Microsporidian Diversity in Soil, Sand, and Compost of the Pacific Northwest

Abstract

Microsporidia are intracellular parasites considered to be ubiquitous in the environment. Yet the true extent of their diversity in soils, sand, and compost remains unclear. We examined microsporidian diversity found in the common urban environments of soil, sand, and compost. We retrieved 22 novel microsporidian sequences and only four from described species. Their distribution was generally restricted to a single site and sample type. Surprisingly, one novel microsporidian showed a wide distribution, and high prevalence, as it was detected in five different compost samples and in soil samples collected over 200 km apart. These results suggest that the majority of Microsporidia appear to have a narrow distribution. Our phylogenetic analysis indicated that the Microsporidia detected in this study include representatives from four of the five major microsporidian groups. Furthermore, the addition of our new sequences calls into question the cohesiveness of microsporidian clade II. These results highlight the importance of increasing our knowledge of microsporidian diversity to better understand the phylogenetic relationships and evolutionary history of this important group of emerging parasites.

A Large Collection of Novel Nematode-Infecting Microsporidia and Their Diverse Interactions with Caenorhabditis elegans and Other Related Nematodes

“…Environmental SSU rDNA microsporidian sequences have been reported from soil, sand and compost samples from North America [41]. (The corresponding species have not been named.)…”

“…SSU rDNA Bayesian inference phylogeny with the sequences of Fig 2 and nine microsporidian sequences (S1 Table) found in environmental samples in soil, sand and compost samples [41]. Model Kimura 2-Parameter (K2P) was applied.…”

Diverse Applications of Environmental DNA Methods in Parasitology

“…Many parasite taxa are Key Table Table 1 85,88,90,91,94] genetically divergent, indicated by their long branches on phylogenetic trees, which means that even primers designed to conserved regions of marker genes fail to amplify from divergent lineages, or do so relatively poorly. This is demonstrably the case for haplosporidians, mikrocytids, plasmodiophorids, trypanosomatids, myxozoans, many alveolates, and microsporidians, among others, because PCR primers designed to amplify those groups specifically or preferentially have revealed significant previously unknown diversity, often in environmental samples [39,[46][47][48][49][50]. Primers can also be designed to exclude unwanted targets, for example general eukaryote primers with an anti-metazoan bias to reduce host and other 'contaminating' metazoan sequences [51].…”

Microsporidia

“…The majority of microsporidian species were obtained from soil (17 species), compost (10 species), and sand (2 species), but none are known to infect humans. In addition, the distribution for each species was usually restricted to a particular site, and that only a small number of species appear to be more widespread, thus highlighting the diversity of Microsporidia in common, urban habitats (Ardila-Garcia et al, 2013). In Korea, 34 farm soil samples were collected from seven different localities along the western side of the Korean Peninsula, and E. hellem (genotype 1B) was identified in three samples (8.8%) by real-time PCR and nucleotide sequencing.…”