Clarifying the Relationships between Microsporidia and Cryptomycota

Abstract

Some protists with microsporidian-like cell biological characters, including Mitosporidium, Paramicrosporidium, and Nucleophaga, have SSU rRNA gene sequences that are much less divergent than canonical Microsporidia. We analysed the phylogenetic placement and environmental diversity of microsporidian-like lineages that group near the base of the fungal radiation and show that they group in a clade with metchnikovellids and canonical microsporidians, to the exclusion of the clade including Rozella, in line with what is currently known of their morphology and cell biology. These results show that the phylogenetic scope of Microsporidia has been greatly underestimated. We propose that much of the lineage diversity previously thought to be cryptomycotan/rozellid is actually microsporidian, offering new insights into the evolution of the highly specialized parasitism of canonical Microsporidia. This insight has important implications for our understanding of opisthokont evolution and ecology, and is important for accurate interpretation of environmental diversity. Our analyses also demonstrate that many opisthosporidian (aphelid+rozellid+microsporidian) SSU V4 OTUs from Neotropical forest soils group with the short-branching Microsporidia, consistent with the abundance of their protist and arthropod hosts in soils. This novel diversity of Microsporidia provides a unique opportunity to investigate the evolutionary origins of a highly specialized clade of major animal parasites.

Keywords: Mitosporidium; Nucleophaga; Paramicrosporidium; Rozella; Rozellida; Rozellomycota.

Figure 1

Phylogenetic relationships among canonical, long‐branching (LB) Microsporidia, metchnikovellids, Rozellida, and a diversity of related short‐branching lineages. LB‐Microsporidia form a clade with a diversity of short‐branching lineages (SB‐Microsporidia) that share key cell biological characters defining the microsporidian clade. Lineages that have been labelled in other studies are labelled: GS xx from Tedersoo et al. (2017), Laz x from Lazarus and James (2015); others as marked. The extent of the expanded Microsporidia is shown by the bracket on the far right. The tree was inferred under the CAT+GTR model in PhyloBayes‐MPI, on a final alignment of 1729 sites from the SSU rRNA gene. Black blobs indicate support values of > 0.96 BPP and > 95% ML bootstrap (actual values also shown). Branch lengths are proportional to the expected number of substitutions per site, as denoted by the scale bar.

Figure 2

Evolutionary placement of tropical soil microsporidian OTUs on the opisthosporidian reference tree. The branch colours correspond to the distribution of OTU placement: The darker a branch, the more OTUs are placed on it. The OTU frequency scaling is logarithmic due to the large range of placement density. The branch labels for Microsporidia are red (characterized taxa in bold), rozellids orange, NCLC1 purple, aphelids blue, chytrids green, and the holozoan outgroup grey. Nucleariids are the sister clade to Fungi+Opisthosporidia.

Figure 3

Maximum Likelihood phylogeny of SSU rRNA gene V4 region OTUs from tropical soil and European marine (Biomarks) samples. The OTUs are aligned to reference sequence dataset of long‐ and short‐branch Microsporidia, metchnikovellids, rozellids, other clades of environmental sequences, and representative aphelids and fungi with a holozoan outgroup. Light and dark grey shading indicates extent of expanded Microsporidia; dark grey box encloses all members of the subclade including long‐branch Microsporidia. Green triangles (collapsed clades) represent OTUs from Neotropical soil samples only, ‘BM’ from Biomarks only, and blue from both.