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

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2018 Apr 6

PMID 29621291

Citations 26

Authors

Loreen Sommermann

Joerg Geistlinger

Daniel Wibberg

Annette Deubel

Jessica Zwanzig

Doreen Babin

Andreas Schluter

Ingo Schellenberg

Affiliations

Soon will be listed here.

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).

Citing Articles

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References

Monard C, Gantner S, Stenlid J . Utilizing ITS1 and ITS2 to study environmental fungal diversity using pyrosequencing. FEMS Microbiol Ecol. 2012; 84(1):165-75. DOI: 10.1111/1574-6941.12046. View

Madi L, Katan T, Katan J, Henis Y . Biological Control of Sclerotium rolfsii and Verticillium dahliae by Talaromyces flavus Is Mediated by Different Mechanisms. Phytopathology. 2008; 87(10):1054-60. DOI: 10.1094/PHYTO.1997.87.10.1054. View

Stockinger H, Peyret-Guzzon M, Koegel S, Bouffaud M, Redecker D . The largest subunit of RNA polymerase II as a new marker gene to study assemblages of arbuscular mycorrhizal fungi in the field. PLoS One. 2014; 9(9):e107783. PMC: 4183475. DOI: 10.1371/journal.pone.0107783. View

Blaalid R, Kumar S, Nilsson R, Abarenkov K, Kirk P, Kauserud H . ITS1 versus ITS2 as DNA metabarcodes for fungi. Mol Ecol Resour. 2013; 13(2):218-24. DOI: 10.1111/1755-0998.12065. View

Weiss M, Sykorova Z, Garnica S, Riess K, Martos F, Krause C . Sebacinales everywhere: previously overlooked ubiquitous fungal endophytes. PLoS One. 2011; 6(2):e16793. PMC: 3039649. DOI: 10.1371/journal.pone.0016793. View

Edgar R . Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010; 26(19):2460-1. DOI: 10.1093/bioinformatics/btq461. View

Liebe S, Wibberg D, Winkler A, Puhler A, Schluter A, Varrelmann M . Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes. FEMS Microbiol Ecol. 2016; 92(2). DOI: 10.1093/femsec/fiw004. View

Magoc T, Salzberg S . FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011; 27(21):2957-63. PMC: 3198573. DOI: 10.1093/bioinformatics/btr507. View

Metsalu T, Vilo J . ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. Nucleic Acids Res. 2015; 43(W1):W566-70. PMC: 4489295. DOI: 10.1093/nar/gkv468. View

10.

Toju H, Tanabe A, Yamamoto S, Sato H . High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples. PLoS One. 2012; 7(7):e40863. PMC: 3395698. DOI: 10.1371/journal.pone.0040863. View

11.

Pawluczyk M, Weiss J, Links M, Aranguren M, Wilkinson M, Egea-Cortines M . Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples. Anal Bioanal Chem. 2015; 407(7):1841-8. DOI: 10.1007/s00216-014-8435-y. View

12.

Maus I, Kim Y, Wibberg D, Stolze Y, Off S, Antonczyk S . Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis. J Microbiol Biotechnol. 2016; 27(2):321-334. DOI: 10.4014/jmb.1605.05083. View

13.

Koljalg U, Larsson K, Abarenkov K, Nilsson R, Alexander I, Eberhardt U . UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol. 2005; 166(3):1063-8. DOI: 10.1111/j.1469-8137.2005.01376.x. View

14.

Vierheilig H, Bennett R, Kiddle G, Kaldorf M, Ludwig-Muller J . Differences in glucosinolate patterns and arbuscular mycorrhizal status of glucosinolate-containing plant species. New Phytol. 2021; 146(2):343-352. DOI: 10.1046/j.1469-8137.2000.00642.x. View

15.

Harman G, Howell C, Viterbo A, Chet I, Lorito M . Trichoderma species--opportunistic, avirulent plant symbionts. Nat Rev Microbiol. 2004; 2(1):43-56. DOI: 10.1038/nrmicro797. View

16.

Balint M, Schmidt P, Sharma R, Thines M, Schmitt I . An Illumina metabarcoding pipeline for fungi. Ecol Evol. 2014; 4(13):2642-53. PMC: 4113289. DOI: 10.1002/ece3.1107. View

17.

Samuels G, Ismaiel A, Mulaw T, Szakacs G, Druzhinina I, Kubicek C . The Longibrachiatum Clade of Trichoderma: a revision with new species. Fungal Divers. 2012; 55(1):77-108. PMC: 3432902. DOI: 10.1007/s13225-012-0152-2. View

18.

Valyi K, Rillig M, Hempel S . Land-use intensity and host plant identity interactively shape communities of arbuscular mycorrhizal fungi in roots of grassland plants. New Phytol. 2014; 205(4):1577-1586. DOI: 10.1111/nph.13236. View

19.

Veresoglou S, Wulf M, Rillig M . Facilitation between woody and herbaceous plants that associate with arbuscular mycorrhizal fungi in temperate European forests. Ecol Evol. 2017; 7(4):1181-1189. PMC: 5306016. DOI: 10.1002/ece3.2757. View

20.

Tkacz A, Cheema J, Chandra G, Grant A, Poole P . Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. ISME J. 2015; 9(11):2349-59. PMC: 4611498. DOI: 10.1038/ismej.2015.41. View