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Seed quantity affects the fungal community composition detected using metabarcoding

Oskay, Funda and Vettraino, Anna Maria and Dogmus, H. Tugba and Lehtijarvi, Asko and Woodward, Stephen and Cleary, Michelle (2022). Seed quantity affects the fungal community composition detected using metabarcoding. Scientific Reports. 12 :1 , 3060
[Research article]

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Abstract

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.

Authors/Creators:Oskay, Funda and Vettraino, Anna Maria and Dogmus, H. Tugba and Lehtijarvi, Asko and Woodward, Stephen and Cleary, Michelle
Title:Seed quantity affects the fungal community composition detected using metabarcoding
Series Name/Journal:Scientific Reports
Year of publishing :2022
Volume:12
Number:1
Article number:3060
Number of Pages:10
Publisher:NATURE PORTFOLIO
ISSN:2045-2322
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Forest Science
URN:NBN:urn:nbn:se:slu:epsilon-p-116512
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-116512
Additional ID:
Type of IDID
DOI10.1038/s41598-022-06997-9
Web of Science (WoS)000760421800036
ID Code:27546
Faculty:S - Faculty of Forest Sciences
Department:(S) > Southern Swedish Forest Research Centre
Deposited By: SLUpub Connector
Deposited On:13 Apr 2022 11:25
Metadata Last Modified:13 Apr 2022 11:31

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