It is rare when discoveries are so groundbreaking, they may rewrite the textbooks. But the discovery of a giant, filamentous, bacteria in a mangrove in Guadeloupe may do just that. The thin, vermicelli-like threads, that are visible to the naked eye and have organelles, may redefine what it means to be a bacterial cell.

“It’s 5,000 times bigger than most bacteria. To put it into context, it would be like a human encountering another human as tall as Mount Everest,” said Jean-Marie Volland, PhD, a scientist at the Laboratory for Research in Complex Systems (LRC) in Menlo Park, CA. In addition to the cells growing orders of magnitude over theoretical limits for bacterial cell size, they also display unprecedented polyploidy of more than half a million copies of a very large genome, and undergo a dimorphic life cycle with asymmetric segregation of chromosomes into daughter cells.

Now, the bacteria’s morphological and genomic features, and life cycle, are published in Science in the paper, “A centimeter-long bacterium with DNA contained in metabolically active membrane-bound organelles.

“The big surprise of the project was to realize that these genome copies that are spread throughout the whole cell are actually contained within a structure that has a membrane,” Volland said. “And this is very unexpected for a bacterium.”

The bacterium itself was discovered in 2009 by Olivier Gros, PhD, professor of marine biology at the Université des Antilles in Guadeloupe. Gros’ research focuses on marine mangrove systems, and he was looking for sulfur-oxidizing symbionts in sulfur-rich mangrove sediments not far from his lab when he first encountered the bacteria. “When I saw them, I thought, ‘Strange,’” he said. “In the beginning I thought it was just something curious, some white filaments that needed to be attached to something in the sediment like a leaf.” The lab conducted microscopy studies over the next couple of years, and realized it was a sulfur-oxidizing prokaryote.

To identify and classify the organism, the team performed 16S rRNA gene sequencing. “I thought they were eukaryotes,” noted Silvina Gonzalez-Rizzo, PhD, associate professor of molecular biology at the Université des Antilles. “I didn’t think they were bacteria because they were so big with seemingly a lot of filaments,” she recalled of her first impression. “We realized they were unique because it looked like a single cell. The fact that they were a ‘macro’ microbe was fascinating!”

The organism was named Candidatus (Ca.) Thiomargarita magnifica. “Magnifica because magnus in Latin means big and I think it’s gorgeous like the French word magnifique,” Gonzalez-Rizzo explained.

View of sampling sites amidst the mangroves in Guadeloupe. [Hugo Bret]

What is this sulfur-oxidizing, carbon-fixing bacterium doing in the mangroves? “Mangroves and their microbiomes are important ecosystems for carbon cycling. If you look at the space that they occupy on a global scale, it’s less than 1% of the coastal area worldwide. But when you then look at carbon storage, you’ll find that they contribute 10–15% of the carbon stored in coastal sediments,” said Tanja Woyke, PhD, microbial genomics program lead at the Joint Genome Insistute (JGI)—a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory.

Volland took on the challenge to visualize these giant cells. Using various microscopy techniques, such as hard X-ray tomography, for instance, he visualized entire filaments up to 9.66 mm long and confirmed that they were indeed giant single cells rather than multicellular filaments, as is common in other large sulfur bacteria. Using confocal laser scanning microscopy and transmission electron microscopy (TEM), he observed novel, membrane-bound compartments that contain DNA clusters. He dubbed these organelles “pepins,” after the small seeds in fruits.

Left to right: Tanja Woyke, Jean-Marie Volland, Olivier Gros, Silvina Gonzalez-Rizzo, and Shailesh Date. [Background image: Hugo Bret; Composite by Susan Brand/Berkeley Lab]

The team learned about the cell’s genomic complexity. “The bacteria contain three times more genes than most bacteria and hundreds of thousands of genome copies (polyploidy) that are spread throughout the entire cell,” noted Volland.

The JGI team then used single-cell genomics to analyze five of the bacterial cells on the molecular level. In parallel, Gros’ lab also used a labeling technique known as BONCAT to identify areas involved in protein-making activities, that confirmed that the entire bacterial cells were active.

Samples of Thiomargarita bacteria were collected amidst the mangroves in Guadeloupe. [Olivier Gros]

For the team, characterizing Ca. Thiomargarita magnifica has paved the way for multiple new research questions. Among them, is the bacterium’s role in the mangrove ecosystem. “We know that it’s growing and thriving on top of the sediment of mangrove ecosystem in the Caribbean,” Volland said. “In terms of metabolism, it does chemosynthesis, which is a process analogous to photosynthesis for plants.” Another outstanding question is whether the new organelles named pepins played a role in the evolution of the Thiomargarita magnifica extreme size, and whether or not pepins are present in other bacterial species. The precise formation of pepins and how molecular processes within and outside of these structures occur and are regulated also remain to be studied.

Gonzalez-Rizzo and Woyke both see successfully cultivating the bacteria in the lab as a way to get some of the answers. “If we can maintain these bacteria in a laboratory setting, we can use techniques that are not feasible right now,” Woyke said. Gros wants to look at other large bacteria. “You can find some TEM pictures and see what look like pepins so maybe people saw them but did not understand what they were. That will be very interesting to check if the pepins are already present everywhere.”

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