Most bacteria are only a few micrometers in size and can only be seen with a microscope. But now researchers have discovered for the first time a bacterium that is visible to the naked eye. The cells of the bacterial species discovered in the water of mangrove forests on Guadeloupe form whitish threads that are up to two centimeters long. Their genome is three times larger than that of typical prokaryotes and contains more gene copies than any other known cell, the team reports. What is also unusual about the bacterium called Thiomargarita magnifica is that it has packed its genetic material together with the protein-producing ribosomes in many small membrane sacs – normally the genetic material of bacteria lies freely in their cell fluid.
Bacteria are not classified as microorganisms for nothing: Most bacterial cells are only a few micrometers in size and cannot be seen with the naked eye. Only in recent years have scientists discovered unusually large representatives of such microbes in the sea and in fresh water. These giant bacteria can grow to be several hundred micrometers in size. The largest bacterial species, Thiomargarita namibiensis, was discovered on the seabed off the coast of Namibia in 1997. It is up to 750 micrometers in size and thus reaches dimensions that are at the limit of what is possible for prokaryotes – at least that’s what was thought. Because unlike the cells of eukaryotic organisms, prokaryotes have no cell nucleus, hardly any active transport mechanisms and only rarely cell compartments. They can therefore only take up nutrients and cell-specific molecules and distribute them in their cells through passive diffusion. This limits the maximum size from which such a simply structured cell is still functional.
White threads in the mangrove mud
But now a team led by Jean-Marie Volland from the Lawrence Berkeley National Laboratory in Berkeley reports the discovery of an even larger bacterium. The marine biologist Olivier Gros from the University of the Antilles on Guadeloupe found it when he was looking for sulfur-oxidizing organisms in the sulphur-rich mud of the mangrove forests. He noticed whitish threads that seemed to be stuck to fallen leaves in the sediment. “These filaments had a stalk-like shape and gradually thinned towards the top, where a kind of buds could be seen,” the researchers report. These white threads were 9.7 millimeters long on average, but some filaments also reached lengths of 20 millimeters. To find out what it was, the scientists collected some samples and then examined them in the laboratory using electron microscopy, fluorescence microscopes and X-ray tomography.
To the surprise of the research team, it turned out that these were not multicellular structures, as initially assumed. Instead, each thread consisted of just a single bacterial cell. “It is 5,000 times larger than most bacteria,” says Volland. “For comparison: A person of this size would be as tall as Mount Everest.” The cell size and also the cytoplasm volume of these cells are thus well above what was previously considered the maximum upper limit for prokaryotic cells. “This discovery raises new questions about the morphotype of the bacteria,” says Gros. The research team has named their new discovery Thiomargarita magnifica. The genus name Thiomargarita indicates that this species is closely related to the previously known giant sulfur-oxidizing bacteria.
Huge genome, individually wrapped
In order to find out why this bacterium was able to grow so large and what its interior is like, Volland and his colleagues subjected their find to DNA analysis and other laboratory tests. These revealed that the genome of Thiomargarita magnifica is also unusually large: It contains 11,788 protein-coding genes – three times as many as an average bacterial cell, the team said. In addition, the genome contains an average of 36,880 gene copies per millimeter of filament length. There can be more than 730,000 gene copies in a thread two centimeters long. “The number of gene copies is thus an order of magnitude higher than in the other giant bacteria,” the researchers report. “Thiomargarita magnifica has the highest number of gene copies ever found in a cell.” Genes for the oxidation of sulfur and the fixation of carbon are particularly enriched, which indicates their chemoautotrophic diet. An atypical set of genes for cell division and cell elongation is also closely linked to the gigantic growth of the cells, as the analyzes showed.
Even more unusual, however, is the way in which the genome is present in the giant bacteria. Typically, the DNA of prokaryotes is exposed in the cytoplasm, there is no nucleus or other compartment for the DNA. This is different with Thiomargarita magnifica: “The big surprise was that the many genome copies are packaged in structures that have a membrane,” says Volland. “This is unexpected for a bacterium.” Microscope images showed that the elongated bacterial cell has a central, fluid-filled cavity, a vacuole. On the outside is the cytoplasm, which contains numerous small membrane sacs, each containing a piece of DNA and a few ribosomes. “This compartmentalization of DNA and ribosomes is reminiscent of the nucleus and compartments of eukaryotes,” write Volland and his colleagues. They have dubbed the newly discovered bacterial organelles “pepins” – corresponding to the French word for the small seeds of kiwis and other fruits.
According to the research team, these pepin organelles, the extremely high copy number in the genome, and the large vacuole at the cell center could provide an explanation for how the newly discovered giant bacterium got so large. Because these adaptations could reduce the diffusion problem by distributing the genome over the entire length of the cell and also by concentrating all components near the cell membrane. “If we study the biology, energy metabolism and the formation, role and nature of the pepins in more detail, this could help us to understand how biological complexity has evolved,” explain Volland and his team. “The discovery of Thiomargarita magnifica suggests that there may be even larger and more complex bacteria unnoticed by us.”
Source: Jean-Marie Volland (Lawrence Berkeley National Laboratory, Berkeley) et al., Science, doi: 10.1126/science.abb3634