Scientists from the Integrated Ocean Drilling Program have announced the findings at the Goldschmidt conference, a meeting of more than 4,000 geochemists, in Florence, Italy.
Fumio Inagaki of the Japan Agency for Marine-Earth Science and Technology, reported that the microbes exist in very low concentrations, of around 1,000 microbes in every tea spoon full of rock, compared with billions or trillions of bacteria that would typically be found in the same amount of soil at Earth's surface.
Alongside the simple single-celled organisms (prokaryotes) found in the deep rocks, Tim Engelhardt of the University of Oldenburg, Germany, showed that viruses are even more abundant, outnumbering microbes by more than 10 to one, with that ratio increasing with depth.
Speaking to BBC News, Dr Engelhardt said of these viruses: "They are quite stable in these sediments, especially as the metabolic rates of the cells are so low, and they exist in sediments up to 100 million years old."
The number of microbes was so low that the distances between them were much greater than those of communities at Earth's surface, so the scientists were surprised to find that they could support a virus' life cycle.
"We're pushing the boundaries of what we understand about how viruses cycle on Earth elsewhere, by studying them in the deep biosphere" Dr Beth Orcutt of Bigelow Laboratory for Ocean Sciences in Maine, US, told BBC News.
Dr Orcutt continued: "One of the biggest mysteries of life below the sea floor is that although there are microbes down there it's really hard to understand how they have enough energy to live and how incredibly slowly they are growing.
"The deeper we look, the deeper we are still finding cells, and the discussion now is where is the limit? Is it going to be depth, is it going to be temperature? Where is the limit from there being life to there being no life?"
Alive, or just un-dead?
The long-lived bacteria metabolise at such a slow rate that some even question whether this constitutes life at all.
"The other question we have is that even though we are finding cells, is it really true to call it alive when it's doubling every thousands of years? It's almost like a zombie state," Dr Orcutt commented.
Despite being very slow-living and slow-acting, Earth scientists have also suggested that the existence of microbial communities deep in Earth's rocks could be changing the chemistry of the rocks, the deeper Earth, and the planet itself.
By locking up and using carbon within the rocks, these deep organisms could be modifying the carbon cycle on Earth, and could ultimately have some impact on the rates of release of carbon dioxide into the atmosphere from volcanoes over Earth's history.
[Source]: Simon Redfern