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J. Plant Biol. (2014) 57:137-149 DOI 10.1007/s12374-014-0110-5

REVIEW ARTICLE

Plant Metabolomics for Plant Chemical Responses to Belowground Community Change by Climate Change Sangkyu Park1*, Young-Su Seo2 and Adrian D. Hegeman3 1

Department of Biological Sciences, Ajou Unviersity, 443-749, Korea Department of Microbiology, Pusan National University, 609-735, Korea 3 Department of Horticultural Sciences, University of Minnesota, MN55108, USA 2

Received: March 5, 2014 / Accepted: March 10, 2014 © Korean Society of Plant Biologists 2014

Abstract General circulation models on global climate change predict increase in surface air temperature and changes in precipitation. Increases in air temperature (thus soil temperature) and altered precipitation are known to affect the species composition and function of soil microbial communities. Plant roots interact with diverse soil organisms such as bacteria, protozoa, fungi, nematodes, annelids and insects. Soil organisms show diverse interactions with plants (eg. competition, mutualism and parasitism) that may alter plant metabolism. Besides plant roots, various soil microbes such as bacteria and fungi can produce volatile organic compounds (VOCs), which can serve as infochemicals among soil organisms and plant roots. While the effects of climate change are likely to alter both soil communities and plant metabolism, it is equally probable that these changes will have cascading consequnces for grazers and subsequent food web components aboveground. Advances in plant metabolomics have made it possibile to track changes in plant metabolomes as they respond to biotic and abiotic environmental changes. Recent developments in analytical instrumentation and bioinformatics software have established metabolomics as an important research tool for studying ecological interactions between plants and other organisms. In this review, we will first summarize recent progress in plant metabolomics methodology and subsequently review recent studies of interactions between plants and soil organisms in relation to climate change issues. Keywords: Altered precipitation, Belowground and aboveground, Climate change, Metabolomics, Soil microbial communities, Volatile organic compounds, Warming

*Corresponding author; Sangkyu Park Tel : +82-31-219-2454 E-mail : [email protected]

Introduction Since industrial revolution in 18th century, dramatic increases of human population and expansion of civilized areas have stimulated global climate changes including global warming (IPCC 2007). Surface air temperature has risen by 0.6±0.2°C during the 20th century (IPCC 2001). General circulation models predict further increase of surface air temperature by 1.7~4.9°C by the year 2100 (Wigley and Rapper 2001). Tundra ecosystems in arctic areas, in particular, are expected to experience dramatic increases of surface air temperature (4~7oC) over the next century (Arctic Climate Impact Assessment 2004). For example, it has been predicted that Cambridge Bay area in Nunavut, Canada would experience an average increase in air temperature of 3.9 and an average increase in precipitation of 18.6 mm by 2040-69 (Bell et al. 2002). Air temperature increase (and resulting increases in soil temperature) and altered precipitation are known to change species composition and functions of soil microbial communities (Singh et al. 2010). One study observed that with increased soil temperature, the total biomass of bacteria and fungi was reduced by 50% and species composition was altered to favor fungi over bacteria (Allison and Treseder 2008). Soil water content is another important factor that can affect soil microbial communities; changes in precipitation patterns are anticipated to dramatically perturb soil microbial community compositions (Singh et al. 2010). Plant roots interact with diverse soil organisms such as bacteria, protozoa, fungi, nematodes, annelids and insects (Gange et al. 2012). Soil organisms may participate in diverse interactions with plants such as competition, mutualism and parasitism, that can result in dramatic changes in plant metabolism (Gange et al. 2012; van Dam 2012). The main theme of this review concerns the effects of changes in soil

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temperature and soil water content that lead to changes in soil communities that, in turn, result in alterations in plant metabolomes. While plants change their metabolomes in response to soil community changes, they are also capable of affecting soil community structure by producing volatile organic compounds (VOCs) (Wenke et al. 2010). In addition to plant roots, various soil microbes including many bacteria and fungi are capable of producing VOCs. As a result, VOCs often function as infochemicals capable of mediating chemical interactions between soil organisms and plant roots (Insam and Seewald 2010; Wenke et al. 2010; Effmert et al. 2012). Recently, a number of studies have focused on the link between aboveground and belowground plant herbivory defenses (Bezemer and van Dam 2005; Rasmann and Agrawal 2008; van Dam 2012). While the number of belowground grazers is relatively small compared with that aboveground, the impact of such grazing on plants can be significant (Rasmann and Agrawal 2008). Alteration in plant metabolism in response to climate chagne-mediated soil community perturbations is likely to influence grazers and subsequent food web components (Bezemer and van Dam 2005; Dicke et al. 2012). Recent progress in plant metabolomics has made it possibile to track subtle changes in plants’ metabolism as they respond to changes in their biotic and abiotic environment (Sardans et al. 2011; Hartley et al. 2012). Traditional phytochemical ecological studies have used bioassay-guided fractionation approach to identify chemcials that mediate those interactions. This approach is, however, quite tedious and time-consuming due to the need for repetitive iteration of multiple fractionation and assay steps before compounds can be isolated at suitable purity for structure elucidation (Koehn and Carter 2005). Recent improvements in analytical instrumentation such as liquid chromatography mass spectrometry (LC-MS), gas chromatography mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) have made metabolomics more accessible as a research tool in biology, pharmacology, medicine and environmental science (Weckwerth and Morgenthal 2005). Metabolomics is fundamentally different from a traditional reductionist approach in that it attempts to elucidate the dynamics of metabolites across an entire metabolomics data set rather than focusing on predetermined target substances in the traditional approaches (Weckwerth and Morgenthal 2005). In this review, we will first summarize recent advances in plant metabolomics methodology (Fig. 1) and subsequently review recent studies on interactions of plants and soil organisms in relation to climate change.

J. Plant Biol. (2014) 57:137-149

Fig. 1. A schematic diagram for metabolomic approach. Abbreviations: GC-MS, gas chromatograpy mass spectrometry; LC-MS, liquid chromatography mass spectrometry; NMR, nuclear magnetic resonance; PCA, principal component analysis; HCA, hierarchical cluster analysis; PLS-DA, partial least squares-discriminant analysis; OPLS-DA, orthogonal partial least squares-discriminant analysis; EI, electron-impact.

Recent Progress in Plant Metabolomics Collection and Preparation of Plant Samples Since sample collection and processing steps can influence the overal metabolomic results, great care should be taken for reproducible and reliable results (Fiehn 2007; Fernie et al. 2011). Many intermediate metabolites such as those of the Calvin cycle and nucleotides have turn-over time within fractions of a second and thus require nearly instantaneous quenching of metabolic enzymes to avoid perturbation of their physiological abundance (Fernie et al. 2011). Metabolites detected by GC-MS usually turn over less quickly, but still rapid quenching is very important (Lisec et al. 2006). For most cases, quick excision and snap-freezing in liquid nitrogen would be the standard collection method recommended (Fernie et al. 2011; Hill and Roessner 2013). In addition to the quenching to avoid enzyme activity and oxidation, protection from light is important to prevent any changes in

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light-sensitive compounds such as catecholamines (Fiehn 2007). A simultaneous quenching and extraction approach such as cold organic solvent at low temperature (-72°C) and subsequent extraction at higher temperature (4°C) has been proposed (Kimball and Rabinowitz 2006). For field collection of plant samples, one report recommended sampling of fresh plant material in a solvent mixture such as methanol: dichloromethane (2:1) (Maier et al. 2010). Generally, storage of aqueous organic solvent extracts even at a low temperatures (-20°C) is not recommended (Fernie et al. 2011). Either freeze drying or quick processing of deep frozen samples minimize changes in metabolite profiles (Villas-Bôas 2007; Hegeman 2010; Fernie 2011; Hill and Roessner 2013). Extraction steps can be very crucial in plant metabolomics studies (Hall 2011). Hot water or alcohol/water mixtures have been used for polar/semipolar metabolites, while chloroform has been popular for lipophylic ones (Hall 2011). Alcohol/water mixtures of 70-90% methanol, ethanol, or isopronanol (30-10% water) have been proposed to be optimal extraction solvents in terms of optimizing the number of metabolites and reproducibility (Villas-Bôas 2007). Isopropanol water mixtures may be a good choice in order to minimize unnecessary esterification (Hegeman 2010). Methanol-waterchloroform mixtures are also popular because of the broad target solubility range and denaturing ability of chloroform (Lisec et al. 2006; Hall 2011). Proper internal standards are very important for quantification and quality control across the large number of sample analyses within a typical metabolomics experiment (Fiehn 2007). Many studies used ribitol as an internal standard for GC-MS analysis although ribitol is naturally occurring in few plants and is hard to separate from xylitol (Lisec et al. 2006; Fiehn 2007). One alternative way is using 13C labeled compounds such as 13C-sorbitol as internal standards (Lisec et al. 2006; Moco et al. 2007). Comparison between Metabolomics Tools Plant metabolomics have utilized recent progress in NMR and mass spectrometry such as GC-MS, LC-MS, and matrixassisted laser desorption ionization (MALDI)-MS (Hegeman 2010). Although MALDI-MS has its merits in the area of the spatial distribution patterns of various metabolites over other tools (Hegeman 2010; Kaspar et al. 2011; Svatoš and Mock 2013), a majority of plant metabolomics studies have used GC-MS, LC-MS, and NMR (Hill and Roessner 2013; Stobiecki and Kachlicki 2013; van der Sar et al. 2013). In this review, we will focus on these three commonly used metabolomics tools for plants. Currently, GC-MS is the most established tool for plant metabolomics in spite of its well documented limitations (Mehmeti et al. 2013). The major advantages of GC-MS are

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stable protocols due to its long history and a relatively broad coverage of compound classes including organic acids, amino acids, sugars and lipophylic compounds (Lisec et al. 2006). Also, GC-MS has a linear relation between signal and concentration, allowing quantification of targeted metabolites (Hegeman 2010). GC-MS is known good for low molecular weight metabolites either volatile or that can be made volatile through chemical derivatization (Hill and Roessner 2013). Therefore, GC-MS has obvious disadvantages in that it can only be used to analyze thermally stable and either volatile or derivatizable compounds of fairly low molecular weight (