References
Alphei, J., & Scheu, S. (1993). Effects of biocidal treatments on biological and nutritional properties of a mull-structured woodland soil. In L. Brussaard & M. J. Kooistra (Eds.), Soil Structure/Soil Biota Interrelationships (pp. 435–448). Elsevier. https://doi.org/10.1016/B978-0-444-81490-6.50035-2
Baldwin, I. T., Halitschke, R., Paschold, A., Dahl, C. C. von, & Preston, C. A. (2006). Volatile Signaling in Plant-Plant Interactions: “Talking Trees” in the Genomics Era. Science , 311 (5762), 812–815. https://doi.org/10.1126/science.1118446
Bardgett, R. D., & van der Putten, W. H. (2014). Belowground biodiversity and ecosystem functioning. Nature , 515 (7528), 505–511. https://doi.org/10.1038/nature13855
Bardgett, R. D., & Wardle, D. A. (2010). Aboveground-Belowground Linkages: Biotic Interactions, Ecosystem Processes, and Global Change . Oxford University Press.
Barry, K. E., Mommer, L., van Ruijven, J., Wirth, C., Wright, A. J., Bai, Y., Connolly, J., De Deyn, G. B., de Kroon, H., Isbell, F., Milcu, A., Roscher, C., Scherer-Lorenzen, M., Schmid, B., & Weigelt, A. (2019). The Future of Complementarity: Disentangling Causes from Consequences. Trends in Ecology & Evolution , 34 (2), 167–180. https://doi.org/10.1016/j.tree.2018.10.013
Benton, H. P., Want, E. J., & Ebbels, T. M. D. (2010). Correction of mass calibration gaps in liquid chromatography–mass spectrometry metabolomics data. Bioinformatics , 26 (19), 2488–2489. https://doi.org/10.1093/bioinformatics/btq441
Bezemer, T. M., De Deyn, G. B., Bossinga, T. M., Van Dam, N. M., Harvey, J. A., & Van der Putten, W. H. (2005). Soil community composition drives aboveground plant–herbivore–parasitoid interactions.Ecology Letters , 8 (6), 652–661. https://doi.org/10.1111/j.1461-0248.2005.00762.x
Bezemer, T. M., Fountain, M. T., Barea, J. M., Christensen, S., Dekker, S. C., Duyts, H., van Hal, R., Harvey, J. A., Hedlund, K., Maraun, M., Mikola, J., Mladenov, A. G., Robin, C., Ruiter, D., C, P., Scheu, S., Setälä, H., Šmilauer, P., Putten, V. D., & H, W. (2010). Divergent composition but similar function of soil food webs of individual plants: Plant species and community effects. Ecology , 91 (10), 3027–3036. https://doi.org/10.1890/09-2198.1
Bezemer, T. M., & van Dam, N. M. (2005). Linking aboveground and belowground interactions via induced plant defenses. Trends in Ecology & Evolution , 20 (11), 617–624. https://doi.org/10.1016/j.tree.2005.08.006
Bowers, M. D., & Puttick, G. M. (1988). Response of generalist and specialist insects to qualitative allelochemical variation.Journal of Chemical Ecology , 14 (1), 319–334. https://doi.org/10.1007/BF01022549
Broz, A. K., Broeckling, C. D., De-la-Peña, C., Lewis, M. R., Greene, E., Callaway, R. M., Sumner, L. W., & Vivanco, J. M. (2010). Plant neighbor identity influences plant biochemistry and physiology related to defense. BMC Plant Biology , 10 (1), 115. https://doi.org/10.1186/1471-2229-10-115
Castagneyrol, B., Jactel, H., Vacher, C., Brockerhoff, E. G., & Koricheva, J. (2014). Effects of plant phylogenetic diversity on herbivory depend on herbivore specialization. Journal of Applied Ecology , 51 (1), 134–141. https://doi.org/10.1111/1365-2664.12175
Chambers, M. C., Maclean, B., Burke, R., Amodei, D., Ruderman, D. L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., & Egertson, J. (2012). A cross-platform toolkit for mass spectrometry and proteomics.Nature Biotechnology , 30 (10), 918–920. https://doi.org/10.1038/nbt.2377
Conrath, U., Beckers, G. J. M., Flors, V., García-Agustín, P., Jakab, G., Mauch, F., Newman, M.-A., Pieterse, C. M. J., Poinssot, B., Pozo, M. J., Pugin, A., Schaffrath, U., Ton, J., Wendehenne, D., Zimmerli, L., & Mauch-Mani, B. (2006). Priming: Getting Ready for Battle.Molecular Plant-Microbe Interactions® , 19 (10), 1062–1071. https://doi.org/10.1094/MPMI-19-1062
Cortois, R., Schröder-Georgi, T., Weigelt, A., van der Putten, W. H., & De Deyn, G. B. (2016). OLD DO NOT USE Plant–soil feedbacks: Role of plant functional group and plant traits. Journal of Ecology , n/a-n/a. https://doi.org/10.1111/1365-2745.12643
de Souza, R. S. C., Armanhi, J. S. L., & Arruda, P. (2020). From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency. Frontiers in Plant Science , 11 . https://doi.org/10.3389/fpls.2020.01179
Ebeling, A., Pompe, S., Baade, J., Eisenhauer, N., Hillebrand, H., Proulx, R., Roscher, C., Schmid, B., Wirth, C., & Weisser, W. W. (2014). A trait-based experimental approach to understand the mechanisms underlying biodiversity–ecosystem functioning relationships.Basic and Applied Ecology , 15 (3), 229–240. https://doi.org/10.1016/j.baae.2014.02.003
Eisenhauer, N. (2012). Aboveground–belowground interactions as a source of complementarity effects in biodiversity experiments. Plant and Soil , 351 (1–2), 1–22. https://doi.org/10.1007/s11104-011-1027-0
Eisenhauer, N., Bonkowski, M., Brose, U., Buscot, F., Durka, W., Ebeling, A., Fischer, M., Gleixner, G., Heintz-Buschart, A., Hines, J., Jesch, A., Lange, M., Meyer, S., Roscher, C., Scheu, S., Schielzeth, H., Schloter, M., Schulz, S., Unsicker, S., … Schmid, B. (2019). Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships. Research Ideas and Outcomes: The Open Science Journal , 5 , e47042. https://doi.org/10.3897/rio.5.e47042
Ferlian, O., Biere, A., Bonfante, P., Buscot, F., Eisenhauer, N., Fernandez, I., Hause, B., Herrmann, S., Krajinski-Barth, F., Meier, I. C., Pozo, M. J., Rasmann, S., Rillig, M. C., Tarkka, M. T., van Dam, N. M., Wagg, C., & Martinez-Medina, A. (2018). Growing Research Networks on Mycorrhizae for Mutual Benefits. Trends in Plant Science ,23 (11), 975–984. https://doi.org/10.1016/j.tplants.2018.08.008
Fernandez, C., Monnier, Y., Santonja, M., Gallet, C., Weston, L. A., Prévosto, B., Saunier, A., Baldy, V., & Bousquet-Mélou, A. (2016). The Impact of Competition and Allelopathy on the Trade-Off between Plant Defense and Growth in Two Contrasting Tree Species. Frontiers in Plant Science , 7 , 594. https://doi.org/10.3389/fpls.2016.00594
Finch, S., & Collier, R. H. (2000). Host-plant selection by insects – a theory based on ‘appropriate/inappropriate landings’ by pest insects of cruciferous plants. Entomologia Experimentalis et Applicata ,96 (2), 91–102. https://doi.org/10.1046/j.1570-7458.2000.00684.x
Gehring, C. A., & Whitham, T. G. (1994). Interactions between aboveground herbivores and the mycorrhizal mutualists of plants.Trends in Ecology & Evolution , 9 (7), 251–255. https://doi.org/10.1016/0169-5347(94)90290-9
Hamilton, E. W., & Frank, D. A. (2001). Can Plants Stimulate Soil Microbes and Their Own Nutrient Supply? Evidence from a Grazing Tolerant Grass. Ecology , 82 (9), 2397–2402. https://doi.org/10.1890/0012-9658(2001)082[2397:CPSSMA]2.0.CO;2
Hol, W. H. G., de Boer, W., Termorshuizen, A. J., Meyer, K. M., Schneider, J. H. M., van Dam, N. M., van Veen, J. A., & van der Putten, W. H. (2010). Reduction of rare soil microbes modifies plant-herbivore interactions. Ecology Letters , 13 (3), 292–301. https://doi.org/10.1111/j.1461-0248.2009.01424.x
Huber, W., Carey, V. J., Gentleman, R., Anders, S., Carlson, M., Carvalho, B. S., Bravo, H. C., Davis, S., Gatto, L., Girke, T., Gottardo, R., Hahne, F., Hansen, K. D., Irizarry, R. A., Lawrence, M., Love, M. I., MacDonald, J., Obenchain, V., Oleś, A. K., … Morgan, M. (2015). Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods , 12 (2), 115–121. https://doi.org/10.1038/nmeth.3252
Huberty, M., Choi, Y. H., Heinen, R., & Bezemer, T. M. (2020). Above-ground plant metabolomic responses to plant–soil feedbacks and herbivory. Journal of Ecology , 108 (4), 1703–1712. https://doi.org/10.1111/1365-2745.13394
Kaplan, I., Halitschke, R., Kessler, A., Sardanelli, S., & Denno, R. F. (2008). Constitutive and induced defenses to herbivory in above- and belowground plant tissues. Ecology , 89 (2), 392–406. https://doi.org/10.1890/07-0471.1
Karban, R., & Baldwin, I. T. (1997). Induced Responses to Herbivory . University of Chicago Press. https://press.uchicago.edu/ucp/books/book/chicago/I/bo3644508.html
Kos, M., Bukovinszky, T., Mulder, P. P. J., & Bezemer, T. M. (2015). Disentangling above- and belowground neighbor effects on the growth, chemistry, and arthropod community on a focal plant. Ecology ,96 (1), 164–175. https://doi.org/10.1890/14-0563.1
Kuhl, C., Tautenhahn, R., Böttcher, C., Larson, T. R., & Neumann, S. (2012). CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets.Analytical Chemistry , 84 (1), 283–289. https://doi.org/10.1021/ac202450g
Latz, E., Eisenhauer, N., Rall, B. C., Allan, E., Roscher, C., Scheu, S., & Jousset, A. (2012). Plant diversity improves protection against soil-borne pathogens by fostering antagonistic bacterial communities.Journal of Ecology , 100 (3), 597–604. https://doi.org/10.1111/j.1365-2745.2011.01940.x
Lohmann, M., Scheu, S., & Müller, C. (2009). Decomposers and root feeders interactively affect plant defence in Sinapis alba.Oecologia , 160 (2), 289–298. https://doi.org/10.1007/s00442-009-1306-0
Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology , 15 (12), 550. https://doi.org/10.1186/s13059-014-0550-8
Martinez-Medina, A., Flors, V., Heil, M., Mauch-Mani, B., Pieterse, C. M. J., Pozo, M. J., Ton, J., van Dam, N. M., & Conrath, U. (2016). Recognizing Plant Defense Priming. Trends in Plant Science ,21 (10), 818–822. https://doi.org/10.1016/j.tplants.2016.07.009
Mithöfer, A., & Boland, W. (2008). Recognition of Herbivory-Associated Molecular Patterns. Plant Physiology , 146 (3), 825–831. https://doi.org/10.1104/pp.107.113118
Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P. R., O’Hara, R. B., Simpson, G. L., Solymos, P., Stevens, M. H. H., Szoecs, E., & Wagner, H. (2020). vegan: Community Ecology Package . https://CRAN.R-project.org/package=vegan
Oliver, S. G., Winson, M. K., Kell, D. B., & Baganz, F. (1998). Systematic functional analysis of the yeast genome. Trends in Biotechnology , 16 (9), 373–378. https://doi.org/10.1016/S0167-7799(98)01214-1
Peñuelas, J., & Sardans, J. (2009). Ecological metabolomics.Chemistry and Ecology , 25 (4), 305–309. https://doi.org/10.1080/02757540903062517
Peters, K., Worrich, A., Weinhold, A., Alka, O., Balcke, G., Birkemeyer, C., Bruelheide, H., Calf, O. W., Dietz, S., Dührkop, K., Gaquerel, E., Heinig, U., Kücklich, M., Macel, M., Müller, C., Poeschl, Y., Pohnert, G., Ristok, C., Rodríguez, V. M., … Dam, N. M. van. (2018). Current Challenges in Plant Eco-Metabolomics. International Journal of Molecular Sciences , 19 (5). https://doi.org/10.3390/ijms19051385
R Core Team. (2020). R: A Language and Environment for Statistical Computing . R Foundation for Statistical Computing. https://www.R-project.org/
Ristok, C., Poeschl, Y., Dudenhöffer, J.-H., Ebeling, A., Eisenhauer, N., Vergara, F., Wagg, C., Dam, N. M. van, & Weinhold, A. (2019). Plant species richness elicits changes in the metabolome of grassland species via soil biotic legacy. Journal of Ecology , 107 (5), 2240–2254. https://doi.org/10.1111/1365-2745.13185
Rivero, J., Gamir, J., Aroca, R., Pozo, M. J., & Flors, V. (2015). Metabolic transition in mycorrhizal tomato roots. Frontiers in Microbiology , 6 , 598. https://doi.org/10.3389/fmicb.2015.00598
Rohart, F., Gautier, S. D. with key contributors B., Singh, A., & Le Cao, K.-A. (2017). mixOmics: An R package for ’omics feature selection and multiple data integration. PLoS Computational Biology ,13 (11), e1005752.
Ryals, J., Neuenschwander, U., Willits, M., Molina, A., Steiner, H., & Hunt, M. (1996). Systemic Acquired Resistance. The Plant Cell ,8 (10), 1809–1819.
Scherling, C., Roscher, C., Giavalisco, P., Schulze, E.-D., & Weckwerth, W. (2010). Metabolomics Unravel Contrasting Effects of Biodiversity on the Performance of Individual Plant Species. PLoS ONE , 5 (9), 1–13. https://doi.org/10.1371/journal.pone.0012569
Smith, C. A., Want, E. J., O’Maille, G., Abagyan, R., & Siuzdak, G. (2006). XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification.Analytical Chemistry , 78 (3), 779–787. https://doi.org/10.1021/ac051437y
Tautenhahn, R., Böttcher, C., & Neumann, S. (2008). Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics ,9 , 504. https://doi.org/10.1186/1471-2105-9-504
Treutter, D. (2006). Significance of flavonoids in plant resistance: A review. Environmental Chemistry Letters , 4 (3), 147–157. https://doi.org/10.1007/s10311-006-0068-8
Trevors, J. T. (1996). Sterilization and inhibition of microbial activity in soil. Journal of Microbiological Methods ,26 (1), 53–59. https://doi.org/10.1016/0167-7012(96)00843-3
van Dam, N. M. (2009). Belowground Herbivory and Plant Defenses.Annual Review of Ecology, Evolution, and Systematics ,40 (1), 373–391. https://doi.org/10.1146/annurev.ecolsys.110308.120314
van Dam, N. M., & Baldwin, I. T. (2001). Competition mediates costs of jasmonate-induced defences, nitrogen acquisition and transgenerational plasticity in Nicotiana attenuata. Functional Ecology ,15 (3), 406–415. https://doi.org/10.1046/j.1365-2435.2001.00533.x
van Dam, N. M., & Heil, M. (2011). Multitrophic interactions below and above ground: En route to the next level. Journal of Ecology ,99 (1), 77–88. https://doi.org/10.1111/j.1365-2745.2010.01761.x
Van Der Heijden, M. G. A., Bardgett, R. D., & Van Straalen, N. M. (2008). The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology Letters ,11 (3), 296–310. https://doi.org/10.1111/j.1461-0248.2007.01139.x
van der Putten, W. H., Bardgett, R. D., Bever, J. D., Bezemer, T. M., Casper, B. B., Fukami, T., Kardol, P., Klironomos, J. N., Kulmatiski, A., Schweitzer, J. A., Suding, K. N., Van de Voorde, T. F. J., & Wardle, D. A. (2013). Plant-soil feedbacks: The past, the present and future challenges. Journal of Ecology , 101 (2), 265–276. https://doi.org/10.1111/1365-2745.12054
van Moorsel, S. J., Hahl, T., Wagg, C., De Deyn, G. B., Flynn, D. F. B., Zuppinger-Dingley, D., & Schmid, B. (2018). Community evolution increases plant productivity at low diversity. Ecology Letters ,21 (1), 128–137. https://doi.org/10.1111/ele.12879
Wardle, D. A., Bardgett, R. D., Klironomos, J. N., Setälä, H., Putten, W. H. van der, & Wall, D. H. (2004). Ecological Linkages Between Aboveground and Belowground Biota. Science , 304 (5677), 1629–1633. https://doi.org/10.1126/science.1094875
Whitehead, S. R., Bass, E., Corrigan, A., Kessler, A., & Poveda, K. (2021). Interaction diversity explains the maintenance of phytochemical diversity. Ecology Letters , 24 (6), 1205–1214. https://doi.org/10.1111/ele.13736
Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis . Springer-Verlag New York. https://ggplot2.tidyverse.org
Wurst, S., Wagenaar, R., Biere, A., & Van der Putten, W. H. (2010). Microorganisms and nematodes increase levels of secondary metabolites in roots and root exudates of Plantago lanceolata. Plant & Soil ,329 (1/2), 117–126. https://doi.org/10.1007/s11104-009-0139-2
Zuppinger-Dingley, D., Flynn, D. F. B., Brandl, H., & Schmid, B. (2015). Selection in monoculture vs. Mixture alters plant metabolic fingerprints. Journal of Plant Ecology , 8 (5), 549–557. https://doi.org/10.1093/jpe/rtu043