Data from: Effects of pesticides on soil bacterial, fungal and protist communities, soil functions and crop quality in vineyards
Cite this dataset
Steiner, Magdalena et al. (2024). Data from: Effects of pesticides on soil bacterial, fungal and protist communities, soil functions and crop quality in vineyards [Dataset]. Dryad. https://doi.org/10.5061/dryad.4tmpg4fjv
Abstract
Pesticides can have unintentional effects on non-target organisms and change biotic communities. Such changes might be particularly important in soil microbial communities which drive many ecosystem functions and may affect crop quality. Here, we investigated, in a 3-year study, how vegetation control (by herbicide application) and soil copper content (from long-term copper-based fungicide application), affect biodiversity and the community structure of soil bacteria, fungi and protists and associated soil functions (respiration, decomposition) in Swiss vineyards. Furthermore, we determined the effects of these two management practices on grape quality as the most direct ecosystem service to farmers. Across all study years, the community composition of microorganisms was affected by herbicide application, however, a significant loss of operational taxonomic units (OTUs) was only observed in fungi and protists. Soil copper content reduced OTU richness of bacteria and protists in some years but had no significant effect on fungal richness. Copper changed the community composition in all three groups of soil microorganisms. While we found no effect of copper on soil functions, herbicide application reduced microbial respiration and biomass by about 39% and 45% respectively. However, decomposition rates remained virtually unchanged by any pesticide. Yeast assimilable nitrogen (YAN) levels in grape must were below the critical threshold of 140 mg/L in 40% of the vineyards without herbicide application and the variety Chasselas , whereas in vineyards with herbicide application it was only 20%. Synthesis and applications: Application of pesticides led to changes in richness and composition of soil microbial communities and directly reduced some soil functions (microbial biomass and respiration), but not all (decomposition). Some grape quality parameters can be indirectly enhanced by pesticide application, highlighting the trade-off between the interests of nature conservation and the interests of the farmer. Balancing these two diverging interests requires the establishment of alternative vineyard management allowing reduced pesticide application.
README: Data from: Effects of pesticides on soil bacterial, fungal and protist communities, soil functions and crop quality in vineyards
Microbial Diversity datasets
OTU tables for microbial groups bacteria, fungi and protist separately for each year 2015, 2016, 2017
-contains information about OTUs and associated number of reads for each DNA_sample_ID
FILENAMES:
"otu_table_bacteria_2015_01_rar_no_single_nomech_no_under_new_pipe.txt"
"otu_table_bacteria_2016_01_rar_no_single_nomech_no_under_new_pipe.txt"
"otu_table_bacteria_2017_01_rar_no_single_nomech_no_under_new_pipe.txt"
"otu_table_Fungi_rar_nomech_0.1_2015_final.txt"
"otu_table_Fungi_rar_nomech_0.1_2016_final.txt"
"otu_table_Fungi_rar_nomech_0.1_2017_final.txt"
"otu_table_protists_2015_01_rar_no_single_nomech_no_under_new_pipe.txt"
"otu_table_protists_2016_01_rar_no_single_nomech_no_under_new_pipe.txt"
"otu_table_protists_2017_01_rar_no_single_nomech_no_under_new_pipe.txt"
FILENAME: "DNA_Sample_ID.xlsx"
"DNA_Sample_ID" = ID number of DNA sample
"Year" = year of sampling
"vineyard" = vineyard DNA sample was taken from
"rowID" = row ID within each vineyard
"unique_rowID" = combination of rowID and year of sampling
"treatment" = Herb - herbicide treated, AltHerb - Herbicide treated in alterneting rows, NoHerb - not treated with herbicide
Taxonomy tables with number of reads for microbial groups bacteria, fungi and protist separately for each year 2015, 2016, 2017
- contains information about the OTU and associated "phylum", "class", "order", "family", "genus" ,"species"
FILENAMES:
"tax_table_bacteria_2015_01_rar_no_single_nomech_no_under_new_pipe.txt"
"tax_table_bacteria_2016_01_rar_no_single_nomech_no_under_new_pipe.txt"
"tax_table_bacteria_2017_01_rar_no_single_nomech_no_under_new_pipe.txt"
"tax_table_Fungi_rar_nomech_0.1_2015_final.txt"
"tax_table_Fungi_rar_nomech_0.1_2016_final.txt"
"tax_table_Fungi_rar_nomech_0.1_2017_final.txt"
"tax_table_protists_2015_01_rar_no_single_nomech_no_under_new_pipe.txt"
"tax_table_protists_2016_01_rar_no_single_nomech_no_under_new_pipe.txt"
"tax_table_protists_2017_01_rar_no_single_nomech_no_under_new_pipe.txt"
FILENAME: "Env_var_row_year_Reference.xlsx"
Sample data (metadata) for each DNA sample separately for each microbial group and year
"vineyard" = number of vineyard site identification
"treatment" = Herb - herbicide treated, AltHerb - Herbicide treated in alterneting rows, NoHerb - not treated with herbicide
"row" = row ID within each vineyard
"unique_row" = combination of riwID and year of sampling
"variety" = Grape variety Chasselas or Pinot nor
"year" = year of sampling
"SOM_perc"= soil organic matter in percent
"CN" = carbon/nitrogen ratio
"N_perc" = Nitrogen contentin percent
"Cu_mg/kg" = copper in mg /kg soil
"pH" = soil pH
"clay" = clay content in percent
"plant_cover%" = plant cover in %
"plant_spec" = average number of plant species
##############################
Microbial functions Data
FILENAME:
"RMS_2015_ok.txt"
"RMS_2016_ok.txt"
"RMS_2017_ok.txt"
Respiration
"vineyard" = number of vineyard site identification
"treatment" = Herb - herbicide treated, AltHerb - Herbicide treated in alterneting rows, NoHerb - not treated with herbicide
"row" = row ID within each vineyard
"unique_row" = combination of riwID and year of sampling
"variety" = Grape variety Chasselas or Pinot nor
"year" = year of sampling
"measurement" = month and year of measurement
"som_perc"= soil organic matter in percent
"CN" = carbon/nitrogen ratio
"N_perc" = Nitrogen contentin percent
"Cu_mg/kg" = copper in mg /kg soil
"pH" = soil pH
"clay" = clay content in percent
"plant_cover%" = plant cover in %
"plant_rich" = average number of plant species
"basal_res" = basal respiration
"cmic" = microbial biomass (no data for 2017)
"bact_rich" = number of bacterial OTUs
"fung_rich" = number of bacterial OTUs
"prot_rich" = number of bacterial OTUs
Decomposition
FILENAMES:
"Decomposition_2015_ok.txt"
"Decomposition_2016_ok.txt"
"vineyard" = number of vineyard site identification
"treatment" = Herb - herbicide treated, AltHerb - Herbicide treated in alterneting rows, NoHerb - not treated with herbicide
"row" = row ID within each vineyard
"unique_row" = combination of riwID and year of sampling
"variety" = Grape variety Chasselas or Pinot nor
"year" = year of sampling
"whloss_recal" = weight loss of recalicrtant substrate in %
"whloss_labile" = weight loss of labile substrate in %
"SOM_perc"= soil organic matter in percent
"CN" = carbon/nitrogen ratio
"N_perc" = Nitrogen contentin percent
"Cu_mg/kg" = copper in mg /kg soil
"pH" = soil pH
"clay" = clay content in percent
"plant_cover%" = plant cover in %
"plant_spec" = average number of plant species
"basal_res" = basal respiration
"cmic" = microbial biomass
"bact_rich" = number of bacterial OTUs
"fung_rich" = number of bacterial OTUs
"prot_rich" = number of bacterial OTUs
##############################
Grape Quality_15_16_17 datasets
FILENAME: "Grape_quality_15_16_17.xlsx"
"vineyard" = number of vineyard site identification
"location" = location (commune) of vinayard
"uniq_viny" = unique sample code
"variety" = Grape variety Chasselas or Pinot nor
"treatment" = Herb - herbicide treated, AltHerb - Herbicide treated in alterneting rows, NoHerb - not treated with herbicide
"year" = year of sampling
"date" = sampling date
"average_berry_weight" = average weight of collected berries in gram
Grape Qualities columns: parameter were measured by FTIR analysis of grape juice
"Brix_Refr" = sugar measurement with Brix refractometer in °Brix
"Oe_Refr" = measure of grape sugar content; measured by refractometer in °Oechsle
"D20_20" = relative denisty measurement of grape juice extract in g/cm3
"Extrait_density" = desnsity measurement of grape juice extract g/L
"pH" = measured pH
"tot_Acidity_g_l" = describes total acidity (g/l)
"tartric_Acid_g_l" = amount of tartric acid (g/l)
"malic_Acid_g_l" = amount of malic acid (g/l)
"N_assimilable_mg_l"= amount of yeast available nitrogen (YAN) as (mg/l)
##############################
For All datasets
"NA" = stands for missing values due to failed measurement
Methods
See the associated Readme file and manuscript part "Materials and methods".
Funding
Swiss National Science Foundation, Award: 40FA40_158390