The quest for the ultra-rare biosphere

Like Comment

Our original paper published in molecular ecology can be found here.

In the past, the microbial world was a hidden world because humans were not able to see it. Microbes then became visible through microscopes, but the extent of their diversity remained unknown. In the early 2000’s a new technology called high throughput sequencing open widely the door to the mysterious microbial world. Cheap and massive sequencing that use ribosomal RNA marker genes, which represented the first revolution in the field in the 80's, allowed researchers from all around the world to report a microbial diversity never expected before. With the discovery of this hidden diversity, we started to better understand the role and the ecology of microbial communities at the global scale. It became also easier to apply ecological concept, such as dominance and rarity, to entire communities of microbes.

Our team is specialized in the comprehension of the mechanisms that maintain wood falls microbial ecosystem in the ocean. These communities have the incredible ability to convert, within less than a month, a piece of sunken wood into a chemosynthetic habitat (Kalenitchenko et al., 2015). From a microbial ecologist point of view, it was amazing to discover that some deep-sea microbes were adapted to colonize wood, which is a strictly terrestrial material. This discovery led us to wonder where these wood colonizing microbes came from. At that time most researches working on sunken wood thought that the associated microbes came from the surrounding sediments but we were not so sure.

In earlier studies we had immersed fresh wood logs in an aquaria with natural filtered seawater and without sediment, and observed the appearance of microbial mat similar to the ones observed in the natural environment (Kalenitchenko et al., 2017; 2018). Contrary to the common assumption, we therefore suspected that wood microbes might indeed come from the seawater and not the sediments. However, when we started looking for the genetic markers of the wood associated microbes (called wood loving microbes in the lab) in the water column we were never able to detect them even within the members of the rare biosphere.

Following this first observation, we designed an experiment to test, first if the wood microbes were present in the water and second to measure how rare they were. We used four aquaria filled with natural seawater diluted with sterile seawater. Each aquarium contained a different dilution ranging from 1/1 to 1/1000. Then, we incubated wood logs in each aquarium to let potential wood loving microbes colonize them, and follow the development of the wood associated chemoautotrophic microbial ecosystem in each aquarium.

Our trap was a success and the immersed wood did capture wood loving microbes present in the natural seawater. We also found that the strength of the initial dilution impacted the capacity of the microbes to transform the wood into a chemosynthetic ecosystem. But most interestingly, we were able to calculate that the microbes that set up the wood chemosynthetic ecosystem represented less than 1 cell in 10L of the original seawater, making them undetectable by modern molecular tools. We therefore described a new kind of microbes, which we called the ultra-rare biosphere, defined as microbes that couldn’t be detected without being enriched by using a suitable substrate. It shows that the full potential of the microbial world that waits in nature remains hidden to our eyes until a change in the environment allow microbes to grow. We think that it's important to bring these results to the scientific community at a time when we are trying to predict the fate of environments under perturbations.


Kalenitchenko D, Fagervold SK, Pruski AM, Vétion G, Yücel M, Le Bris N, et al. (2015). Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater. ISME J 9: 2657–2670.

Kalenitchenko D, Le Bris N, Dadaglio L, Peru E, Besserer A, Galand PE. (2017). Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. ISME J 12: 367-379.

Kalenitchenko D, Péru E, Pereira LC, Petetin C, Galand PE, Le Bris N. (2018). The early conversion of deep-sea wood falls into chemosynthetic hotspots revealed by in situ monitoring. Scientific Reports 8: 907.

Dimitri Kalenitchenko

Postdoctoral student, Laval University