# Long Term Copepod Culture Houses a Rich Microbial Eukaryotic Community Including New and Known Symbionts

## TL;DR

This study explores the microbial eukaryotic community in a long-term copepod culture, revealing new symbionts and highlighting the importance of studying eukaryotic microbes.

## Contribution

The study identifies a rich and previously underexplored microbial eukaryotic community in copepods, including new symbionts like Perkinsea.

## Key findings

- The copepod eukaryome includes saprotrophs, bacterivores, and known parasites, differing from inlet water.
- Perkinsea, Ascomycota, and Basidiomycota form the core eukaryome in most copepods.
- Eukaryotic microbial richness varies among individual copepods, suggesting diverse symbiotic relationships.

## Abstract

Copepods, dominant marine zooplankton, are hosts to microbial eukaryotic symbionts, but the copepod eukaryome remains largely unexplored. We used 18S rRNA gene primers with reduced metazoan amplification to identify microbial eukaryotes in a culture of
Calanus finmarchicus
(Copepoda). Samples were taken from the inlet water (99.5% of reads from non‐copepod sources) and the contents of the culture, which included ambient water (99.7%), bulk (many crushed copepods, 60.2%), individual copepods (1%–41%, mean = 7.4), and bulk fecal pellets (74%). The microbial eukaryotic community in the culture differed from the inlet water. The culture contained saprotrophs and bacterivores typical of eutrophic aquacultures and known parasites of copepods. Individual copepod eukaryomes varied in richness (8–33 operational taxonomic units, mean = 16.1) and revealed variation in non‐copepod read yields related to specific taxa. Perkinsea, not previously reported in copepods, as well as Ascomycota and Basidiomycota (Fungi), formed the core eukaryome (found in > 90% of individuals), indicating potentially important symbiosis. The small eukaryome, relative to reported microbiomes in
C. finmarchicus
, suggests that ecological inferences from microbiomes, which largely address bacteria, are not readily applicable to the eukaryotic microbes. The study underpins the need for investigations of eukaryomes.