References:
Allaby R.G., Stevens C.J., Kistler L. & Fuller D.Q. (2022) Emerging evidence of plant domestication as a landscape-level process.Trends in ecology & evolution 37 , 268–279.
Amrhein V. & Greenland S. (2018) Remove, rather than redefine, statistical significance. Nature human behaviour 2 , 4.
Bergmann J., Weigelt A., van der Plas F., Laughlin D.C., Kuyper T.W., Guerrero-Ramirez N., … Mommer L. (2020) The fungal collaboration gradient dominates the root economics space in plants. Science advances 6 .
Berner D. & Amrhein V. (2022) Why and how we should join the shift from significance testing to estimation. Journal of evolutionary biology 35 , 777–787.
Bulgarelli D., Garrido-Oter R., Münch P.C., Weiman A., Dröge J., Pan Y., … Schulze-Lefert P. (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell host & microbe 17 , 392–403.
Csardi G. & Nepusz T. (2006) The igraph software package for complex network research. InterJournal , 1695.
Fernandez A.R., Sáez A., Quintero C., Gleiser G. & Aizen M.A. (2021) Intentional and unintentional selection during plant domestication: herbivore damage, plant defensive traits and nutritional quality of fruit and seed crops. The New phytologist 231 , 1586–1598.
Flores-Moreno H., Fazayeli F., Banerjee A., Datta A., Kattge J., Butler E.E., … Reich P.B. (2019) Robustness of trait connections across environmental gradients and growth forms. Global ecology and biogeography: a journal of macroecology 28 , 1806–1826.
Guo H., Ayalew H., Seethepalli A., Dhakal K., Griffiths M., Ma X.-F. & York L.M. (2021) Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture. The New phytologist 232 , 98–112.
Halsey L.G. (2019) The reign of the p-value is over: what alternative analyses could we employ to fill the power vacuum? Biology letters 15 , 20190174.
Han M., Chen Y., Sun L., Yu M., Li R., Li S., … Zhu B. (2023) Linking rhizosphere soil microbial activity and plant resource acquisition strategy. The Journal of ecology .
He N., Li Y., Liu C., Xu L., Li M., Zhang J., … Yu G. (2020) Plant Trait Networks: Improved Resolution of the Dimensionality of Adaptation. Trends in ecology & evolution 35 , 908–918.
Honvault N., Houben D., Nobile C., Firmin S., Lambers H. & Faucon M.-P. (2021) Tradeoffs among phosphorus-acquisition root traits of crop species for agroecological intensification. Plant and soil461 , 137–150.
Isaac M.E., Nimmo V., Gaudin A.C.M., Leptin A., Schmidt J.E., Kallenbach C.M., … Lu X. (2021) Crop Domestication, Root Trait Syndromes, and Soil Nutrient Acquisition in Organic Agroecosystems: A Systematic Review. Frontiers in Sustainable Food Systems 5 .
Kong X., Zhang M., De Smet I. & Ding Z. (2014) Designer crops: optimal root system architecture for nutrient acquisition. Trends in biotechnology 32 , 597–598.
Kumar A., Kuzyakov Y. & Pausch J. (2016) Maize rhizosphere priming: field estimates using 13C natural abundance. Plant and soil409 , 87–97.
Kumar A. & Pausch J. (2022) Microbial nutrient limitation and catalytic adjustments revealed from a long‐term nutrient restriction experiment.Journal of Sustainable Agriculture and Environment 1 , 142–148.
Kumar A., Shahbaz M., Blagodatskaya E., Kuzyakov Y. & Pausch J. (2018) Maize phenology alters the distribution of enzyme activities in soil: Field estimates. Applied soil ecology: a section of Agriculture, Ecosystems & Environment 125 , 233–239.
Kuzyakov Y. (2002) Review: Factors affecting rhizosphere priming effects. Journal of Plant Nutrition and Soil Science165 , 382–396.
Martín-Robles N., García-Palacios P., Rodríguez M., Rico D., Vigo R., Sánchez-Moreno S., … Milla R. (2020) Crops and their wild progenitors recruit beneficial and detrimental soil biota in opposing ways. Plant and soil 456 , 159–173.
Martín-Robles N., Lehmann A., Seco E., Aroca R., Rillig M.C. & Milla R. (2018) Impacts of domestication on the arbuscular mycorrhizal symbiosis of 27 crop species. The New phytologist 218 , 322–334.
Marx M.-C., Wood M. & Jarvis S.C. (2001) A microplate fluorimetric assay for the study of enzyme diversity in soils. Soil biology & biochemistry 33 , 1633–1640.
McGonigle T.P., Miller M.H., Evans D.G., Fairchild G.L. & Swan J.A. (1990) A new method which gives an objective measure of colonization of roots by vesicular-arbuscular mycorrhizal fungi. The New phytologist 115 , 495–501.
Meister R., Rajani M.S., Ruzicka D. & Schachtman D.P. (2014) Challenges of modifying root traits in crops for agriculture. Trends in plant science 19 , 779–788.
Meyer R.S., DuVal A.E. & Jensen H.R. (2012) Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops. The New phytologist 196 , 29–48.
Milla R., Osborne C.P., Turcotte M.M. & Violle C. (2015) Plant domestication through an ecological lens. Trends in ecology & evolution 30 , 463–469.
Oksanen J., Simpson G.L., Guillaume Blanchet F., Kindt R., Legendre P., Minchin P.R., … Weedon J. (2022) Community Ecology Package [R package vegan version 2.6-4].
Parada A.E., Needham D.M. & Fuhrman J.A. (2016) Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environmental microbiology 18 , 1403–1414.
Pausch J., Loeppmann S., Kühnel A., Forbush K., Kuzyakov Y. & Cheng W. (2016) Rhizosphere priming of barley with and without root hairs.Soil biology & biochemistry 100 , 74–82.
Peres-Neto P.R., Jackson D.A. & Somers K.M. (2003) Giving meaningful interpretation to ordination axes: Assessing loading significance in principal component analysis. Ecology 84 , 2347–2363.
Pérez-Jaramillo J.E., Carrión V.J., Bosse M., Ferrão L.F.V., de Hollander M., Garcia A.A.F., … Raaijmakers J.M. (2017) Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. The ISME journal 11 , 2244–2257.
Pérez-Jaramillo J.E., Mendes R. & Raaijmakers J.M. (2016) Impact of plant domestication on rhizosphere microbiome assembly and functions.Plant molecular biology 90 , 635–644.
Phillips J.M. & Hayman D.S. (1970) Improved procedures for clearing roots and staining parasitic and vesicular-arbuscular mycorrhizal fungi for rapid assessment of infection. Transactions of the British Mycological Society 55 , 158-IN18.
Phillips R.P., Erlitz Y., Bier R. & Bernhardt E.S. (2008) New approach for capturing soluble root exudates in forest soils. Functional ecology 22 , 990–999.
Preece C., Livarda A., Christin P.-A., Wallace M., Martin G., Charles M., … Osborne C.P. (2017) How did the domestication of Fertile Crescent grain crops increase their yields? Functional ecology31 , 387–397.
Richman M.B. (1988) A cautionary note concerning a commonly applied eigenanalysis procedure. Tellus 40 , 50–58.
Rillig M.C., Aguilar-Trigueros C.A., Camenzind T., Cavagnaro T.R., Degrune F., Hohmann P., … Yang G. (2019) Why farmers should manage the arbuscular mycorrhizal symbiosis. The New phytologist222 , 1171–1175.
Ripley B. (2023) MASS: Support Functions and Datasets for Venables and Ripley’s MASS. Comprehensive R Archive Network (CRAN) .
Rose L. (2017) Pitfalls in Root Trait Calculations: How Ignoring Diameter Heterogeneity Can Lead to Overestimation of Functional Traits.Frontiers in plant science 8 , 898.
Rose L. & Lobet G. (2019) Accuracy of image analysis tools for functional root traits: A comment on Delory et al. (2017). Methods in ecology and evolution / British Ecological Society 10 , 702–711.
Roucou A., Violle C., Fort F., Roumet P., Ecarnot M. & Vile D. (2018) Shifts in plant functional strategies over the course of wheat domestication. The Journal of applied ecology 55 , 25–37.
Schindelin J., Arganda-Carreras I., Frise E., Kaynig V., Longair M., Pietzsch T., … Cardona A. (2012) Fiji: an open-source platform for biological-image analysis. Nature methods 9 , 676–682.
Schneider H.M. & Lynch J.P. (2020) Should Root Plasticity Be a Crop Breeding Target? Frontiers in plant science 11 , 546.
Seethepalli A., Dhakal K., Griffiths M., Guo H., Freschet G.T. & York L.M. (2021) RhizoVision Explorer: open-source software for root image analysis and measurement standardization. AoB plants 13 , lab056.
Simpson K.J., Wade R.N., Rees M., Osborne C.P. & Hartley S.E. (2017) Still armed after domestication? Impacts of domestication and agronomic selection on silicon defences in cereals. Functional ecology31 , 2108–2117.
Smith A.G., Han E., Petersen J., Olsen N.A.F., Giese C., Athmann M., … Thorup-Kristensen K. (2022) RootPainter: deep learning segmentation of biological images with corrective annotation. The New phytologist 236 , 774–791.
Sun L., Ataka M., Han M., Han Y., Gan D., Xu T., … Zhu B. (2021) Root exudation as a major competitive fine-root functional trait of 18 coexisting species in a subtropical forest. The New phytologist229 , 259–271.
Tracy S.R., Nagel K.A., Postma J.A., Fassbender H., Wasson A. & Watt M. (2020) Crop Improvement from Phenotyping Roots: Highlights Reveal Expanding Opportunities. Trends in plant science 25 , 105–118.
Turcotte M.M., Turley N.E. & Johnson M.T.J. (2014) The impact of domestication on resistance to two generalist herbivores across 29 independent domestication events. The New phytologist204 , 671–681.
Vance E.D., Brookes P.C. & Jenkinson D.S. (1987) An extraction method for measuring soil microbial biomass C. Soil Biology and Biochemistry 19 , 703–707.
Vierheilig H., Coughlan A.P., Wyss U. & Piche Y. (1998) Ink and vinegar, a simple staining technique for arbuscular-mycorrhizal fungi.Applied and environmental microbiology 64 , 5004–5007.
Wang X.-X., Zhang J., Wang H., Rengel Z. & Li H. (2023) Plasticity and co‐variation of root traits govern differential phosphorus acquisition among 20 wheat genotypes. Oikos 2023 .
Wen Z., Pang J., Tueux G., Liu Y., Shen J., Ryan M.H., … Siddique K.H.M. (2020) Contrasting patterns in biomass allocation, root morphology and mycorrhizal symbiosis for phosphorus acquisition among 20 chickpea genotypes with different amounts of rhizosheath carboxylates.Functional ecology 34 , 1311–1324.
Wen Z., White P.J., Shen J. & Lambers H. (2022) Linking root exudation to belowground economic traits for resource acquisition. The New phytologist 233 , 1620–1635.
Wickham H., Chang W., Henry L., Pedersen T.L., Takahashi K., Wilke C., … Posit P.B.C. (2023) ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics.
Xie J., Wang Z. & Li Y. (2022) Stomatal opening ratio mediates trait coordinating network adaptation to environmental gradients. The New phytologist 235 , 907–922.
Yang G., Roy J., Veresoglou S.D. & Rillig M.C. (2021a) Soil biodiversity enhances the persistence of legumes under climate change.The New phytologist 229 , 2945–2956.
Yang G., Ryo M., Roy J., Hempel S. & Rillig M.C. (2021b) Plant and soil biodiversity have non-substitutable stabilising effects on biomass production. Ecology letters 24 , 1582–1593.
York L.M., Cumming J.R., Trusiak A., Bonito G., von Haden A.C., Kalluri U.C., … Yang W.H. (2022a) Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production. The Plant Phenome Journal 5 .
York L.M., Griffiths M. & Maaz T.M. (2022b) Whole-plant phenotypic engineering: moving beyond ratios for multi-objective optimization of nutrient use efficiency. Current opinion in biotechnology75 , 102682.
Zachary F., Grunwald N. & Gilmore R. (2023) Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data [R package metacoder version 0.3.6].
Zhalnina K., Louie K.B., Hao Z., Mansoori N., da Rocha U.N., Shi S., … Brodie E.L. (2018) Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nature microbiology 3 , 470–480.
Zuur A.F., Ieno E.N. & Elphick C.S. (2010) A protocol for data exploration to avoid common statistical problems. Methods in ecology and evolution / British Ecological Society 1 , 3–14.