Different microbiomes associated with the two copepod species Acartia tonsa and Temora longicornis from the same marine environment

Microbiomes of the neritic copepod species Acartia tonsa and Temora longicornis collected in coastal Danish waters were investigated by use 16s rRNA gene-amplicon high-throughput sequencing. In contrast to current assumptions and findings, microbiomes of the two copepod species from the same environment were significantly different both in terms of bacterial species composition (i.e. presence/absence of specific taxa) and, in particular, in terms of relative abundance of bacteria associated with each copepod species. The microbiomes of both species, likewise, differed from that of A. tonsa reared in laboratory culture, but similarities were also observed between wild and laboratory-reared A. tonsa. Alphaproteobacteria dominated A. tonsa microbiomes, whereas Gammaproteobacteria were most abundant in T. longicornis microbiomes. The overall diversity of bacteria associated with the two copepod species was to some extent in harmony with previous findings, but several of the most abundant operational taxonomic units (OTUs) correspond to bacteria that have not previously been found in association with marine copepods. The results thus add to the knowledge of the diversity of microbiomes of marine zooplankton organisms and, first and foremost, document that different planktonic copepod species from the exact same environment may host significantly different microbiomes. Hence, different copepod species are either not colonized by the same bacteria assemblages or support colonization/growth of different bacteria populations, leading to distinct copepod microbiomes.