Last month GigaScience published a new approach for assessing and understanding biodiversity, using the slightly unusual sounding method of combining DNA-soup made from crushed-up insects and the latest sequencing technology. This bulk-collected insect goo has the potential to reveal, rapidly and cost-effectively, the diversity and make-up of both known and unknown species collected at a particular time and place. The new method devised by Xin Zhou and colleagues at BGI Shenzhen, China (see the related Author Q&A), is a more accurate and quantitative version of a new biodiversity analysis technique called metabarcoding. Doing some initial validation on the analyses has already revealed how diverse and poorly characterized insect communities (or diversity) can be, even from two small sites within the researchers’ own backyard- literally.
Combining DNA barcoding, which utilizes a standard gene fragment for species identification, with next generation sequencing technologies, metabarcoding looks at multiple markers simultaneously to compare species. Previous metabarcoding methods, however, have required a step to amplify the amount of DNA collected that uses the polymerase chain reaction (PCR). This step can introduce problematic errors into the analysis. The authors of this study have found a way to carry out this method without this step, giving it the potential to be more accurate. In addition to assessing species diversity, it also allows the researcher to determine the total quantity of mitochondrial DNA present for each species, making it possible to reveal relative abundance and biomass of each species. Allowing more consistent and rapid sampling, this may simplify the study of changes in biodiversity over space and time and transform the way we study ecosystems.
Testing the technique on species collected on a hillside behind their laboratory, the authors were very surprised by what they managed to find in their own neighborhood. BGI, the world’s largest genomics organization, is situated on the edge of Shenzhen, a city of 12 million people in the densely urbanized Pearl River delta. Setting up two traps close to each not only revealed how much diversity there was, but also detected species not currently present in online databases. The findings demonstrated how little is known about insect diversity in China, and by opening up the ability to carry out these types of systematic and high-throughput analyses — enabling it to be tested if this is the case everywhere else in the world.
“In some sense, the contribution of next generation sequencing technology to biodiversity research is equivalent to what microscopes did to microbiology.”
Of the study, Dr. Zhou said: ‘The two sampling sites were very close to each other, yet there were only around 10% of the total species being shared between them. The fact that only very few of our barcoded specimens received a sequence match from the Barcode of Life Data Systems, the world’s largest barcode reference database, suggests that much of China’s arthropod fauna still remains as a mystery, at least from a molecular aspect.” With the ability to detect and discover tiny organisms, stomach contents and partial samples without the usual visual cues, he also adds, “In some sense, the contribution of next generation sequencing technology to biodiversity research is equivalent to what microscopes did to microbiology.”
Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification
GigaScience 2013, 2:4 (27/03/2013)
Go to article >>