Substantial methodological biases in soil fungal diversity were demonstrated by an Estonian-German research consortium ( University of Tartu and EMBL ). It turns out that even sophisticated and innovative approaches such as DNA barcoding and PCR-free analyses are likely to end up with biased information when researching the taxonomic community composition of soil biota. The study is published in both open access journal MycoKeys and Science magazine.
High-throughput Illumina sequencing of DNA metabarcodes and the whole soil metagenome revealed strong methodological biases in taxonomic insights into soil fungal diversity. All methods had their inherent biases and shortcomings, but reached roughly similar ecological conclusions indicating the greatest role of floristic variables on soil fungal communities in the mountainous Papua New Guinea.
"I was motivated by a criticism on our last year's Science article on global fungal diversity, where the abundance of certain fungi were suspected of being underestimated", explained Dr. Leho Tedersoo, soil ecologist and mycologist from the University of Tartu, Estonia, and leading author of the present paper.
"The most intriguing result is that all these innovative, high-throughput molecular methods have their serious inherent biases. For example, amplicon-based methods depend strongly on taxonomic resolution of the barcode (DNA fragment used for identification), primer-template mismatches, the presence of introns and the overall length of the barcode; but conversely, PCR-free methods are affected strongest by the availability of taxonomic reference information, which differs enormously for fungal classes and phyla", added Leho.
In conclusion, Dr. Tedersoo pointed out that the recently developed PCR-free methods do not provide a magic wand for understanding the taxonomic community composition of soil biota, but nonetheless, these methods have a great potential in understanding the functional capacity of microorganisms.
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Original source
Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Bork P, Hildebrand F, Abarenkov K. 2015. Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10: 1-43. doi: 10.3897/mycokeys.10.4852
Tedersoo L, Bahram M, Põlme S, Anslan S, Riit T, Kõljalg U, Nilsson RH, Hildebrand F, Abvarenkov K. 2015. Response to Comment on "Global diversity and geography of soil fungi": Analytical biases in microbial diversity studies. Science 359: 936. doi: 10.1126/science.aaa5594
Additional Information
Schadt CW, Rosling A. 2015. Global diversity and geography of soil fungi: minus at least one widespread group. Science 348: 1438. doi: 10.1126/science.aaa4269
Tedersoo L, Bahram M, Cajthaml T, Põlme S, Hiiesalu I, Anslan S, Harend H, Buegger F, Pritsch K, Koricheva J, Abarenkov K. 2015. Tree diversity and species identity effects on soil fungi, protists and animals are context-dependent. The ISME Journal, in press. doi:10.1038/ismej.2015.116
Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou NS, Wijesundera R, Villarreal-Ruiz L, Vasco-Palacios A, Quang Thu P, Suija A, Smith ME, Sharp C, Saluveer E, Saitta A, Ratkowsky D, Pritsch K, Riit T, Põldmaa K, Piepenbring M, Phosri C, Peterson M, Parts K, Pärtel K, Otsing E, Nouhra E, Njouonkou AL, Nilsson RH, Morgado LN, Mayor J, May TW, Kohout P, Hosaka K, Hiiesalu I, Henkel TW, Harend H, Guo L, Greslebin A, Grelet G, Geml J, Gates G, Dunstan W, Dunk C, Drenkhan R, Dearnaley J, De Kesel A, Dang T, Chen X, Buegger F, Brearley FQ, Bonito G, Anslan S, Abell S, Abarenkov K. 2014. Global diversity and geography of soil fungi. Science 346: 1078. doi: 10.1126/science.1256688
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