CHAPTER 5: GENERAL DISCUSSION, CONCLUSIONS AND PERSPECTIVES153
There is a considerable work left to be done concerning deep-sea benthic foraminifera.
Many issues remain unsolved and new molecular methods have just opened a door on a tremendous world never seen before.
It is really important that our knowledge on “early foraminifera” improves in the near future. Each new description of monothalamous species adds an important piece of information regarding this largely overlooked group, which is, however, the core richness of the entire phylum. This kind of investigations should include molecular data for a much larger set of species, which is the only possible way to establish a solid phylogenetic classification of this group.
We wish to expand physico-chemical analyses on xenophyophores. We propose notably to further investigate radioactive elements contained in their stercomata and their possible origins. Additionally, it could be worthwhile to get the RNA of some specimens and obtain sequences of functional genes. This might give us some clues to understand biological functions linked to the particular feature of fecal pellets sequestration, which drastically modify the concentrations of metallic compounds within the deep-sea sediment.
We should acknowledge that it was particularly frustrating failing to establish komokiaceans origin by molecular tools. This project should be continued by collecting fresh specimens, and enlarged to other described species of Komokiacea.
Concerning the chapter on “hidden” foraminiferal richness (including numerous cosmopolite unidentified taxa and squatters) we should design specific fluorescent probes and apply them to sediment samples to reveal targeted undescribed species.
The applications of massive sequencing methods are countless. Our preliminary analyses probably still retain a lot of information we are not able to unscramble yet. For that reason and because the costs of analyses are not so high (at least in the case of Solexa), we should multiply basic tests to settle properly those new methods. However, it will be hard to
wait for starting a new project and screening the deep-sea sediment on a large scale. We believe that massive sequencing could be a way to circumnavigate the problematic issue of deep-sea sampling and its lack of representativeness. It is now possible to perform far more replicates, which should increase the accuracy of any environmental analysis.
Among numerous analyses, which could be performed using massive sequencing approach, three in particular, have retained our attention: 1) testing possible correlations between foraminiferal richness and some environmental parameters such as depth, latitude and the species richness of other meiofaunal group (for instance nematodes); 2) testing the ubiquity or wide dispersal of target species; and finally 3) monitoring foraminiferal populations in a reduced area over time by massive sequencing of DNA and RNA extracts.
Last but not least, the extracellular DNA obviously amplified during our 454 project should be investigated. It might be possible to estimate its concentration by real time PCR and determine its profile in the sediment.
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