Cade Mirchandani

We used ultra-accurate DNA sequencing and computational modeling to estimate how many genetically distinct symbiotic bacteria are passed from parent to offspring in a deep-sea hydrothermal vent clam. Our results reveal that the genetic bottleneck is far more severe than previously thought — only about 8 symbionts per generation, compared to hundreds or thousands estimated by traditional cell counting methods.

Many animals depend on symbiotic bacteria for survival, much like our own cells depend on mitochondria — which were themselves once free-living bacteria. Each generation, only a small number of these symbionts are transmitted from parent to offspring, creating a genetic bottleneck that causes symbiont genomes to gradually degrade over millions of years. Understanding how severe this bottleneck is has been difficult because traditional methods rely on physically counting cells, which overestimates the number of genetically distinct founders. We applied two ultra-accurate DNA sequencing methods to a deep-sea hydrothermal vent clam and its sulfur-oxidizing symbiont, then used demographic modeling to estimate the effective genetic bottleneck size. Our results reveal that only about 8 genetically distinct symbionts are transmitted per host generation — orders of magnitude below previous census-based estimates. Despite this severe bottleneck, the symbiont genome remains surprisingly intact, supporting the hypothesis that occasional horizontal transmission between symbiont lineages counteracts genome degradation.