Soil fungal communities
Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing
Published in PLOS ONE
AuthorsLoreen Sommermann1, Joerg Geistlinger1, Daniel Wibberg2, Annette Deubel3, Jessica Zwanzig1, Doreen Babin4, Andreas Schlüter2, Ingo Schellenberg1
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms (GRIM), Bielefeld University, Bielefeld, North Rhine-Westphalia, Germany
- Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, Bernburg, Saxony-Anhalt, Germany
- Institute for Epidemiology and Pathogen Diagnostics, Julius-Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Lower Saxony, Germany
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.
Two-dimensional principal component analysis (PCA) including all differentially abundant OTUs retrieved from the ITS1 dataset. Each colored dot represents one dataset originating from a distinct replicate of a specific soil treatment. Data points representing the same cluster are color-coded and framed by circles based on Ward’s minimum variance. WW1 – pre-crop maize, WW2 – pre-crop rapeseed, MP – mould-board plough, CT – conservation tillage cultivator, ext – extensive N-fertilization intensity, int – intensive N-fertilization intensity.
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).
AMF genera detected in two winter wheat fields with different pre-crops. Each dot/triangle represents one DNA sample originating from the separately analyzed 4 replicates per soil treatment (WW1 pre-crop maize, WW2 pre-crop rapeseed). Archaeospora was only detectable with the ITS1 (designated with a red dot) and Paraglomus only with the ITS2 (designated with a blue triangle) primers. WW1 – pre-crop maize, WW2 – pre-crop rapeseed, MP – mould-board plough, CT – conservation tillage cultivator, ext – extensive N-fertilization intensity, int – intensive N-fertilization intensity.
