Ecological insights into circular putative plasmids in Stylissa carteri microbiomes across the Indo-Pacific

Aims
The main goal of this study was to investigate the diversity, genetic composition, and potential ecological relevance of circular putative plasmids within the microbiomes of the sponge Stylissa carteri across thousands of kilometers (~6000 km) in the Indo-Pacific region.

Methods and results
To achieve this, we applied a selective multiply-primed rolling circle amplification method combined with high-throughput sequencing to enrich and characterize circular putative plasmids from sponge samples. Our results revealed highly diverse and site-specific plasmid assemblages, primarily consisting of small cryptic plasmids (<5 kbp) of unknown function. We also observed the widespread distribution of two putatively cryptic plasmids across all sampling locations, and 22 additional plasmids present in at least three locations. We, furthermore, detected a striking prevalence of putative genes encoding for immunoglobulin-like (Ig-like) and eukaryotic-like protein (ELP) domains, such as Calx-beta, fibronectin type III (fn3), ankyrin (ANK), and scavenger receptor cysteine-rich, as well as RVT-CRISPR-related reverse transcriptases (RVTs) and unclassified RVTs. The widespread presence of genes encoding ELPs in putative plasmids, which may play key roles in host colonization and immune evasion, underscores the need for a deeper understanding of how these plasmid-carried genes influence microbe–sponge ecological interactions.

Conclusions
Our findings shed new light on the potential role of plasmids as a reservoir of genetic diversity in the context of sponge microbe symbioses.