EcoFAB Workshop 2016

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.

Browse 2016 EcoFAB Report

EcoFAB workshop cover


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.


  • 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?


  • 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?


  • What is the criteria for selecting the model plant?
  • What would be the initial plant to use?
  • How is the plant maintained and disseminated?


  • 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?


  • 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?


  • 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