title: Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics.
abstract: Environmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism-environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored.
authors.affiliation: UMR ECOBIO, Centre National de la Recherche Scientifique, Université de Rennes, France. philippe.vandenkoornhuyse@univ-rennes1.fr
authors.forename: Philippe
authors.initials: P
authors.lastname: Vandenkoornhuyse
authors.forename: Alexis
authors.initials: A
authors.lastname: Dufresne
authors.forename: Achim
authors.initials: A
authors.lastname: Quaiser
authors.forename: Gwenola
authors.initials: G
authors.lastname: Gouesbet
authors.forename: Françoise
authors.initials: F
authors.lastname: Binet
authors.forename: André-Jean
authors.initials: AJ
authors.lastname: Francez
authors.forename: Stéphane
authors.initials: S
authors.lastname: Mahé
authors.forename: Myriam
authors.initials: M
authors.lastname: Bormans
authors.forename: Yvan
authors.initials: Y
authors.lastname: Lagadeuc
authors.forename: Ivan
authors.initials: I
authors.lastname: Couée
mesh_terms: D000818:Animals; D019295:Computational Biology; D017753:Ecosystem; D004777:Environment; D015870:Gene Expression; D056186:Metagenomics; D040901:Proteomics