Abstract
Fungal communities in agricultural soils are assumed to be affected by soil and crop management. Our intention was to investigate the impact of different tillage and fertilization practices on fungal communities in a long-term crop rotation field trial established in 1992 in Central Germany. Two winter wheat fields in replicated strip-tillage design, comprising conventional vs. conservation tillage, intensive vs. extensive fertilization and different pre-crops (maize vs. rapeseed) were analyzed by a metabarcoding approach applying Illumina paired-end sequencing of amplicons generated by two recently developed primer pairs targeting the two fungal Internal Transcribed Spacer regions (ITS1, ITS2). Analysis of 5.1 million high-quality sequence reads uncovered a diverse fungal community in the two fields, composed of 296 fungal genera including 3,398 Operational Taxonomic Units (OTUs) at the 97% sequence similarity threshold. Both primer pairs detected the same fungal phyla (Basidio-, Asco-, Zygo-, Glomero- and Chytridiomycota), but in different relative abundances. OTU richness was higher in the ITS1 dataset, while ITS2 data were more diverse and of higher evenness. Effects of farming practice on fungal community structures were revealed. Almost two-thirds of the fungal genera were represented in all different soil treatments, whereas the remaining genera clearly responded to farming practice. Principal Component Analysis revealed four distinct clusters according to tillage practice and pre-crop. Analysis of Variance (ANOVA) substantiated the results and proved significant influences of tillage and pre-crop, while fertilization had the smallest and non-significant effect. In-depth analysis of putative phytopathogenic and plant beneficial fungal groups indicated distinct responses; for example Fusarium was significantly enriched in the intensively fertilized conservation tillage variants with the pre-crop maize, while Phoma displayed significant association with conventional tillage and pre-crop rapeseed. Many putative plant beneficial fungi also reacted differentially to farming practice with the most distinct responders identified among the Glomeromycota (arbuscular mycorrhizal fungi, AMF).
Highlights
Fungi are involved in several soil functions like decomposition of organic material, nutrient cycling, mineral mobilization, formation of soil aggregates, elevated water holding capacity, plant growth promotion and suppression of phytopathogens
In this study, which was conducted within the DiControl Project of the BonaRes Program, we investigated root-proximate soil layers of two winter wheat fields that are part of a 6 ha large long-term strip-tillage field trial established in Central Germany in 1992
In long-term average (2005–2014) crop yield from the long-term field trial was comparable in both tillage treatments, but varied within single years depending on weather conditions
Summary
Fungi are involved in several soil functions like decomposition of organic material, nutrient cycling, mineral mobilization, formation of soil aggregates, elevated water holding capacity, plant growth promotion and suppression of phytopathogens. Another beneficial feature of especially mutualistic root endophytic fungi is the induction of systemic resistance in host plants via ethylene/jasmonate or salicylic acid pathways and thereby increasing tolerance levels of crops to biotic and abiotic stress factors [1]. Compared to undisturbed natural ecosystems, fungal soil communities in agro-ecosystems are exposed to additional influencing factors related to soil and crop management practices. The impact of different agricultural management regimes on fungal community composition gains rising interest, up to date, only few studies were dedicated to determine the effects of tillage, fertilization and crop rotation on microbial diversity [3,4,5]
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