Data for: Contrasting dynamics of soil fungal functional groups in the plant rhizosphere
Description
Soil microbiomes, critical for plant productivity and ecosystem functioning, mediate essential functions such as pathogenesis, mutualism, and decomposition through different fungal functional groups. Yet, our understanding of the dynamics of co-existing soil fungal functional groups in the plant rhizosphere remains limited. By leveraging a ‘natural’ experiment in urban farming with fields of varying ages and multiple plant genotypes, we tracked the relative abundance, richness, and microbial networks of plant pathogens, mycorrhizal fungi, and saprotrophic fungi across fields over two years. We observed an increase in the relative abundance of plant pathogens in older fields relative to younger fields, supporting the prediction of pathogen accumulation over time. In contrast, there was a decrease in the relative abundance of mycorrhizal fungi in older fields. Unlike plant pathogens and mycorrhizal fungi, the relative abundance of saprotrophic fungi remained similar among fields. For fungal richness, the richness of plant pathogens and saprotrophic fungi showed no significant differences among fields. However, the richness of mycorrhizal fungi declined in older fields and over the two years. These dynamics led to distinct microbial networks, with decreased network links for mycorrhizal fungi and increased links for saprotrophic fungi in older fields, whereas the links for plant pathogens remained similar across fields. Our study reveals contrasting dynamics of essential soil fungal functional groups in the plant rhizosphere, and provides a predictive insight into the potential shifts in soil function and their impact on plant productivity.
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We conducted this study at an urban farm in Chesterland, Ohio (41.554652ºN, 81.324045ºW). Four perennial strawberry fields, denoted as field A (planted in 2019), field B (2018), field C (2017), and field D (2016), were selected for investigation (Table S1). Each field (c. 50 m × 100 m) consisted of 35–55 matted rows growing 3–6 genotypes (cultivars; Fragaria ×ananassa “AC Valley Sunset”, “Allstar”, “DaRoyal”, “DarSelect”, “Earliglow”, and “Wendy”; Table S1). Within each field, we collected soil microbiome samples from the plant rhizosphere in three randomly selected subplots (20 cm × 20 cm) per genotype across non-adjacent rows during June 14–15, 2021. We repeated the sampling at the same locations on June 21, 2022, with the exception of field B, which was removed by the farm in 2022. Specifically, for soil microbiome collection, we took soil at 5 cm depth from the root zone of a strawberry plant using an ethanol-cleaned stainless steel hand transplanter. Each sample, comprising 0.5 mL of soil, was transferred into a sterile 2 mL microcentrifuge tube. The samples (N = 96) were stored at -20 ºC within 3 h after collection. Soil microbial DNA was extracted using cetyltrimethylammonium bromide (CTAB) and purified using polyethylene glycol (PEG) 8000. The DNA samples were sent to the Argonne National Laboratory for fungal (ITS1f–ITS2) library preparation and sequencing using Illumina MiSeq (paired-end 250 bp). Fungal sequences were used for identifying fungal amplicon sequence variants (ASVs) using package DADA2 v1.20.0. Fungal functional groups (e.g., potential plant pathogens, mycorrhizal fungi including both arbuscular and ectomycorrhizal fungi, and saprotrophic fungi) were identified using FungalTraits v1.2.