Environmental Sequencing Fills the Gap Between Parasitic Haplosporidians and Free‐living Giant Amoebae

Abstract

Class Ascetosporea (Rhizaria; Endomyxa) comprises many parasites of invertebrates. Within this group, recent group-specific environmental DNA (eDNA) studies have contributed to the establishment of the new order Mikrocytida, a new phylogeny and characterization of Paramyxida, and illuminated the diversity and distribution of haplosporidians. Here, we use general and lineage-specific PCR primers to investigate the phylogenetic “gap” between haplosporidians and their closest known free-living relatives, the testate amoeba Gromia and reticulate amoeba Filoreta. Within this gap are Paradinium spp. parasites of copepods, which we show to be highly diverse and widely distributed in planktonic and benthic samples. We reveal a robustly supported radiation of parasites, ENDO-3, comprised of Paradinium and three further clades (ENDO-3a, ENDO-3b and SPP). A further environmental group, ENDO-2, perhaps comprising several clades, branches between this radiation and the free-living amoebae. Early diverging haplosporidians were also amplified, often associated with bivalves or deep-sea samples. The general primer approach amplified an overlapping set of novel lineages within ENDO-3 and Haplosporida, whereas the group-specific primer strategy, targeted to amplify from the earliest known divergent haplosporidians to Gromia, generated greater sequence diversity across part of this phylogenetic range.

Rhizarian ‘Novel Clade 10’ Revealed as Abundant and Diverse Planktonic and Terrestrial Flagellates, including Aquavolon n. gen.

“…,b; Ward et al. , ), but others are free‐living protists, e.g. the reticulopodial amoeba Filoreta marina (Bass et al.…”

“…Neuhauser et al 2014), and animals (e.g. Hartikainen et al 2014a,b;Ward et al 2016Ward et al , 2018, but others are free-living protists, e.g. the reticulopodial amoeba Filoreta marina (Bass et al 2009a), which also has mitochondria with tubular cristae (Myl'nikov and Myl'nikov 2011).…”

Ultrastructure, phylogeny and histopathology of two novel haplosporidians parasitising amphipods, and importance of crustaceans as hosts

“…Molecular analyses (Reece et al 2004) support this ontogenic hypothesis and confirm the monophyly of Urosporidium, Bonamia and Minchinia. However, Haplosporidium is currently paraphyletic, highlighting the need for taxonomic revisions based on molecular characterizations, his topathological and ultrastructural descriptions to facilitate the erection of novel monophyletic genera (Burreson & Ford 2004, Hartikainen et al 2014, Ward et al 2018. Attention is increasingly being focussed on haplosporidian infections in non-molluscan invertebrates, including crabs and amphipods, as definitive or intermediate hosts.…”

Revised Taxonomy and Expanded Biodiversity of the Phytomyxea (Rhizaria, Endomyxa)

“…Those are mainly based on symptoms of the host (hypotrophies or no hypertrophies) and the arrangement of the resting spores. Especially species of plasmodiophorids that do not form hypertrophies are discussed to play major roles in the rhizosphere (Bass et al 2018, Fiore-Donno et al 2019) but data on those are still sparse in terms of available voucher sequences. Non-galling plasmodiophorids are (mainly) placed within the genera Polymyxa and Ligniera.…”

“…nine are placed within the plasmodiophorid clade and five within the phagomyxids (Neuhauser et al 2014). Phytomyxid biodiversity is still understudied (Bass et al 2018, Neuhauser et al 2014, and current data indicate that the diversity of this group of parasites is relatively low compared to their free living (Berney et al 2013) and parasitic relatives (Hartikainen et al 2014a, Hartikainen et al 2014b, Ward et al 2016, Ward et al 2018. Phytomyxea are regularly detected in environmental sequencing studies, but do not get systematic attention in those studies because they are rare in terms of reads and there are usually few operational taxonomic units recovered (Ciaghi et al unpublished).…”