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September 3, 2010
Things are finally returning back to normal. I’m back in NYC (indefinitely) and have finally begun to conquer my jet-lag (I slept a full 8 hours last night!), and classes start again on Tuesday, which I’m so excited about. I spent the other morning helping Dustin move into the new laboratory where I’ll be spending lots of time this fall, in between processing all that soil with Krista McGuire. Here is more about Dustin’s lab:
http://www.columbia.edu/~dr2497/HOME.html
And I turn 31 tomorrow! The first year of my 30’s was definitely one of the best of my life, I’m sad to see it end. I have a lot of goals for this coming year though, and one of them is to be able to explain microbiology as intelligently and thoroughly as this Caltech grad student, Jeffrey Marlow. I’ve become a bit enamored with him after following the blog he’s been keeping for the NY Times, where he’s been discussing his summer research studying microbes in the deep sea methane vents at Hydrate Ridge–my dream job! I reprinted my favorite report of his below. Hope you enjoy!
Also, here is the original article if the formatting on my blog is too annoying to read:
http://scientistatwork.blogs.nytimes.com/2010/09/03/readers-questions-on-deep-ocean-biology/
xH
Readers’ Questions on Deep-Ocean Biology
By JEFFREY MARLOWAfter a smooth cruise into San Diego, where Atlantis would be embarking on her next expedition, the science teams went their separate ways, cars brimming with cooler-packed samples. We’ve had a couple of weeks to sort things out (a process which involved many brushes with frostbite, as samples were carefully arranged in freezers set at minus 80 degrees Celsius), and we are continuing to design and conduct experiments to tease out the secrets of the Hydrate Ridge ecosystem.
And with that, I’d like to address a few of the science-based questions that came up in the comments.
Fascinating life-forms, these creatures that do not need sun. Apparently, quite a few have been discovered during the last decades and their adaptability to various sources of “life energy” is remarkable.
Do they have something in common? That is, the lowest part of the chain that actually creates organic material (proteins?) from inorganic sources. How did they evolve? Do they have relatives, close or distant, in the world outside the darkness?
— Ladislav Nemec, Big Bear, Calif.
It’s true: the range of ways for microbes to make a living is impressive. Organisms can be classified by the source of their biomass (how they take atoms and molecules from the environment and turn them into cell stuff) and the source of their energy. Some microbes at the bottom of the ocean get energy from chemicals in their environments, while the grass in your front yard taps into the sun. As long as you can find two chemicals or minerals that can transfer an electron between them, you’ve got an energy source, a microscopic battery of sorts. This process is called chemosynthesis, and a lot of different microbes can do it, microbes living in rocks and soils all over the world. There’s a huge microbial biosphere hidden beneath the surface of the earth – possibly comparable in biomass to the plant life we can see on the surface.
The question of evolution is tricky. We generally approach evolutionary relationships by sequencing a particular gene of various organisms (e.g. the 16S rRNA — one of the genes that makes ribosomal RNA, for those of you keeping score) and seeing how closely related the sequences are. If they’re very similar, the organisms probably evolved around the same time; if they’re really different, then they don’t have much in common. (This trend was first observed by Carl Woese, and is explained at length in his 1987 paper “Bacterial Evolution,” which was published in Microbiology and Molecular Biology Reviews.)
No one really knows how archaea and bacteria evolved, but the cool thing about a lot of these chemolithoautotrophs, including methane-producing and sulfur-respiring micro-organisms, is that they appear very close to the “root” of the tree of life. So it seems pretty likely that life on earth got a toehold via chemolithoautotrophy, not by harvesting solar energy.
Microbes are finely tuned to inhabit specific chemical or physical niches where they’ve got an advantage. For example, if there’s a lot of sulfate in a given patch of mud, pretty soon an organism will show up that can use that sulfate to its advantage. Just about anywhere on earth where similar chemical or physical constraints/opportunities exist, related micro-organisms will pounce. Thus, the high-temperature-loving microbes that swarm around deep-sea hydrothermal vents are often genetically and metabolically similar to the microbes in the hot springs of Yellowstone. By the same token, the methane-eating archaea and bacteria we find at the cold seeps of Hydrate Ridge are similar to methane-eating microbes found in shallow organic-rich anoxic environments like salt marsh sediments, up here on the surface.
Doesn’t the methane on the ridge come from layers of deeply buried organic material, just like other oil and gas deposits? If so, wouldn’t it be more correct to say that the life forms that live on it are still dependent on energy from the sun, just not its direct rays of light? Oil and gas deposits are products of solar energy stored for millions of years.
— JB, California
JB brings up a good point, something that a number of readers pointed out. Natural gas, composed largely of methane, is generally found in huge reservoirs beneath the earth’s surface, derived from a combination of heat and microbial reworking of organic goo produced by photosynthesis in the sunlit ocean waters. However, there are a few other ways to make methane. Methane-producing archaea (methanogens) are a type of chemolithotroph that can use carbon dioxide and hydrogen to make methane without ever seeing the sun. In fact, this process is continually happening in much of the rock at the bottom of the ocean, building up methane stocks within sediments or rocks. As seafloor rock slips beneath a continental tectonic plate, organic matter that has fallen from higher in the water column is cooked and broken down into methane and other organic molecules. This methane, as well as that produced by methanogens, is squeezed out of the rock and percolates up toward the seafloor. In other words, the methane comes from a combination of sources, some of which were ultimately sun-based and some of which weren’t.
As I read your article, I found myself wondering about the changes your samples must undergo as they transition from enormous deep-sea pressures to 1 atmosphere when they are brought to the surface. How does the physiognomy of these organisms change when they are brought out of the depths?
— Mfumbi, Los Angeles
“… but deep-ocean organisms have evolved more stable cell membranes – strong enough to withstand extreme forces without snapping, but flexible enough to allow nutrients in and wastes out.”
Is this correct? Seems that it’s the pressure differential across membranes that is critical; not the absolute pressure. The deep-sea creatures would have a problem only if they move to a different depth quickly — which would cause a pressure imbalance between internal and external pressures.
— jimvj, California
It’s certainly true that you need pressures across a membrane to be similar, but the absolute pressure also plays a role, testing the mechanical strength of a membrane. Think of it like the cell membrane being crushed between two walls, Indiana Jones-style: without strength conferred by branching lipid molecules, the membranes would crumple. The extreme pressure can actually be a good thing for organisms seeking certain dissolved gases. For example, our methane oxidizing archaea benefit from the pressure because methane is more soluble at such depths compared with surface waters. When we bring these organisms up from the deep, there’s no disadvantage to having strong membranes. It may be unnecessary — a needless extra input of energy to build fancy membranes — but it doesn’t impair transport of food and wastes.
I’m wondering how these sites are even found in the first place. Did Alvin drive around the seafloor and just happen to get lucky? How frequent are sites like Hydrate Ridge?
— Paul, Seattle
Analogous to the revolutionary discovery of hydrothermal vents in the late ’70s, methane-driven ‘cold’ seeps were found mostly by accident. In 1983, an Alvin crew was examining large underwater cliffs and landslides off the west coast of Florida when they discovered tube worms and mussels — dead giveaways for the presence of energetic fluids and an active, sulfide-producing microbial community. Other discoveries of cold seeps came about from bottom trawls that brought clams up from the deep ocean and from photographs of the ocean floor taken by robotic submersibles. Once a few sites had been found, scientists began to notice geologic patterns that informed subsequent exploration. Today, dozens of these environments are known in subduction zones near Costa Rica; Monterey Bay, Calif.; Japan; Alaska and Antarctica.
So how are the foram cages you left on the seabed located a year later? Sounds impossible, but obviously there is a reliable technique.
— Barry, California
Finding samples left on the seafloor is all about documentation, documentation, documentation. The easiest way to locate something is with the GPS coordinates, depth and the sub’s heading. If you know where you were when you deployed an experiment and which direction you were facing, you should be able to find it. To make samples easier to see, we usually attach large and/or brightly colored floats or markers that stick up above the seafloor. During my dive, I was surprised by how many experiments are down there — experiments from other expeditions that are seeking answers to very different questions. If for some reason you’re missing the coordinates of a given sample, you can always go back to the video. The sub itself has several video cameras running at all times throughout each dive, looking at different angles at the sub’s surroundings. By seeing when in the dive the sample was deployed, you can work backward or forward with some good old-fashioned dead reckoning to find it.
