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Commit 28f77b6c authored by Felix Zimmermann's avatar Felix Zimmermann :speech_balloon:
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**Destructive Sampling Protocol**
After 64 days (set one) and 58 days (set two) of cultivation, we sampled all above- and belowground parts of the plants destructively (Table S2). We measured total plant biomass, followed by a separate weighing of above and below ground plant parts. We further divided above ground biomass into stem, leaves from the newest shoot flush, leaves from the second newest shoot flush, remaining leaves, and buds. We counted leaves from the last two shoot flushes and scanned them using an EPSON Perfection V700 Photo scanner (SEIKO Epson CORPORATION, Tokyo, Japan) to determine leave area. The root system was scanned with the same EPSON Perfection V700 Photo scanner and analyzed with WinRhizo 2003b (Regent Instruments, Québec, Canada) to quantify root parameters (total root length, total root surface area, average root diameter, total root volume, number of root tips, number of root forks, number of root crossings, length of fine roots (0–1mm diameter), surface area of fine roots (0–1 mm diameter), and volume of fine roots (0–1mm diameter)). We separated and weighed principal and lateral roots (the latter defined as diverging more than 1 cm from the principal roots). To assess mycorrhization rate, we examined root tips from ~10% of the lateral roots for colonization by *C. geophilum* and *P. croceum* versus non-mycorrhized tips. Finally, we dried all plant materials at 55°C for two weeks and measured dry weights.
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File added
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Zurich
tzcode source: internal
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_1.2.0 ggbeeswarm_0.7.2 emmeans_1.10.4 MASS_7.3-61 rstatix_0.7.2
[6] psych_2.4.12 ggpubr_0.6.0 magick_2.8.5 viridis_0.6.5 viridisLite_0.4.2
[11] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[16] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] beeswarm_0.4.0 gtable_0.3.5 lattice_0.22-6 tzdb_0.4.0 vctrs_0.6.5
[6] tools_4.4.1 generics_0.1.3 parallel_4.4.1 sandwich_3.1-0 fansi_1.0.6
[11] pkgconfig_2.0.3 Matrix_1.7-0 lifecycle_1.0.4 compiler_4.4.1 munsell_0.5.1
[16] mnormt_2.1.1 codetools_0.2-20 carData_3.0-5 vipor_0.4.7 pillar_1.9.0
[21] car_3.1-2 abind_1.4-5 multcomp_1.4-26 nlme_3.1-166 tidyselect_1.2.1
[26] mvtnorm_1.3-1 stringi_1.8.4 splines_4.4.1 colorspace_2.1-1 cli_3.6.3
[31] magrittr_2.0.3 survival_3.7-0 utf8_1.2.4 broom_1.0.6 TH.data_1.1-2
[36] withr_3.0.1 scales_1.3.0 backports_1.5.0 timechange_0.3.0 estimability_1.5.1
[41] gridExtra_2.3 ggsignif_0.6.4 zoo_1.8-12 hms_1.1.3 coda_0.19-4.1
[46] rlang_1.1.4 Rcpp_1.0.13 xtable_1.8-4 glue_1.8.0 rstudioapi_0.16.0
[51] R6_2.5.1
".y.","group1","group2","n1","n2","statistic","p","p.adj","p.adj.signif","Part"
"DW_Shoot","Control","Pilo",19,21,142,0.124,0.124,"ns","Shoot"
"DW_Shoot","Control","Ceno",19,24,328,0.015,0.03,"*","Shoot"
"DW_Shoot","Control","Co_Inoc",19,23,282,0.112,0.124,"ns","Shoot"
"DW_Shoot","Pilo","Ceno",21,24,479,2.56e-07,1.536e-06,"****","Shoot"
"DW_Shoot","Pilo","Co_Inoc",21,23,400,0.000103,0.000309,"***","Shoot"
"DW_Shoot","Ceno","Co_Inoc",24,23,201,0.113,0.124,"ns","Shoot"
"DW_Roots_Total","Control","Pilo",19,21,115.5,0.024,0.048,"*","Root"
"DW_Roots_Total","Control","Ceno",19,24,291,0.127,0.1905,"ns","Root"
"DW_Roots_Total","Control","Co_Inoc",19,23,246,0.495,0.594,"ns","Root"
"DW_Roots_Total","Pilo","Ceno",21,24,430.5,5.13e-05,0.0003078,"***","Root"
"DW_Roots_Total","Pilo","Co_Inoc",21,23,373,0.002,0.006,"**","Root"
"DW_Roots_Total","Ceno","Co_Inoc",24,23,252,0.62,0.62,"ns","Root"
"group1","group2","n1","n2","statistic","p","p.adj","p.adj.signif"
"Ceno","Co_Inoc",24,23,211,0.171,0.2052,"ns"
"Ceno","Control",24,19,132,0.018,0.036,"*"
"Ceno","Pilo",24,21,69,1.01e-05,6.06e-05,"****"
"Co_Inoc","Control",23,19,175,0.28,0.28,"ns"
"Co_Inoc","Pilo",23,21,100,0.000626,0.001878,"**"
"Control","Pilo",19,21,127,0.05,0.075,"ns"
"Treatment","response","SE","df","lower.CL","upper.CL","Part"
"Control",0.453567514597558,0.0275055266994483,82,0.383318509711376,0.52381651948374,"Shoot"
"Pilo",0.47366276586997,0.0291267922686154,82,0.399273055221825,0.548052476518115,"Shoot"
"Ceno",0.351858330159944,0.0256275976469571,82,0.286405548542847,0.41731111177704,"Shoot"
"Co_Inoc",0.395743444153842,0.0253353168124786,82,0.331037146615882,0.460449741691802,"Shoot"
"Control",0.332049163229227,0.0261926790038616,82,0.265153166092717,0.398945160365736,"Roots"
"Pilo",0.385646437453976,0.0277365610424506,82,0.314807371782272,0.456485503125679,"Roots"
"Ceno",0.323345119635379,0.0244043841131146,82,0.261016420478317,0.385673818792442,"Roots"
"Co_Inoc",0.337522080037482,0.0241260539375056,82,0.27590423503275,0.399139925042215,"Roots"
"contrast","estimate","SE","df","t.ratio","p.value","Part"
"Control - Pilo",-0.0200952512724119,0.0399122214934747,82,-0.503486163397278,0.615972401884668,"Shoot"
"Control - Ceno",0.101709184437615,0.0376885469832781,82,2.69867619154279,0.0253534911944604,"Shoot"
"Control - Co_Inoc",0.0578240704437162,0.0374470841340624,82,1.54415415194153,0.189602536279991,"Shoot"
"Pilo - Ceno",0.121804435710026,0.0412341308669473,82,2.95397121629798,0.0245565260402311,"Shoot"
"Pilo - Co_Inoc",0.0779193217161281,0.0399514120665197,82,1.950352132395,0.109101535219373,"Shoot"
"Ceno - Co_Inoc",-0.0438851139938983,0.0351525595011496,82,-1.24841873868283,0.258516587745045,"Shoot"
"Control - Pilo",-0.0535972742247492,0.0380071982381118,82,-1.41018745683297,0.418945708063114,"Roots"
"Control - Ceno",0.00870404359384718,0.0358896604323072,82,0.242522316706344,0.878399868322438,"Roots"
"Control - Co_Inoc",-0.00547291680825584,0.0356597226830697,82,-0.153476146096174,0.878399868322438,"Roots"
"Pilo - Ceno",0.0623013178185964,0.0392660124491575,82,1.5866474320321,0.418945708063114,"Roots"
"Pilo - Co_Inoc",0.0481243574164934,0.0380445182324155,82,1.26494853010096,0.418945708063114,"Roots"
"Ceno - Co_Inoc",-0.014176960402103,0.0334747164538472,82,-0.423512486555317,0.878399868322438,"Roots"
File added
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Zurich
tzcode source: internal
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_1.2.0 ggsignif_0.6.4 rstatix_0.7.2 ggtext_0.1.2 tidybayes_3.0.7
[6] bayestestR_0.15.0 bayesnec_2.1.3.0 posterior_1.6.1 brms_2.22.0 Rcpp_1.0.13
[11] ggpubr_0.6.0 viridis_0.6.5 viridisLite_0.4.2 lubridate_1.9.3 forcats_1.0.0
[16] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1
[21] tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] svUnit_1.0.6 tidyselect_1.2.1 loo_2.8.0 TH.data_1.1-2
[5] tensorA_0.36.2.1 estimability_1.5.1 timechange_0.3.0 lifecycle_1.0.4
[9] survival_3.7-0 magrittr_2.0.3 compiler_4.4.1 rlang_1.1.4
[13] tools_4.4.1 utf8_1.2.4 bridgesampling_1.1-2 xml2_1.3.6
[17] abind_1.4-5 multcomp_1.4-26 withr_3.0.1 fansi_1.0.6
[21] xtable_1.8-4 colorspace_2.1-1 emmeans_1.10.4 scales_1.3.0
[25] MASS_7.3-61 insight_1.0.1 cli_3.6.3 mvtnorm_1.3-1
[29] generics_0.1.3 RcppParallel_5.1.9 rstudioapi_0.16.0 tzdb_0.4.0
[33] splines_4.4.1 operator.tools_1.6.3 bayesplot_1.11.1 parallel_4.4.1
[37] matrixStats_1.3.0 vctrs_0.6.5 Matrix_1.7-0 sandwich_3.1-0
[41] carData_3.0-5 car_3.1-2 hms_1.1.3 arrayhelpers_1.1-0
[45] ggdist_3.3.2 glue_1.8.0 chk_0.10.0 codetools_0.2-20
[49] distributional_0.5.0 stringi_1.8.4 gtable_0.3.5 munsell_0.5.1
[53] pillar_1.9.0 Brobdingnag_1.2-9 R6_2.5.1 formula.tools_1.7.1
[57] evaluate_0.24.0 lattice_0.22-6 backports_1.5.0 gridtext_0.1.5
[61] broom_1.0.6 rstantools_2.4.0 coda_0.19-4.1 gridExtra_2.3
[65] nlme_3.1-166 checkmate_2.3.2 zoo_1.8-12 pkgconfig_2.0.3
This diff is collapsed.
"Treatment","estimate_absolute","se","lower_absolute","upper_absolute","estimate_relative","lower_relative","upper_relative","Significant"
"Control",3.75158564355395,0.30341765154836,3.08962655148966,4.27991445006125,0.269119327398317,-0.392839764665974,0.797448133905616,FALSE
"Ceno",2.43735227620854,0.310976910164312,2.01642282012821,2.99497488017923,-1.04511403994709,-1.46604349602742,-0.487491435976401,TRUE
"Co_Inoc",3.04927506522306,0.21381284865162,2.53520651345949,3.61145133992785,-0.433191250932575,-0.947259802696141,0.128985023772215,FALSE
"Pilo",4.69165227963698,0.295340289419153,4.06884731164184,5.1051039569049,1.20918596348135,0.586380995486205,1.62263764074927,TRUE
This diff is collapsed.
"Treatment1","Treatment2","First_Significant_Day"
"Control","Ceno",21
"Control","Pilo",33
"Control","Co_Inoc",45
"Ceno","Pilo",6
"Ceno","Co_Inoc",36
"Pilo","Co_Inoc",4
"group1","group2","n1","n2","statistic","p","p.adj","p.adj.signif","stage"
"Ceno","Co_Inoc",25,23,385,0.045,0.0675,"ns","A"
"Ceno","Control",25,21,393.5,0.004,0.012,"*","A"
"Ceno","Pilo",25,27,540.5,2e-04,0.0012,"**","A"
"Co_Inoc","Control",23,21,292,0.238,0.2856,"ns","A"
"Co_Inoc","Pilo",23,27,427.5,0.022,0.044,"*","A"
"Control","Pilo",21,27,325,0.392,0.392,"ns","A"
"Ceno","Co_Inoc",10,18,102,0.572,0.7236,"ns","B"
"Ceno","Control",10,18,89,0.98,0.98,"ns","B"
"Ceno","Pilo",10,23,144.5,0.226,0.678,"ns","B"
"Co_Inoc","Control",18,18,145.5,0.603,0.7236,"ns","B"
"Co_Inoc","Pilo",18,23,231,0.518,0.7236,"ns","B"
"Control","Pilo",18,23,259.5,0.149,0.678,"ns","B"
"Ceno","Co_Inoc",14,23,65.5,0.002,0.012,"*","C"
"Ceno","Control",14,24,118,0.117,0.234,"ns","C"
"Ceno","Pilo",14,29,108,0.008,0.024,"*","C"
"Co_Inoc","Control",23,24,314.5,0.409,0.4908,"ns","C"
"Co_Inoc","Pilo",23,29,388,0.301,0.4515,"ns","C"
"Control","Pilo",24,29,333.5,0.797,0.797,"ns","C"
"Ceno","Co_Inoc",23,31,420.5,0.263,0.3156,"ns","D"
"Ceno","Control",23,27,437,0.013,0.078,"ns","D"
"Ceno","Pilo",23,35,534.5,0.034,0.102,"ns","D"
"Co_Inoc","Control",31,27,522.5,0.102,0.204,"ns","D"
"Co_Inoc","Pilo",31,35,635.5,0.229,0.3156,"ns","D"
"Control","Pilo",27,35,413,0.392,0.392,"ns","D"
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R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Zurich
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_1.2.0 ggpubr_0.6.0 corrplot_0.94 psych_2.4.12 viridis_0.6.5
[6] viridisLite_0.4.2 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[11] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1
[16] tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] utf8_1.2.4 generics_0.1.3 rstatix_0.7.2 stringi_1.8.4 lattice_0.22-6
[6] hms_1.1.3 magrittr_2.0.3 grid_4.4.1 timechange_0.3.0 backports_1.5.0
[11] gridExtra_2.3 fansi_1.0.6 scales_1.3.0 abind_1.4-5 mnormt_2.1.1
[16] cli_3.6.3 rlang_1.1.4 munsell_0.5.1 withr_3.0.1 tools_4.4.1
[21] parallel_4.4.1 tzdb_0.4.0 ggsignif_0.6.4 colorspace_2.1-1 broom_1.0.6
[26] vctrs_0.6.5 R6_2.5.1 lifecycle_1.0.4 car_3.1-2 pkgconfig_2.0.3
[31] pillar_1.9.0 gtable_0.3.5 glue_1.8.0 tidyselect_1.2.1 rstudioapi_0.16.0
[36] nlme_3.1-166 carData_3.0-5 compiler_4.4.1
This diff is collapsed.
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