Please select your home edition
Edition
Marine Resource 2016

Deep Biosphere home to growing communities of microorganisms

by Woods Hole Oceanographic Institution on 19 Jun 2013
A cell’s DNA carries the instructions, or genes, to make the proteins that are needed to build cell structures and to perform necessary functions. To make a protein, the instructions in the DNA are transcribed, or copied, to a molecule of messenger RNA (mRNA). Other molecules in the cell then help translate those instructions to assemble the protein by stringing together more than 20 different kinds of amino acids in a specific sequence. Messenger RNA provides vital clues about the processes a cell uses to survive, because it shows which genes are being used at a given time. Katherine Joyce
According a new study by scientists at Woods Hole Oceanographic Institution (WHOI) and the University of Delaware (UD), the deep biosphere—the realm of sediments far below the seafloor—harbors a vast ecosystem of bacteria, archaea and fungi that are actively metabolizing, proliferating and moving.

'This is the first molecular evidence for active cell division in the deep biosphere,' says WHOI postdoctoral investigator Bill Orsi, who was the lead author on the study. Previous studies and models had suggested cells were alive, but whether the cells were actually dividing or not had remained elusive.

The finding of so much activity in the deep biosphere has implications for our understanding of global biogeochemical cycles, say the study’s authors.

'Cells are very abundant there, but they do not have high activity levels,' says WHOI microbial ecologist Virginia Edgcomb. 'But it’s a huge biosphere, and when you do the math, you see we’re talking about a potentially significant contribution. Carbon is being turned over, and that has important implications for models of carbon and nitrogen cycling.'

The researchers analyzed messenger RNA (mRNA) from different depths in a sediment core collected off the coast of Peru in 2002 during Leg 201 of the Ocean Drilling Program. Their work was published in Nature on June 12.

This first glimpse into the workings of the heretofore hidden ecosystem was made possible by the first successful extraction of total mRNA, or the 'metatranscriptome,' from the deep biosphere.

Messenger RNA is highly sought-after by microbial ecologists because its presence indicates that the cells that made it are alive, and because it carries the instructions for the proteins the cells are making. That gives researchers valuable information about the biochemical mechanisms and processes the organisms are using to function.

But because the metabolic rates in the deep biosphere are very low, and because mRNA is present in such small amounts—only four to 10 percent of the total RNA in most environmental samples —that extracting enough of it to analyze from deep sediments has been thought by many scientists to be impossible, says Edgcomb.

'It’s not easy,' says Orsi, who developed the extraction technique while a postdoctoral investigator in Edgcomb’s lab at WHOI. 'There’s a certain amount of banging your head against the wall before it works.'

Among the proteins they found coded for in the mRNA, many are involved in cell division, indicating that the cells that made them belong to growing, multiplying populations.

The group found mRNAs related to cell division at all depths tested, from 5 to 159 meters below the seafloor. Such messages were most abundant in zones where cell numbers were the highest, says Orsi, which indicates that the larger cell populations there were likely due to dividing cells.

The study also identified mRNAs for specific biochemical pathways that reveal much about the workings of the deep biosphere ecosystem and its significance to global cycles. The mRNAs came from bacteria and archaea, which have long been recognized as major players in the subseafloor ecosystem; and from fungi, which have recently been suggested to have an important ecological role there.

'Until recently, the fungi in deep sediments have been ignored,' says Orsi. 'The fact that fungi are metabolically active in deep sediments refines our understanding of the extent of the deep biosphere.'

Messenger RNAs coding for enzymes involved in sulfate reduction and nitrate reduction, processes cells use to generate the energy-storing molecule ATP, were also found.

'It’s been theorized that much of the energy that microbes get in this environment comes from sulfate reduction,' says Orsi. 'Basically, instead of breathing with oxygen, they ‘breathe’ with sulfate.'

Until now, models of microbial activity in deep sediments have included sulfate reduction but have not included significant use of nitrate. The current research found comparable numbers of mRNAs involved in nitrate reduction and sulfate reduction, suggesting that both processes are important in the deep biosphere community.



The researchers also found evidence that cells in the deep biosphere are eating amino acids, which are a rich source of carbon and nitrogen and can only come from other living (or recently-deceased) organisms.

'To be a reliable food source for these cells, previous studies have indicated that there probably have to be a lot of dying and/or dead cells to provide the amino acids,' says Orsi. He and his colleagues think those dead or dying cells are native to the deep biosphere rather than remnants that drifted down through the water, because most of the dead material that reaches the seafloor from above is rapidly eaten. Deeper than a few centimeters down, most of the amino acids come from cells that lived and died there.

The experiment turned up another surprise: Many of the cells in the deep biosphere are making proteins to make flagella, the whip-like 'tails' that propel them through a fluid environment. The researchers were even able to show that cells making flagellar proteins occurred in areas of the sediment where the pore spaces are large enough to permit flagella-driven locomotion. Other cells produced mRNAs related to gliding and twitching. In sum, the work provided strong evidence that cells in deep sediments are capable of a variety of kinds of movement.

'The take-home story there is, if there’s room to move, they move,' says Orsi.

The current project grew out of earlier studies in 2005 and 2008 by UD microbiologist Jennifer Biddle showing that DNA from fungi occurs in deep sediments from various sites, including the one the current samples came from.

After further work by Biddle, Edgcomb, and other colleagues in 2010 suggested the presence of active populations of living fungi in the sediments, Orsi and Edgcomb obtained funding from the Center for Dark Energy Biosphere Investigations, an NSF-funded Science and Technology Center, to further pursue the activity of fungi in the deep biosphere.

Orsi says obtaining the mRNA was just one of the technical challenges in the complex study. His extraction yielded more than one billion readable mRNA sequences.

'We had a huge matrix of information—a billion sequences and millions of bits of information associated with those,' he says. 'How do you parse out what’s important and find correlations?'

Orsi worked with Glenn Christman, a bioinformatics programmer at UD, to integrate several bioinformatics tools to address specific ecological questions. Their approach allowed for efficient and high-throughput data analysis that facilitated examination of the immense amount of data.

The Woods Hole Oceanographic Institution is a private, non-profit organization on Cape Cod, Mass., dedicated to marine research, engineering, and higher education. Established in 1930 on a recommendation from the National Academy of Sciences, its primary mission is to understand the oceans and their interaction with the Earth as a whole, and to communicate a basic understanding of the oceans’ role in the changing global environment. For more information, please click here.

Naiad/Oracle SupplierAncasta Ker 33 660x82Wildwind 2016 660x82

Related Articles

A Few Rays - What is Broad Spectrum Protection?
What is Broad Spectrum sunscreen? Ultraviolet rays only make up a small proportion of all of the sun’s rays. What is Broad Spectrum sunscreen? Ultraviolet rays (UVA, UVB and UVC) only make up a small proportion of all of the sun’s rays. UVA and UVB sun-rays are however the biggest contributors to skin damage from sun.
Posted on 19 Apr
Frigid flying – Coast Guard aircrews take on New England Winter
Freezing rain? Teeth-chattering temperatures? Limited visibility? Coast Guard aircrews are still ready to fly. Freezing rain? Teeth-chattering temperatures? Limited visibility? Coast Guard aircrews are still ready to fly. At Air Station Cape Cod, aviation maintenance and electronic technicians work around the clock to ensure the MH-60 Jayhawk helicopters are prepared and ready to launch. There is one thing the maintenance crews and pilots cannot control: winter weather.
Posted on 9 Feb
When whales meet sails
CAMPER helmsman Roberto ‘Chuny’ Bermudez found himself nearly face to face with whale in middle of North Atlantic Ocean. Currently the database for marine mammal strikes is very sparse. We are requesting sailors and boaters help to submit information on current and past incidents, however long ago that may be. By giving a location, date, identification if possible, and any other relevant information you can help scientists better understand where marine mammals are at risk for strikes
Posted on 8 Jan
Vendée Globe – Uncertainty about weather condition in North Atlantic
Alex Thomson and Armel le Cléac'h are probably looking closely at the wind models for the North Atlantic. Alex Thomson and Armel le Cléac'h are probably looking closely at the wind models for the North Atlantic. It does not seem to be easy.
Posted on 4 Jan
10,000 metric tons of plastic enter Great Lakes every year
A new study inventories and tracks high concentrations of plastic in Great Lakes could help inform cleanup efforts A new study by Rochester Institute of Technology that inventories and tracks high concentrations of plastic in the Great Lakes could help inform cleanup efforts and target pollution prevention.Researchers found that nearly 10,000 metric tons—or 22 million pounds—of plastic debris enter the Great Lakes every year from the United States and Canada.
Posted on 2 Jan
The Deepwater Horizon aftermath
Researchers analyze 125 compounds from oil spilled in Gulf of Mexico to determine their longevity at different levels. Researchers analyze 125 compounds from oil spilled in the Gulf of Mexico to determine their longevity at different contamination levels. The oil discharged into the Gulf of Mexico following the explosion and sinking of the Deepwater Horizon (DWH) rig in 2010 contaminated more than 1,000 square miles of seafloor.
Posted on 1 Jan
What happened to Deepwater Horizon Oil?
What happened to the 160 million gallons of oil that gushed for 87 days into the Gulf of Mexico in 2010? Six years after the Deepwater Horizon oil spill, we are continually asked two questions. What happened to the 160 million gallons of oil that gushed for 87 days into the Gulf of Mexico in 2010? Was discharging 1.67 million gallons of chemicals into the ocean to disperse the oil a good or bad idea?
Posted on 24 Dec 2016
Vendée Globe – Light winds for Banque Populaire and Hugo Boss
The first one to get out of it will have a nice north-westerly flow on the edge of the high pressure system. Banque Populaire and Hugo Boss are sailing in a complex weather system in a light wind zone. The first one to get out of it will have a nice north-westerly flow on the edge of the high pressure system.
Posted on 15 Dec 2016
Great Barrier Reef managers and industry prepare for summer
Marine park managers, scientists and experts recently met for the annual pre-summer workshop Marine park managers, scientists and experts recently met for the annual pre-summer workshop to assess climate-related risks to the Great Barrier Reef over the coming months. Current predictions by the Bureau of Meteorology and National Oceanic and Atmospheric Administration are for a summer of average sea temperatures across the Great Barrier Reef.
Posted on 7 Dec 2016
Fourth Blog from on board Perie Banou II
Oh no - not the coffee cup Oh no - not the coffee cup - Jon keeps us all entertained as he approaches Reunion Island. The B&G chartplotter tells me since leaving the pleasant mid Western Australian town of Carnarvon (by world standards, an isolated town), that I have sailed some 2559 NM and have 751nm to go to Le Port Reunion Island. French. Reunion is a Suburb (department) of Paris. Population 844,000.
Posted on 23 Nov 2016