Microbial diversity from subsurface sediments (Group presentation: )
Microbiologists participating in the Ocean Drilling Program for the past decade have demonstrated that over 10 4 microbial cells per gram of sediment reside in the subsurface marine sediments, even in several million year old layers at depths close to 1,600m. The discovery of this deep biosphere represents obviously one of the more important conceptual discoveries of the last decades.
Several data contributed to the demonstration of the presence of a subsurface biosphere. They include: microscopic cell counts using fluorescent cationic dyes intercalating between nucleic acids (acridine orange, DAPI), detection of intact lipids, sequences of high molecular weight prokaryotic DNA, microbial activity measurements with radiotracers, culture and isolation of diverse prokaryotes from deep sediment layers, and hybridization of microbial 16S rRNA sequences with fluorescently-labelled probes. The prokaryotes of this “hidden biomass” have been estimated to constitute as much as one third of Earth’s total living biomass, exceeding the biomass in surface terrestrial and oceanic environments.
The discovery of this substantial prokaryotic biomass has profoundly altered our perspective on the distribution of living organisms on Earth and raises a number of interesting questions. Which are the prokaryotic species present in the deep sediments? Do they represent well-preserved remnants of a microbial burial at sea or were they transported by the circulating fluids? How many are they and how are they distributed along the sedimentary gradient? What are the limits of the deep biosphere? Are the prokaryotes active or dormant? Are the microbial cohorts associated with viral suites? What are the carbon and energy sources for the deep prokaryotes? How do the micro-organisms maintain complex functions under the a priori extreme energy limitation? How do they and how are they affected by their geological and geochemical settings? Some elements of answer were provided in the last years by the microbiologists participating in the Integrated Ocean Drilling program IODP ,but the available data remain too limited to be extrapolated to the global sedimentary cover. The composition of the deep microbial communities and the diversity of their metabolic activities are starting to be documented, but the respective functions of the microbial groups are not still identified. The relationships between the deep biosphere and the geological settings remain so far largely unknown.
The involvement of the LM2E in the study of the “deep biosphere” began with the DEEP BUG European program. Concretely, our laboratory contributed to the microbiological analysis of oceanic sediments collected in the Oriental Pacific Ocean (ODP Leg 190) and the North-West Atlantic Ocean (ODP Leg 210). These samples have been collected during international drilling programs (‘ODP Ocean Drilling Program’, and then ‘IODP Integrated Ocean Drilling Program’). The results of the work done on leg 210 samples were published by Roussel et al., (2008). They suggest the existence of a sub-seafloor biosphere as deep as 1600 m in the sediments. These results have a direct impact on the importance of the deep-sea biosphere and are largely discussed as seen in the following commentaries.
Today, the LM2E is further developing its project on the deep biosphere. With this objective, a research group composed of a CNRS research scientist (K. Alain) and an associate professor (F. Duthoit) has been established. The work of this group will be based on the analysis of subsurface sediments collected in the framework of the program IODP. Their studies will combine molecular, cultural, biogeochemical and functional approaches and will integrate the data obtained by a network of local, national and international collaborations (geophysical, geochemical and sedimentological analyses).
The research program will aim at:
(i) determining and measuring global microbial activities,
(ii) identifying and quantifying the prokaryotes along the sedimentary gradient, and determining the activities of the abundant and ubiquitous groups,
(iii) characterizing the physiology and the metabolism of model organisms isolated from deep sea sediments and selected for their representativeness in the ecosystem or for their metabolic or phylogenetic originality.
These 3 research axis correspond, respectively, to 3 levels of Life organisation :
(i) the scale of the ecosystem. At this scale, the challenges are to identify the main microbial activities taking place in this singular ecosystem and to identify the energy sources (>microbiological and biogeochemical analyses),
(ii) the scale of the community. At the community scale, the objectives are: (1) to identify the microbial groups, their abundance and their distribution (with the ultimate objective, to determine the boundaries of the deep biosphere and the physico-chemical limits of Life) (>molecular and cultural analyses of the diversity), and (2), to determine the function of abundant groups of uncultivated prokaryotes (>functional and metagenomic approaches),
(iii) the scale of the individual. At this scale, the work will consist in the characterization of prokaryotes originating from this « extreme » habitat (>physiological analyses and metabolic biochemistry).