Inside the discovery of the largest bacteria ever found

A closer look revealed these white threads to be something entirely new

It wasn't recklessness that led Gross to assume that the eyelash-sized creatures he found in the mangrove were eukaryotes. Prior to this research, almost all known organisms large enough to be seen with the naked eye were eukaryotic cells. That wasn't a coincidence. Only eukaryotic cells were known to have the organelles thought to be required to sustain life at macroscopic size (that is, large enough to be seen without a microscope).  

"I brought them back to the lab, took some pictures with a binocular microscope, and begin to observe them with electron microscopy," he said. He needed the microscope to search for the hallmark of eukaryotic cells: mitochondria. "But I couldn't find any," he said.

That's when he turned to a colleague, physicist, and co-author Jean-louis Mansot, to take a closer look at the samples. The pair saw that the cells' cytoplasm was packed with granules of sulfur. That's not unheard of: scientists know about some bacteria that oxidize sulfur and live together, forming fibrous mats. But there was a big difference between those bacteria and Gros' sample: each eyelash-sized creature from the mangrove was just one cell.

Then... nothing. While working on other projects, Gros set the anomaly aside for a few years. The next breakthrough came when molecular biologist Silvina Gonzalez-Rizzo investigated the creatures. She used genetic analysis to figure out how they fit into the tree of life. RNA revealed that despite their gargantuan size, the strange white threads were closely related to known species of bacteria. "She showed without a doubt that it was a bacterial species belonging to the well-known genus Thiomargarita," Gros said.

Now that the researchers knew what the creature was, they turned to colleagues at other institutions to see what else could be gleaned from its genome.

The genetic analysis brings T. magnifica into clearer focus

T. magnifica's genetic code is 12 million bases long. (For reference, the human genome is roughly 250 times larger, at 6 billion bases.) "For a bacterium that's not unheard of, but it's in the upper size range — and it's twice the size of some of its relatives," according to genomicist Tanja Woyke, a principal investigator at the U.S. Department of Energy's Joint Genome Institute and a co-author on the paper.

She told reporters that despite its superlative size T. magnifica is quite similar to its close genetic cousins, with two exceptions. For one thing, a huge chunk of the newly discovered species' genome — roughly one in four base pairs — code for secondary metabolism. Those functions "that are not essential for cell survival," Woyke says. Many plants, for example, use secondary metabolism to create the chemicals they use to make their leaves bitter and to ward off predators. T. magnifica may do something kind of similar. Its large genetic dedication to secondary metabolism, "may explain why we don't see bacteria attached to the outside [of these bacteria.] They might use some of these compounds to keep other bacteria away."

The second thing that's unique about T. magnifica's genome is the number of copies each bacterium contains. This is one of the ways that the new species overturns what scientists thought they knew about bacteria. In most bacterial cells, the genetic material floats around in the cytoplasm without much structure, according to biologist Jean-Marie Volland, another co-author. But that isn't so with T. magnifica.

"These giant cells have their DNA inside small membrane-bound compartments. These compartments represent a new type of bacterial organelle that we named the pepins, which means, in French, the small seeds in fruits," Volland says. 

That's a big deal because it's completely out of step with what scientists thought they knew about bacteria. "Until now, the packing of the cell's DNA inside membrane-bound organelles was considered to be strictly limited to the eukaryotic cells, which are the building blocks of organisms such as humans, other animals, or plants," Volland said.

Incredibly, each T. magnifica bacterium maintains roughly 500,000 copies of its genetic code. That means each cell contains roughly 6,000,000,000,000 (6 trillion) bases. "This means that T. magnifica stores several orders of magnitude more DNA in itself as compared to a human cell," Woyke says.

Why's it so big?

There is, of course, one gigantic question looming over this discovery: why did T. magnifica grow so incredibly large? What evolutionary pressure could have nudged this species' ancestors to balloon more than fifty times bigger than their neighbors? It's far too early to say for sure, but the researchers on this paper think the answer comes down to food... sort of.

Instead of eating plants or animals, T. magnifica makes its own food. But it doesn't use sunlight or rely on energy from hydrothermal vents. Instead, the bacteria extract chemical energy from their environment. "They need sulfide, and they need CO2," Gros says. The sulfide is found in the black sediment on the mangrove floor, and the carbon dioxide is dissolved in the seawater.

Volland compares the process to photosynthesis. "Plants are able to use the energy coming from light... to produce more complex molecules — sugars — from carbon dioxide," he says. The bacteria uses an analogous process called chemosynthesis, which biologists were already familiar with. "It uses the energy contained in the hydrogen sulfide, in reduced sulfur species that are full of electrons," he says.

This sounds like a piece of cake. All a sulfur-oxidizing bacterium has to do is find a spot where the sediment meets the water, and voila! Energy from chemosynthesis. But there's a bit of a problem. "They have to position themselves exactly at the right interface... because these two chemicals cannot remain together in the same environment. They react with each other. Most bacteria that are microscopic face a huge challenge, which is to access both hydrogen sulfide and oxygen at the same time," he said.

How could a species get a leg up under these conditions? Growing incredibly large seems like a good solution. "These giant bacteria maybe have a big advantage by being giants and by being able to... sit right at this interface," he said. 

For now, it's just speculation. But these are early days for research into the macroscopic bacteria. For instance, the researchers don't know what cycles determine where T. magnifica will be at what time of the year. That's important because lab research depends on maintaining a steady supply of samples — the researchers have not yet figured out how to grow the bacteria in the lab. For now, that supply has been cut off.

At the press conference before the announcement, Gros told reporters, "in these last two months, I cannot find them. I don't know where they are. They are not here for the moment." 

That may be disappointing news if you're on the edge of your seat, wanting to learn more about this textbook-rewriting species. But it shouldn't be a surprise. In science, every discovery spawns far more answers than questions.