High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities
By Aibin Zhan, M. Hulák, F. Sylvester, Xiaoting Huang, Abisola A. Adebayo, C. Abbott, S. Adamowicz, D. Heath, M. Cristescu, H. MacIsaac. 2013
259 citations recorded by the source corpus.
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.
Subfields: Ecology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/94643ad393439cb49f0debb1865d0a292c4f84e9
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Citations in the corpus
- Ascidians as models for studying invasion success (2015, background): “Moreover, these genetic techniques are very powerful at detecting species at low population abundance (Zhan et al. 2013) and may be used to powerfully screen for all invasive ascidian species simultaneously as long as technical issues are well addressed (e.g., Zhan et al. 2014a, b; Zhan and…”
- Tackling Invasive Alien Species in Europe: the Top 20 Issues (2014, methodology): “Molecular methods based on detecting DNA in water (environmental DNA or eDNA) or using DNA in organisms may greatly enhance surveillance programs (Jerde et al. 2011; Dejean et al. 2012; Zhan et al. 2013).”
- Introduction and use of non‐native species for aquaculture in China: status, risks and management solutions (2015, background): “…to develop high-throughput and effective inspection tools, especially genetic tools based on newly emerged technologies, such as gene probe, microarray, and highly sensitive tools such as 454 pyrosequencing to effectively detect small organisms and low-density populations (Zhan et al. 2013).”
- Particle size distribution and optimal capture of aqueous macrobial eDNA (2014, background): “There is broad interest in research on the reliability of eDNA-based ecological monitoring (Sutherland et al. 2013; Zhan et al. 2013; Schmidt et al. 2013).”
- Early detection of aquatic invaders using metabarcoding reveals a high number of non‐indigenous species in Canadian ports (2016, methodology): “…method has been demonstrated to have high sensitivity; that is, species can be detected when present at very low biomass (Hajibabaei et al., 2011; Pochon et al., 2013; Zhan et al., 2013), making it possible to sample rare taxa that are present but not detectable by traditional means.”
- Scraping the bottom of the barrel: are rare high throughput sequences artifacts? (2015, background): “However, Zhan et al. (2013) sequenced aquatic communities and spiked the samples with known indicators to test sensitivity.”
- Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol: advantage of enclosed filter (2017, methodology): “…sensitive technique for revealing species distributions (e.g. Jane et al. 2015; Valentini et al. 2016), early detection of invasive species (e.g. Smart et al. 2015; Simmons et al. 2016) and monitoring rare and/or threatened species for conservation (e.g. Zhan et al. 2013; McKee et al. 2015).”
- How will the ‘molecular revolution’ contribute to biological recording? (2015, background): “The ability of metabarcoding to detect very rare species in complex samples such as mixed plankton or ballast has been demonstrated by artificial spiking of indicator species with known biomass (Zhan et al., 2013).”