EC-US Working Group on Environmental Biotechnology

Ioannis Economidis, EC DG ResearchAnna Palmisano, Dept. of Energy

June 2009

Working Group Mission

To foster the collaboration of researchers in the EU and US in the field of environmental biotechnology.

Special Focus: To increase scientific interchange and collaborative research between early career scientists in the US and in the EU.

Current Working Group Members

Prof. Spiros Agathos, BelgiumProf. Jerome Kukor, USDr. Barb Methe*, USDr. Ivonne Nijehuis*, GermanyDr Balbina Nogales*, SpainDr. Juan Ramos, SpainProf. Joseph Suflita, USProf. Judith Wall, US

Prof. Lily Young, USProf. Gerben Zylstra, USDr. Ioannis Economidis, EC co-chairDr. Anna Palmisano, US co-chair

Dr. Victor de Lorenzo, Spain Special Advisor

* Former participants in WG activities for early career scientists

Summary of Working Group Activities

US-EC WorkshopsUse of Molecular Methods in Bioremediation

(Granada, Spain -1996)Genomics and Environmental Biotechnology

(Rockville, US - 2004) 10 year Celebration of Working Group

Activities (Brussels, 2005)Metabolomics and Environmental

Biotechnology (Mallorca, Spain – 2008)

Summary of Working Group Activities (cont’d)

Short Courses:EC-US Short courses on environmental biotech with lab and field elements– Rutgers Univ. 1998 – U. of Madrid 2003 – U. Oklahoma 2009

Fellowships:US-EC Short Term Exchange Fellowships 1999--2007

US-EU Exchange of Early Career Scientists

• Short term, trans-Atlantic exchange fellowships

• Learn new skill/expertise in environmental biotech

• 1-6 month tenure• Require leveraging of costs from host, parent institution

Workshop on Environmental Biotechnology and Metabolomics, Mallorca, June 16-17, 2008

Workshop Goal: To identify important advances in environmental

biotechnology derived from the use new approaches in metabolomics of microorganisms and microbial communities.

EU EU OrganizersOrganizers: Dr. : Dr. BalbinaBalbina Nogales (U. de les Nogales (U. de les IllesIllesBalearsBalears) and Dr. Juan Ramos (CSIC, Granada)) and Dr. Juan Ramos (CSIC, Granada)

US Organizer: Dr. Lily Young (Rutgers University)US Organizer: Dr. Lily Young (Rutgers University)(Jointly funded by the European Commission, National (Jointly funded by the European Commission, National

Science Foundation, Dept. of Energy, USDA, and Office of Science Foundation, Dept. of Energy, USDA, and Office of Naval Research) Naval Research)

Workshop on Environmental Biotechnology and Metabolomics - Format

• The WG brought together 20 renowned, senior scientists from the EU and the US.

• Each senior scientist was asked to identify a very promising young scientist to attend the workshop, as well.

Discussion Objective: To identify realistic research objectives for the next decade for

Microbial Environmental Biotechnology

The implicit background of the debate was

[i] the growing penetration of systems biology, with all its technological developments (omics and the like) in every field of biological research (including environmental microbiology), [ii] the shift of the emphasis of the field from environmental cleanup to environmental sustainability e.g. clean energy and CO2-neutral processes, and [iii] the promise of synthetic biology to address longstanding environmental problems on the basis of synthetic genomes and engineering non-naturalbiological catalysts.

Research ObjectivesMicrobial Environmental Biotechnology

- Discovery science is as fundamental to Environmental Biotechnology as isapplication-directed research.- A well-trained, creative research force is essential. Because of the rapid pace ofdata accumulation and technological improvements, it is essential that microbiologists remain flexible in their outlook and expertise.- A current challenge is the need to integrate vast amounts of information. Thequantity of ever-increasing sequencing information has resulted in large sets of omicsdata that need reliable storage, accessibility, and trained personnel for exploration and exploitation.- Partnerships among disciplines are needed to address the complexity ofenvironmental microbial processes. Computational experts, engineers, hydrologists,geologists, ecologists, and microbiologists trained in physiology and biochemistry will all contribute.- While sequences of well-studied microbes are now available, large percentages ofthe predicted open reading frames remain un-annotated or poorly annotated. A concerted biochemical effort should be made to decrease this list and reveal the true array of functional activities.

Research ObjectivesMicrobial Environmental Biotechnology

- The recognition of microbial diversity underscores the need of improved culturingtechniques for previously uncultured organisms. Some of these bacteria may be syntrophs or live in consortia. Techniques for culture and analysis of robust consortia and defined communities are needed.- Much of the microbial biomass in the environment is now known to exist as biofilms. Tools for the analysis of biofilms at multiple levels, including development, structure, and function, should be perfected. Are all biofilms alike? Can biofilms be infected? Can biofilms die? A model system for biofilms allowing extrapolation of resultsfrom one research group to another might facilitate the rate of elucidation of this life style.- Nanobiology tools should be pursued that will open the examination of singlecells at the molecular, metabolic and biochemical levels.- A systems biology approach should be used for integrating all aspects of the fateof chemicals in the environment, including global modelling and predictive methods that could guide further experimentation and decision-making.

Research ObjectivesMicrobial Environmental Biotechnology

- Omics tools, i.e., the methods of determining cellular transcripts, proteins, andmetabolite concentrations and fluxes, are currently being perfected and applied. However, the relationships among these data sets are not understood. The use of these various sources of information for prediction of function is still rather poor. Modeling efforts are needed to integrate the data so that meaningful predictions from variable inputs can be approached.- The environmental impacts of bacteriophages on microbes and the functioning ofmicrobial communities is currently a mystery, one that needs solving.- The variety and flexibility of microbial metabolism in extreme environmentscontinue to surprise. These extremophiles should be aggressively examined if we are to understand the total physiological space of life.- Questions of evolution of life and the derivation of an evolutionary frame formicrobes are now being approached. - There is a realistic danger of niche loss for microbes, especially for plantendosymbionts. There should be a special effort to take a closer look at this issue to avoid the loss of biochemical diversity.

Research ObjectivesMicrobial Environmental Biotechnology

- Synthetic biology offers a splendid opportunity to take up again the notion ofdesigner microorganisms for environmental cleanup. The emphasis in robust designconcepts, e.g. modularity, orthogonality (i.e. context independency) and definition ofsystems boundaries –along with a growing easiness for massive DNA synthesis-open new scenarios for environmental interventions that could not materialize before.

This indicative list of challenges for microbial biotechnology represents opportunities for increased understanding and for the elucidation of solutions compatible with our fragile environment.To meet these challenges EU-US collaboration at all career levels will be required.Establishing strong ties across the Atlantic through efforts such as this Workshop is onestep on this critical journey.

Theoretical and Practical Course on Molecular Approaches for in situ Biodegradation

• Held at the University of Oklahoma from May 27 to June 6, 2009

• Led by Profs. Joe Sulfita and Kathleen Duncan• Faculty from US and EU countries• 24 early career scientists (12 from EU, 12 from US)• EU countries included: Belgium,Denmark, Estonia,

Germany, Italy, Netherlands, Spain, others• US states included Alaska, California, New Jersey,

Oklahoma, Minnesota,Montana, Washington, and others

• Seminars, hands-on field and laboratory experiments, poster sessions

• Strong focus on anaerobic microbiology

• Topics included:– Metagenomics– Metabolomics and microbial

physiology– Bioinformatics– Field Research

•• Jointly funded by the Jointly funded by the European Commission, European Commission, National Science Foundation, National Science Foundation, Dept. of Energy, USDA, and Dept. of Energy, USDA, and Office of Naval Research Office of Naval Research

Quotes from Students“Meeting other young scientists that are also

excited about this field was fantastic.”“This was the first time I had an opportunity to

study and have discussions with international scientists---to get their perspectives and ideas.”

“Some of us have already started to discuss collaborations between and within EU and USA.”

“I now know 23 other young career scientists that I can easily contact and collaborate with.”

More from the students…“It was great to work with people from all around

the world, shoulder to shoulder in the lab, encouraging each other.”

“All lectures were extremely interesting and provided the opportunity of meeting famous scientists from all over the globe!”

“The course was such a wonderful experience that it’s difficult for me to find the words to express my thoughts and feelings—thank you very much!”

“Global problems will only be solved with global teams.”

Proposed Activity: Short Course• A short course is proposed to be held

at the U. Lausanne for July 2011. • Follow-on to highly successful short

courses at Rutgers U., 1998, U. of Madrid, 2003 and U. Oklahoma 2009

• Students, lecturers shared equally between US, EU

• Course will include lecture/lab/field activities with state-of-the-art techniques, including bioinformatics, metabolomics, and metagenomics)

EC-US Working Group on Biotechnology for the Environment:

Vision Statement

“Training the next generation of scientific leaders in environmental biotechnology to work collaboratively across the Atlantic.”