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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. [PMID: 33669773 PMCID: PMC7921978 DOI: 10.3390/biom11020318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/02/2022] Open
Abstract
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.
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Affiliation(s)
- Anna Rucińska
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
| | - Marcin Olszak
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Sebastian Świerszcz
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland; (M.N.); (S.Z.)
- Research Laboratory ‘Herbarium’, National Research Tomsk State University, 634050 Tomsk, Russia
| | - Szymon Zubek
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland; (M.N.); (S.Z.)
| | - Grzegorz Kusza
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland;
| | - Maja Boczkowska
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute (IHAR)–National Research Institute, Radzików, 05-870 Błonie, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland;
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Hiiesalu I, Pärtel M, Davison J, Gerhold P, Metsis M, Moora M, Öpik M, Vasar M, Zobel M, Wilson SD. Species richness of arbuscular mycorrhizal fungi: associations with grassland plant richness and biomass. THE NEW PHYTOLOGIST 2014; 203:233-244. [PMID: 24641509 DOI: 10.1111/nph.12765] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/13/2014] [Indexed: 06/03/2023]
Abstract
Although experiments show a positive association between vascular plant and arbuscular mycorrhizal fungal (AMF) species richness, evidence from natural ecosystems is scarce. Furthermore, there is little knowledge about how AMF richness varies with belowground plant richness and biomass. We examined relationships among AMF richness, above- and belowground plant richness, and plant root and shoot biomass in a native North American grassland. Root-colonizing AMF richness and belowground plant richness were detected from the same bulk root samples by 454-sequencing of the AMF SSU rRNA and plant trnL genes. In total we detected 63 AMF taxa. Plant richness was 1.5 times greater belowground than aboveground. AMF richness was significantly positively correlated with plant species richness, and more strongly with below- than aboveground plant richness. Belowground plant richness was positively correlated with belowground plant biomass and total plant biomass, whereas aboveground plant richness was positively correlated only with belowground plant biomass. By contrast, AMF richness was negatively correlated with belowground and total plant biomass. Our results indicate that AMF richness and plant belowground richness are more strongly related with each other and with plant community biomass than with the plant aboveground richness measures that have been almost exclusively considered to date.
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Affiliation(s)
- Inga Hiiesalu
- Department of Botany, University of Tartu, 40 Lai St, 51005, Tartu, Estonia; Institute of Botany, Czech Academy of Sciences, 135 Dukelská St, 37982, Třeboň, Czech Republic
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Pärtel M, Hiiesalu I, Öpik M, Wilson SD. Below-ground plant species richness: new insights from DNA-based methods. Funct Ecol 2012. [DOI: 10.1111/j.1365-2435.2012.02004.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Meelis Pärtel
- Institute of Ecology and Earth Sciences; University of Tartu; Lai 40; 51005; Tartu; Estonia
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences; University of Tartu; Lai 40; 51005; Tartu; Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences; University of Tartu; Lai 40; 51005; Tartu; Estonia
| | - Scott D. Wilson
- Department of Biology; University of Regina; Regina; Saskatchewan; S4S 0A2; Canada
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Chase R, Darbyson E, Horn KE, Samarova E. A mechanism aiding simultaneously reciprocal mating in snails. CAN J ZOOL 2010. [DOI: 10.1139/z09-121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The majority of hermaphroditic animals mate on a given occasion as either male or female, but terrestrial snails and slugs generally mate reciprocally with each partner participating in both sexual roles. This manner of mating requires that the genitalia be exactly opposed prior to copulation attempts, a task made difficult in snails and slugs by the absence of hearing and very limited vision. In the brown garden snail, Cornu aspersum (Müller, 1774), we found that a small protruding structure associated with the genital atrium plays an important role in positioning the snails prior to copulation. Lesions of the penial lobe reduced mating success rates, delayed mating, increased the number of attempted intromissions, and increased the number of unilateral intromissions. The sensory capacity of the penial lobe is demonstrated by histological and electrophysiological evidence, and behavioral data suggest that the lobe is also a stimulus for the partner snail. A literature review suggests that structures functionally equivalent to the penial lobe may be present in many gastropod molluscs that mate simultaneously and reciprocally, but in none that mate in other ways.
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Affiliation(s)
- R. Chase
- Department of Biology, McGill University, 1205, avenue Docteur Penfield, Montréal, QC H3A 1B1, Canada
| | - E. Darbyson
- Department of Biology, McGill University, 1205, avenue Docteur Penfield, Montréal, QC H3A 1B1, Canada
| | - K. E. Horn
- Department of Biology, McGill University, 1205, avenue Docteur Penfield, Montréal, QC H3A 1B1, Canada
| | - E. Samarova
- Department of Biology, McGill University, 1205, avenue Docteur Penfield, Montréal, QC H3A 1B1, Canada
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