Microsporidia are obligate parasites that are closely related to Fungi. While the widely known “long-branch” Microsporidia infect mostly metazoans, the hosts of “short-branch” Microsporidia are only partially characterized or not known at all. Here, we used network analyses from Neotropical rainforest soil metabarcoding data, to infer co-occurrences between environmental lineages of short-branch microsporidians and their potential hosts. We found significant co-occurrences with several taxa, especially with Apicomplexa, Cercozoa, and Fungi, as well as some Metazoa. Our results are the first step to identify potential hosts of the environmental lineages of short-branch microsporidians, which can be targeted in future molecular and microscopic studies.

Microsporidia are obligate parasites that are closely related to Fungi. While the widely-known long-branch Microsporidia infect mostly animals, the hosts of short-branch Microsporidia are only partially characterized or not known at all. Here, we used network analyses from Neotropical rainforest soil metabarcoding data, to infer co-occurrences between environmental lineages of short-branch microsporidians and their potential hosts. We found significant co-occurrences with several taxa, especially with Apicomplexa, Cercozoa, Fungi, as well as some Metazoa. Our results are the first step to identify potential hosts of the environmental lineages of short-branch microsporidians, which can be targeted in future molecular and microscopic studies.

Ciliates have a long history of being central in evolutionary and ecological studies on eukaryotic microorganisms. Although thousands of species have been discovered, their total diversity still remains unknown. Here, we will discuss two unsolved problems that hinder the further exploration of ciliate diversity at the species level, and potential solutions to these problems are proposed. First, ciliate morphospecies are difficult to identify because the different silver stains are not scalable (they do not represent high-throughput methods) and basic supplies are lacking (e.g., protargol); a solution may be the development of fluorescent staining techniques. Second, ciliate phylogenetic species are difficult to identify because of extensive paralogy in nuclear-protein-coding genes; a solution may be to concentrate on sequencing mitochondrial genomes. These two approaches could be integrated into a high-throughput fluorescent-single-cell sorting and mitochondrial genomes sequencing process that would enable the observation and better understanding of ciliate species on a massive scale.