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.

Microorganisms persist at record depths in the subseafloor of the Canterbury Basin

“…Our culture data support this hypothesis. Genome and metagenome analyses would allow functions to be predicted on a finer scale to assess and hypothesize the individual ecological functions within the analyzed habitat or ecosystem (Vandenkoornhuyse et al, 2010). The detection of fungal sequences at great depths and our success in the cultivation of fungal strains leads us to ask what role they play in deep carbon cycling and what involvement they have in dynamics/regulation of prokaryotic populations, if they are active in situ.…”

Herbicide Contamination of Freshwater Ecosystems: Impact on Microbial Communities

“…Finally, the introduction of "omic" methods opens a new area in the assessment of the impact of pesticides on microbial communities. The use of metagenomic, metatranscriptomic and metaproteomic methods in recent years has shown that environmental microbial ecology is already entering the "Omics" era (see for example Nelson et al, 2006;Vandenkoornhuyse et al, 2010). Despite some restrictions, there is no doubt that all these methods will soon be major tools for ecotoxicological studies.…”

Mesocosm Experiments as a Tool for Ecological Climate-Change Research

“…Beveridge et al, 2010;Petchey et al, 1999). Understanding the functional roles of these organisms in situ is far more challenging and until recently they have been confined to a 'black box' in field studies (Purdy et al, 2010;Vandenkoornhuyse et al, 2010), despite early recognition that they are probably the main drivers of most ecosystem processes (e.g. Azam et al, 1983;Finlay and Esteban, 1998;Pomeroy, 1974;Pomeroy et al, 2007).…”