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Cropping systems comprising winter catch crops followed by spring wheat could reduce N leaching risks compared to traditional winter wheat systems in humid climates. We studied the soil mineral N (N inorg ) and root growth of winterand spring wheat to 2.5 m depth during 3 years. The roots of the winter and spring wheat penetrated the soil at a similar rate (1.3 mm o C day −1 ) and by virtue of its longer growing period, winter wheat reached depths of 2.2 m, twice that of spring wheat (1.1 m). The deeper rooting of winter wheat was related to much lower amounts of N inorg left in the 1 to 2.5 m layer after winter wheat (81 kg N inorg ha −1 less). When growing winter catch crops before spring wheat, N content in the 1 to 2.5 m layer after spring wheat was not different from that after winter wheat. The results suggest that due to its deep rooting, winter wheat may not lead to as high levels of leaching as it is often assumed in humid climates. Deep soil and root measurements (below 1 m) in this experiment were essential to answer the questions we posed.

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Unused inorganic nitrogen (N inorg ) left in agricultural soils will typically leach to deeper soil layers. If it moves below the root zone it will be lost from the system, but the depth of the root zone depends on the crop species grown. In this experiment we studied the effect of 3-year crop sequences, with different combinations of deep-rooted and shallow-rooted crops, on soil N inorg dynamics to 2.5 m soil depth and the possibility of crop utilization of N leached to deep soil layers. We grew ten different crop sequences for 3 years. The crops and catch crops grown were selected to allow different sequences of deeprooted and shallow-rooted crops. Very different rooting depths were obtained, from only 0.5 m (leek), to~1.0 m (ryegrass and barley), 1.5 m (red beet), 2.0 m (fodder radish and white cabbage) and more than 2.5 m by the chicory catch crop. The results showed a significant retention of N inorg within the 2.5 m soil profile from one year to the next, but the retained N had leached to deeper parts of the profile during the winter season. Only little N inorg was retained over two winter seasons. The retention in the deeper soil layers allowed N inorg to be taken up by succeeding deep-rooted main crops or catch crops. The effects of crop rooting depth on N inorg in the subsoil layers from 1.0 to 2.5 m were striking. White cabbage reduced N inorg below 1.0 m with up to 113 kg N ha -1 during its growth. Grown after catch crops, leek and red beet left on average 60 kg N ha -1 less below 1.0 m than leek and red beet grown without a preceding catch crop. We conclude that it is possible to design crop rotations with improved nitrogen use efficiency by using the differences in crop rooting patterns; deep-rooted crops or catch crops can be used to recover N inorg leached after previous crops, and catch crops can be grown before shallow-rooted crops to lift the deep N inorg up to layers where these crops have their roots.

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ABSTRACTal., 1998). Cultivated plants are thought to have the major part of their root system within this depth, but (Robinson, 1986; ing in the ability of catch crops to take up NO 3 from deep soil layers. Strebel and Duynisveld, 1989), and thus for reducing Nitrogen uptake was studied over a 6-d period at the end of October NO 3 leaching to ground water (Thorup-Kristensen, 2001). (Borg and Grimes, 1986). Studies of the root growth of radish, winter rye, and ryegrass, respectively. The measurements obcatch crops below 1-m depth have shown large differtained with the minirhizotron method were highly relevant for evaluatences in root depth and distribution from one species ing N uptake from different soil layers, and root depths of the catch to the next (Barraclough, 1989; Materechera et al., 1993; crops were important for N depletion. Knowledge about root growth Thorup-Kristensen, 2001). and catch crops in soils below 1-m depth. Significant N uptake has been found at 0.9 to 1.5 m for winter wheat (Triticum aestivum L.), winter barley (Hordeum vulgare L.), sugarbeet (Beta vulgaris L. var. altissima Dö ll), corn

We present RootPainter, a GUI-based software tool for the rapid training of deep neural networks for use in biological image analysis. RootPainter facilitates both fully-automatic and semiautomatic image segmentation. We investigate the effectiveness of RootPainter using three plant image datasets, evaluating its potential for root length extraction from chicory roots in soil, biopore counting and root nodule counting from scanned roots. We also use RootPainter to compare dense annotations to corrective ones which are added during the training based on the weaknesses of the current model. Deep Learning | GUI | Segmentation | Phenotyping | Biopore | Rhizotron | Root nodule | Interactive segmentation Correspondence: ags@di.ku.dk Fig. 1. RootPainter corrective annotation concept. (a) Roots in soil. (b) AI root predictions. (c) Human corrections. (d) AI learns from corrections. Smith et al. | bioRχiv | April 16, 2020 | 1-16

This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues.Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. b s t r a c tOne of the core ideas behind organic production is that cropping systems should be less dependent on import of resources, and minimize negative effects on the surrounding environment compared to conventional production. However, even when clearly complying with regulations for organic production, it is not always obvious that these goals are reached. As an example, strong dependence on import of manure is often seen in current organic production, especially in systems producing high value crops such as vegetable crops.The aim of the present study was to test novel approaches to organic rotations, designed to reduce the reliance on import of external resources significantly. We compared a conventional system (C) and an organic system relying on manure import for soil fertility (O1) to two novel systems (O2 and O3) all based on the same crop rotation. The O2 and O3 systems represented new versions of the organic rotation, both relying on green manures and catch crops grown during the autumn after the main crop as their main source of soil fertility, and the O3 system further leaving rows of the green manures to grow as intercrops between vegetable rows to improve the conditions for biodiversity and natural pest regulation in the crops. Reliance on resource import to the systems differed, with average annual import of nitrogen fertilizers of 149, 85, 25 and 25 kg N ha −1 in the C, O1, O2 and O3 systems, respectively. As expected, the crop yields were lower in the organic system. It differed strongly among crop species, but on average the organic crops yielded c. 82% of conventional yields in all three organic systems, when calculated based on the area actually grown with the main crops. In the O3 system some of the area of the vegetable fields was allocated to intercrops, so vegetable yields calculated based on total land area was only 63% of conventional yields.Differences in quality parameters of the harvested crops, i.e. nutrient content, dry matter content or damages by pests or diseases were few and not systematic, whereas clear effects on nutrient balances and nitrogen leaching indicators were found. Root growth of all crops was studied in the C and O2 system, but only few effects of cropping system on root growth was observed. However, the addition of green manures to the systems almost doubled the average soil exploration by active root systems during the rotation from only 21% in C to 38% in O2 when measured to 2.4 m depth. This relates well to the observed differences in subsoil inorganic N content (N inorg , 1-2 m depth) across the whole rotation (74 and 61 kg N ha −1 in C and O1 vs. only 22 and...