Molecular characterisation of the Microsporidia of the amphipod Gammarus duebeni across its natural range revealed hidden diversity, wide-ranging prevalence and potential for co-evolution

Microsporidia comprise an unusual group of intracellular, eukaryotic parasites that exhibit ubiquitous distribution throughout the animal kingdom. We analysed the small subunit ribosomal gene (SSUrDNA) using PCR and sequencing and screened 894 Gammarus duebeni (Crustacea, Amphipoda) specimens from 35 European marine and freshwater populations. We discovered considerable hidden microsporidian diversity. Blast searches, sequence analysis and phylogenetic analysis revealed intraspecific sequence variants of known species Dictyocoela duebenum,Dictyocoela muelleri, Pleistophora mulleri and Nosema granulosis. For seven SSUrDNA sequences, we did not find corresponding GenBank entries; they likely represent new species, provisionally classified within the genus Microsporidium. Phylogenetic reconstructions revealed their position as polyphyletic, thereby lending support to the hypothesis of an early microsporidian radiation within this host group. Nevertheless, four of the presumptive novel species formed a discrete and well-supported subclade in the phylogenetic analysis. The respective host specimens were collected from disjunct freshwater sites in Wales, Ireland and Brittany (France) and may represent a new, G. duebeni-specific, microsporidian genus. At the population level, our screening showed that parasitism through Microsporidia is the rule rather than the exception in G. duebeni. We found Microsporidia in 91% of sampled G. duebeni populations. This finding may have considerable consequences for the interpretation of results from ecological, behavioural, physiological and evolutionary studies of the host, as parasitism can significantly influence these traits. Because the host G. duebeni has a complex phylogeography and evolutionary history, the studied host–parasite system may have potential as a model system for investigating processes of co-evolution.