2014 Fiscal Year Research-status Report
Travelling DNA: a study in DNA dispersal and connectivity between marine ecosystem
| Project/Area Number |
26870917
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| Research Institution | Japan Agency for Marine-Earth Science and Technology |
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Principal Investigator |
フレデリック シニゲル 独立行政法人海洋研究開発機構, 海底資源研究開発センター, ポストドクトラル研究員 (10625940)
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| Project Period (FY) |
2014-04-01 – 2016-03-31
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| Keywords | eDNA / coral reef / hydrothermal vent |
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| Outline of Annual Research Achievements |
During this FY2014, samples were obtained in various coral reef environments as well as in the Iheya North Hydrothermal vent field. DNA from the sediments was extracted. A student was hired to assist with this process. Amplicon librairies were constructed and preliminary sequences were obtained.
In addition, sequences were obtained from individual organisms to compare fine scale differences in some of the coral species exhibiting a broad bathymetric distribution.
The first sequences obtained showed a surprisingly low amount of coral DNA in the environmental DNA extracted from sediment samples. This preliminary result might result either from the low sequencing depth obtained in the test round, or in the low contribution of corals to the pool of environmental DNA.
Sequences of individual organisms contributed to understand the connectivity between shallow and deep reefs and these results are included in a manuscript now in review for the journal Coral Reefs.
Overall, the results so far suggest a low dispersal of medium to large size DNA fragments in the environment although similarities can be found between sites within an ecosystem.
The preliminary results of this project were presented at the 2nd International Workshop on Mesophotic Ecosystems in Eilat, Israel in October 2014.
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| Current Status of Research Progress |
Current Status of Research Progress
3: Progress in research has been slightly delayed.
Reason
The preliminary sequencing retrieved only low amounts of coral DNA in the pool of envrionmental DNA. This results combined to the fact the Roche 454 sequencing will be discontinued in the near future motivated the decision to shift to Illumina sequencing. Adpating the protocols for Illumina requires a bit of time, however Illumina sequencing should provide a much higher amount of sequences from the samples facilitating the detection of rare DNA (coral DNA appeared to be rare).
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| Strategy for Future Research Activity |
The second part of this project will focus on obtaining amplicon librairies for Illumina sequencing using both already sampled sediments and newly collected samples. Following the preliminary results showing rare coral DNA in sedimentary eDNA, the research will target Symbiodinium protists living in symbiosis with corals as well as in the water column and in the sediments. These protists are dependent on photosythesis, and, if found in deep-sea sediments, will be good indicators of DNA originating from the water surface. The results from this research will be presented either at the next Deep Sea Biology Symposium in Portugal or at the next meeting of the Japanese Benthic and Plankton Research Societies in Hokkaido (overlapping schedules). A closed system experiment will be set up to test the contribution of corals to sedimentary DNA.
Using the preliminary findings of this research, the second part of the project will aim to demonstrate the potential of eDNA to detect local variations of benthic communities in the sediments (i.e. a relative absence of transfer of medium to large sized DNA fragments between different marine ecosystems).
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| Causes of Carryover |
The main reason for the lower usage of budget is the change of sequencing platform from 454 to Illumina.
Because only little coral DNA was found, in addition of searching for rare coral DNA, I will look for protist DNA, especially Symbiodinium dinoflagellates living in association with shallow corals. For this purpose, Illumina platform is more appropriate than 454.
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| Expenditure Plan for Carryover Budget |
The budget will be used for developing Symbiodinium specific primers to build the amplicon libraries that will then be sequenced on an Illumina platform. Additional samples in different locations in the Ryukyu Archipelago will be collected in order to obtain robust data on the resolution of eDNA in coral reef ecosystems. De novo sequencing of coral/metazoan eDNA using Illumina will be performed. In addition, a closed circuit system will be created to investigate the contribution of coral DNA to sedimentary DNA.
The results from this research will be presented either at the next Deep Sea Biology Symposium in Portugal or at the next meeting of the Japanese Benthic and Plankton Research Societies in Hokkaido (overlapping schedules).
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