REVIEW PAPER Ecological metabolomics: overview of current developments and future challenges Jordi Sardans • Josep Pen ˜ uelas • Albert Rivas-Ubach Received: 11 November 2010 / Accepted: 1 June 2011 / Published online: 23 June 2011 Ó Springer Basel AG 2011 Abstract Ecometabolomics, which aims to analyze the metabolome, the total number of metabolites and its shifts in response to environmental changes, is gaining impor- tance in ecological studies because of the increasing use of new technical advances, such as modern HNMR spec- trometers and GC-MS coupled to bioinformatic advances. We review here the state of the art and the perspectives of ecometabolomics. The studies available demonstrate eco- metabolomic techniques have great sensitivity in detecting the phenotypic mechanisms and key molecules underlying organism responses to abiotic environmental changes to biotic interactions. But such studies are still scarce, and in most cases they are limited to the direct effects of a single abiotic factor or of biotic interactions between two trophic levels under controlled conditions. Several exciting chal- lenges remain to be achieved through the use of ecometabolomics in field conditions, involving more than two trophic levels, or combining the effects of abiotic gradients with intra- and inter-specific relationships. The coupling of ecometabolomic studies with genomics, transcriptomics, ecosystem stoichiometry, community biology and biogeochemistry may provide a further step forward in many areas of ecological sciences, including stress responses, species lifestyle, life history variation, population structure, trophic interaction, nutrient cycling, ecological niche and global change. Keywords Abiotic relationships Á Atmospheric changes Á Biotic relationships Á Competition Á Ecology Á Ecophysiology Á Eutrophication Á GC-MS Á Global change Á HPLC–MS Á Invasiveness Á Metabolome Á NMR Á Nutrients Á Plant-animal Á Pollution Á Stoichiometry Á Trophic webs Á Water Introduction The possibility of using progressively improved meta- bolomic techniques in ecophysiological and ecological studies has opened up a new way to advance knowledge of the structure and function of organisms and ecosystems. Metabolomics is the analysis of the complete metabolome (all the metabolites that one organism produces) at one moment (Fiehn 2002). It provides the phenotypical response at the metabolic level in a particular environ- mental circumstance. Moreover, it is also a powerful tool to monitor the phenotypic variability of one genotype in response to environmental changes in drought (Fumagalli et al. 2009), nutrient availability (Hirai et al. 2004, 2005), pollutants (Jones et al. 2007; Bundy et al. 2008), salinity (Fugamalli et al. 2009), temperature (Michaud and Delinger 2007) and biotic interactions (Choi et al. 2006), among other ecological factors. These studies are espe- cially adequate in plants because metabolomic studies enable the simultaneous analysis of primary compounds together with secondary compounds, which have a defen- sive and protective function. Metabolomics provides a better analysis of the different response capacities conferred by the phenotypic plasticity of each species, allowing to ascertain what metabolic pathways are involved in a phenotypic response. Moreover, this facilitates transcriptomics change research (Hirai et al. J. Sardans (&) Á J. Pen ˜uelas Á A. Rivas-Ubach Global Ecology Unit CSIC-CEAB-CREAF, Center for Ecological Research and Forestry Applications, Edifici C. Universitat Auto `noma de Barcelona, Bellaterra, 08193 Barcelona, Spain e-mail: j.sardans@creaf.uab.cat Chemoecology (2011) 21:191–225 DOI 10.1007/s00049-011-0083-5 CHEMOECOLOGY 123