Microscope What? Next Gen Sequencing reporting in for More Discovery!

Diversity of plankton is always a topic of discussion among marine scientists. Each discovery timeline yields new findings by new techniques to sample, analyze and store data from observations. Microscopes are one of breakthrough inventions, with the discovery of microscopic organisms changing the way mankind views how the world works and many great findings since microscope exists. But as time advances, we are now entering the era of DNA sampling via genetical sequencing. This paper aims to “compare and contrast the taxon richness of whole community zooplankton samples traditional microscope base morphological analysis with the metagenetic analysis” and also addressing the strength and weakness between the two approachs (Lindeque et.al, 2013).

New technological progression changes how effective genetic coding and sequencing are on providing accurate information about species, clades and group of organisms and are necessary to identify more zooplankton and other planktonic assemblages. Morphological identification may be the starting key for diversity and new discoveries, but genetic coding and sequencing shows us DNA similarity and a common ancestor in a wide range of samples. In early era of genetic coding, we were only able to sequence limited and specific amount of sample, but now introducing next gen metabarcoding where the user is able to code and sequence whole zooplankton assemblages, we have more precision. As new technology enhances amplification of replication we are now able to sample a whole range of groups, consuming less time.

454 sequencing (similar to illumina sequencing : read here, but able to sequence longer reads) was used, the data was processed using Qiime (Quantitative Insights into Microbial Ecology, v1.3.0) and  followed the Qiime 18s data tutorial guidlines: read here. Chimera were identified using Chimera slayer in Qiime, and rejected few chimera from the dataset before the constructing the OUT table.

Zooplankton’s morphological features were observed using a microscope after field sampling and treated with formalin preserve. On acquiring 200 samples, they broke it down to 1/4 or 1/8 of the sub-sample and identified larger and rare species that they might have missed in their previous identification, using an Olympus SZX16 microscope.

The results show that metagenetic (next generation) technology outcompetes the traditional microscope morphological analysis,which metagenetic generated three times more OTU. This paper states that ‘the increase in taxonomic resolution is due to improved identification of meroplanktonic larvae as well as some copepoda that are difficult to identify trough microscopy’. There is some missing taxonomic data from both methods such as Cirripedia absence in 2010 sample data (from morphological observation), Amphipoda and Appendicularia missing from 2010 sample data (from metagenetics sampling) and Amphipoda missing from 2011 metagenetic samples. This shows that the metagenetic analysis does have the edge in terms of identifying morphologically similar plankton but morphological identification is not necessarily out of date as well.

This paper explains its method in high detail; from how they start off the sampling process to how they conduct the observations, sequencing tools and techniques. It also has well-described and visual diagrams to show the findings and percentage of results. The lack of comparison to older sequencing methods is a down side of this paper, as this would have provided a more relevant concept. Also, the title seems arguably misconception to what is currently doing as the paper is doing a comparison between two methods instead of making new discoveries using the next gen sequencing method in my opinion.

Reviewed article:

Lindeque PK, Parry HE, Harmer RA, Somerfield PJ, Atkinson A (2013) Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton

Assemblages . PLoS ONE 8(11): e81327. doi:10.1371/journal.pone.0081327