Temporal variations of Microsporidia diversity and discovery of new host–parasite interactions in a lake ecosystem

Abstract

Microsporidia are a large group of obligate intracellular eukaryotic parasites related to Fungi. Recent studies suggest that their diversity has been greatly underestimated and little is known about their hosts other than metazoans, and thus about their impact on the communities at the base of the food web. In this work, we therefore studied the diversity of Microsporidia over one year and identified potential new hosts in small-sized fractions (<150 μm) in a lake ecosystem using a metabarcoding approach coupled with co-occurrence networks and tyramide signal amplification-fluorescent in situ hybridization. Our analysis shows a great Microsporidia diversity (1 472 OTUs), with an important part of this diversity being unknown. Temporal variations of this diversity have been observed, which might follow temporal variations of their potential hosts such as protists and microzooplankton. New hosts among them were identified as well as associations with phytoplankton. Indeed, repeated infections were observed in Kellicottia (rotifers) with a prevalence of 38% (infected individuals). Microsporidia inside a Stentor (ciliate) were also observed. Finally, potential infections of the diatom Asterionella were identified (prevalence <0.1%). The microsporidian host spectrum could be therefore even more important than previously described, and their role in the functioning of lake ecosystems is undoubtedly largely unknown.

Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of marine parasites

“…In our study, parasitic Dinoflagellates (Syndiniales) represented 22% of metabarcodes and only 0.4% (1 537 metabarcodes) could be assigned to a referenced genus, being the major contributor to the unassigned marine protist microbiome. To capture efficiently Syndiniales diversity, an alternative would be to design specific primers as it has been done to target Perkinsea and Microsporidia [43], or a combination of distinct genetic markers should be favored (e.g. 18S and ITS or COI) [43].…”

“…To capture efficiently Syndiniales diversity, an alternative would be to design specific primers as it has been done to target Perkinsea and Microsporidia [43], or a combination of distinct genetic markers should be favored (e.g. 18S and ITS or COI) [43]. The cytochrome c oxidase 1 (COI) barcode has successfully identified different cultured dinoflagellate species [44].…”

“…Our FAIR (Findable, Accessible, Interoperable and Reusable) computational workflow that allows to integrate data from heterogeneous ecosystem sampling protocols, such as coastal time-series and open sea campaigns and can be applied to any targeted protist group of any metabarcoding dataset, of the same marker gene, for example originating from the metaPR2 database [54] and Ocean Barcode Atlas [55]. The taxa identified by the network could then be specifically targeted for in situ hybridisation [43] and isolation for single-cell omics [31]. Other approaches to reduce the unassigned taxonomic load encompass long-read sequencing [16], sequencing multiple metabarcoding markers [30] and combining metabarcoding and microscopy [34].…”

Microsporidia: a new taxonomic, evolutionary, and ecological synthesis

“…These features remain important, but molecular and genomic technologies are rapidly providing evidence to revise microsporidian systematics and ecological affiliations, becoming the gold standard for species identification and broader phylogenetic placement [1,3]. With these tools, we are beginning to unravel a more complete picture of microsporidian diversity and the role of microsporidians in ecological systems, including the indirect impacts of infection on host populations and their ecosystem services [4,5].…”

“…The Microsporidia are classified within the Opisthosporidia (Eukaryota: Opisthokonta) [6,7]. Early work using the small-subunit (SSU) rRNA gene for a large number of species to determine microsporidian phylogenies identified three environmentally defined groups (Aquasporidia, Marinosporidia, and Terresporidia), which were originally classified into five genetically distinct clades, sometimes referenced using Roman numerals (I, II, III, IV, V) and sometimes with Arabic numerals (1,2,3,4,5) [8]henceforth, we use Arabic numerals when referring to the cladebased taxonomy. Recently, multiple phylogenetic studies involving the long-and short-branch Microsporidia (including 'Cryptomycota') suggested an alternative configuration of clade numbers [9,10], supported additional smaller clades or 'orphan' lineages [11,12], and presented a somewhat different configuration of the main five well-supported 'clades' (1, 3, 4a, 4b, 5) [12].…”