I am Deputy Business Unit Manager Bioscience and Professor of Plant Metabolomics at Wageningen University, Laboratory of Plant Physiology. For the last 20 years my research activities have been centred around the development and application of metabolomics technology for plants, with particular emphasis on crop species. We use metabolomics approaches to gain a better understanding of the biochemical composition of plant materials and to ascertain how this is influenced by genotype and environment. We work on both fresh plant materials (regarding e.g. whole plant development, fruit ripening, seed maturation, plant-pathogen interactions etc) as well as processed plant (food) materials (e.g. fruit juices, tomato paste, roasted coffee beans, tea etc). We have established an extensive plant metabolomics platform comprising 8 LC and GC Mass Spectrometers supported by all required in silico tools for data management, processing and statistical analysis and (our in house) metabolite databases.
Metabolomics is growing in importance as a tool for analysis of food - both in academia and in industry. Metabolomics is giving us ever deeper insights into the biochemical composition of our food and how this is impacted by aspects such as shelf-life, processing methods, additives. See our recent cover article on Soy sauce or other recent papers on food quality where we have a strong focus on flavour and fragrance of both fresh and processed foodstuffs.
- DIEZ-SIMON, C., EICHELSHEIM, C., MUMM, R., HALL, R.D. (2020) Chemical and sensory characteristics of soy sauce: A review. Journal of Agriculture and Food Chemistry 68, 11612-11630 DOI: 10.1021/acs.jafc.0c04274
- BAKIR, S., CAPANOGLU, E., HALL, R.D., DE VOS, C.H.R. (2020) Untargeted semi-polar metabolite analysis of a unique set of tomato accessions collected in Turkey. Food Chemistry 317, 12406 pp 1-9 https://doi.org/10.1016/j.foodchem.2020.126406
- JACOBS, D.M., VAN DEN BERG, M., HALL, R.D. (2021) Towards superior plant-based foods using metabolomics. Current Opinion in Biotechnology 70, 23-28
- PEGIOU, E., MUMM, R., DE VOS, R.C.H., HALL, R.D. (2020) Green and white asparagus (Asparagus officinalis) – a source of developmental, chemical and urinary intrigue! Metabolites 10, https://doi.org/10.3390/metabo10010017
Metabolomics and plant Phenotyping
There is a growing interest in being able to deeply phenotype plant populations. Many academic institutions and private companies have invested heavily in automated phenotyping systems based on robotics and sensor technology. Metabolomics has gret potential to contribute this although there ar estill some technological challenges to overcome. Wantto see how this could be achieved? Please see our cover article in Trends in Plant Science!
HALL, R.D., D’AURIA, J.C., SILVA-FERREIRA, A.C., GIBON, Y., KRUSKZA, D., MISHRA, P., van de ZEDDE, R. (2022) High-throughput plant phenotyping: a role for metabolomics? Trends in Plant Science 27 (6) (https://doi.org/10.1016/j.tplants.2022.02.001) pp549-563
New developments in plant metabolomics
Plant metabolomics is the technology used to study the biochemical composition of living materials in an untargeted manner. We look specifically at the smaller molecules such as the amino acids, fatty acids, organic acids, alkaloids, phenolics and many other secondary metabolites etc. We have facilities to look at both volatile and non-volatile metabolites which play important roles in food / nutritional quality, flavour and fragrance, plant (a)biotic stress physiology and plant signalling mechanisms, to name but a few. We develop new wet lab procedures as well as data analysis approaches to optimise data generation and data mining strategies. The variety of applications of these approaches is tremendous.
Want to know more? For example - how we used metabolomics approaches to understand feed related methane production in cows – see our cover article in Metabolomics;
- BECKER, P.M., WIKSELAAR, P.G., FRANSSEN, M.C.R., DE VOS, R.C.H., HALL, R.D., BEEKWILDER, J. (2014) Evidence for a hydrogen-sink mechanism of (+)catechin-mediated emission reuction of the ruminant greenhouse gas methane. Metabolomics 10, DOI 10.1007/s11306-013-0554-5
or to understand how changes occur when making vegetable soup:
- LOPEZ-SANCHEZ, P. DE VOS, R.C.H., MUMM, R., HALL, R.D., BIALEK, L., LEENMAN, R., STRASSBURG, K., VREEKEN, R., HANKEMEIER, T., SCHUMM, S., VAN DUYNHOVEN, J. (2015). Comprehensive metabolomics to evaluate the impact of industrial processing on the phytochemical composition of vegetable purees. Food Chemistry 168, 348-355
– or how metabolites are treated and taken up in our gut:
- TOYDEMIR, G., BOYACIOGLU, D., CAPANOLU, E., VAN DER MEER, I.M., TOMASSEN, M., HALL, R.D., MES, J., BEEKWILDER, J. (2013) Transport of anthocyanins from unprocessed fruit and processed fruit juice from sour cherry (Prunus cerastus L.) through intestinal epithelial cells. Journal of Agriculture and Food Chemistry 61, 11434-11441
In vivo / spatial metabolomics
Plants are a tremendously rich source of biochemicals. Many compounds play a day-to-day role in the life of the plant while others contribute to plant reproduction, fitness, disease prevention etc. Many others have, as yet, an unknown function. Knowing where, why and when plants accumulate metabolites within their tissues is important for our understanding of the mechanisms behind the control of plant metabolism. Furthermore, it is becoming increasingly evident that the location of specific metabolites within plant organs and tissues is highly heterogeneous. Ideally, we would like to be able to look inside living plant tissues and locate individual metabolites. A new technology, LAESI-MSI (Laser Ablation Electro-Spray Ionisation Mass Spectrometric Imaging) has the potential to give us direct insight into the distribution of metabolites across cells and tissues. We have been using LAESI to assess the potential and limitations of using this approach to make metabolic maps of plant tissues.
ETALO, D., DE VOS, R.C.H., JOOSTEN, M.H.A.J., HALL, R.D. (2015) Spatially-resolved plant metabolomics: some potentials and limitations of Laser-Ablation Electrospray Ionization (LAESI) Mass Spectrometry metabolite imaging. Plant Physiology 169, 1424-1435
Metabolomics on rice
Rice is the world’s most important food crop. It provides more than 20% of the total calorific need of the global population and is the staple food stuff of approximately half of the world’s consumers. There are actually many different kinds of rice which are linked to strongly-embedded cultural and societal needs for rice grains with contrasting quality attributes. Typical examples are e.g. basmati and jasmine rices which differ considerably in terms of e.g aroma, taste, grain size and shape (which determine mouth feel). However, despite the importance of the crop we still have relatively poor knowledge of the biochemical differences behind these different quality features. We have been developing and applying metabolomics approaches to look at both the volatile and non-volatile chemicals present in rice grains of diverse origin. This research has revealed not only how complex rice grain biochemistry is but also, is helping to point us to those compounds which potentially play the most important role in fragrance and flavour attributes. With this knowledge we can now assist plant breeders to select for quality attributes as well as for yield and disease resistance.
- FITZGERALD, M.E., McCOUCH, S., HALL, R.D. (2009) More than a grain of rice: the quest for quality. Trends In Plant Science 14: 133-138
- CALINGACION, M., FANG, L., QUIATCHON-BAEZA, L., MUMM, R,. RIEDEL, A., HALL, R.D., FITZGERALD, M. (2015) Delving deeper into technological innovations to understand differences in rice quality. Rice 8: 6.
- MUMM, R., HAGEMAN, J.A., CALINGACION, M.N., DE VOS, R.C.H., JONKER, H.H., ERBAN, A., KOPKA, J., HANSEN, T.H., LAURSEN, K.H.,SCHOERRING, J., WARD, J.L., BEALE, M.H., JONGEE, S., RAUF, A., HABIBI, F., INDRASARI, S.D., SAKHAM, S., RAMLI, A., ROMERO, M., REINKE, R.F., OHTSUBO, K., BOUALAPHANH, C., FITZGERALD, M.A., HALL, R.D. (2016) Multi-platform metabolomics analyses of a broad collection of fragrant and non-fragrant rice varieties reveals the high complexity of grain quality characteristics. Metabolomics 12 :38. DOI 10.1007/s11306-015-0925-1
Metabolomics and plant and fruit development
The growth of plants and the development of plant organs are paired with paradigm shifts in plant metabolism. An unripe strawberry which is green/white astringent, hard and unpleasant to eat is transformed into a red ripe, juicy, aromatic, sweet fruit in just a matter of days. Understanding which biochemical changes take place and how these are coordinated and controlled is very important in helping us gain greater control of these processes – either through breeding or through crop / product management practices.
For an overview of the potential of metabolomics in this field please see our overview cover article in Trends in Plant Science or one of our other publications:
- BINO, R.J., HALL, R.D., FIEHN, O., KOPKA, J., SAITO, K., DRAPER, J., NIKOLAU, B.J., MENDES, P., ROESSNER-TUNALI, U., BEALE, M.H., TRETHEWEY, R.N., LANGE, B.M., WURTELE, E.S., SUMNER, L.W. (2004) Potential of metabolomics as a functional genomics tool. Trends in Plant Science 9, 418 - 424
- MOING, A., ALLWOOD, J.W., AHARONI, A., BAKER, J., BEALE, M.H., BEN-DOR, S., BIAIS, B., BRIGANTE, F., BURGER, Y., DEBORDE, C., ERBAN, A., FAIGENBOIM, A., GUR, A., HANSEN, T.H., GOODACRE, R., JACOB, D., KATZIR, N., KOPKA, J., MAUCOURT, M.,`MILLER, S., MUMM, R., OREN, E., PARIS, H.S, ROGACHEV, I., ROLIN, D., SAAR, U., SCHJOERING, J.K., TADMOR, Y., TSURI, G., DE VOS, R.C.H., WARD, J.L., YESELSON, E., HALL, R.D.* , SCHAFFER*, A.A. (2020) Comparative metabolomics and molecular phylogenetics of melon (Cucumis melo, Cucurbitaceae) biodiversity. Metabolites 10: doi:10.3390/metabo10030121
- BUTELLI, E., TITTA, L., GEORGIO, M., MOCK, H-P.,MATROS, A., PETEREK, S., SCHIJLEN, E.G.W.M., HALL, R.D., BOVY, A.G., MARTIN, C.A. (2008) Induced anthocyanin biosynthesis in purple fruit with enhanced antioxidant, dietary and health-inducing properties. Nature Biotechnology 26: 1301 - 1308
Model plant metabolomics
Arabidopsis has been the model plant of choice for many years, especially regarding molecular biology research. Exploiting some of the existing standard genomics-based approaches in combination with metabolomics analysis has become a powerful approach to link metabolites to the genome and also to link genotype to phenotype / chemotype. In this way are finding QTLs and even individual genes which play key roles in plant metabolism. And of course, extrapolating this further, towards other Brassica species, we can find important metabolites and genes determining phenotypic traits in crops such as broccoli and cabbage.
Want to know more? Please see our publications:
KEURENTJES, J.J.B., FU, Y, DE VOS C.H.R., LOMMEN, A, HALL, R.D., BINO, R.J., VAN DER PLAS, L.H.W., JANSEN R.C., VREUGDENHIL, D, KOORNNEEF, M. (2006). The genetics of plant metabolism. Nature Genetics 38, 842-849.
DE VOS, C.H.R., MOCO, S., LOMMEN, A., KEURENTJES, J.J.B., BINO, R.J., HALL, R.D. (2007). Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nature Protocols 2: 778-791
HALL, R.D., DE VOS, R.C.H., WARD, J.L. (2010) Plant metabolomics applications in the Brassicaceae: added value for science and industry. Acta Horticulturae 867, 191-205
Applications of Plant Metabolomics
Want a broad overview? Check out these books on Plant Metabolomics – one is for people wanting to apply the technologies. The other gives a range of overviews on how metabolomics approaches can and are being applied in a broad diversity of biological topics – from crops to model plants and from plant pathogen interactions to systems biology.
HARDY, N.G. & HALL, R.D. (Eds) (2012) Methods for Plant metabolomics, Springer-Humana Press, 340 pp
HALL, R.D. (Ed.) (2011) The biology of plant metabolomics . Annual Plant Reviews Vol 43. Blackwell/Wiley pp 420