Microbiologists discover unknown microbial life

Microbiologists discover unknown microbial life in deeply buried marine sediments off Peru and Oregon: Diverse, yet uncultivated, microbes inhabit the deep-biosphere.
The deep sub-seafloor biosphere is the least explored habitat on Earth. Microbial abundance in deep marine sediments exceeds 100 000 cells/cm3, even at a depth of one kilometer below the seafloor. This huge population of microscopic cells is believed to play an important role for the long-term controls on global biogeochemical cycles. However, until now it was unknown what types of microbes are living there and how they interact with geochemical and geological processes in deep marine sediments. An international team of microbiologists from different research institutes, including the Max Planck Institute for Marine Microbiology in Bremen and the Japan Agency for Marine-Earth Science and Technology in Japan, identified the genetic diversity of microbes in 400 meter deep sediment cores obtained from the eastern Pacific margin off Peru and Oregon during two research cruises (no. 201 and 204) of the Ocean Drilling Program (ODP). The scientists analyzed over 2,800 DNA clones by molecular biological techniques and found that the microbes in the deep sediments mostly consist of species that are previously uncultured, unidentified, and basically unknown. The researchers also found that a particular microbial community inhabits the methane hydrate-bearing deep sediments, regardless of their location in the Pacific Ocean. These molecular results reveal the microbial diversity and geographic distribution of the deep biosphere, a significant step toward determining the role that deep microbes play in the essential biogeochemical processes on Earth.
Top row left: Microbiologists study deep marine sediments during the Ocean Drilling Program Cruise 201, off Peru. Researchers had to put on gas mask on deck because some cores release large amounts of toxic hydrogen sulfide. The photo shows the core splitting process on the drilling research vessel JOIDES Resolution.
Top row right: Microbiologist on Leg 201 is processing microbiological samples in the cold room at 4ºC on the drilling ship.
Bottom row left: Image of a sediment core from the Peru Margin. The red patch indicates iron oxide that can be used for the respiration of deeply buried microbes.
Bottom row right: Some of the microbes have been cultivated onboard during Cruise 201. Light blue dots show the fluorescence of DNA-stained cells of cultivated spore-forming bacteria.
Until a few decades ago, the microbial world was thought to be limited to the upper meters of the seabed, while the deeper sediments were thought to be sterile in spite of significant amounts of organic material buried to much greater depths. Exploration of the deep sub-seafloor ecosystem started when the first evidence of microbial activity was provided by studies of methane formation and sulfate reduction in cores obtained from the Deep Sea Drilling Project (DSDP). In the late 1980s, systematic counting of microbial cells in Ocean Drilling Program (ODP) cores was initiated, an endeavor that over the following two decades has led to a large database on the population size of deep biosphere microorganisms. For many years, these bacterial numbers were considered with skepticism among microbiologists, mainly because they contradicted the general understanding of minimum energy requirements for life and because of the difficulty to convincingly prove that the cells were not a result of contamination from the surface world. As the reality of a deep sub-seafloor ecosystem became accepted, however, a bold global extrapolation was made, based on the available data. The astonishing conclusion is that the prokaryotes (bacteria and archaea) of sub-seafloor sediments constitute a “hidden majority” equivalent to 1/2 to 5/6 of Earth's prokaryotic biomass and 1/10 to 1/3 of Earth's total living biomass. This vast population must play a critical role in global carbon cycling by controlling the amount of organic material that becomes buried to great depth in the seabed and stored there for many millions of years. This ecosystem also controls the microbial formation of methane that is the main source of modern gas hydrates accumulating in the seabed, a reduced carbon reservoir that exceeds the amount of carbon in all living organisms on Earth.
New results
In the spring of 2002, research cruise no. 201 of the Ocean Drilling Program drilled deep-sea sediments in the eastern equatorial Pacific and in ocean margin sediments off Peru. Co-chiefs on the drillship were Prof. Bo Barker Jørgensen from the Max Planck Institute (MPI) for Marine Microbiology in Bremen, Germany, and Prof. Steven D’Hondt from the University of Rhode Island, USA. Among the scientists on board were Dr. Fumio Inagaki from the Japan Agency for Marine Earth-Science and Technology (JAMSTEC), currently a guest of the MPI in Bremen as a research fellow of the Alexander Humboldt Foundation, as well as Dr. Timothy Ferdelman from the MPI. Cruise 201 was the first ODP expedition that directly targeted the deep biosphere. An international team of microbiologists and biogeochemists collected drilled core sediments for the exploration of deeply buried microbial communities (see images).

By molecular ecological techniques, Dr. Fumio Inagaki and his German and US colleagues studied the diversity and biogeographical distribution of microbial communities in methane hydrate-bearing and hydrate-free deep sediments from the Peru Margin as well as from the Cascadia Margin, off Oregon, collected during the Cruise 204. They amplified genes encoding for a specific and universal component in the molecular machinery of all cells, the small subunit ribosomal RNA (16S rRNA). They also amplified several genes that have key functions, e.g. by microbial methane formation, by polymerase chain reaction (PCR) technique.

Based on such phylogenetic analyses using over 2,800 clone sequences of 16S rRNA genes, the scientists revealed that microbes in the deep marine sediments are mostly composed of previously uncultivated, unidentified, and unknown species. Interestingly, when the vast data set of sequences is statistically compared to sequence data reported from other methane hydrate-bearing and hydrate-free sediments of western and eastern Pacific Margins, an indigenous (specific) microbial community can be identified at the methane hydrate sites, regardless of the location in the Pacific Ocean. This finding provides novel evidence that the geochemical and geological environment of sub-surface sediments strongly affects the deep microbial community.

Since most discovered DNA sequences were derived from phylogenetically unknown species, the metabolic function and physiological characteristics of the organisms remain largely unknown. Nevertheless, the recognition that the biogeographic distribution of specific microbial populations is consistent with the presence of methane hydrates serves as a starting point for defining their ecological and biogeochemical significance. Many questions arise, however, from these findings. How do these cells affect the cycling of carbon in the deep biosphere? How do they survive the low energy availability of the deep sub-seafloor? What types of microbes are producing or consuming deeply buried methane hydrates? Future research during the Integrated Ocean Drilling Program (IODP), which is the next generation of ODP, will provide answers to these and other urgent questions concerning the deep biosphere.
Fumio Inagaki, Takuro Nunoura, Satoshi Nakagawa, Andreas Teske, Mark Lever, Antje Lauer, Masae Suzuki, Ken Takai, Mark Delwiche, Frederick S. Colwell, Kenneth H. Nealson, Koki Horikoshi, Steven D’Hondt, and Bo. B. Jørgensen. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margins.
Proc. Natl. Acad. Sci. USA, vol. 103, p.2815-2820, February 21, 2006.


Prof. Dr. Bo Barker Jørgensen

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