The objective of Tara Pacific is challenging: to study as fully as possible all the microscopic organisms associated with coral. To investigate this diversity and hope to understand the still unresolved functioning of the coral holobiont, scientists are using a relatively new and rapidly evolving tool: the study of genes, made possible in particular by the high-speed sequencing carried out by the Genoscope (CEA).
Bacteria, viruses, microalgae and fungi – Coral is definitely not just a simple assembly of small polyps in pretty limestone houses. This is all our eye can see, but in fact coral is teeming with microorganisms. It’s a dynamic ecosystem whose functioning is not really understood, but is already dangerously threatened: 20% of coral reefs have already been destroyed and scientists estimate that another 40% could disappear within 40 years.
The surface of a Diploastrea heliopora - © Vincent Hilaire / Fondation Tara Expéditions
In the case of corals as well as other complex biological systems, scientists were until recently insufficiently equipped to understand them. Coral, soil, our microbiota, ocean waters – all these environments have one thing in common: they are populated by thousands of different microorganisms in constant interaction. This invisible and very complex biodiversity has long remained outside the reach of microbiologists.
Too many, too diverse
A little more than 4 centuries ago, the microscope became a common tool on laboratory benches. Scientists then started to realize how limited our vision of biodiversity really was. We contemplate nature on a human scale, in the image of what our eyes can see. In reality, the diversity and complexity of life are much greater in the heart of this microscopic world impossible to grasp with our eyesight.
Beyond the size barrier, scientists soon encountered another difficulty: microorganisms are very, very diverse. On average, one liter of sea water contains millions of protists, billions of viruses, and thousands of different species. The careers of hundreds of biologists with high-power microscopes would not be sufficient to draw up a map (even an approximate one) of the diversity and functioning of complex ecosystems such as coral, plankton or microbiota. Nature still eludes us.
Dropping off DNA on the MinION, a small sequencer that allows the sequencing of DNA directly on board – © Loïc Menard
Recently, scientists have added metagenomics to their toolbox. New advances in sequencing methods, data storage and bioinformatic analysis now offer the opportunity to directly interrogate the genes of organisms present in laboratory samples. Result: no need to constrain, isolate, or cultivate them in labs. In very little time, biologists have developed a precise vision of the diversity and abundance of microorganisms present in a handful of soil or a liter of seawater.
Updating an invisible diversity
The power of these genomic analyses depends in part on the properties of the DNA molecule: universal but sufficiently differentiating. Each type of organism and each species has its own genetic characteristics, so the analysis of their genome makes it possible to distinguish, identify and classify them precisely. We know what species are present in the environment and in what proportions.
Buffer solution and beads used for separating components of coral samples - © Noëlie Pansiot / Tara Expeditions Foundation
Discovering new species
When analyzing samples, scientists may discover a new species or gene. To confirm this, they compare their results with public databases that have collected everything that has already been referenced. If nothing corresponds, then they’ve discovered and observed something totally new. Analysis of the Tara Oceans expedition samples has already helped to increase the taxonomic and genetic diversity of ocean plankton by several thousand species and millions of genes. Metagenomics thus reveals above all, and without surprise, the extent of our ignorance of the microbial world.
This inventory of diversity is the first necessary step. Once we know who is in the ecosystem, we can begin to ask ourselves how this small world interacts, organizes, evolves and adapts. Here again, genomic analyses will prove to be invaluable.
Evolution and functioning of ecosystems
Beyond the aspect of diversity, by comparing samples collected at the same location at different times or in distinct areas with dissimilar environmental conditions, one can get an idea of the spatial and temporal evolution of the ecosystem. The objective is to predict its reaction to changes in temperature, oxygen concentration or pH for example. In the case of coral, by comparing the samples collected along a temperature gradient we can speculate on how this parameter influences the diversity and functionality of the reefs.
From an evolutionary standpoint, by comparing the sequenced genomes of different organisms, relationships between them are identified, and our understanding of the path of evolution is refined, or sometimes upset.
Even more recently, scientists have adapted the methods of DNA analysis to RNA, ie, the genes that are actually expressed and therefore used by organisms. A gene present in a sample may not be expressed and thus have no function in the ecosystem. Analysis of RNA thus makes it possible to understand the variability of gene expression and the functioning of organisms. This sheds light on the complexity of interactions and the way in which organisms adapt to environments that are sometimes very particular and changing.
More generally, linking genetic data to environmental and morphological parameters gives scientists a global vision of the natural system they are studying. More importantly, it opens up completely new research paths upon which they might never have ventured.
Margaux Gaubert, scientific journalist
* Holobiont: The holobiont is an assemblage of all microbial communities that are associated with organisms, here coral, that would be the true unit of evolution of the genome and likely to be the place of biological adaptations.
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