March 2016 EcoFAB workshop: This one-day workshop brought together a group of thought leaders with diverse expertise (microbial genomics, systems biology, soil science, microbial ecology, and bioinformatics) and included scientists from multiple national labs, industry, and academia. The goal was set to define initial model microbial communities for construction in reproducible, highly controlled, and instrumented model soil habitats and to determine the types of integrated measurements and standards required to accurately predict and model microbiome activities.
Agenda
March 22, 2016
9:00am Trent Northen: Opening and Introductions
9:15am Karsten Zengler: Multi-dimensional Interactions Define Dynamics in Microbial Communities
9:45am Barbara Campbell: Microbial Community Structure and Function in Atlantic Coastal Waters
10:15am Break
10:30am Chuck Pepe-Ranney: Tracking Carbon Into and Through the Soil Microbial Community with DNA-SIP
11:00am Sur Herrera-Paredes: Who, What and Eventually How: Bacterial Combinatorics for Plant Phenotypes
11:30am Breakout Session Assignments
11:45am Working Lunch
1:45pm Break
2:00pm Define 3 Model Systems
3:30pm Summary, Next Steps & Leads
4:00pm Close
Workshop Charge Questions
The following are some key aspects of the EcoFABs to be addressed. Please determine the minimum that is required for the 1.0 design and what should be the target for the 2.0 design.
Ecology
- Is it important to base the model ecosystems on natural ecosystems?
- What are the attributes of a native system to be selected for modelling in the laboratory?
- What native systems will be used as a reference for the model ecosystems?
- How will validity of the model ecosystem be determined?
Soil Science
- What soil or model soil should be used?
- How is the soil prepared?
- Does it need to be sterilized? If so, how?
- How can it be reproduced?
- How will the soil be disseminated?
Microbiology
- What are the criteria for selecting microbes to include in the model ecosystems?
- Recommendations for key taxa to be included?
- How do we know we have the right microbes?
- How many different microbes are required?
- How will these microbes be maintained and disseminated?
Plants
- What is the criteria for selecting the model plant?
- What would be the initial plant to use?
- How is the plant maintained and disseminated?
Fabrication
- What is the appropriate scale for cultivation?
- Which aspects of the EcoFAB should be controlled?
- What should be physically or chemically manipulated?
- How can we design the EcoFAB to be both reproducible and flexible?
- How is the design standardized and disseminated?
Sampling, Sensing and Imaging
- Rank the most important parameters that should be monitored?
- What needs to be sampled and at what resolution?
- What needs to be imaged? What kind of imaging and what resolution?
- Does this need to be standardized?
Sample Measurement
- What would be the most informative sample measurements?
- Does this constrain the other aspects of the design?
Implementation
- What information is required for a lab to effectively set-up an EcoFAB?
- How do they know that they have done it correctly?
- What forum is needed to share designs?
Data Capture and Sharing
- What is the minimum set of parameters that must be recorded to reproduce an EcoFAB state?
- How is the information reported?
Modeling
- Any special aspects of the EcoFAB that should be constrained to improve computational modeling efforts?
2016 EcoFAB Workshop Participants
| Name | Institution | Role |
| Adam Deutschbauer | LBNL | Participant |
| Adam Rivers | LBNL | Participant |
| Alvin Tamsir | Pivot Bio | Participant |
| Barbara Campbell | Clemson University | Speaker |
| Ben Bowen | LBNL | Participant |
| Ben Brown | LBNL | Participant |
| Charles Pepe-Ranney | Cornell University | Speaker |
| Daniel van der Lelie | FMC Corporation | Participant |
| Eoin Brodie | LBNL | Participant |
| Hector Garcia Martin | LBNL | Participant |
| Javier Ceja Navarro | LBNL | Participant |
| Jennifer Pett-Ridge | LBNL | Participant |
| Jenny Mortimer | LBNL | Participant |
| Jian Gao | LBNL | Participant |
| John Vogel | LBNL | Participant |
| Jorge Rodrigues | UC Davis | Participant |
| Kabir Peay | Stanford | Breakout Lead: Growth Promotion |
| Karsten Zengler | UC San Diego | Speaker |
| Katherine McMahon | University of Wisconsin | Participant |
| Katy Christiansen | LBNL | Participant, Author |
| Kirsten Hofmockel | PNNL | Participant |
| Margaret McFall-Ngai | University of Hawaii | Participant |
| Mary Firestone | UC Berkeley | Breakout Lead: Carbon Cycling |
| Matt Smith | UC Berkeley | Participant |
| Matt Traxler | UC Berkeley | Participant |
| Matthew Francis | UC Berkeley | Participant |
| Michalis Hadjithomas | LBNL | Participant |
| Michi Taga | UC Berkeley | Participant |
| Natalia Ivanova | LBNL | Participant |
| Nikos Kyrpides | LBNL | Co-Chair |
| Peter Nico | LBNL | Participant |
| Romy Chakraborty | LBNL | Participant |
| Steve Singer | LBNL | Participant |
| Sue Celniker | LBNL | Participant |
| Sur Herrera-Paredes | University of North Carolina | Speaker |
| Susannah Tringe | LBNL | Co-Chair |
| Tanja Woyke | LBNL | Breakout Lead: Community Assembly |
| Trent Northen | LBNL | Co-Chair |
| Yasuo Yoshikuni | LBNL | Participant |
| Jose Dinneny | Carnegie Institute | Contributor |
| Jeff Dangl | University of North Carolina, Chapel Hill | Contributor |