By Marisa Sloan
Dr. Julie Huber, an associate scientist of marine chemistry and geochemistry at the Woods Hole Oceanographic Institution, has rubbed shoulders with the likes of United Nations officials and Bill Nye. On Nov. 8, Huber spoke to a lecture hall full of UNCG chemistry and biology students about her research on microorganisms deep beneath the sea floor.
Microorganisms have a diversity of forms and functions. For example, they play a huge role in the fermentation of every college student’s favorite beverage, beer. In the pharmaceutical industry, microorganisms are used to produce antibiotics, vaccines and medically-useful enzymes. When an explosion on the Deepwater Horizon oil rig caused the largest marine oil spill in history in 2010, the first responders were microorganisms that naturally eat hydrocarbons and methane found on the seafloor.
In shallow ocean waters, they survive by converting light from the sun into energy through photosynthesis. But thousands of meters beneath the sea floor, there are microorganisms living in total darkness.
“You can think of the ocean’s crust as a jar of marbles that water can move through,” said Huber. “We now know, especially in the last decade, that there are microbes living within that rocky matrix…All of these communities are living in the dark, often very hot or very cold, across a whole range of environmental niches.”
Here, microorganisms must get their energy in another way: from chemicals produced when seawater reacts with certain rocks in the earth’s crust. Depending on what rocks are present in the environment below, underwater volcanoes and hydrothermal vents spew fluids containing these chemicals along with the microorganisms that survive on them. Huber studies these active sites to get an idea of what life is like beneath the sea floor.
As part of her research, she spent three years monitoring sites off the coast of Washington and Oregon. The sites—a small sulfide mound, an eruptive fissure on a rift, and a lava pillar on top of old lava—were chosen because their vent fluid compositions represented a wide range of oxygen, hydrogen and nitrate levels despite being within only a kilometer of each other.
“We filtered the vent fluid on the seafloor, we extracted all the DNA, we sequenced everything, and then we tried to stick it all back together again,” said Huber. “This allows us to access the genomes of these organisms, to look at their functional potential, evolution and many other things. We mostly wanted to know ‘who are they?’ and ‘what are they doing?’”
Through this process, Huber discovered that although each of the three sites housed different microorganisms, the genetic makeup of the communities were similar across the board. In other words, each contained a range of microorganisms with similar DNA.
Next, Huber wanted to figure out which of the genes that showed up in her initial findings were actually being expressed by the microorganisms. Gene expression occurs when a sequence of DNA is transcribed and made into RNA, but it doesn’t happen to every bit of DNA in an organism. In fact, one Oxford study has claimed that less than 10 percent of human DNA is actually functionally useful.
By freezing the RNA of the microorganisms while on the sea floor, and then converting that back to DNA, Huber determined the gene expression of the three sites.
What she found was surprising. Many of the genes that she knew were present in the microorganisms’ genomes weren’t being expressed at the moment the samples were taken, and the genetic expression varied wildly from site to site. This meant that despite a shared genetic potential existing across the different communities, they each hosted fairly distinct populations.
“Despite being this one little kilometer sitting on the sea floor, we have really isolated populations and they’re not showing a lot of exchange between the different sites,” said Huber. “How do you maintain separation in a place that has water flowing through it? This is not the islands of the Galapagos or Darwin’s finches.”
Huber’s best guess is that it has to do with the plumbing beneath the sea floor. She believes the physical structure of the sea floor keeps these populations away from one another by altering things like chemical compositions and flow paths and rates. But it’s just a hypothesis. After spending three years focusing on a single square kilometer, Huber is excited to find out what else she can learn from exploring the rest of the vast ocean floor, although her opportunities to do so may be disappearing.
“Even though the deep sea is really out of sight and out of mind, it is now under pressure from consumerism,” said Huber. “The latest is deep-sea mining. This has been on the table for about 20 years, but was never financially possible. We didn’t really know enough about the deep sea to know what the resources were, but we do now.”
As research on the deep sea has expanded, so has knowledge about where valuable rocks and minerals can be found. Unfortunately, these places are generally near underwater volcanoes and hydrothermal vents, where vibrant communities of microorganisms often live. And because deep-sea mining occurs in international waters, many nations don’t feel the need to report the toll their actions are taking on these ecosystems.
“The scientific community has come out and been very clear that these active hydrothermal systems should be off-limits,” said Huber. “There are too many endemic, rare species there that will not recover if their habitat is destroyed…If you think about losing a habitat, you also lose a lot of potential for new discoveries that are really just the beginning to our access of the deep ocean.”
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