Looking for life in unimaginable places
Original story by Laura Poppick
When she was a kid, Karen Lloyd enjoyed mucking around along estuaries and beaches on the coast of North Carolina where she lived. With net in hand, the future microbial geochemist dredged up seaweed and mud squirming with snails, crab larvae and other small invertebrates. To the young Lloyd, these were marvelous hidden worlds, out of sight but no less interesting than fish and whales. These childhood experiences made an impression, instilling in her a belief that there is “a lot more to reality than we can see with our eyes,” she said.
She has since built her career around this belief. Using tools from bioinformatics and geochemistry, Lloyd, now at the University of Southern California, makes organisms visible that are doubly beyond our view — in terms of their microscopic size and their hard-to-reach locations. She studies single-celled microbes that manage to survive in rock 5 kilometers or more below the Earth’s surface, where they live impossibly far from sunlight and oxygen, and push the boundaries of life’s relationship with time and energy.
Until the 1980s, these subsurface ecosystems were unknown to science; Earth’s crust was considered lifeless. Then, after microbiologists cultured cells from aquifer sediments located 30 meters beneath the surface, the race was on to find microbes in more extreme, unexpected habitats. But it would take several decades to begin identifying these organisms using their DNA.
In 2013, taking advantage of advances in DNA sequencing, Lloyd’s team published the first whole-genome sequences of microbial cells living in marine sediments beneath the seafloor in Aarhus Bay, Denmark. The trailblazing study revealed that those sediments teemed with microbes that sit deep on the branches of the tree of life and feed by slowly degrading bits of protein buried in the sediment. This was a previously unknown feeding mechanism for archaea, a branch of single-celled organisms separate from bacteria.
The scientific community has now accepted that bacteria and archaea thrive in the subsurface, representing a massive biome that collectively outweighs more than 200 million blue whales, according to Lloyd’s calculations. In the decade since their discovery, she and her colleagues have sifted through more genomic data and conducted laboratory experiments on the cells. Their findings have expanded their perception of life’s metabolic limits. From the ability to “breathe” rocks to possibly living for hundreds of thousands or even millions of years, these subsurface microbes — known as “intraterrestrials” for their ability to survive within the planet — have forced Lloyd to evolve her own understanding of biology’s universal laws.
While an organism that lives for millions of years may sound extraordinary to us, these ultra-long-lived microbes may actually be quite ordinary on Earth. In a recent comment in Nature Microbiology, Lloyd and her fellow USC microbiologist Andrew Steen advocated for naming these long-lived subsurface microbes “aeonophiles” in reference to their love of eons, or immeasurable lengths of time.
Beyond expanding our perceptions of reality, these microbes may also offer more practical applications. The enzymes that stabilize these cells underground for millennia may be able to stabilize other types of materials, such as medicines in transit to remote areas, Lloyd suggested. Thousands of gene sequences with potential candidates for this type of practical application now exist in the public domain thanks to the work of Lloyd and her colleagues. “It’s just a matter of sifting through the firehose of possibility and finding gold,” Lloyd said. “It’s improbable that there’s nothing useful in there.”
With two TED Talks under her belt, and the recent publication of her book Intraterrestrials: Discovering the Strangest Life on Earth, Lloyd has become something of an ambassador for the microbes that live in our planet’s deep rocks and sediments. Quanta Magazine spoke with her about her experience researching these hard-to-reach biomes and what they can teach us about the limits of life on Earth.