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Abstract. Plant phenotyping is an emerging discipline in plant biology. Quantitative measurements of functional and structural traits help to better understand gene-environment interactions and support breeding for improved resource use efficiency of important crops such as bean (Phaseolus vulgaris L.). Here we provide an overview of state-of-the-art phenotyping approaches addressing three aspects of resource use efficiency in plants: belowground roots, aboveground shoots and transport/allocation processes. We demonstrate the capacity of high-precision methods to measure plant function or structural traits non-invasively, stating examples wherever possible. Ideally, high-precision methods are complemented by fast and high-throughput technologies. High-throughput phenotyping can be applied in the laboratory using automated data acquisition, as well as in the field, where imaging spectroscopy opens a new path to understand plant function noninvasively. For example, we demonstrate how magnetic resonance imaging (MRI) can resolve root structure and separate root systems under resource competition, how automated fluorescence imaging (PAM fluorometry) in combination with automated shape detection allows for high-throughput screening of photosynthetic traits and how imaging spectrometers can be used to quantify pigment concentration, sun-induced fluorescence and potentially photosynthetic quantum yield. We propose that these phenotyping techniques, combined with mechanistic knowledge on plant structure-function relationships, will open new research directions in whole-plant ecophysiology and may assist breeding for varieties with enhanced resource use efficiency varieties.

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Summary• Root colonization by arbuscular mycorrhizal fungi (AMF) was investigated in industrially polluted grassland characterized by exceptionally high phosphorus levels (up to 120 g kg − 1 soil).• Along a pollution-induced nitrogen gradient, soil and tissue element concentrations of Artemisia vulgaris plants and their mycorrhizal status were determined. Additionally, we compared mycorrhization rates and above-ground biomass of A. vulgaris at N-fertilized and control plots in the N-poor area.• Despite high soil and tissue P concentrations, plants from N-deficient plots, which were characterized by low tissue N concentrations and N : P ratios, were strongly colonized by AMF, whereas at a plot with comparable P levels, but higher soil and plant N concentrations and N : P ratios, mycorrhization rates were significantly lower. Correlation analyses revealed a negative relationship between percentage root colonization of A. vulgaris by AMF and both tissue N concentration and N : P ratio. Accordingly, in the fertilization experiment, control plants had higher mycorrhization rates than N-fertilized plants, whereas the species attained higher biomass at Nfertilized plots.• The results suggest that N deficiency stimulates root colonization by AMF in this extraordinarily P-rich field site.