Seed quantity affects the fungal community composition detected using metabarcoding

Funda Oskay, Anna Maria Vettraino* (Corresponding Author), H. Tuğba Doğmuş, Asko Lehtijärvi, Stephen Woodward, Michelle Cleary

*Corresponding author for this work

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Pest introductions via trade in tree seed may result from a lack of adequate survey and validation protocols. Developing better diagnostic protocols to identify potentially harmful pests and pathogens in forest tree seed is of critical importance. High-throughput sequencing-based barcoding and metabarcoding provide effective tools for screening potentially harmful organisms in various plant materials, including seeds. However, the sample size needed to detect the total microorganism diversity of a community is a major challenge in microbiome studies. In this work, we examined how increasing sample size (ranging between 100 and 1000 seeds) influences diversity of fungal communities detected by high throughput sequencing in Pinus sylvestris seeds. Our results showed that as sample size increased, fungal alpha diversity also increased. Beta-diversity estimators detected significant differences between the mycobiota from different samples. However, taxonomic and functional diversity were not correlated with sample size. In addition, we found that increasing the number of PCR replicates resulted in a higher abundance of plant pathogens. We concluded that for the purpose of screening for potentially harmful pathogens using HTS, greater efforts should be made to increase the sample size and replicates when testing tree seed.
Original languageEnglish
Article number3060
Number of pages10
JournalScientific Reports
Issue number1
Early online date23 Feb 2022
Publication statusPublished - 23 Feb 2022

Bibliographical note

We gratefully acknowledge COST Action FP 1406 “Pine pitch canker—strategies for management of Gibberella circinata in greenhouses and forests” (PINESTRENGTH), for supporting F.O. in this work. M.C. is supported by Te Swedish Research Council FORMAS (grant number 2018-00966). S.W. was part-funded by the UK Forestry
Commission. Permission has been obtained for collection of seeds for the study.


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