Strain-level diversity of symbiont communities between individuals and populations of a bioluminescent fish

Abstract

The bioluminescent symbiosis involving the urchin cardinalfish, Siphamia tubifer, and Photobacterium mandapamensis, a luminous member of the Vibrionaceae, is highly specific compared to other bioluminescent fish-bacteria associations. Despite this high degree of specificity, patterns of genetic diversity have been observed for the symbionts from hosts sampled over relatively small spatial scales. We characterized and compared sub-species, strain-level symbiont diversity within and between S. tubifer hosts sampled from the Philippines and Japan using PCR fingerprinting. We then carried out whole genome sequencing of the unique symbiont genotypes identified to characterize the genetic diversity of the symbiont community and the symbiont pangenome. We determined that an individual light organ contains six symbiont genotypes on average, but varied between 1–13. Additionally, we found that there were few genotypes shared between hosts from the same location. A phylogenetic analysis of the unique symbiont strains indicated location-specific clades, suggesting some genetic differentiation in the symbionts between host populations. We also identified symbiont genes that were variable between strains, including luxF, a member of the lux operon, which is responsible for light production. We quantified the light emission and growth rate of two strains missing luxF along with the other strains isolated from the same light organs and determined that strains lacking luxF were dimmer but grew faster than most of the other strains, suggesting a potential metabolic trade-off. This study highlights the importance of strain-level diversity in microbial associations and provides new insight into the underlying genetic architecture of intraspecific symbiont communities within a host.

Comparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences

“…nov. In contrast, apogonid hosts in the genus Siphamia associate with a much narrower range of P. ‘mandapamensis’ strains [1, 11, 21]. It remains unclear why this degree of specificity exists for the bioluminescent symbiosis with Siphamia and not for the other hosts examined, but it could be due to the fish’s distinct behavioural ecology as a cryptic reef fish [47].…”

“…This could indicate that a major selective pressure acting on this operon is the host niche. While luxF is not required for light production, its presence appears to increase light emission [ 21 , 46 ], which may be required for the bioluminescent symbiosis with Siphamia and Acropoma hosts, and perhaps, is a key feature for these hosts to recognize specific symbionts from the environmental pool of bacteria.…”

“…Two strains, StP .2.23 and StJ .4.81, also had Illumina short reads (150 bp paired-end reads) available from a recent study [ 21 ] that were used along with the ONT reads as input for Unicycler v0.5.0 [ 22 ] to produce hybrid assemblies. The short reads were first quality filtered and trimmed using fastp v0.23.2 [ 23 ].…”