Environmental genomics and environmental metagenomics
18-20 November , 2004
Congress and Exhibition Centre, Granada, Spain

Organisers:

Juan L. Ramos: CSIC, Granada, Spain
Víctor De Lorenzo: CNB, CSIC, Madrid, Spain
Kenneth N. Timmis: GBF, Braunschweig, Germany
Christa Schleper: University of Bergen, Bergen, Norway

Report

The European Science Foundation Workshop on Environmental Genomics and Environmental Metagenomics was held in Granada on 18-20 November, 2004. The workshop was organized by 4 European head scientists in the area of Environmental Genomics: Prof. Víctor de Lorenzo (Spain), Prof. Kenneth N. Timmis (Germany), Prof. Christa Schleper (Germany) and Prof. Juan L. Ramos (Spain).

This workshop was conceived to serve as a forum for scientists, biotechnologists, and scientists working in bioinformatics to discuss the progress made in genomics and proteomics in the area of environmental sciences. Current advances in genomics and proteomics are contributing to the development of new concepts regarding the biology and social behaviour of living organisms. These advances are expected to result in new biotechnological products of importance for the environment and public health and will provide strategic information on the vulnerability of human beings, animals, plants and microbes to environmental insults.

Environmental problems are complex but common to many different countries worldwide and there is an existing need for wide-reaching international collaboration among scientists and technology developers to assure fast advances in the field.

The goals of the ESF workshop on Environmental Genomics and Environmental Metagenomics have not only tried to address issues related to basic science, technology development in the field and bioinformatics for the environment, but also those pertaining to international collaboration in environmental genomics and environmental metagenomics.
A selected group of international key speakers covering 3 continents were gathered for these purposes.

Speakers

Siv Andersson (Uppsala University, Uppsala, Sweden)
Amos Bairoch (Swiss Institute of Bioinformatics, Geneva, Switzerland)
Oded Beja (Israel Institute of Technology, Haifa, Israel)
Peer Bork (EMBL, Heidelberg, Germany)
Ildefonso Casés (Centro Nacional de Biotecnología-CSIC, Madrid, Spain)
Víctor de Lorenzo (Centro Nacional de Biotecnología-CSIC, Madrid, Spain)
Eduardo Díaz (Centro Nacional de Biotecnología-CSIC, Madrid, Spain)
Steven Gill (The Institute for Genomic Research, Rockville, USA)
Frank O. Gloekner (Max-Planck Inst. for Marine Microbiology, Bremen, Germany)
Shigeaki Harayama (Marine Biotechnology Institute, Iwate, Japan)
Matthew Holden (The Sanger Centre, Cambridge, UK)
Dick B. Janssen (University of Groningen, Groningen, The Netherlands)
Vasantha Nagarajan (DuPont Company, Wilmington, USA)
Karin A. Remington (The Venter Institute, Rockville, USA)
Christa Schleper (University of Bergen, Bergen, Norway)
Chris M. Thomas (University of Birmingham, Birmingham, UK)
Kenneth N. Timmis (GBF, Braunschweig, Germany)
Burkhard Tümmler (Medizinsche Hochschule, Hannover, Germany)
Alfonso Valencia (Centro Nacional de Biotecnología-CSIC, Madrid, Spain)

Final programme for the meeting

18 November

8:30-8:55 Registration

9:00-9:15 Welcome to the ESF workshop meeting

Chair: Víctor de Lorenzo

9:15-10:00 Matthew Holden "Expanding environmental genomics: the sequencing, annotation and analysis of microbial genomes"

10:00-10:45 Peer Bork "Function prediction by combining homology and network analysis"

10:45-11:15 coffee break

11:15-12:00 Ildefonso Casés "Evolution of Transcription Networks and Environmental Adaptation"

12:00-12:45 Alfonso Valencia "A bioinformatics approach to the study of protein interactions in the context of the biodegradation network"

12:45-13:30 Karin Remington "Comparative metagenomics of the global oceans"

13:30-15:00 lunch break

Chair: Oded Beja

15:00-15:20 Invited poster - Mike Allen "A genomic approach to investigate infection dynamics of marine phytoplankton viruses"

15:20-15:40 Invited poster - Roland Siezen "Genome diversity in Lactobacillus plantarum"

15:40-16:10 tea break

16:10-16:55 Burkhard Tümmler "In silico and functional analyses of the Pseudomonas putida KT2440 genome"

16:55-17:40 Eduardo Díaz "Genome and functional analysis of the catabolic potential of
Pseudomonas putida KT2440 towards aromatic compounds"

19 November

Chair: Christa Schleper

9:15-10:00 Kenneth N. Timmis "A cold-adapted chaperone: a new tool to extend microbial growth windows and aid mining of metagenome libraries for functions of psychrophiles"

10:00-10:45 Frank Oliver Gloekner "Genome analysis of environmentally relevant marine bacteria - lessons from the Rhodopirellula baltica SH1T genome"

10:45-11:15 coffee break

11:15-12:00 Oded Beja "Coast to coast: Walking with marine proteorhodopsins"

12:00-12:45 Shigeaki Harayama "Metabolic potential of Rhodococcus deduced from its genomic sequence"

12:45-13:30 Siv Andersson "When the environment is a eukaryote: Genomic analyses of
the alpha-proteobacteria"

13:30-15:00 lunch break

Chair: Eduardo Díaz

15:00-15:45 Vasantha Nagarajan "Plasmid diversity in wastewater bioreactors"

15:45-16:05 Invited Poster - Margaret Wexler "Construction of metagenomic libraries from a waste-water treatment plant and identification of a novel alcohol/aldehyde dehydrogenase gene"

16:05-16:25 Invited Poster - Christian Leggewie "Novel biocatalysts from the metagenome"

16:25-17:00 tea break

17:00-17:45 Christa Schleper "Environmental soil libraries: Digging out clues on the metabolism of uncultured crenarchaeota"

20 November

Chair: Ken Timmis

9:00:9:45 Víctor de Lorenzo "Tools for addressing biodegradation from a systems biology
perspective"

9:45:10:30 Christopher Thomas "Genomics of Pseudomonas plasmids"

10:30-11:00 coffee break

10:30-11:15 Steven Gill "Genomics of the human gastrointestinal microbiome"

11:15-12:00 Dick B. Janssen "Bacterial enzymes in biotransformations: lessons from
(meta)genomics"

12:00-12:45 Amos Bairoch "HAMAP: Microbial proteins annotation"

12:45 Closing of the meeting

List of participants

Mr. Alejandro Acosta (Spain)
Prof. Spiros Agathos (Belgium)
Dr. Mike Allen (UK)
Ms. Patricia Bernal (Spain)
Mrs. Carmilla Bernasconi (Italy)
Dr. Dietmar Boeltner (Spain)
Dr. Philip Bond (UK)
Dr. Tim Booth (UK)
Dr. Pedro F.B. Brandao (Germany)
Dr. Kim Brügger (Denmark)
Mr. Antonio Caballero (Spain)
Dr. Inés Canosa (Spain)
Dr. Manuel Carmona (Spain)
Ms. Teresa Del Castillo (Spain)
Dr. Estrella Duque (Spain)
Dr. Said El Fantroussi (Belgium)
Dr. Manuel Ferrer (Spain)
Dr. Takeshi Fujii (Japan)
Dr. Mª Trinidad Gallegos (Spain)
Ms. M. Eugenia Guazzaroni (Argentina)
Mr. Fredrik Hardeman (Sweden)
Prof. Hermann Heipieper (Germany)
Ms. Mª Carmen Herrera (Spain)
Dr. Linda Hiwatig (The Philipinnes)
Dr. Mª José Huertas (Spain)
Dr. José Ignacio Jiménez (Spain)
Dr. Howard Junca (Germany)
Dr. Inmaculada Llamas (Spain)
Dr. Christian Leggewie (Germany)
Dr. Diana Marco (Argentina)
Dr. Silvia Marqués (Spain)
Dr. Francisco Martínez-Abarca (Spain)
Mr. Manuel Martínez-Bueno (Spain)
Dr. Joaquín Martínez Martínez (UK)
Dr. Ramón Massana (Spain)
Mr. Javier I. Medina Bellver (Spain)
Dr. Jesús Muñoz (México)
Dr. Gerard Muyzer (The Netherlands)
Dr. Juan Nogales Enrique (Spain)
Dr. Balbina Nogales (Spain)
Dr. Lesley Ogilvie (UK)
Dr. Reeta Piskonen (Finland)
Dr. Cayo Ramos (Spain)
Dr. Hugo Ramírez Saad (México)
Ms. Olga Revelles (Spain)
Dr. Manuel Rey (Spain)
Dr. Alia Rodríguez (Germany)
Dr. Juan José Rodríguez-Herva (Spain)
Mr. Luc Schuler (Belgium)
Dr. Ana Segura (Spain)
Prof. Roland Siezen (The Netherlands)
Dr. Antonio Suarez (Spain)
Mr. Benoit Stenuit (Belgium)
Dr. Hideto Takami (Japan)
Dr. Hanno Teeling (Germany)
Mr. Wilson Terán (Spain)
Prof. Robert Van Der Geize (The Netherlands)
Dr. Pieter Van Dillewijn (Spain)
Dr. Margaret Wexler (UK)
Dr. Paul Wilmes (UK)
Dr. Erwin Zoetendal (The Netherlands)