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Zhan, A.; Hulák, M.; Sylvester, F.; Huang, X.; Adebayo, A.A.; Abbott, C.L.; Adamowicz, S.J.; Heath, D.D.; Cristescu, M.E.; Macisaac, H.J. "High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities" (2013) Methods in Ecology and Evolution. 4(6):558-565
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Abstract:

Summary: Concerns regarding the rapid loss of endemic biodiversity, and introduction and spread of non-indigenous species, have focused attention on the need and ability to detect species present in communities at low abundance. However, detection of rare species poses immense technical challenges, especially for morphologically cryptic species, microscopic taxa and those beneath the water surface in aquatic ecosystems. Next-generation sequencing technology provides a robust tool to assess biodiversity, especially for detection of rare species. Here, we assess the sensitivity of 454 pyrosequencing for detection of rare species using known indicator species spiked into existing complex plankton samples. In addition, we develop universal small subunit ribosomal DNA primers for amplification of a wide range of taxa for detailed description of biodiversity in complex communities. A universality test of newly designed primers for the hypervariable V4 region of the nuclear small subunit ribosomal DNA (V4-nSSU) using a plankton sample collected from Hamilton Harbor showed that 454 pyrosequencing based on this universal primer pair can recover a wide range of taxa, including animals, plants (algae), fungi, blue-green algae and protists. A sensitivity test showed that 454 pyrosequencing based on newly designed universal V4-nSSU primers was extremely sensitive for detection of very rare species. Pyrosequencing was able to recover spiked indicator species with biomass percentage as low as approximately 2·3 × 10-5% when 24 artificially assembled samples were tagged and sequenced in one PicoTiter plate (i.e. sequencing depth of an equivalent of 1/24 PicoTiter plate). In addition, spiked rare species were sometimes recovered as singletons (i.e. Operational Taxonomic Units represented by a single sequence), suggesting that at least some singletons are informative for recovering unique lineages in 'rare biospheres'. The method established here allows biologists to better investigate the composition of aquatic communities, especially for detection of rare taxa. Despite a small-scale pyrosequencing effort, we demonstrate the extreme sensitivity of pyrosequencing using rare species spiked into plankton samples. We propose that the method is a powerful tool for detection of rare native and/or alien species. © 2013 British Ecological Society.

Registro:

Documento: Artículo
Título:High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities
Autor:Zhan, A.; Hulák, M.; Sylvester, F.; Huang, X.; Adebayo, A.A.; Abbott, C.L.; Adamowicz, S.J.; Heath, D.D.; Cristescu, M.E.; Macisaac, H.J.
Filiación:Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China
Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genetica y Evolucion, Consejo Nacional de Investigaciones, Científicas y Técnicas, Universidad de Buenos Aires, Buenos Aires, Argentina
Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, QC, H3A 1B1, Canada
Palabras clave:Alien invasive species; Biodiversity; Endangered species; Next-generation sequencing (NGS); Non-indigenous species; nSSU rDNA; Plankton; Universal primers; algae; Animalia; Chlorophyta; Fungi; Protista
Año:2013
Volumen:4
Número:6
Página de inicio:558
Página de fin:565
DOI: http://dx.doi.org/10.1111/2041-210X.12037
Título revista:Methods in Ecology and Evolution
Título revista abreviado:Methods Ecol. Evol.
ISSN:2041210X
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_2041210X_v4_n6_p558_Zhan

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Citas:

---------- APA ----------
Zhan, A., Hulák, M., Sylvester, F., Huang, X., Adebayo, A.A., Abbott, C.L., Adamowicz, S.J.,..., Macisaac, H.J. (2013) . High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Methods in Ecology and Evolution, 4(6), 558-565.
http://dx.doi.org/10.1111/2041-210X.12037
---------- CHICAGO ----------
Zhan, A., Hulák, M., Sylvester, F., Huang, X., Adebayo, A.A., Abbott, C.L., et al. "High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities" . Methods in Ecology and Evolution 4, no. 6 (2013) : 558-565.
http://dx.doi.org/10.1111/2041-210X.12037
---------- MLA ----------
Zhan, A., Hulák, M., Sylvester, F., Huang, X., Adebayo, A.A., Abbott, C.L., et al. "High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities" . Methods in Ecology and Evolution, vol. 4, no. 6, 2013, pp. 558-565.
http://dx.doi.org/10.1111/2041-210X.12037
---------- VANCOUVER ----------
Zhan, A., Hulák, M., Sylvester, F., Huang, X., Adebayo, A.A., Abbott, C.L., et al. High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Methods Ecol. Evol. 2013;4(6):558-565.
http://dx.doi.org/10.1111/2041-210X.12037