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Open AccessArticle

Looking for Hidden Enemies of Metabarcoding: Species Composition, Habitat and Management Can Strongly Influence DNA Extraction while Examining Grassland Communities

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Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland
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Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
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The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
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Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
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Research Laboratory ‘Herbarium’, National Research Tomsk State University, 634050 Tomsk, Russia
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Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland
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National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute (IHAR)–National Research Institute, Radzików, 05-870 Błonie, Poland
*
Author to whom correspondence should be addressed.
Academic Editor: Nurhayat Tabanca
Biomolecules 2021, 11(2), 318; https://doi.org/10.3390/biom11020318
Received: 20 January 2021 / Revised: 15 February 2021 / Accepted: 17 February 2021 / Published: 19 February 2021
(This article belongs to the Section Molecular Genetics)
Despite the raising preoccupation, the critical question of how the plant community is composed belowground still remains unresolved, particularly for the conservation priority types of vegetation. The usefulness of metabarcoding analysis of the belowground parts of the plant community is subjected to a considerable bias, that often impedes detection of all species in a sample due to insufficient DNA quality or quantity. In the presented study we have attempted to find environmental factors that determine the amount and quality of DNA extracted from total plant tissue from above- and belowground samples (1000 and 10,000 cm2). We analyzed the influence of land use intensity, soil properties, species composition, and season on DNA extraction. The most important factors for DNA quality were vegetation type, soil conductometry (EC), and soil pH for the belowground samples. The species that significantly decreased the DNA quality were Calamagrostis epigejos, Coronilla varia, and Holcus lanatus. For the aboveground part of the vegetation, the season, management intensity, and certain species—with the most prominent being Centaurea rhenana and Cirsium canum—have the highest influence. Additionally, we found that sample size, soil granulation, MgO, organic C, K2O, and total soil N content are important for DNA extraction effectiveness. Both low EC and pH reduce significantly the yield and quality of DNA. Identifying the potential inhibitors of DNA isolation and predicting difficulties of sampling the vegetation plots for metabarcoding analysis will help to optimize the universal, low-cost multi-stage DNA extraction procedure in molecular ecology studies. View Full-Text
Keywords: DNA quality; belowground diversity; graminoid vegetation; Central Europe; roots; DNA extraction DNA quality; belowground diversity; graminoid vegetation; Central Europe; roots; DNA extraction
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MDPI and ACS Style

Rucińska, A.; Olszak, M.; Świerszcz, S.; Nobis, M.; Zubek, S.; Kusza, G.; Boczkowska, M.; Nowak, A. Looking for Hidden Enemies of Metabarcoding: Species Composition, Habitat and Management Can Strongly Influence DNA Extraction while Examining Grassland Communities. Biomolecules 2021, 11, 318. https://doi.org/10.3390/biom11020318

AMA Style

Rucińska A, Olszak M, Świerszcz S, Nobis M, Zubek S, Kusza G, Boczkowska M, Nowak A. Looking for Hidden Enemies of Metabarcoding: Species Composition, Habitat and Management Can Strongly Influence DNA Extraction while Examining Grassland Communities. Biomolecules. 2021; 11(2):318. https://doi.org/10.3390/biom11020318

Chicago/Turabian Style

Rucińska, Anna; Olszak, Marcin; Świerszcz, Sebastian; Nobis, Marcin; Zubek, Szymon; Kusza, Grzegorz; Boczkowska, Maja; Nowak, Arkadiusz. 2021. "Looking for Hidden Enemies of Metabarcoding: Species Composition, Habitat and Management Can Strongly Influence DNA Extraction while Examining Grassland Communities" Biomolecules 11, no. 2: 318. https://doi.org/10.3390/biom11020318

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