Database of soil fungi and bacteria affected by commonly used pesticides in a pot experiment

Database of soil fungi and bacteria affected by commonly used pesticides in a pot experiment Contributors: Veronika Řezáčová, Ema Némethová, Oushadee A.J. Abeyawardana, Markéta Mayerová Affiliation: Czech Agrifood Research Center, Drnovská 507/73, CZ-160 00 Prague 6, Czech Republic This database contains species-level abundance data for soil fungal and bacterial taxa detected after short-term direct exposure to selected herbicides and fungicides in a pot experiment. The dataset includes untreated controls and different pesticide treatments applied to three agricultural soils. It is intended as supporting documentation for the interpretation of microbial species abundance data across pesticide treatments and soil types. Supporting information on pesticide applications, soil properties, sampling design, DNA isolation, sequencing, and bioinformatic processing is provided. Database structure The database is provided as an Excel workbook with two worksheets: Fungi and Bacteria. Each worksheet contains species-level relative abundance data expressed as percentage of sequences. The first six columns contain taxonomic classification fields: Phylum, Class, Order, Family, Genus, and Species. The remaining 108 columns represent individual experimental samples from the pot experiment. Samples are organized by three soil types, nine treatments including untreated controls, and four biological replicates per soil–treatment combination. Header rows specify the soil type, pesticide treatment, and individual sample identifier. The fungal worksheet contains 1,477 taxon records, and the bacterial worksheet contains 1,448 taxon records. Values in the sample columns represent the relative abundance of each taxon in the corresponding sample. Dataset documentation and experimental metadata Study design The data were generated in a pot experiment arranged as a fully factorial design with two factors: pesticide treatment and soil type. The database reports microbial taxon abundances for individual experimental samples and includes the corresponding treatment and soil metadata required for data interpretation. Pesticides and soil selection The experiment included eight commercially available pesticides: three fungicides (Mirador XTRA, Kuprikol 50, and Captan 80 WG) and five herbicides (Basagran, CORUM, Stomp 400 SC, Targa Super 5 EC, and Sharpen 40 SC; Table 1). The selected products represent pesticides commonly used for legume protection. To assess microbial communities under different soil conditions, three agricultural soils were collected from ecologically managed fields differing in pH and other physicochemical properties (Table 2). These fields had been free of pesticide application for approximately 10 years, as documented by Némethová et al. (2026). Soil physicochemical characteristics were determined before the experiment was established using air-dried and homogenized soil samples from all three soil types (Table 2). Available phosphorus (P), potassium (K), magnesium (Mg), and calcium (Ca) were measured using the Mehlich III extraction method (Mehlich, 1984) and quantified with an Agilent ICP-OES 5110 VDV instrument (Agilent Technologies, Santa Clara, CA, USA). Nitrate nitrogen (NO₃⁻) and ammonium nitrogen (NH₄⁺) were determined according to ISO 14255:1998 using calcium chloride as the extractant and analysed with an automated chemistry analyser (Skalar Analytical B.V., Breda, The Netherlands). Soil pH was assessed in a water slurry (1:5, w:v) after 1 h of shaking using a pH meter (Hanna Instruments, Woonsocket, RI, USA). Two technical replicate measurements were performed per sample. Table 1. Pesticides used in the pot experiment and corresponding application parameters. Pesticide Manufacturer Active compound Dose used (l/ha) Recommended dose range (l/ha) Dilution (l/ha) Recommended dilution (l/ha) Basagran BASF AG, Agricultural Products Bentazone 2 2 200 200 - 400 CORUM BASF AG, Agricultural Products Imazamox, bentazone 1.25 1.25 100 100 – 400 Sharpen 40 SC Sharda Worldwide Exports Pvt. Ltd. Pendimethalin 4.1 4.1 400 400 – 600 Stomp 400 SC BASF AG, Agricultural Products Pendimethalin 4.1 4.1 400 400 – 600 Targa Super EC Nissan Chemical Ind. Ltd Quizalofop-P-ethyl 2.5 1.5 – 2.5 200 200 – 400 Captan 80 WG Arysta LifeScience S.A.S Captan 2.1 2.1 500 500 Kuprikol NeraAgro, spol.s.r.o. Copper oxychloride 5 5 200 200 Mirador XTRA Adama CZ, s.r.o. Azoxystrobin, cyproconazole 1 1 200 200 - 400 Table 2. Description of sampling locations and physicochemical profiles of the collected soils. Soil_1 Soil_2 Soil_3 Field owner VH AGROTON, s.r.o., Velké Hostěrádky BIOFARMA Sasov, Jihlava Ing. Přemysl Čech, Zábřeh GPS coordinates 49°1′52.43″ N, 16°52′20.64″ E 49° 22′ 51.69″ N, 15° 36′18.014″ E 49°52′59.41″ N, 16°51′50.47″ E available P (mg/kg) 11.25 111.50 101.60 Mg (mg/kg) 410.00 178.80 114.90 K (mg/kg) 214.00 271.00 280.80 Ca (mg/kg) 7854.00 1863.00 2198.00 Hot water extractable P (mg/kg) 3.29 12.37 11.93 NH₄⁺ (mg/kg) 6.34 10.15 11.18 NO₃⁻ (mg/kg) 7.95 13.31 13.95 pH (H2O) 8.20 6.40 7.00 Pot experiment Before pesticide application, one-liter black plastic pots sterilized with 96% ethanol (Penta, Prague, Czech Republic) were filled with homogenized fresh soil and watered to near field capacity, allowing slight leaching from the bottom. The pots were randomly arranged to minimize positional effects. Pesticide solutions were prepared according to the manufacturers’ recommended field application doses (Table 1) and evenly sprayed onto the soil surface of each pot (169 cm2 per pot). The experiment was maintained in a room with an average temperature of 21.4°C. Four biological replicate pots were established for each combination of soil type and treatment, including an untreated control for each soil type. In total, the experiment comprised 108 pots (3 soils × 9 treatments × 4 replicates). Soil was sampled two weeks after pesticide application, providing data on microbial taxa detectable after short-term direct exposure. Samples were taken randomly from a depth of 0–10 cm in each pot using a sterile metal spoon and pooled to obtain one composite homogenized sample per pot. DNA isolation and sequencing Total genomic DNA was isolated from 0.25 g of air-dried, homogenized soil sieved through a 2 mm mesh using the DNeasy PowerSoil DNA Isolation Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. Fungal communities were characterized by amplicon sequencing of the internal transcribed spacer (ITS) region using the gITS7 and ITS4 primer pair. Bacterial communities were characterized by amplicon sequencing of the V4 region of the 16S rRNA gene. Amplicon libraries were prepared from pooled equimolar PCR products and sequenced using Illumina MiSeq paired-end sequencing. The resulting sequence data were used to generate fungal and bacterial taxon abundance datasets for the experimental treatments and untreated controls. Bioinformatic processing and derived datasets Raw sequence data were processed using the SEED 2.1.2 pipeline. Fungal ITS and bacterial 16S rRNA sequences were clustered into operational taxonomic units (OTUs) and taxonomically assigned to the species level. Fungal OTUs were assigned using the UNITE reference database, and bacterial OTUs were assigned using the SILVA reference database. Before standardization, sequence data were rarefied to the same number of sequences per sample to allow comparison among samples. The resulting species-level abundance tables were then standardized. Derived datasets include fungal and bacterial species abundance tables across pesticide treatments, soil types, and untreated controls. Funding This database was developed with support from the Technology Agency of the Czech Republic, project SS07020100 “The impact of plant protection products on non-target biodiversity: soil microorganisms, invertebrates and wild plants”, and from institutional support provided by the Ministry of Agriculture of the Czech Republic, MZE-RO0426. References Mehlich A. (1984). Mehlich 3 soil test extractant. A modification of the Mehlich 2 extractant. Commun. Soil Sci. Plant Anal.15, 1409–1416. doi: 10.1080/00103628409367568. Némethová E., Řezáč M., Gryndler M., Abeyawardana O.A.J. and Řezáčová V. (2026). Soil pH mediates the impact of pesticides on bacterial communities, diversity, and abundance. Front. Microbiol. 16,1670425. doi: 10.3389/fmicb.2025.1670425.