This unusual size is remarkable because the bacteria are usually invisible without the help of a microscope. “It’s 5,000 times larger than most bacteria,” said ean-Marie Volland, a scientist at the U.S. Department of Energy’s (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility located in Lawrence Berkeley National The Berkeley Lab and the Complex Systems Research Laboratory (LRC) in Menlo Park, CA, have joint appointments. In the June 24, 2022 issue of Science, Volland and colleagues, including researchers from JGI and Berkeley Lab, LRC, and the University of Guadeloupe Antilles, describe this giant filamentous bacterium morphological and genomic characteristics, and its life cycle.
For most bacteria, their DNA floats freely in the cytoplasm of their cells. This newly discovered bacterial species has its DNA more organized. “The biggest surprise of the project was the realization that these copies of the genome, which are spread throughout the cell, are actually contained in a membrane with a structure,” Volland said. “And that’s pretty unexpected for a bacterium.”
Strange encounters in the mangroves
The bacterium itself was discovered in 2009 by Olivier Gros, a professor of marine biology at the University of the Antilles in Guadeloupe. Gros, whose research focuses on marine mangrove systems, was looking for symbionts of sulfur oxides in sulfur-rich mangrove sediments not far from his lab when he first encountered the bacteria. He said: “When I saw them, I thought, ‘weird’. At first 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 researchers spent the next few years doing some microscopy studies and realized it was a sulfur-oxidizing prokaryote.
Silvina Gonzalez-Rizzo, associate professor of molecular biology at the University of the Antilles and co-first author of the study, performed 16S rRNA gene sequencing to identify and classify this prokaryotic organism. “I thought they were eukaryotes; I didn’t think they were bacteria because they were so large and seemed to have a lot of filaments,” she recalled her first impressions. “We realized they were unique because it looked like a single cell. They were a ‘macro’ microbe, which was fascinating!”
“She understood that it was a bacterium belonging to the genus Thiomargarita,” Gros noted. “She named it Ca. Thiomargarita magnifica.”
“Magnifica is because magnus means big in Latin, and I think it’s as gorgeous as the French word magnifique,” explains Gonzalez-Rizzo. “This discovery opens up new questions about bacterial morphology that have never been studied before.”
Characterizing Giant Bacteria
When Volland returned to the Gros lab as a postdoctoral researcher, he was involved in the study of the giant Thiomargarita bacteria. He will be at JGI when he applies for a discovery position at LRC, and Gros has allowed him to continue working on the project.
At JGI, Volland began studying Ca. T. magnifica’s single-cell group at Tanja Woyke to better understand the role of this sulfur-oxidizing, carbon-fixing bacterium in mangroves. “Mangroves and their microbiome are important ecosystems for the carbon cycle. If you look at the space they take up on a global scale, it’s less than 1 percent of the world’s coastal areas. But when you look at carbon storage, You’ll find that they contribute 10-15% of the carbon stored in coastal sediments,” said Woyke, who also leads the JGI Microbiology Program and is one of the paper’s senior authors. The team also had to study these large bacteria, given their potential interactions with other microbes. “We started this project under the strategic thrust of JGI’s Inter-Organism Interactions, as large sulfur bacteria have been shown to be hotspots for symbionts,” Woyke said. She added, “However, this project brought us to a A very different direction.”
Volland took up the challenge to visualize these giant cells in 3D at relatively high magnification. For example, using various microscopy techniques, such as hard X-ray tomography, he saw whole filaments up to 9.66 mm long and confirmed that they were indeed giant single-celled, rather than multicellular filaments, as is seen in other large sulfur bacteria very common in. He was also able to use Berkeley Lab’s existing imaging facilities, such as confocal laser scanning microscopy and transmission electron microscopy (TEM), to observe filaments and cell membranes in greater detail. These techniques allowed him to observe new, membrane-bound compartments containing DNA clusters. He called these organelles “pepins,” after the small seeds in the fruit. DNA clusters are very abundant in single cells.
The team learned about the genomic complexity of cells. As Volland points out, “These bacteria contain three times more genes than most bacteria, as well as hundreds of thousands of copies of the genome (polyploidy) spread throughout the cell.” The JGI team then used single-cell genomics at the molecular level Five bacterial cells were analyzed. They amplified, sequenced and assembled the genome. Meanwhile, Gros’ lab also used a labeling technique called BONCAT to identify regions involved in protein-making activity, which confirmed that the entire bacterial cell was active.
Shailesh Date, one of the paper’s senior authors and founder and CEO of LRC, said: “This project is a great opportunity to demonstrate how complexity evolves in some of the simplest organisms. What we have demonstrated One of the things is that there is a need to look at and study the complexity of living things in more detail than is currently done. So we think there might be some surprises in very, very simple organisms.”
The LRC provided funding for Volland through grants from the John Templeton Foundation and the Gordon and Betty Moore Foundation. Sara Bender of the Gordon and Betty Moore Foundation added: “This groundbreaking discovery underscores the importance of supporting fundamental, creative research projects to advance our understanding of the natural world. We look forward to learning about Ca. We look forward to To understand how the characteristics of Ca. Thiomargarita magnifica challenge the current paradigm of what constitutes bacterial cells and advance microbial research.”
One giant bacterium, multiple research questions
For the team, describing Ca. Thiomargarita magnifica paves the way for multiple new research questions. Among them, the role of the bacteria in the mangrove ecosystem. “We know it grows and thrives on top of the sediments of mangrove ecosystems in the Caribbean,” says Volland. “In terms of metabolism, it undergoes chemical synthesis, which is a process similar to photosynthesis in plants.” Another open question is , whether new organelles named pepins played a role in the evolution of the extreme size of Thiomargarita magnifica, and whether pepins are present in other bacterial species. The precise formation of pepins and how molecular processes within and outside these structures occur and are regulated also remain to be studied.
Both Gonzalez-Rizzo and Woyke believe that successfully growing these bacteria in the lab is the way to get some answers. “If we could maintain these bacteria in a laboratory setting, we could use techniques that aren’t feasible right now,” Woyke said. “You can find some TEM pictures and see what looks like pepins, so maybe people see them, But don’t understand what they are. It would be very interesting to examine if pepins were already everywhere.”