institution) An ocean of single cell genomes
4:40 PMDanny Ionescu (Leibniz Institute of Freshwater Ecology and Inland Fisheries) Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum
5:00 PMFrancisco Latorre (Institute of Marine Sciences - CSIC) Single-cell genomics illuminates the eco-evolution of a cosmopolitan lineage of tiny ocean grazers
5:20 PMJulia McGonigle (Unviersity of Utah) Metabolic strategies of the dense biofilms inhabiting the lost city hydrothermal vent field
5:40 PMBeth Orcutt (Bigelow Laboratory for Ocean Sciences) TBD
6:00 PMDinner

Tuesday, September 24. Focus: Microbial single cell genomics in translational research

8:15 AMLogistics update (Brian Thompson)
8:30 AM KEYNOTE: Michael Wagner (University of Vienna) Linking chemical microscopy and single cell genomics
9:30 AMTanja Woyke (US DOE Joint Genome Institute) Hot spring single cell genomics
10:10 AMCoffee break
10:40 AMDiane Dickel (University of California Berkeley) High throughput single cell transcriptomics in plants and animals
11:20 AMKarsten Zengler (University of California San Diego) Unraveling microbial interactions at a single cell level
12:00 PMLunch break
1:30 PMKasturi Venkateswaran (NASA Jet Propulsion Laboratory) Utilization of state-of-the-art molecular techniques to measure microbial communities associated with the International Space Station
1:50 PMMorgan Sobol (Karlsruhe Institute of Technology) Targeted cell sorting combined with single cell genomics
2:10 PMFranziska Hemmerling (ETH Zurich) Identifying metabolic functions of uncultivated microbiota
2:30 PM Yi Zhang (JAMSTEC) Accurate high-throughput screening based on digital protein synthesis in a massively parallel femtoliter droplet array
2:50 PMBreakout group discussions with coffee: Unique research opportunities offered by microbial single cell genomics
4:00 PMBreakout group presentation
4:30 PMDeparture for Bigelow Laboratory
5:00 PMTours and BBQ at Bigelow Laboratory, celebrating SCGC's 10th anniversary
8:00 PMReturn to Spruce Point Inn

Wednesday, September 25. Focus: New technologies for studies of individual cells

8:15 AMLogistics update (Brian Thompson)
8:30 AMKEYNOTE: Victoria Orphan (Caltech) Activity-based cell sorting in deep sea sediments: genomic insights into methane-oxidizing syntrophic consortia
9:30 AMA. Murat Eren (University of Chicago) TBD
10:10 AMCoffee break
10:40 AMAaron Wright (Pacific Northwest National Laboratory) Function-dependent profiling and sorting of microbiomes
11:20 AMRamunas Stepanauskas (Bigelow Laboratory for Ocean Sciences) From genome to phenomes of microbial individuals
12:00 PMLunch break
1:30 PMPoster lightning-talks (1 minute per poster)
1:50 PMPoster session 2 (coffee available)
4:00 PMMircea Podar (Oak Ridge National Laboratory) Targeted isolation and cultivation of microbial "dark matter" through reverse genomics
4:20 PMBen Twining (Bigelow Laboratory for Ocean Sciences) Connecting function to form: studying ocean biogeochemistry through single-cell element analysis
4:40 PMChuan Ku (Institute of Plan and Microbial Biology) Single-cell RNA-seq for microbial eukaryotes: insights into infection of a cosmopolitan alga by its large DNA virus
5:00 PMFlora Vincent (Weizmann Institute of Science) Revealing heterogeneous dynamics of active host-virus infection as a function of viral pressures using single cell single molecule RNA FISH in controlled and natural environments
5:20 PMOpen discussions about new technologies
5:30 PMClosing remarks

Thursday, September 26

8:00 AMInformal discussions and networking on a trip to Monhegan Island, Maine
5:00 PM Arrival back at Spruce Point Inn

Workshop goals are to stimulate progress in single cell genomics (SCG) through the exchange of breakthroughs in research applications and method development, with a focus on microorganisms and the prediction of cell’s phenome. Although invisible to human eyes, unicellular microorganisms are the oldest, most abundant and diverse organisms on Earth. The vast majority of microorganisms are the uncultured, making them inaccessible to many classical microbiology methods. Uncultured microorganisms shape many functions of the biosphere, including the productivity of the oceans, the fertility of soils, the health of plants and animals, including humans, and the global cycles of carbon, nitrogen, and other elements. This “microbial uncultured majority” also harbors an enormous reservoir of the genetic resources. When combined with the current breakthroughs in synthetic biology, we anticipate that microbial SCG will be increasingly important in the discovery of novel enzymes, small molecules, gene editing systems and other applications for bioenergy, biotech and pharmaceutical industries. During this four-day workshop, we aim to create an opportunity for effective, creative interactions among principal investigators, postdocs and students who utilize microbial SCG in research and/or develop SCG technology, building on the success of our prior SCG workshops that were held in 2007, 2010 and 2015.

The 2015 workshop had 72 participants, including 16 students, 13 postdocs, and 32 principal investigators and 11 other professionals from 15 countries. Throughout the workshop, discussions were encouraged and were open, frank, and diverse. After the workshop, all participants were requested to fill out workshop evaluation forms. The obtained feedback was overwhelmingly positive; e.g., to the question whether the workshop met their expectations, 82% and 18% answered “completely agree” and “agree”, respectively. Several attendees expressed their desire for microbial single cell genomics workshops to be held more frequently. We anticipate an even greater interest in the workshop of 2019, given the rapid advances in technology and the growth of SCG applications in a broad spectrum of studies that address questions in biogeochemistry, microbial ecology, evolution, and biotechnology.

Available bus transportation

Due to the fact that there is no regular public transportation between Portland and the workshop venue, we have arranged for bussing on specific dates.

Bus transportation from Portland to the workshop venue Sunday, September 22
3:00-3:30 PM = pickup at airport (PWM)
3:45-4:00 PM = pickup at bus terminal (Portland Transportation Center)
7:30-8:00 PM = pickup at airport (PWM)
8:15-8:30 PM = pickup at bus terminal (Portland Transportation Center)

Bus transportation from the workshop venue to Portland Wednesday (PM), September 25
Bus departs Spruce Point Inn at 6:00 pm for arrival at Portland International Jetport (PWM) and bus station (Portland Transportation Center) between 7:30 pm and 8:30 pm.

Bus transportation from the workshop venue to Portland Thursday (PM), September 26
Bus departs Spruce Point Inn at 6:00 pm for arrival at Portland International Jetport (PWM) and bus station (Portland Transportation Center) between 7:30 pm and 8:30 pm.

Bus transportation from the workshop venue to Portland Friday (AM), September 27
Bus departs Spruce Point Inn at 8:30 am for arrival at Portland International Jetport (PWM) and bus station (Portland Transportation Center) between 10:00 am and 11:00 am.