Into the deep

Katrina Edwards builds condominiums for microbes. The housing is simple: basalt and silicate chips are pushed into cylindrical boreholes in the muddy sediment to provide a nucleus for microbial growth. The environment – a shallow sediment pool on the western flank of an undersea mountain range in the mid Atlantic Ocean – may seem a less than desirable habitat. It’s a strange place to find life; the micro-organisms that live here could wait millions of years for their next meal. Yet despite a lack of oxygen, light or nutrients, life beneath the sea floor is more vibrant than you might expect. It’s also relatively obscure – we know less about the basement of the world than we do about space, and the implications of these extremophiles’ day-to-day activities range from a better comprehension of our planet’s carbon cycle, to new directions in astrobiology research.

Edwards, who is based at the University of Southern California in Los Angeles, is one of only a few hundred scientists worldwide trying to better understand the nature of the billions of microbes that make marine sediments their home. “I think of the world beneath the seafloor as part of the ocean – though it’s an unusual part of the ocean. It’s not the part that people usually think about,” says Steve D’Hondt, an oceanographer at the University of Rhode Island in the USA.

In 1998, a team of scientists led by William Whitman, from the University of Georgia in Athens, U.S., estimated the number of deep-sea microbes to be around 35 x 1029 – that’s 3,500 billion billion billion. This suggested that an incredible 55% of all microbial cells on Earth were living in the deep seabed – while most of the rest lived underground on land. The research kick-started a flurry of scientific interest in the deep-sea environment.

A key component of this knowledge acquisition was the 2010 launch of the Centre for Dark Energy Biosphere Investigations (C-DEBI), based at the University of Southern California. The use of the phrase ‘dark energy’ may seem odd in this context. But the phrase comes from Whitman’s 1998 paper in the journal Proceedings of the National Academy of Sciences. Whitman’s “dark energy biosphere” referred to the fact that there are still extensive amounts of biomass that aren’t included in the global carbon cycle, Edwards explains. Like the dark energy in our universe that mystifies physicists, the dark energy biosphere “is the biomass that’s missing in our own planetary system”.

This dark energy biosphere is under increasing scrutiny as scientists develop new tools to access the inhabitants who live there. Underwater drilling and submarines are able to dive further than ever before, while undersea observatories and drilling programs yield more data. “We have unprecedented connectivity to the ocean and more access than ever before,” says Julie Huber, an assistant scientist with the Marine Biological Laboratory in Woods Hole, Massachusetts, USA.

In mid 2012, D’Hondt and a team of scientists refined Whitman’s study and published a new count of the number of microbes in the Proceedings of the National Academy of Sciences. They tied the number of micro-organisms to sedimentation rate and distance from the coast, and approximated the total number of cells below seafloor to be 2.9 x 10^29 (290 billion billion billion) – a reduction by a single order of magnitude on Whitman’s calculation, but still an extraordinarily high number.

Life in the deep-sea substrate is one of deprivation. The colonies that dwell beneath the seabed can be millions of years old. The microbes themselves have extremely slow metabolism and very low levels of respiration, pushing the boundaries of what it means to be alive. They respire using oxygen, but can also make do with nitrate, oxidised metals, sulphates and, as a last resort, carbon dioxide. Far from the surface, they do not photosynthesise, but rely instead on buried organic matter as a food source. “They are starvation artists. They manage to hold their cellular machinery together with very little food,” says Andreas Teske, a marine scientist at the University of North Carolina in Chapel Hill, USA.

The dark energy group’s objective is simple: to explore life beneath the seafloor. With 70% of the planet covered in water, there’s a lot to pursue. Edwards, D’Hondt, Huber and Teske are all part of this initiative, which is designed to serve as a repository of information and coordinate and share data collection and analysis activities. “It’s hard to interpret the data. It takes an interdisciplinary approach,” says Edwards, whose expertise lies at the crossroads of ecology, mineralogy and microbiology. Part of C-DEBI’s purpose is to provide a “framework of communication, to share data for context,” she adds.

The project is in its infancy, but is already producing results. For example, Edwards, who heads C-DEBI, has recently found that microbial populations will migrate depending on the availability of food: as one population’s food source or environment changes, it moves away, while a new population will ingress and live off the nutrients the first group eschewed. Micro-organisms that thrive on hot fluid methane and sulphur at active hydrothermal vents, for example, are supplanted, once the vents go cold, by microbes that feed on the solid iron and sulphur that make up the vents themselves.

In another experiment, Edwards put colonisation substrates in igneous rock in the Juan de Fuca Ridge, a relatively young, three-million-year-old underwater mountainous area near the coast of Vancouver, Canada, in the eastern Pacific Ocean. The 3mm x 3mm x 1mm mineral chips were placed in bore holes that are 600m from the surface of the water and more than 100m below the ocean’s crust. These chips were exposed to allow the free ebb and flow of the borehole fluids. Edwards left the tiny ‘houses’ for four years, tracking the changes in the microbial communities.

When she removed the substrates at the conclusion of the experiment, she found a dynamic she didn’t expect. There had been an early colonisation of bacteria that consumed iron oxide, but then something changed in the borehole hydrogeology that caused these bacteria to leave and a new colony of thermophilic (heat-loving) microbes to take their place. “We saw two completely distinct populations of bacteria move in and move out in a relatively short period,” she says. “The colony can sense and respond accordingly.”

Huber has also noted the ability of microbes to respond to the environment. She was a graduate student when she first visited the ocean’s floor using a remotely operated vehicle. She cruised over an active deep-sea volcano, with fresh lava flows, that was only six months old but was already teeming with microbes. Like Edwards, Huber studies microbial diversity, although she is most interested in populations near underwater volcanoes with an eye towards possible astrobiological implications. What lives in extreme environments on Earth may give us hints as to what could survive on other planets.

“We need to know who eats whom,” she says, describing much of her lab’s work as “exploratory”. It involves a constant search for new hydrothermal vents and sub-seafloor systems. “It isn’t easy and is often frustrating, but it is always fun,” she says.

It’s obviously challenging to go deep enough, often enough, to acquire the kind of data on the denizens of the deep that biosphere researchers would like to have.
The ocean bottom is extremely varied. In places, Earth’s crust is particularly active; volcanoes, thermal vents and underground aquifers constantly swish sediments about. The amount of iron delivered annually to the ocean from these sub-seafloor circulation aquifer systems is equal to all the iron carried by rivers on Earth, says Edwards. That’s a lot of underwater movement, and much of the dynamics of this environment – and the creatures that thrive here – are relatively unknown.

In other areas, like the abyssal plains that cover much of Earth’s seabeds, activity moves at a glacial pace and sediment accumulation is much slower, ranging from a few centimetres per million years to several metres per 1,000 years, says D’Hondt. In such regions, it may be hundreds or even millions of years before a new nutrient is added to the food pile. Surviving here takes patience.

There are other problems with this research. For a start, back in the lab, growing microbes that have been collected on expeditions is not easy. “We’re not doing a good enough job at replicating the growth environment of microbes in the lab,” Teske says. And the bacteria that do grow don’t necessarily represent the diversity or a dominant species found in situ. The micro-organisms scientists can investigate in a petri dish are extreme even for extremophiles.

Another of Teske’s problems is that it is difficult to isolate individual cell behaviour from the complex microbial mixture in nature. When he obtains a sample and analyses it, it is so mixed “you can feed it some glucose but you don’t know who is using it and who is doing what with it”. The burgeoning field of ‘single cell genomics’ could address this, enabling scientists to “take a wild sample with a mixed microbial community and to pick out individual cells for physiological and genomic analysis,” he says.

“With the current technology, we can get DNA and genetics but nothing else. What we’d like to do is take a single cell and grow it in the laboratory and do tests on it.” But the devil is in the detail, he says. “You can get a single cell out of samples, but inferring the right culture conditions for it is another matter.” He estimates that in the deep subsurface of the seafloor, there are approximately one million cells per cubic centimetre. So, Teske has taxonomic and genetic goals in decoding these bottom dwellers: “We want to understand them and talk about them like biologists, and we do not want to regard them as mysterious microbial monsters. The window that is most accessible to looking at [these] organisms is genetic analysis.”

Undersea microbes are thought to have a “profound influence” on global cycles, like the carbon, nitrogen and sulphur cycles, says Edwards. Huber agrees: “Most of Earth’s history is microbes,” she adds, referring to the two billion plus years that Earth’s life history was dominated by microbes. For billions of years, microbes have driven and responded to changes in the chemistry and temperature of the ocean and atmosphere, so the more we know about them, the better we can understand current state of play regarding the Earth’s climate and atmosphere. “The whole chemical environment on this planet is driven by micro-organisms,” says Hans Røy, a geomicrobiologist at Aarhus University in Denmark.

Ultimately, if we can gain a greater appreciation for the extreme nature of deep ocean microbes, it may give us clues about potential life on other planets. These long-term survivalists are prime candidates for the hypothetical microbes inside meteorites in the theory known as panspermia – the idea that life could be seeded by asteroids. The microbes “are [literally] stuck between a rock and a hard place and for this reason they are not very active,” says Teske. D’Hondt adds: “There are odd implications for survival. How slowly can things go and still survive?”