Deep sea challenges of microbes and men

How do marine microbes cope with extreme life in the deep sea? And how do scientists study these challenging environments?
11 June 2011

Interview with 

Professor Douglas Bartlett and Kevin Hardy, Scripps Institution of Oceanography


DOV Karen brought onboard - glass buoyancy and communication sphere seen in yellow housing.


Sarah visits the Scripps Institution of Oceanography in San Diego, in the US, to find out how masses of marine microbes deal with the challenges life in the deep. And she gets to play with some high-tech gadgets that bring samples of the deep sea back to the lab.

Douglas - There's so much diversity of  microbial life in the ocean in general and especially in the deep sea and we just don't know a lot of what's there. So there's all this biology that's just waiting to be explored. And so we've been taken up with that.

I have been told of this quote that came out of the Census from Marine Microbial Life that there's something like 30 full frown African elephants-worth of microbes for every man, woman, and child on the planet. And most of those microbes in the ocean are in the deep ocean. Maybe not in extreme deep ocean environments but found at depth.

So there's a lot of diversity of life down there. We're interested in the adaptations of microbial life to deep ocean sediments because they are so different - they're dark, the way microbes get nutrients in the deep ocean is very different from that in surface waters, they're adapted to low temperatures as a rule, and they're adapted to high hydrostatic pressure. And it's this last parameter, high pressure, that we've really been focusing on.

And it would be wonderful to be able to get those organisms into culture to more easily do biochemistry and genetics. It would also be useful to look at their genomes and do culture independent molecular analyses, and to look at processes like CO2 fixation and other biogeochemical cycles.

Sarah - So, if you look at something like a bacterium or a microorganism, something that's very small, do they face different challenges to the high pressure than something like a larger bodied animal?

Douglas - The general problems that a microbe would face would be very similar to the cells of any organisms, an invertebrate or a vertebrate. It all has to do with high pressure influences on volume changes, on equilibria, activation, so biochemical processes are very different under high pressure. And all organisms are going to face that issue.

Sarah - And so how do they get around these issues. What adaptations have they come up with that help them solve it?

Douglas - The most well-studied adaptation has to do with membrane lipids. The membrane lipids of deep ocean organisms - fish the bacteria - are loaded with highly unsaturated fatty acids. And that's critical to keeping the membrane in the right physical state - a semi-liquid state. So that it can function for transport and for energetics and for other processes.

Sarah - So, how exactly do you go and retrieve samples of these things? Is that what you do, you go and then you bring them back and study them in the lab? I guess you can't necessarily study them in situ because you just look at them and think I don't really know what's going on there?

Douglas - Yeah, it's hard to explore microbial activities and processes in situ. But that's a growing area of development in the ocean sciences that is coming up with more autonomous instruments that allow you to go where you need to go and to measure those parameters that you'd like to measure.

But what we usually do is, we work with an engineer here at Scripps who comes up with these wonderful untethered toys that can be deployed from relatively small ocean craft and sink all the way down to the deepest ocean depth and can be used to collect water samples and mud and to collect animals using baited traps, and things like that.

And after a prescribed time will release their ballast, close the doors of whatever they're sampling, sea water or animals like crustaceans, and come back up to the surface. And we get those samples at the surface and then we process them.

So far it's been valuable. We've been getting new kinds of microbes. In some cases not just new species or genera of microbes but even new sub-phyla and phyla of microbes coming up that hadn't been cultured previously from deep ocean environments.

Sarah - And finally, I spotted earlier that little tiny polystyrene cup on your window sill. Is that something that was taken down in one of these little unmanned subs?

Douglas - What a great question! You know, I don't even remember where this came from. It is either came from one of those small untethered instruments or it looks like in this case it came from a dive with the Alvin submersible. And so that probably went down just a couple of kms in depth.

But some of these instruments that we deploy have been used at depths as great as 9km or so.

Sarah - So I'm guessing this was once a normal sized polystyrene cup and it's now the size of a very mall egg cup. It's an illustration of the pressures that we're looking at, I suppose.

Douglas - It is. It is. This is a perfect example of how high pressure promotes volume decreases and it does that to a Styrofoam cup. The Styrofoam cups get compressed to something like ceramic and greatly decreased in size.

Sarah - So I guess that is a great illustration of the problems that microbes like that face in the deep sea.

Douglas - It is. And also for people who want to deploy instruments in the deep ocean. Because everything ahs to be designed so that it can cope with high pressure. So, pressure housing are necessary for every component of equipment that gets deployed down deep. Whether it's a manned submersible or an autonomous instrument, or some cabled array, is all has to be pressure resistant.

Sarah - Well, speaking of taking stuff down to the deep ocean and how exactly we go about looking at all the microbes and all the life down there, we're now joined by Kevin Hardy. Kevin, hello.

Kevin - Hi.

Sarah - So I hear that you have quite a lot of exciting gadgets and instruments that you might be able to show us?

Kevin - We have some of the tools of science that get us down to the deepest ocean depths. So, just across the hall...

Sarah - Let's go. Let's go.

Wow, this is quite an exciting room full of gadgets and big yellow spheres. What exactly am I looking at here?

A Deep Ocean VehicleKevin - This here is actually is one of our deep ocean vehicles. It's a small 17-inch outside diameter glass sphere with an acoustic transponder up on top so we can acoustically communicate with it at depth. And gives us about 54 pounds of buoyancy as well as command control so that gives us a payload capability which means we can haul stuff down to the deep ocean.

Sarah - And then haul stuff back up, I guess?

Kevin - And then haul stuff back up, yes. It should be a round trip. So we have one of our frames right here. We actually try to use fiberglass reinforced plastic, FRP, because the water weight is so much lighter and then we attached plastic bottles onto here. So even though it looks large, underwater it really weights nothing so we can carry large volumes of water back to the surface.

Sarah - Well, it's quite noisy in here so shall we take a couple of your exciting gadgets back to the office and we can have a a look at them in more depth. As it were. Fantastic pun there!

Kevin - So, we have a few things we do. Each of the vehicles is a composite of a variety of technologies and we're experimenting with some new ideas. These are lithium ion batteries which are actually really cool because they're vacuum packed and you can see it's sort of like a Ziploc bag that hold a jelly sandwich.

Sarah - Oh yea. So that's pretty small. It's about 3 or 4 inches long, it's about an inch wide. How much power does that thing give out?

Kevin - Yes, this will give us quite a bit actually. It's almost 12 volts at about 2 amp hours. So you can really pack a lot of punch. But the other great thing about this you can package these in an oil environment so they're pressure compensated, and we've done that running them down to pressures greater than the deepest ocean depths. So we can put these outside and we never have to open up those glass spheres on board the small ship, so it makes turnaround very easy.

So we're excited about that, so rather than bringing water up to be processes on the ship we can bring our little factory with us down to the sea floor and leave it down there for a long period of time and actually get a lot more of the microbes that we're looking for.

Sarah - So obviously pressure is something that these are calibrated for. Is pressure the major problem that we look at when we're going down to study the deep sea?

Kevin - Yeah, it's really the first order problem because it'll effect your buoyancy so it's really a buoyancy game - it's like having a lift to the deep sea. So we can put a big anchor on these things, send them down and we have to design them to either tolerate pressure or to be stronger than the pressure.

Once you're down there it's actually pretty benign, temperatures are fairly constant, there's no light to deal with, currents are pretty nominal, corrosion is one of the problems we have to deal with - so a secondary problem. But those things are easily engineering around. So we've got some experience doing this.

So, some of the problems remains the same. The core extraction problem is the one where we go down and get sediments from the seafloor. It's well known that it's like trying to take a core sample out of peanut butter. You plunge in a core tube and you pull it out and it really has a lot of adhesion.

So, one of the techniques that was first proposed in 1960 was by a guy named David Moore here in Sand Diego. And that was actually a technique where you take a steel core tube and it's lined with a plastic sleeve.

Sarah - Oh I see. So this is kind of, it's almost like a drainpipe size, a metal tube here and it's surrounded with this rather sturdy looking plastic rings and things. How does this work?

Kevin - Well, this is really great because what he decided to do was rather than fight the sea floor he was going to give it up. And what he did was he took this steel tube and it would go down to the sea floor, hit the bottom and then the mud would push up on this release and would leave the steel tube behind. And then draw up the plastic liner and leave the steel casement in the bottom which actually rusts away in a short period of time and it's fairly cheap.

That works out actually pretty well, especially for free vehicles when you only have a limited amount of buoyancy.

Sarah - So I guess one of the problems is not just being able to get the sample into your machine it's being able to get the machine off the seafloor because I guess it's like getting stuck in that goopy mud at the beach where you get your feet stuck and you can't out and you're making that splatchy noise. But you're obviously under so much pressure under the sea as well, so I guess it's a bit of a problem.

Kevin - It is. Some of the core samples have a line that goes all the way back up to the ship with a big powerful winch. They can haul this thing with hundreds of pounds. But with the free vehicles which are really just remote vehicles that go down on their own, all you have on board is the buoyancy you have which might only be in the order of 40 or 50 pounds. And so we had to become a little more clever about how to get our vehicle back.

Sarah - And is this still a system that's still used today?

Kevin - Oh yeah. We just used on the Philippines Sea. It's been used down in Fiji. It's really the best way to go, I think. It's still something of the holy grail for us to get this working perfectly every time. But once we do that we have microbial scientists working here on new medicines from the sea, both antibiotics and actually cancer cure drugs, and they really need to harvest the sediments to find those animals. And so they're very good at that, I' very good at this, together we can do things that really help mankind.

Sarah - And we're talking about all these untethered, unmanned vehicles. But haveNOAA Okeanos Explorer Program, deep sea sub either of you ever been down inside something like the Alvin submersible where I guess you get packed into this tiny little room, have either of you ever been down in one of those?

Douglas - I have, I've been down on a few dives in the Alvin, and it's a wonderful experience looking out that porthole. In my case we were looking at cold seeps off the NW coast of the US. Beautiful trip. It's cramped in there, as you indicated. You have three people crammed in an uncomfortable position, everybody trying to look out the porthole window.

And there are real advantages to being right there when it comes to sampling and thinking about the science that you're going to do.

Kevin - So I've been down in a couple of smaller submarines, not the Alvin. And it's quite an experience, first hand observation. Roger Revelle, our former director, once said that instruments will only see what you tell them to look for. So if you're measuring temperature, that's what you get. So, having a human eye behind the portal is really pretty nice. The great thing about free vehicles, unmanned vehicles, is there persistence - they can stay down there quite a long time, 2 years perhaps. If you want to study an entire annual cycle of the deep ocean you can do that. Whereas manned vehicles the great advantage is the human eye and their mobility.

We're picking up some more mobility with AUVs which are like a first order solution to survey a large area. But I think still that there's still quite a bit of opportunity for manned observation down deep.

It's really an exciting place to be. It's a whole other planet. It's a whole other earth. Things happen there that don't happen topside - spreading centers, subduction zones, all sorts of weird and strange animals, many of which we've yet to find. Every time we go down with a camera we find something brand new with samples, we find something brand new. It's still a remarkable place to go.

Find out more

Professor Douglas Bartlett's lab at Scripps


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