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Life 2 km below the seafloor: depth records are broken!

New frontiers have been established for life within subseafloor sediments! Microbial molecular signatures were found along the entire length of a two-kilometer core, and some of these micro-organisms could be cultivated in the laboratory.

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Although once hardly conceivable in the abysses, life was found in the whole oceanic mass and is now known to extend below the bottom of the sea: sediments and underlying rocks indeed provide a habitat for large numbers of microbial cells. Molecular archives have shown that life still exists at more than 1000 m below the seafloor, with complex and diversified communities hosting cells belonging to the three domains of the living world: archaea, bacteria and eukaryotes. Yet most deep-subsurface organisms are refractory to cultivation. The extreme depths where active organisms were found in the sediment (518 m for bacteria, 1626 m for archaea and 159 m for micro-eukaryotes) are thus not necessarily the actual limits of their distribution. A better knowledge of these limits would make possible to estimate the volume of the subseafloor biosphere and to guide the search for deep life capabilities/adaptation and the role of microorganisms in global nutrient cycles.

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Deep core drilling requires specialized vessels such as the Joides Resolution, used for the IODP 317 expedition (© William Crawford, IODP/TAMU)

This work concerned microbial communities within a 1927 m-long core, drilled into the oceanic floor of the Canterbury Basin (New Zealand) under 344 m of water. During the drilling operations, the major concern was to avoid sample contamination by external micro-organisms. For this purpose, samples were collected only from the center parts of unconsolidated sediments (which had no contact with the solid and liquid materials used form drilling) and from intact pieces of rocks that had been exposed to ultraviolet radiation after washing. The use of fluorescent micro-spheres made possible to detect the contaminations, the impact of which was found negligible according to several tests.

DNA was extracted from samples collected from all along the core, amplified by polymerase chain reaction and sequenced. Prokaryote (bacteria and archaea) cells were counted in 13 samples. Quantifying the abundance of the different groups was done through the detection of their specific RNA and of several functional DNA genes. The results of sequencing were compared to databases to determine the taxonomic affiliation of the organisms. The cells were cultivated without oxygen and in culture media targeting different metabolic pathways.

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Work on microbiology samples in an anaerobic chamber to prevent contamination (© William Crawford, IODP/TAMU)

The core is composed of three lithological units, from unconsolidated sediments of the seafloor to hard rocks. The temperature at the bottom of the hole was estimated to be in the range of 60 °C–100 °C. Porosity decreased with depth and mean pore size was around 2–4 µm at the base of the core.

The average number of cells also decreased with depth, from around 1,500,000 cells/cm3 at the surface to 25,000 in the deepest samples.

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Richness of the microbial community according to depth

Archaea were most abundant in the first meters and were no more detectable beyond 650 m. Bacteria dominated in the rest of the core, and the abundance of eukaryotes remained somewhat constant at all depths. Sequences were detected down to 1740 m for eukaryotes and 1922 m for bacteria. Species richness was extremely low in comparison with other microbial habitats investigated so far, including extreme environments. Richness decreased very rapidly with depth for archaea and eukaryotes. Archaeal populations were dominated by two groups typically found in subseafloor sediments. Among eukaryotes, few protists but mostly fungi were identified. Bacteria were dominated by two groups well represented in subsurface sediments but distributed in a complementary manner along the core.

The analysis of various environment parameters showed that depth is the main factor explaining diversity and composition changes within the microbial community.

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Epifluorescence microphotographs of cell cultures

Procaryote and eukaryote strains could be cultivated. Strains of fungi could be obtained from samples collected between 21 and 765 m, one which had already been found in extreme environments and 57 which are currently under description. Bacterial strains collected at 1827 and 1922 m were also cultivated, but with very low densities and growth rates. These cells were able to grow at atmospheric pressure as well as at in situ pressure, i.e. 220 times higher. They were very small (0.3 to 0.8 µm in diameter) and often formed aggregates. They could have survived during the progressive burial of sediments or been transported by circulating fluids, and might have acquired metabolic capabilities enabling them to resist the associated environmental changes.

These results confirm the existence, at depths never observed so far, of micro-organisms able to revive, at least to a certain extent: archaea (650 m), bacteria (1922 m), eukaryotes (1740 m). Beyond this discovery, they raise many research perspectives, on the causes of the low phylogenetic diversity of these communities, the microbial metabolic versatility, the concept of species or the role fungi play in deep carbon cycling and in regulation of prokaryotic populations.

 

The paper

Ciobanu M.-C., Burgaud G., Dufresne A., Breuker A., Redou V., Ben Maamar S., Gaboyer F., Vandenabeele-Trambouze O., Lipp J.S., Schippers A., Vandenkoornhuyse P., Barbier G., Jebbar M., Godfroy A., Alain K., 2014. Microorganisms persist at record depths in the subseafloor of the Canterbury Basin. The ISME Journal 8, 1370-1380.

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The authors

The fifteen co-authors of this work are members of French (LMEE of IUEM, LUBEM, ECOBIO) and German (BGR, Hannover; Department of Geosciences and MARUM Center, University of Bremen) laboratories.

 

The journal

ISME Journal is published jointly by the International Society for Microbial Ecology and Nature Publishing Group. This reference journal for microbial ecology (bacteria, archaea, microbial eukaryotes, viruses) covers fields like population ecology, microbe-microbe and microbe-host interactions, evolutionary genetics, genomics and post-genomics approaches, microbial engineering, microbial contributions to geochemical cycles, functional diversity of natural habitats.

 

Contacts

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Communication and scientific mediation service: communication.iuem@univ-brest.fr


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