At the American Society for Microbiology's annual meeting held in New Orleans, La., this week, Yale University's Nancy Moran outlined her group's investigations of symbiotic bacterial genomes that are as small as 145 kb — and shrinking. The pea aphid's mutual obligate symbiont Buchnera aphidicola has shown a reduction in the size of its genome over time. By sequencing the genomes of Buchnera — which, according to an upper limit estimate contains 580 genes — and other species with the "tiniest bacterial genomes," like the 145 kb Hodgkinia, Moran said her group has found that some even lack genes generally considered essential: those that encode certain transporters, cell envelope components, certain small ribosomal proteins, and some tRNA synthetases.
Through sequencing, Moran's group is reconstructing biological pathways that speak to the bugs' symbiotic relationship with their hosts. For example, the Buchnera genome sequence supports the idea that the bacterium provides its host with certain essential amino acids that the aphid does not itself produce, nor acquires from its dietary staple, phloem sap. "Clearly, looking at these genomes tells us a lot about the biological roles of these symbionts within these systems," Moran said, adding that "the other thing that's striking about these genomes, though, is that they're extremely small."
Indeed, it appears some are continuing to shrink, she added. "The only changes occurring [in these genomes] are just further loss of genes. So they are small, and they're getting smaller, and they never get larger because they don't gain any genes," Moran said. "There's no horizontal gene acquisition, no uptake at all, so all they can do is lose genes and become smaller and smaller."
During her talk, Moran said that perhaps this "extreme pattern of evolution" her team and others have observed in Buchnera and other small bacterial genomes could help researchers understand how evolutionary processes occur in other microbes. However, Moran said that it remains unclear how these increasingly small genomes are viable. "How is all of this happening? What [are] the real drivers that allow this to happen? If genetic drift is causing this long-term genomic erosion, further loss of genes, what is compensating? What allows these things to exist?" Moran asked. Are these symbiotic bacterial genomes become smaller as a result of horizontal gene transfers to their hosts? "We usually aren't able to give a conclusive answer to that," she said. But in the case of Buchnera and the pea aphid — for which researchers have published complete genome sequences — researchers have been able to "look exhaustively for genes" to suggest symbiont-host transfer. But of the 11 transferred genes in the aphid genome, Moran's team found that none are from Buchnera. "So what is the answer?" Moran asked. "We really don't know at this point," she said, adding that these tiny genomes could be, at the very least, "useful as examples of the way in which things can go under certain conditions."