The microbe with the smallest genome that still pushes the boundaries of life

Symbiotic bacteria living inside insect cells have the smallest genomes known for any organism. The findings further blur the distinction between cellular organelles such as mitochondria and most barebones microbes in nature.

“Exactly where this highly integrated symbiont ends and where the organelle begins is very difficult to say,” he says Piotr Łukasik at the Jagiellonian University in Krakow, Poland. “This is a very blurred line.

Planthoppers are insects that feed exclusively on plant sap and supplement their nutrition through an ancient relationship with symbiotic bacteria. Over many millions of years, these microbes have evolved to live in specialized cells in the bellies of shellfish and produce nutrients that shellfish cannot obtain from their sweet diet. Many of these bacteria are completely dependent on their hosts and have allowed their genetic tools to deteriorate to a fraction of the size of their ancestors.

Łukasik and his colleagues were interested in the evolution of this relationship between bacteria and bugs and how small these bacterial genomes can be. The team sampled 149 individual insect species from 19 planthopper families and extracted DNA from the insects’ abdominal tissues. The scientists analyzed and sequenced the DNA and reconstructed the genomes of the symbiotic bacteria Visions and Sulcia.

Bacterial genomes were exceptionally small. The length of a genome can be measured in the number of base pairs, the sequence of paired “letters” in the genetic code. Bacterial genomes were less than 181,000 base pairs long. By comparison, the human genome is billions of base pairs long.

Some of the Visions genomes were only 50,000 base pairs long, the smallest known for any life form. She used to be the smallest Nasuiaa symbiotic bacterium hosted by relatives of planthoppers called leafhoppers measuring just over 100,000 base pairs.

At 50,000 base pairs Visions genomes are at the level of those found in viruses that are not considered living: for example, the virus responsible for covid-19 has a genome approximately 30,000 base pairs long. Some of the Visions they have only about 60 protein-coding genes, among the lowest numbers on record.

The bacteria co-evolved with their insect hosts for about 263 million years, independently evolving extremely small genome sizes in two different groups of planthoppers. One of the few things these bacteria do is produce the amino acid phenylalanine, which is a chemical precursor for building and strengthening insect exoskeletons.

Łukasik and his team believe that massive gene loss can occur when insects eat new foods with nutrients that were previously supplied by bacteria, or when more microbes move in and take over those roles.

Highly reduced bacteria resemble mitochondria and chloroplasts—the energy-producing organelles inside animal and plant cells descended from ancient bacteria. Symbiotic bacteria similarly reside in host cells and are passed down between generations.

“‘Organelles’ is just a word, so it’s good to call these organelles if someone wants to include them in the definition,” he says Nancy Moran at the University of Texas at Austin, who was not involved in the research. “However, differences from mitochondria or chloroplasts remain.”

Mitochondria are much older, originating 1.5 billion years ago or more, and their genomes are still smaller—about 15,000 base pairs.

“These symbionts live only in specialized host cells, not in most cells throughout the organism, as seen in mitochondria and chloroplasts,” says Moran.

Łukasik sees these bacteria and mitochondria as simply being at different points on an evolutionary “gradient of dependence” on their hosts. He suspects that even smaller symbiont genomes have yet to be discovered.

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