Abstract
Purpose
Measuring continuous root growth with less time- and resource-intensive methods is challenging for plant ecologists. We propose an approach where photos of fine root growth were taken with smartphones and analyzed by the deep learning method-based program RootPainter.
Methods
Picea abies saplings were grown in transparent boxes in growth chambers at either moderate (mRH) or elevated air humidity (eRH) and in nitrate (NO3−) or ammonium (NH4+) dominated soil. To evaluate the partitioning of roots, we analyzed both fine root projection area (PA) of total and young white roots. We aimed to measure the ability of RootPainter to pick up on variation in fine root growth caused by changes in air humidity and soil nitrogen source.
Results
Trees growing at mRH-NH4+ had the highest total PA, 9.4 ± 1.9 cm2, while the lowest was in trees growing at eRH-NO3−, 3.9 ± 0.6 cm2. The young root PA was highest at the beginning of the experiment and was affected by the initial soil nitrogen source. The older (brown) root PA increased over time. At mRH, the relative growth peak of root browning followed the peak of white roots, while at eRH, the peaks coincided. We found strong agreement between the automatic segmentation and manual annotation (F-measure = 0.88); the error measures showed no treatment-specific bias.
Conclusions
We conclude that the increased air humidity reduced the fine root growth and diminished sequential developmental peaks. The combination of smartphone images and RootPainter gives reliable results and is easy to use in future plant growth manipulation experiments.
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Data availability
The photo dataset used in the current study will be available from Zenodo. RootPainter is available from this link: https://colab.research.google.com/drive/104narYAvTBt-X4QEDrBSOZm_DRaAKHtA.
References
Adamczyk B, Sietiö OM, Straková P, Prommer J, Wild B, Hagner M, Pihlatie M, Fritze H, Richter A, Heinonsalo J (2019) Plant roots increase both decomposition and stable organic matter formation in boreal forest soil. Nat Commun 10:3982. https://doi.org/10.1038/s41467-019-11993-1
Adobe Inc. (2019) Adobe Illustrator. Retrieved from https://adobe.com/products/illustrator
Agerer R (ed) (1997) Colour Atlas of Ectomycorrhizae. Einhorn-Verlag Eduard Dietenberger GmbH, Schwäbisch-Gmünd, Germany
Bagniewska-Zadworna A, Arasimowicz-Jelonek M, Smoliński DJ, Stelmasik A (2014) New insights into pioneer root xylem development: evidence obtained from Populus trichocarpa plants grown under field conditions. Ann Botany 113(7):1235–1247. https://doi.org/10.1093/aob/mcu063
Bartsch N (1987) Response of root systems of young Pinus sylvestris and Picea abiesplants to water deficits and soil acidity. Can J For Res 17:805–812. https://doi.org/10.1139/x87-128
Caudullo G, Tinner W, de Rigo D (2016) Picea abies in Europe: distribution, habitat, usage and threats. In: San-Miguel-Ayanz J, de Rigo D, Caudullo G, Houston Durrant T, Mauri A (Eds.) European Atlas of Forest Tree Species. Luxembourg, pp 114–116
Cramer MD, Hawkins HJ, Verboom GA (2009) The importance of nutritional regulation of plant water flux. Oecologia 161:15–24. https://doi.org/10.1007/s00442-009-1364-3
Defrenne CE, Childs J, Fernandez CW, Taggart M, Nettles WR, Allen MF, Hanson PJ, Iversen CM (2021) High-resolution minirhizotrons advance our understanding of root-fungal dynamics in an experimentally warmed peatland. Plants People Planet 3(5):640–652. https://doi.org/10.1002/ppp3.10172
Esri Inc. (2021) ArcGIS Pro 2.8. Retrieved from https://www.esri.com/enus/arcgis/products/arcgis-pro/
Estonian Environment Agency NFI (2019) ISSN (e-väljaanne):2382–7068. pp 23
Ferri C, Hernández-Orallo J, Modroiu R (2009) An experimental comparison of performance measures for classification. Pattern Recognit Lett 30(1):27–38. https://doi.org/10.1016/j.patrec.2008.08.010
French A, Ubeda-Tomás S, Holman TJ, Bennett MJ, Pridmore T (2009) High-throughput quantification of root growth using a novel image-analysis tool. Plant Physiol 150(4):1784–1795. https://doi.org/10.1104/pp.109.140558
Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska-Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon-Cochard C, Rose L, Ryser P, Scherer-Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde-Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Å, Lambers H, Salmon V, Tharayil N, McCormack ML (2021) A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. New Phytol 232(3):973–1122. https://doi.org/10.1111/nph.17572
Fusseder A (1987) The longevity and activity of the primary root of maize. Plant Soil 101:257–265. https://doi.org/10.1007/BF02370653
Gessler A, Schneider S, Von Sengbusch D, Weber P, Hanamann U, Huber C, Rothe A, Kreutzer K, Rennenberg H (1998) Field and laboratory experiments on net uptake of nitrate and ammonium by the roos of spruce (Picea abies) and beech (Fagus sylvatica) trees. New Phytol 138:275–285
Godbold D, Tullus A, Kupper P, Sõber J, Ostonen I, Godbold JA, Lukac M, Ahmed IU, Smith AR (2014) Elevated atmospheric CO2 and humidity delay leaf fall in Betula pendula, but not in Alnus glutinosa or Populus tremula × tremuloides. Ann For Sci 71(8):831–842. https://doi.org/10.1007/s13595-014-0382-4
Goldfarb D, Hendrick R, Pregitzer K (1990) Seasonal nitrogen and carbon concentrations in white, brown and woody fine roots of sugar maple (Acer saccharum Marsh). Plant Soil 126(1):144–148
González A, Sevillano X, Betegón-Putze I, Blasco-Escámez D, Ferrer M, Caño-Delgado AI (2020) MyROOT 2.0: An automatic tool for high throughput and accurate primary root length measurement. Comput Electron Agric 168:105125. https://doi.org/10.1016/j.compag.2019.105125
Han E, Smith AG, Kemper R, White R, Kirkegaard JA, Thorup-Kristensen K, Athmann M (2021) Digging roots is easier with AI. J Exp Bot 72(13):4680–4690. https://doi.org/10.1093/jxb/erab174
Henry CM, Deacon JW (1981) Natural (non-pathogenic) death of the cortex of wheat and barley seminal roots, as evidenced by nuclear staining with acridine orange. Plant Soil 60:255–274. https://doi.org/10.1007/BF02374110
Holden J (1975) Use of nuclear staining to assess rates of cell death in cortices of cereal roots. Soil Biol Biochem 7:333–334
Kupper P, Sõber J, Sellin A, Lõhmus K, Tullus A, Räim O, Lubenets K, Tulva I, Uri V, Zobel M, Kull O, Sõber A (2011) An experimental facility for free air humidity manipulation (FAHM) can alter water flux through deciduous tree canopy. Environ Exp Bot 72(3):432–438. https://doi.org/10.1016/j.envexpbot.2010.09.003
Kupper P, Rohula-Okunev G, Tullus A, Tulva I, Merilo E, Sellin A (2022) Long-term effect of elevated air humidity on seasonal variability in diurnal leaf conductance and gas exchange in silver birch. Can J For Res (in press). https://doi.org/10.1139/cjfr-2021-0236
Lehtonen A, Palviainen M, Ojanen P, Kalliokoski T, Nöjd P, Kukkola M, Penttilä T, Mäkipää R, Leppälammi-Kujansuu J, Helmisaari H-S (2016) Modelling fine root biomass of boreal tree stands using site and stand variables. For Ecol Manag 359:361–369. https://doi.org/10.1016/j.foreco.2015.06.023
Lu W, Li Y, Deng Y (2019) Root phenotypic detection of different vigorous maize seeds based on Progressive Corrosion Joining algorithm of image. Plant Methods 15(137). https://doi.org/10.1186/s13007-019-0518-5
Lupi C, Morin H, Deslauriers A, Rossi S, Houle D (2013) Role of soil nitrogen for the conifers of the boreal forest: A critical review. Int J Plant Soil Sci 2(2):155–189
McCormack ML, Dickie IA, Eissenstat DM, Fahey TJ, Fernandez CW, Guo D, Helmisaari HS, Hobbie EA, Iversen CM, Jackson RB, Leppälammi-Kujansuu J, Norby RJ, Phillips RP, Pregitzer KS, Pritchard SG, Rewald B, Zadworny M (2015) Redefining fine roots improves understanding of belowground contributions to terrestrial biosphere processes. New Phytol 207(3):505–518. https://doi.org/10.1111/nph.13363
McCrady RL, Comerford NB (1998) Morphological and anatomical relationships of loblolly pine fine roots. Trees 12:431–437
Menze BH, Jakab A, Bauer S, Kalpathy-Cramer J, Farahani K, Kirby J, Burren Y, Porz N, Slotboom J, Wiest R, Lanczi L, Gerstner E, Weber MA, Arbel T, Avants BB, Ayache N, Buendia P, Collins DL, Cordier N, van Leemput K (2015) The multimodal brain tumor image segmentation benchmark (BRATS). IEEE Trans Med Imaging 34(10):1993–2024. https://doi.org/10.1109/TMI.2014.2377694
Mohamed A, Monnier Y, Mao Z, Lobet G, Maeght JL, Ramel M, Stokes A (2017) An evaluation of inexpensive methods for root image acquisition when using rhizotrons. Plant Methods 13(11). https://doi.org/10.1186/s13007-017-0160-z
Naeem A, French AP, Wells DM, Pridmore TP (2011) High-throughput feature counting and measurement of roots. Bioinformatics 27(9):1337–1338. https://doi.org/10.1093/bioinformatics/btr126
Narisetti N, Henke M, Seiler C, Junker A, Ostermann J, Altmann T, Gladilin E (2021) Fully-automated root image analysis (faRIA). Sci Rep 11(16047). https://doi.org/10.1038/s41598-021-95480-y
Nordborg F, Nilsson U (2003) Growth, damage and net nitrogen uptake in Picea abies (L.) Karst. seedlings, effects of site preparation and fertilisation. Ann For Sci 60(7):657–666. https://doi.org/10.1051/forest:2003058
Ostonen I, Truu M, Helmisaari H-S, Lukac M, Borken W, Vanguelova E, Godbold DL, Lõhmus K, Zang U, Tedersoo L, Preem J-K, Rosenvald K, Aosaar J, Armolaitis K, Frey J, Kabral N, Kukumägi M, Leppälammi-Kujansuu J, Lindroos A-J, Merilä P, Napa Ü, Nöjd P, Parts K, Uri V, Varik M, Truu J (2017) Adaptive root foraging strategies along a boreal-temperate forest gradient. New Phytol 215:977–991. https://doi.org/10.1111/nph.14643
Psarras G, Merwin IA, Lakso AN, Ray JA (2000) Root growth phenology, root longevity, and rhizosphere respiration of field grown ‘Mutsu’ apple trees on ‘Malling 9’ rootstock. J Am Soc Hortic Sci 125(5):596–602. https://doi.org/10.21273/JASHS.125.5.596
Puhe J (2003) Growth and development of the root system of Norway spruce (Picea abies) in forest stands-a review. For Ecol Manag 175:253–273
Rewald B, Seehra L, Hadar O, Sofer A, Baykalov P, Elmakies M, Bodner G, Zhou K, Lazarovitch N (2020) Enabling next level research on roots: Automatizing Minirhizotron Image Acquisition and Analysis (NextMR-IAA) for Research and Agricultural Management. ATTRACT Final Conference, Sep 2020, Online Conference, Switzerland, hal-02927075
Rogers WS (1939) Root studies VIII. Apple root growth in relationto rootstock, soil, seasonal and climatic factors. J Pomology Hortic Sci 17:99–130. https://doi.org/10.1080/03683621.1940.11513533
Rongsawat T, Peltier JB, Boyer JC, Véry AA, Sentenac H (2021) Looking for Root Hairs to Overcome Poor Soils. Trends Plant Sci 26(1):83–94. https://doi.org/10.1016/j.tplants.2020.09.001
Rosenvald K, Tullus A, Ostonen I, Uri V, Kupper P, Aosaar J, Varik M, Sõber J, Niglas A, Hansen R, Rohula G, Kukk M, Sõber A, Lõhmus K (2014) The effect of elevated air humidity on young silver birch and hybrid aspen biomass allocation and accumulation–Acclimation mechanisms and capacity. For Ecol Manag 330:252–260. https://doi.org/10.1016/j.foreco.2014.07.016
Scoccimarro E, Gualdi S, Bellucci A, Zampieri M, Navarra A (2013) Heavy precipitation events in a warmer climate: results from CMIP5 models. J Clim 26(20):7902–7911. https://doi.org/10.1175/JCLI-D-12-00850.1
Seethepalli A, Dhakal K, Griffiths M, Guo H, Freschet GT, York LM (2021) RhizoVision Explorer: open-source software for root image analysis and measurement standardization. AoB Plants 13(6). https://doi.org/10.1093/aobpla/plab056
Sell M, Ostonen I, Rohula-Okunev G, Rusalepp L, Rezapour A, Kupper P (2022) Responses of fine root exudation, respiration and morphology in three early successional tree species to increased air humidity and different soil nitrogen sources. Tree Physiol 42(3):557–569. https://doi.org/10.1093/treephys/tpab118
Sellin A, Alber M, Keinänen M, Kupper P, Lihavainen J, Lõhmus K, Oksanen E, Sõber A, Sõber J, Tullus A (2017) Growth of northern deciduous trees under increasing atmospheric humidity: possible mechanisms behind the growth retardation. Reg Envriron Chang 17(7):2135–2148. https://doi.org/10.1007/s10113-016-1042-z
Smith AG, Han E, Petersen J, Olsen NAF, Giese C, Athmann M, Dresbøll DB, Thorup-Kristensen K (2020) RootPainter: Deep learning segmentation of biological images with corrective annotation. Bioarxiv. https://doi.org/10.1101/2020.04.16.044461
Smith AG, Petersen J, Selvan R, Rasmussen CR (2020b) Segmentation of roots in soil with U-Net. Plant Methods 16(13). https://doi.org/10.1186/s13007-020-0563-0
Soares PP, de Cairo S, da Silva PAR, Matsumoto LD, do Bonfim SN, Barbosa RAA, Sá MP, Almeida MC, Mesquita MF (2021) Mitigating water stress by increasing NO3–: NH4 + ratio in young Eucalyptus urophylla plants. Trees. https://doi.org/10.1007/s00468-021-02183-y
Svane SF, Dam EB, Carstensen JM, Thorup-Kristensen K (2019) A multispectral camera system for automated minirhizotron image analysis. Plant Soil 441(1):657–672. https://doi.org/10.1007/s11104-019-04132-8
Tullus A, Kupper P, Sellin A, Parts L, Sober J, Tullus T, Lohmus K, Sober A, Tullus H (2012) Climate change at northern latitudes: rising atmospheric humidity decreases transpiration, N-uptake and growth rate of hybrid aspen. PLoS ONE 7(8):e42648. https://doi.org/10.1371/journal.pone.0042648
Tullus A, Kupper P, Kaasik A, Tullus H, Lõhmus K, Sõber A, Sellin A (2017) The competitive status of trees determines their responsiveness to increasing atmospheric humidity – a climate trend predicted for northern latitudes. Glob Change Biol 23(5):1961–1974. https://doi.org/10.1111/gcb.13540
Vincent C, Rowland D, Na C, Schaffer B (2017) A high-throughput method to quantify root hair area in digital images taken in situ. Plant Soil 412(1–2):61–80. https://doi.org/10.1007/s11104-016-3016-9
Wang T, Rostamza M, Song Z, Wang L, McNickle G, Iyer-Pascuzzi AS, Qiu Z, Jin J (2019) SegRoot: A high throughput segmentation method for root image analysis. Comput Electron Agric 162:845–854. https://doi.org/10.1016/j.compag.2019.05.017
Wells CE, Eissenstat DM (2001) Marked differences in survivorship among apple roots of different diameters. Ecology 82(3):882–892. https://doi.org/10.1890/0012-9658(2001)082[0882:MDISAA]2.0.CO;2
Wells CE, Eissenstat DM (2003) Beyond the roots of young seedlings: The influence of age and order on fine root physiology. J Plant Growth Regul 21(4):324–334. https://doi.org/10.1007/s00344-003-0011-1
Wells CE, Glenn DM, Eissenstat DM (2002) Soil insects alter fine root demography in peach (Prunus persica). Plant Cell Environ 25:431–439. https://doi.org/10.1046/j.1365-3040.2002.00793.x
Withington JM, Reich PB, Oleksyn J, Eissenstat DM (2006) Comaprisons of structure and life span in roots and leaves among temperate trees. Ecol Monogr 76(3):381–397
Wojciechowska N, Sobieszczuk-Nowicka E, Bagniewska-Zadworna A (2018) Plant organ senescence – regulation by manifold pathways. Plant Biol 20(2):167–181. https://doi.org/10.1111/plb.12672
Wojciechowska N, Marzec-Schmidt K, Kalemba EM, Ludwików A, Bagniewska-Zadworna A (2020) Seasonal senescence of leaves and roots of populus trichocarpa-is the scenario the same or different? Tree Physiol 40(8):987–1000. https://doi.org/10.1093/TREEPHYS/TPAA019
Xiao M, Yu Z, Kong D, Gu X, Mammarella I, Montagnani L, Arain MA, Merbold L, Magliulo V, Lohila A, Buchmann N, Wolf S, Gharun M, Hörtnagl L, Beringer J, Gioli B (2020) Stomatal response to decreased relative humidity constrains the acceleration of terrestrial evapotranspiration. Environ Res Lett 15(9). https://doi.org/10.1088/1748-9326/ab9967
Xie L, Zhou X, Liu Q, Zhao C, Yin C (2021) Inorganic nitrogen uptake rate of Picea asperata curtailed by fine root acclimation to water and nitrogen supply and further by ectomycorrhizae. Physiol Plant 173(4):2130–2141. https://doi.org/10.1111/ppl.13562
Yasrab R, Atkinson JA, Wells DM, French AP, Pridmore TP, Pound MP (2019) RootNav 2.0: Deep learning for automatic navigation of complex plant root architectures. GigaScience 8(11):1–16. https://doi.org/10.1093/gigascience/giz123
Zadworny M, Eissenstat DM (2011) Contrasting the morphology, anatomy and fungal colonization of new pioneer and fibrous roots. New Phytol 190(1):213–221. https://doi.org/10.1111/j.1469-8137.2010.03598.x
Zeng G, Birchfield ST, Wells CE (2008) Automatic discrimination of fine roots in minirhizotron images. New Phytol 177(2):549–557. https://doi.org/10.1111/j.1469-8137.2007.02271.x
Acknowledgements
We thank Dr. Katrin Rosenvald for the pre-submission review of the manuscript and Prof. Krista Lõhmus for her advice in statistics. This study was funded by the Estonian Research Council grants (PRG916, PUT1350), the European Regional Development Fund (Center of Excellence EcolChange), and the Academy of Finland (PEATSPEC, decision no 341963, Iuliia Burdun).
Funding
This study was funded by the Estonian Research Council grants (PRG916, PUT1350), the European Regional Development Fund (Center of Excellence EcolChange), and the Academy of Finland (PEATSPEC, decision no 341963, Iuliia Burdun).
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This research was designed by Ivika Ostonen and Marili Sell. The growth chamber experiment was led by Priit Kupper. Marili Sell, Gristin Rohula-Okunev and Priit Kupper took care of plants on a daily basis. Marili Sell and Ivika Ostonen performed the imaging and analysis. Abraham G. Smith and Iuliia Burdun introduced deep-learning approach. Marili Sell, Iuliia Burdun and Ivika Ostonen conducted statistical analysis. Marili Sell wrote the manuscript with the support from Ivika Ostonen. All authors contributed to the manuscript revisions and improvements until the final version.
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Sell, M., Smith, A.G., Burdun, I. et al. Assessing the fine root growth dynamics of Norway spruce manipulated by air humidity and soil nitrogen with deep learning segmentation of smartphone images. Plant Soil 480, 135–150 (2022). https://doi.org/10.1007/s11104-022-05565-4
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DOI: https://doi.org/10.1007/s11104-022-05565-4