The international team used a submersible, designed to withstand immense pressures, to study the bottom of the 10.9km-deep underwater canyon.
Their early results reveal that ocean trenches are acting as carbon sinks.
This suggests that they play a larger role in regulating the Earth's chemistry and climate than was thought.
Although two explorers, Jacques Piccard and Don Walsh, reached the deepest part of the Marianas Trench - a point called the Challenger Deep - in 1960, no humans have been back since.
And the handful of scientific missions, including this recent visit to this deepest spot, have been carried out using unmanned underwater vehicles.
Lead researcher Professor Ronnie Glud, from the University of Southern Denmark and the Scottish Association for Marine Science (Sams), said that working at more than 1,000 atmospheres of pressure was challenging, but advances in technology had made it possible.
He told BBC News: "This is the first time we have been able to set down sophisticated instruments at these depths to measure how much carbon is buried there."
Professor Glud, working with scientists from the Japan Agency for Marine Earth Science and Technology (Jamstec) and from the UK and Germany, used a lander equipped with special sensors packed in a titanium cylinder that was able to resist the remarkable pressures.
The lander was launched from a ship and took three hours to free-fall to the sea bottom, where it carried out pre-programmed experiments before releasing its ballast and returning to the surface.
The tests helped the scientists to assess the abundance of carbon at those murky depths.
Professor Glud said: "Basically, we are interested in understanding how much organic material - that is all the material produced by algae or fish in the water above - settles at the sea bed, and is either eaten by bacteria and degraded or is buried.
"The ratio that is either degraded or buried is the ultimate process determining what are the oxygen and carbon dioxide concentrations of the oceans and the atmosphere, and this gives us an overall picture of how efficiently the sea can capture and sequester carbon in the global carbon cycle."
While this has been studied in other parts of the ocean, such as the abyssal plain - the large flat area of the ocean that lies between 4.6km and 5.5km of depth - the role deep sea trenches play in the carbon cycle has until now remained largely unknown.
Professor Glud said: "Although these trenches cover just 2% of the ocean, we thought they might be disproportionately important, because it was likely that they would accumulate much more carbon because they would act as a trap, with more organic matter drifting to the bottom of them than in other parts of the ocean."
He explained that preliminary data from his experiments suggested that this was the case.
He said: "Our results very strongly suggest that the trenches do act as sediment traps. And they also had high activity, meaning that more carbon is turned over by bacteria in the trenches than is turned over at 6,000m of depth in the abyssal plain.
"What it means is that we have carbon storage going on in these trenches that is higher than we thought before, and this really means that we have a carbon dioxide sink in the deep ocean that wasn't recognised before."
The next stage for the team is to quantify their results and work out exactly how much more carbon is stored in deep sea trenches compared with other parts of the sea, and how much carbon turnover by bacteria is being carried out.
This, the researchers said, should help them to better establish the role of the ocean trenches in regulating climate.
This is not the first time deep sea trenches have surprised scientists.
Recent studies by University of Aberdeen's Oceanlab team have revealed that marine life is much more abundant in this hostile habitat than was previously thought.
In 2008, they filmed the deepest living fish ever to be caught on camera - a 17-strong shoal found at depths of 7.7km in the Japan Trench, and the revealed other animals such as amphipods were present in large numbers even deeper.
Dr Alan Jamieson, from Oceanlab, said the new study was helping researchers to build up a better idea of what happens in the deepest of the deep.
He said: "The trenches continue to amaze us.
"And to see an experiment such as this carried out at these extreme depths is a great leap forward in deep-sea science.
"These studies will greatly enhance our understanding of how the deep trenches contribute to carbon cycling in the world's oceans."