Natural populations of the putative ancient asexual Darwinula stevensoni (Crustacea, Ostracoda) differ in their microbiomes

Abstract

Although ostracods are important components in aquatic ecosystems, little is known about their microbiomes. Here, we analyzed the microbiomes of the putative ancient asexual ostracod species, Darwinula stevensoni, in three natural populations from different freshwater habitats in the UK, Belgium, and Spain. We applied high-throughput amplicon sequencing approaches to analyze the V3-V4 part of the bacterial 16S rRNA region. We tested for host-specific microbiomes by comparing bacterial assemblages of ostracods with those of sediment and water samples from the same locations. Around 2,200 Amplicon Sequence Variants (ASVs) were identified from ostracod samples with universal primers and 1,700 ASVs with endosymbiotic-specific primers, illustrating a high microbiome diversity in D. stevensoni. Most bacterial taxa were unique to the microbiome of D. stevensoni as compared to other freshwater invertebrates and to non-marine ostracods. Alpha diversity of ostracod microbiomes did not differ significantly between the three populations, but PERMANOVA detected significant differences in bacterial compositions. Microbiomes varied highly among ostracod specimens from the same population. Possible factors shaping ostracod microbiomes could be latitude, food, age, and environmental variables. Preliminary functionality analyses showed that Darwinula-specific microbiomes contribute to lipid, carbohydrate, nucleotide, and amino acid metabolic processes and the synthesis of co-factors and vitamins.