Bacterial symbionts residing inside insect cells possess the smallest known genomes for any living entities. These findings further blur the line differentiating cellular organelles, such as mitochondria, from the most primitive microbes found in nature. The results of this new research were recently published in the journal Nature Communications.
“Pinpointing exactly where this highly integrated symbiont ends and an organelle begins, I think, is quite challenging,” observes Piotr Łukasik from Jagiellonian University in Krakow, Poland. “It’s a very fluid boundary.”
Leafhoppers are insects that subsist entirely on plant sap, supplementing their diet through ancient relationships with symbiotic bacteria. Over countless millennia, these microbes have adapted to dwell within specialized cells in the leafhopper’s abdomen, manufacturing nutrients that the leafhoppers cannot acquire from their sugary food source. A significant number of these bacteria are completely reliant on their hosts, allowing their genetic material to degenerate to just a fraction of their ancestral size.
Łukasik and his colleagues were interested in the evolution of these bacterium-insect interactions and the ultimate limits of how small these bacterial genomes could become. The research team examined 149 individual insects spanning 19 leafhopper families, extracting DNA from the abdominal tissues of the insects. The researchers meticulously analyzed and sequenced the DNA, reconstructing the genomes of the symbiotic bacteria Vidania and Sulcia.
The bacterial genomes turned out to be remarkably minute. Genome size is quantified by the number of base pairs, which are the sequential, paired “letters” in the genetic code. The bacterial genomes measured less than 181,000 base pairs in length. For context, the human genome contains billions of base pairs.
Some Vidania genomes were as small as 50,000 base pairs, representing the smallest genomes identified among extant organisms. Previously, the smallest recorded genome belonged to Nasuia, a symbiotic bacterium associated with closely related leafhoppers, measuring just over 100,000 base pairs.
These Vidania genomes, reaching 50,000 base pairs, are comparable in size to those of viruses, which are not considered living organisms; for example, the COVID-19 virus genome is approximately 30,000 base pairs long. Certain Vidania strains harbor only about 60 protein-coding genes, one of the lowest counts ever documented.
These bacteria have co-evolved with their insect hosts for roughly 263 million years, independently achieving extremely reduced genome sizes in two distinct lineages of leafhoppers. One of the few remaining functions of these bacteria is the synthesis of the amino acid phenylalanine, which acts as a chemical precursor necessary for building and strengthening the insects’ exoskeletons.
Łukasik and his team hypothesize that massive gene loss can be triggered when insects adopt a new diet that provides nutrients previously supplied by the bacteria, or when new microorganisms colonize the host and take over those functions.
These highly reduced bacteria bear a resemblance to mitochondria and chloroplasts—the energy-producing organelles inside animal and plant cells that originated from ancient bacteria. These symbiotic bacteria also exclusively inhabit host cells and are transferred vertically from one generation to the next.
“‘Organelle’ is just a word, so I could call these bacteria organelles if someone wanted to incorporate them into the definition,” says Nancy Moran of the University of Texas at Austin, who was not involved in the study. “But there are still distinctions from mitochondria or chloroplasts.”
Mitochondria are substantially older, having originated 1.5 billion years ago or even earlier, and their genomes are even smaller, around 15,000 base pairs.
“These symbionts live only in specialized host cells, rather than in most cells of the organism, which is what we see with mitochondria and chloroplasts,” Moran notes.
Łukasik suggests that these bacteria and mitochondria are simply positioned at different points along an evolutionary ‘gradient of dependence’ on their hosts. He speculates that even tinier symbiont genomes are yet to be discovered.
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