Title |
Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol
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Published in |
BMC Ecology and Evolution, December 2012
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DOI | 10.1186/1472-6785-12-28 |
Pubmed ID | |
Authors |
Mehrdad Hajibabaei, Jennifer L Spall, Shadi Shokralla, Steven van Konynenburg |
Abstract |
Characterizing biodiversity in a habitat or in targeted taxonomically or socioeconomically important groups remains a challenge. Standard DNA-based biodiversity identification tools such as DNA barcoding coupled with high-throughput Next-Generation Sequencing (NGS) technologies are rapidly changing the landscape of biodiversity analysis by targeting various habitats and a wide array of organisms. However, effective use of these technological advances requires optimized protocols and benchmarking against traditional tools. Here we investigate the use of commonly used preservative ethanol as a non-destructive and inexpensive source of DNA for NGS biodiversity analysis of benthic macroinvertebrates. We used the preservative ethanol added to field collected organisms (live sorted bulk benthic samples) as a source of community DNA for NGS environmental barcoding. We directly compare this approach with a DNA barcode library generated using Sanger sequencing of all individuals separated from abenthic sample as well as with NGS environmental barcoding of DNA extracted from mixed/homogenized tissue specimens of the same benthic sample. We also evaluate a multiplex PCR strategy, as compared to commonly used single amplicon workflow, using three newly designed primer sets targeting a wide array of benthic macroinvertebrate taxa. |
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Geographical breakdown
Country | Count | As % |
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United States | 1 | 13% |
Canada | 1 | 13% |
Sweden | 1 | 13% |
Unknown | 5 | 63% |
Demographic breakdown
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Members of the public | 4 | 50% |
Scientists | 3 | 38% |
Practitioners (doctors, other healthcare professionals) | 1 | 13% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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France | 4 | 1% |
Spain | 3 | <1% |
United States | 3 | <1% |
Canada | 2 | <1% |
Brazil | 2 | <1% |
Australia | 1 | <1% |
United Kingdom | 1 | <1% |
Germany | 1 | <1% |
New Zealand | 1 | <1% |
Other | 3 | <1% |
Unknown | 350 | 94% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 97 | 26% |
Student > Ph. D. Student | 63 | 17% |
Student > Master | 58 | 16% |
Student > Bachelor | 41 | 11% |
Professor > Associate Professor | 16 | 4% |
Other | 53 | 14% |
Unknown | 43 | 12% |
Readers by discipline | Count | As % |
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Agricultural and Biological Sciences | 183 | 49% |
Environmental Science | 70 | 19% |
Biochemistry, Genetics and Molecular Biology | 35 | 9% |
Computer Science | 3 | <1% |
Earth and Planetary Sciences | 3 | <1% |
Other | 17 | 5% |
Unknown | 60 | 16% |