Awesome Jobs: Meet Julie Huber, Deep Sea Microbiologist

By Erin Biba

Julie Huber, a marine microbiologist at Woods Hole Oceanographic Institution, specializes in finding itty bitty lifeforms in the deepest parts of the ocean.

There's life in the deepest part of the ocean. And some of that life is microscopic. It's not easy to find the world's tiniest organisms on land and it's even harder when they live in one of the most out of reach places on Earth. Julie Huber, a marine microbiologist at Woods Hole Oceanographic Institution, specializes in finding these itty bitty lifeforms. She talked to us about operating underwater ROVs, doing research off the side of a ship, how understanding the weirdest forms of life on Earth teaches us new lessons about our planet, and what it's like to battle seasickness when your career requires you to spend your life among the waves.

Photo credit: Thom Hoffman

What is the focus of your work?

The big picture is that I'm an oceanographer and I study microbial life in the deep ocean. When I say deep, I mean really deep. I'm mostly interested in places where no sunlight penetrates. I'm especially interested in life living beneath the seafloor within the rocks and fluids that are moving through the crust. The oceans cover 70% of the planet's surface. Oceanic crust is formed by the process of plate tectonics. We constantly have new crust being generated and recycled. Within oceanic crust, seawater is moving through it. It's like a jar of marbles. It's porous, water moves through it. Because there is space and water, there is life.The estimates are that 2% of the global volume of the ocean is in the crust at any single point in time.

The water in the ocean is always moving. New ocean water sinks in the North Atlantic and moves through the conveyor belt, and at some point, it was also move through the crust as it makes its way around the planet's oceans.

Plate tectonics make Earth a really unique place. In our solar system other planets don't have plate tectonics. Ever since I started in this field I've been thinking about life beyond our planet. That is something that I didn't appreciate. You have this fundamental process that keeps exposing fresh rock. Water reacts with it and you get this amazing chemistry that allows life to exist.

There are certainly not plate tectonics going on on Mars right now.

What's the difference between the ocean floor and the ground we walk on?

Continental crust is made of different types of rocks, like granite, than the oceanic crust, gives it a different density. It's is less dense than oceanic crust, which is one of the reasons why it's at a higher elevation than the ocean floor. There are surface expressions of oceanic crust on our planet. If you've been to Iceland or Hawaii, those are basaltic -- what most of the ocean crust is made out of. The first time I walked around the volcano on the big island of Hawaii, it was like walking on the seafloor.

Iceland is actually the very end, the Northern reach of the Mid Atlantic Ridge, which forms the beginning of the world's largest mountain range.

So why do we care about microbes?

You have microbes to thank for just about everything. The oxygen you breathe, most importantly. For most of Earth's history we have been a microbial planet. They think that some of the most ancient eukaryotic cells, which were very primitive in nature, were from about 2.5 billion years ago. So the best evidence for life on our planet is 3.8 billion years. It wasn't really until the rise of oxygen, the ability to generate oxygen through photosynthesis that allowed eukaryotic life to evolve. Microbes are doing the same thing now they were 3 billion years ago, they are eating hydrogen, eating sulfur compounds, eating nitrogen compounds, eating iron, and a lot of people think that doesn't matter, but there are many examples where it does. In soils where the cycling of nitrogen is really important to allowing plants to grow, microbes are the link to breaking that nitrogen down into a form the plant can use. And most importantly the ability to do photosynthesis, turn carbon dioxide into oxygen. Microbes were the first on the planet to be able to do that.

In the ocean a lot of the carbon dioxide from our atmosphere gets eaten by single celled organisms. Instead of eating a hamburger (we eat carbon made from somebody else) these guys take carbon and some other energy sources from the oceanic atmosphere. In the deep ocean they're taking hydrogen sulfide or methane or hydrogen and combining that to create carbon.

Photo credit: Thom Hoffman

Carbon is complicated. It's just one example of a reason to study microbes. What's happening in terms of our atmosphere is there's too much carbon. A lot of it gets consumed right away on the surface of the ocean and a lot of it trickles down to the deep ocean. And in the deep ocean microbes can extract energy from rocks or volcanic systems. We don't know that much about them or how they're affecting this global system.

We know that in the ocean iron is a really important element for life. It's a trace nutrient that lots of life in the ocean needs. It comes from two places: rocks and sand blowing from the desert. A lot of the iron is actually coming from underwater volcanoes. They spew out dissolved iron and then life can use it.

How do you study all of this?

You start somewhere, go to one place and ask questions: who lives here, how are they living, what metabolisms are they using, how are they linked to this often very complex and dynamic geologic environment?

"A lot of the places I study are active volcanoes where brand new oceanic crust is being formed. How does life survive an environment like that?"

A lot of the places I study are active volcanoes where brand new oceanic crust is being formed. How does life survive an environment like that? Is it related to the earliest form of life on earth?

So what do you need to take with you when you go to an underwater volcano?

I take a ship. That's kind of the most important thing. Then we need a way to get to the sea floor. Some of these systems I study, they exist in more shallow waters, but most of them are deep and that's where I mainly study them. The ocean is mostly deep, with an average depth around 3700 meters or 10,000 to 13,000 feet. It's deep.

That involves a ship. On the ship we need to have some sort of submersible. That can be a submarine that puts people in it or a remotely operated vehicle. For me, more common is using a remotely operated vehicle, with no people inside. Some of that is because of safety, like when we are studying actively erupting volcanoes, and some of that is because I need to spend more time on the seafloor than a human can to get my science done. In the US at least we only have one federally funded submersible that can carry humans and that's ALVIN. There have been a couple others, the Pisces in Hawaii is still operated off and on. ALVIN has always been the deepest diving.

Why aren't human-based subs more common?

Generally speaking there's a lot more ROVs then submersibles right now. Sometimes for the type of science I do it's nice to be able to stay on the seafloor for a long time. ALVIN can only stay down for 9 or 10 hours and an ROV can stay down for days and days on end.

They're the ultimate utility tool -- we often add a lot of pumps, sort of like vacuum cleaners. We want to suck up water or microbial mats and put them in containers. We add boxes to collect rocks or animals. Cameras and sensors to measure temperature and PH. It really depends on the science we're doing. The ROV has arms to pick stuff up. We retool the vehicle depending on what the need is.

How long is a typical research trip?

Photo courtesy of Julie Huber

Sometimes the travel adds a lot of time to it. My last cruise was in and out of Guam. You're in the air for 20 hours just getting to Guam. That cruise is an example where there are some sites within a few hours because there's an arc of volcanoes. Others are three days away. From Woods Hole to the Mid Atlantic Ridge is a six day trip. We've done some work in the Caribbean where we've been able to leave from Jamaica or Grand Cayman and that's 12 or 18 hours. The middle of the ocean is, well, the middle of the ocean. Not much there

Depending on the science the average cruise is between 2 and 4 weeks long. We try to work 24 hours around the clock. We try to get ourselves on watch schedules, just like the ship's crew. A lot of them work four hours on eight hours off. For science operations, when you have a vehicle in the water, there's a lot going on. Then when it comes back you have to process all your samples and start all your experiments.

What's a lot?

The ROV team is driving the vehicle and keeping an eye on it. Our job as scientists is to stand watches, so two or three are present at all times saying where we want go, logging observations, making measurements, taking imagery. Different types of scientists want to do different things. A geologist might want to follow a crack on the seafloor, a biologist might want to sit in front of a bunch of tube worms and watch their behavior.

A lot of our sample taking is run through the ROV. I'm telling the pilot "put the sampling wand over there" and I start running my pump. We're filming the whole thing to make sure the cameras are running and there are sensors looking at the sample.

Is it a struggle to agree on what to study among the different scientists?

It starts even before you've gotten the idea to go to sea. One of the things I like about this science is it's multidisciplinary. Studying microbes in isolation without understanding the chemistry and geology doesn't make much sense.

There's always a leader, a chief scientist, that has to represent all the different interests. Yes, it can get testy at times, but we plan the dives. We're gonna sample animals, take some chemistry samples, do some microbiology.

Photo courtesy of Julie Huber

What are the biggest things that can go wrong out at sea?

One of the biggest things is weather. Weather is not something we can control. It's just not safe to launch a vehicle in a bad weather state. Sometimes we bring the ROV up, sometimes we leave it down until the bad weather passes. It depends on the situation. There have been many cruises where we pull the ROV and we sit in the water for days, just waiting.

The other thing that can go wrong is the vehicle or the ship has a problem. There are six to 10 vehicle engineers on each trip, plus a full ships crew, usually around 25 people. I often say that those ROV pilots are often an honorary member of the science team. They have a much better three-dimensional feeling for how it works because they're constantly trying to create a 2D world out of the many screens they have in front of them. They're a wonderful resource for getting things done.

Do you ever get seasick?

I get really sick. I've sort of just learned to deal with it. You'll talk to different oceanographers and they'll tell you different things to do. I take a medication for the first couple days and I'm a little out of it. But by day three or four I have my sea legs. If a big storm comes up I might not feel well. Over all I've learned to manage it. As a grad student I didn't realize how seasick I could get until I went off into the North Pacific. Big storms come in, ocean swell is big, it's just nasty.

Photo credit: Carola Buchner

The chief scientist was an old salty dog. I was 22. He sat me down and said: "This is the medication I take, this is what you should try." I realized that tons of people get sick. For most of us you just get used to it. Your brain and your body and your eyes start working together better. You figure out coping skills. It's one of those things, obviously I didn't realize when I got into this, I just wanted to study the ocean. I have found a coping mechanism.

What sorts of discoveries have you made studying the deep ocean?

We've learned lots of things. I think we've learned that these systems are incredibly dynamic and they have a cycle to them that isn't really driven by seasons but underlying geophysical processes like an underwater eruption. The diversity of microbial life is much higher than previous work had shown and that's partly due to new methods we've developed.

"The diversity of microbial life is much higher than previous work had shown and that's partly due to new methods we've developed."

When I first started working in Woods Hole, we took advantage of what was at the time very new sequencing technologies that really allowed us to fully query an individual sample. What is the full compliment of life in the sample -- similar to how you would walk through the forest and count the trees. This is incredibly challenging because there is so much diversity. The field has really taken off from there. It's now one of the most commonly used tools.

We've also really begun to understand who some of the keystone microbial species are in terms of fixing carbon. That's to help us understand how ecosystems work.

Do you worry at all about funding now that the US Government is turning away from science research?

The federal budget for science has been flat for years now. It really has to do with actions in Congress. I worry about it all the time. We have a flatline budget that isn't growing in the way our economy is growing. I'm always concerned, though. It hasn't always followed who's in the White House. One of the reasons I study our planet is because I care deeply about it. I want it to be here for my children's grandchildren. The best way I've found to advocate for science is by being public facing -- personally and professionally.

Photo courtesy of Julie Huber

How do you think the average person that cares about science can help?

By participating in the scientific process, even if it doesn't seem that important. Participating in water quality monitoring volunteering, for example. Most of the water monitoring that goes on in Cape Cod is volunteer work. You don't need a PhD to be a scientist. We're all inquisitive people. People get scared off by this elitist ivory tower view of scientists, but there's lots of ways to participate in the process as an individual, as a community. There's fundraising people can do. Where it's most effective, where you're surrounded by natural beauty, give your time and money and effort to it. The more we can connect people to the natural world the more they appreciate it.

The deep sea volcanoes are a gateway drug to STEM. They capture your imagination and make people think about life elsewhere in the solar system, engineering, and enzymes that can do wild things. No matter what, it's helping them get engaged in the natural world. That's especially hard for people who live in very urban areas. I grew up in the Midwest and there's no ocean there -- it was really books, TV, the aquarium -- those are important resources. Individuals sometimes forget they're welcome to call their Congressperson any time they want. It's very interesting when people don't understand how my lab runs -- a lot of work is funded by their tax dollars and it costs them very little in terms of the whole budget.

Not all science is done in a lab by guys in white coats staring into microscopes. Lots of discoveries require brave men and women to put their boots on the ground and get down and dirty in dangerous environments. We profile one of these field scientists, tell you how they do their job, and explain the science behind what they do. If there's a scientist or field of science you're dying to hear more about shoot us an email or a tweet: erin at erinbiba dot com, @erinbiba