DOI: 10.5061/dryad.kh189324t
title: Inconsistent effects of agricultural practices on soil fungal communities across twelve European long‐term experiments

description: Cropping practices have a great potential to improve soil quality through
 changes in soil biota. Yet the effects of these soil improving cropping
 systems on soil fungal communities are not well known. Here, we analysed
 soil fungal communities using standardized measurements in 12 long‐term
 experiments and 20 agricultural treatments across Europe. We were
 interested in whether the same practices (i.e. tillage, fertilization,
 organic amendments and cover crops) applied across different sites have
 predictable and repeatable effects on soil fungal communities and guilds.
 The fungal communities were very variable across sites located in
 different soil types and climatic regions. The arbuscular mycorrhizal
 fungi (AMF) were the fungal guild with most unique species in individual
 sites while plant pathogenic fungi were most shared between the sites. The
 fungal communities responded to the cropping practices differently in
 different sites and only fertilization showed a consistent effect on AMF
 and plant pathogenic fungi while the response to tillage, cover crops and
 organic amendments were site, soil and crop species specific. We further
 show that the crop yield is negatively affected by cropping practices
 aimed at improving soil health. Yet, we show that these practices have the
 potential to change the fungal communities and that change in plant
 pathogenic fungi and in AMF is linked to the yield. We further link the
 soil fungal community and guilds to soil abiotic characteristics and
 reveal that especially Mn, K, Mg and pH affect the composition of fungi
 across sites. In summary, we show that fungal communities vary
 considerably between sites and that there are no clear directional
 responses in fungi or fungal guilds across sites to soil improving
 cropping systems but that the responses vary based on soil abiotic
 conditions, crop type, and climatic conditions.   Details on
 experiments related to the data is provided in supplementary materials of
 the related article
description: Fungi: DNA was extracted using the modified Power Soil protocol
 (Harkes et al., ), with 0.25 g soil per sample and Lysing matrix E beads
 tubes (MP Biomedicals). Fungal DNA was amplified using primers ITS4ngs and
 ITS3mix1‐5 (Tedersoo et al., , ) and purified using AMPure magnetic beads
 (Beckman Coulter). Polymerase chain reactions (PCRs) were performed with
 12.5‐μL Hotstart ready mix (Fisher scientific) and approximately 50 ng of
 DNA per reaction. Dual tags were added to samples (Illumina dual indexing
 kits v1‐3) using seven cycles of PCR. PCR products were further purified
 using magnetic beads. The DNA was quantified using a Qubit fluorometer and
 equimolar pooled into libraries of 285 and 250 samples each. Mock
 community samples with eight fungal strains were sequenced along with the
 experimental samples. Sequencing was performed using Illumina MiSeq
 pair‐end 2x300bp. Here we give the OTU table and taxa files as well as
 report all OTUs unique to one site. Soil Chemistry:
 Chemical soil properties were determined by AgroCares BV (Wageningen, the
 Netherlands). Soils for chemical analysis were dried at 50°C using fruit
 dryers, crushed and sieved (2 mm sieve). One part of the soil sample was
 homogenized and pulverized (&lt;0.2 mm) using a planetary micro mill
 with 10 clean metal balls for 3 min with speed 500 rpm. This sample was
 used to measure the total C and N by heating it to 900°C in the presence
 of O<sub>2</sub>, forming CO<sub>2</sub> and
 N<sub>2</sub>, which were quantitatively measured with a
 thermal conductivity detector. Peak areas are correlated with validated
 calibration curves, to obtain element weight for C and N, which is
 recalculated to percentage by considering the sample mass. Total organic
 carbon (TOC) was measured using the Elementar Rapid CS cube (Elementar
 Analysensysteme, Germany) after removal and quantification of the total
 inorganic carbon (TIC) fraction as carbonates through acid (1 M HCl)
 treatment. Samples for soil texture were weighed and treated with 30%
 H<sub>2</sub>O<sub>2</sub> for the removal of
 organic material, treated with dithionite solution (40 g/L
 Na<sub>2</sub>S<sub>2</sub>O<sub>4</sub> in 0.3 M NaOAc, pH 3.8) for the removal of iron oxide, and treated with 1 M HCl for the removal of carbonates. After this sample treatment, the samples were measured with the Mastersizer 3,000 (Malvern Panalytical B.V., Almelo, the Netherlands) to determine the particle size distribution using laser diffraction. Soil pH (KCl) was determined using a pH electrode. The procedure for the extraction of soils using Mehlich‐3 solution as extractant was validated and executed according to Wolf and Beegle (), with one exception, the shaking time was increased from 5 to 10 min. The measurement of samples for the determination of bulk multi‐element concentrations in dry soil samples (RT: Real Totals) was carried out using the PANalytical Epsilon 3 ED‐XRF (Malvern Panalytical B.V., Almelo, the Netherlands). The procedure is in accordance with ISO18227:2014 and validated. The samples were prepared as pellets with a soil to wax ratio of 9:1. Lastly, cation exchange capacity (CEC) and the content of exchangeable cations (Al<sup>3+</sup>, Ca<sup>2+</sup>, Fe<sup>2+</sup>, K<sup>+</sup>, Mg<sup>2+</sup>, Mn<sup>2+</sup>, Na<sup>+</sup>, B<sup>+</sup>, Cu<sup>2+</sup>, Mo<sup>2+</sup>, Ni<sup>2+</sup> and Zn<sup>2++</sup>) and anions (S<sup>2−</sup>, P<sup>3−</sup>) in soils were determined after extraction with hexamminecobalt trichloride solution. The procedure was validated and is in accordance with ISO 23470:2007.