This readme file was generated on 2023-03-01 by Jake Allen GENERAL INFORMATION Title of Dataset: Data from `Fertility and tillage intensity affect weed community diversity and functional structure in long-term organic systems.` Principal Investigator Name: Jake Allen Institution: Cornell University, Soil and Crop Sciences Section, School of Integrative Plant Science Email: jpa77@cornell.edu Associate Investigator Name: Matthew R. Ryan Institution: Cornell University, Soil and Crop Sciences Section, School of Integrative Plant Science Associate Investigator Name: Guillaume Deux Institution: INRAE Agroecologie Associate Investigator Name: Uriel Menalled Institution: Cornell University, Soil and Crop Sciences Section, School of Integrative Plant Science Associate Investigator Name: Ashley Jernigan Institution: Cornell University, Department of Entomology Associate Investigator Name: Sandra Wayman Institution: Cornell University, Soil and Crop Sciences Section, School of Integrative Plant Science Associate Investigator Name: Christopher Pelzer Institution: Cornell University, Soil and Crop Sciences Section, School of Integrative Plant Science Associate Investigator Name: Stephane Cordeau Institution: INRAE Agroecologie Associate Investigator Name: Antonio DiTommaso Institution: Cornell University, Soil and Crop Sciences Section, School of Integrative Plant Science Date of data collection: 2017-08-31 - 2023-10-25 Geographic location of data collection: Cornell Musgrave Research Farm, Aurora, NY, USA (42.73 °N, 76.65 °W) Funding information: USDA NIFA Organic Agriculture Research and Extension Initiative (2020-51300-32183) Denison Graduate Fellowship provided by the Cornell University School of Integrative Plant Sciences SHARING/ACCESS INFORMATION Licenses/restrictions placed on the data: CC0. This dataset is shared under a Creative Commons 1.0 Universal Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/). The material can be copied, modified and used without permission, but attribution to the original authors is always appreciated. Links to publications: DOI to be added upon publication Recommended citation for this dataset: Jake Allen, Uriel D. Menalled, Guillaume Adeux, Christopher J. Pelzer, Sandra Wayman, Ashley B. Jernigan, Stéphane Cordeau, Antonio DiTommaso, Matthew R. Ryan. (2023) Fertility and tillage intensity affect weed community diversity and functional structure in long-term organic systems. [dataset] Cornell University eCommons Repository. https://doi.org/10.7298/eym5-3s34 DATA & FILE OVERVIEW File List: 'AllenEtal_emergentdata.csv': emergent weed biomass data by species collected in each crop of rotation from 2017-2021 'AllenEtal_seedbankdata.csv': weed seed bank density data by species from seed bank emergence assays done in 2017 and 2022 'AllenEtal_traitdata.csv': trait values used for functional trait analysis for every weed species found in emergent and seed bank data METHODOLOGICAL INFORMATION Description of methods used for collection/generation of data: All data collected and generated as described in Allen et al. (publication forthcoming) These files contain data supporting all results reported in Allen et al., which tested the effects of fertility and tillage intensity gradients on weed communities in long-term organic cropping systems. This study assessed the seed banks and weed communities of a long-term experiment initiated in 2005, which compared four organic systems differing in nutrient inputs and soil disturbance. The high fertility (HF) system received high-rate nutrient applications, low fertility (LF) received low-rate applications, enhanced weed management (EWM) focused on weed control through frequent soil disturbance, and reduced tillage (RT) prioritized soil health with less intense or frequent soil disturbance. Soil samples for greenhouse germination assays were collected at the beginning (2017) and end (2022) of the experiment’s last crop rotation cycle to explore how these four systems influenced seed bank dynamics over time. Weed community biomass was also sampled in each crop. Treatment effects on weed abundance, taxonomic diversity, and community-weighted means and functional dispersion of weed traits were analyzed with generalized mixed effect models. The RT system had the highest weed seed bank taxonomic diversity and EWM had the lowest. RT and LF had higher functional dispersion of traits than HF in the seed bank. Weed seed bank communities in HF and RT were characterized by short, small-seeded, and early germinating weed species. However, seed banks were also labile: differences between systems in seed density and mean trait values were dependent on the crop which preceded seed bank sampling. Likewise, while the traits of emergent weed communities differed in the four system treatments, they depended on an interaction between crop species and their planting year. Results suggest that resource availability and intensity of disturbance act as weed community assembly filters in organic cropping systems. Organic growers seeking to design systems that balance weed management and production goals can use relatively low soil disturbance and nutrient application to increase weed community taxonomic or functional diversity without necessarily increasing weed biomass or seed bank density. Methods for processing the data: Emergent biomass - raw biomass (g) of each species standardized to g/m2 by multiplying by 2 or 4 for 0.25 m2 and 0.5 m2 sampling areas, respectively Seed bank density - raw counts for each species summed across three weed seed bank emergence flushes Trait data - retrieved from online databases as described in Allen et al. Instrument- or software-specific information needed to interpret the data: R version 4.1.2 (2021-11-01) used for all analysis 'glmmTMB' version 1.1.3 used for generalized linear mixed effect models 'DHARMa' version 0.4.5 used for model residual simulations 'monet' version 0.1-1 used for likelihood tests of model terms 'emmeans' version 1.7.0 used for post-hoc mean comparisons 'vegan' version 2.5-7 used for redundancy analysis, diversity calculations 'FD' version 1.0-12 used for functional dispersion and community-weighted mean calculations DATA-SPECIFIC INFORMATION FOR: 'AllenEtal_emergentdata.csv' Number of variables: 114 Number of cases/rows: 824 Variable List: 'Year' [factor]: year of biomass sampling (2017,2018,2019,2020,2021) 'Crop' [factor]: code for crop sampled (SS = sorghum-sudangrass, CR = cereal rye, Sb = soybean, C = corn, INTCC = intercropped cover crops, Tr = triticale, RC = red clover, SAF1/2 = summer forages cut 1/2) 'Block' [factor]: experimental block (1,2,3,4) 'System' [factor]: organic cropping system (HF = high fertility, LF = low fertility, EWM = enhanced weed management, RT = reduced tillage) 'Entry' [factor]: entry point into rotation (A, B) 'Subplot' [factor]: sampling area for quadrat within each System:Entry (a,b,c,d or 1,2 for uniformity trial) 'Description' [free text]: more detailed description of the crop being sampled 'Sample date' [date]: date of biomass sampling 'quad.size.meter' [factor]: size of sampling area in m2 'total.crop.bm.g.m2' [numeric]: total crop biomass in the sampling area in g/m2 'total.weed.bm.g.m2' [numeric]: total weed biomass in the sampling area in g/m2 '1AMAG' - 'VICVI' [numeric]: biomass of individual weed species in g/m2. Column names are EPPO codes for each species. Missing data codes: NA = not sampled Specialized formats or other abbreviations used: EPPO codes (https://www.eppo.int/RESOURCES/eppo_databases/eppo_codes) used for species names DATA-SPECIFIC INFORMATION FOR: 'AllenEtal_seedbankdata.csv' Number of variables: 62 Number of cases/rows: 64 Variable List: 'Year' [factor]: year of biomass sampling (2017,2022) 'Block' [factor]: experimental block (1,2,3,4) 'System' [factor]: organic cropping system (HF = high fertility, LF = low fertility, EWM = enhanced weed management, RT = reduced tillage) 'Entry' [factor]: entry point into rotation (A, B) 'ABUTH' - 'VESTH' [numeric]: seedling counts of individual weed species in seeds/60cm2. Multiply by 167 to get seed density in seeds/m2. Column names are EPPO codes for each species. Missing data codes: none Specialized formats or other abbreviations used: EPPO codes (https://www.eppo.int/RESOURCES/eppo_databases/eppo_codes) used for species names DATA-SPECIFIC INFORMATION FOR: 'AllenEtal_traitdata.csv' Number of variables: 11 Number of cases/rows: 95 Variable List: 'Species' [factor]: species EPPO code 'RLF' [factor]: Raunkiaer life form (T = therophyte, H = hemicryptophyte, G = geophyte) 'ABP' [factor]: Life history (A = annual, P = perennial) 'COT' [factor]: Cotyledon type (0 = dicotyledon, 1 = monocotyledon) 'SDM' [numeric]: Seed dry mass in mg 'PLH' [numeric]: Plant height in meters 'SLA' [numeric]: Specific leaf area in mm2/mg 'ELN' [factor]: Ellenberg N indicator value (1-9) 'GRS' [factor]: Germination seasonality (a = fall to early-spring, b = mid-spring, c = late-spring to summer) 'FLO' [numeric]: Flowering onset in month of year 'FLD' [numeric]: Flowering duration in months Missing data codes: blank cell = trait value not available Specialized formats or other abbreviations used: EPPO codes (https://www.eppo.int/RESOURCES/eppo_databases/eppo_codes) used for species names