Cellular Identity of a Novel Small Subunit rDNA Sequence Clade of Apicomplexans: Description of the Marine Parasite Rhytidocystis polygordiae n. sp. (Host: Polygordius sp., Polychaeta)

Coinfection of slime feather duster worms (Annelida, Myxicola) by different gregarine apicomplexans (Selenidium) and astome ciliates reflects spatial niche partitioning and host specificity

Individual organisms can host multiple species of parasites (or symbionts), and one species of parasite can infect different host species, creating complex interactions among multiple hosts and parasites. When multiple parasite species coexist in a host, they may compete or use strategies, such as spatial niche partitioning, to reduce competition. Here, we present a host–symbiont system with two species of Selenidium (Apicomplexa, Gregarinida) and one species of astome ciliate co-infecting two different species of slime feather duster worms (Annelida, Sabellidae, Myxicola) living in neighbouring habitats. We examined the morphology of the endosymbionts with light and scanning electron microscopy (SEM) and inferred their phylogenetic interrelationships using small subunit (SSU) rDNA sequences. In the host ‘Myxicola sp. Quadra’, we found two distinct species of Selenidium; S. cf. mesnili exclusively inhabited the foregut, and S. elongatum n. sp. inhabited the mid to hindgut, reflecting spatial niche partitioning. Selenidium elongatum n. sp. was also present in the host M. aesthetica, which harboured the astome ciliate Pennarella elegantia n. gen. et sp. Selenidium cf. mesnili and P. elegantia n. gen. et sp. were absent in the other host species, indicating host specificity. This system offers an intriguing opportunity to explore diverse aspects of host–endosymbiont interactions and competition among endosymbionts.

Patterns of host-parasite associations between marine meiofaunal flatworms (Platyhelminthes) and rhytidocystids (Apicomplexa)

Microturbellarians are abundant and ubiquitous members of marine meiofaunal communities around the world. Because of their small body size, these microscopic animals are rarely considered as hosts for parasitic organisms. Indeed, many protists, both free-living and parasitic ones, equal or surpass meiofaunal animals in size. Despite several anecdotal records of "gregarines", "sporozoans", and "apicomplexans" parasitizing microturbellarians in the literature-some of them dating back to the nineteenth century-these single-celled parasites have never been identified and characterized. More recently, the sequencing of eukaryotic microbiomes in microscopic invertebrates have revealed a hidden diversity of protist parasites infecting microturbellarians and other meiofaunal animals. Here we show that apicomplexans isolated from twelve taxonomically diverse rhabdocoel taxa and one species of proseriate collected in four geographically distinct areas around the Pacific Ocean (Okinawa, Hokkaido, and British Columbia) and the Caribbean Sea (Curaçao) all belong to the apicomplexan genus Rhytidocystis. Based on comprehensive molecular phylogenies of Rhabdocoela and Proseriata inferred from both 18S and 28S rDNA sequences, as well as a molecular phylogeny of Marosporida inferred from 18S rDNA sequences, we determine the phylogenetic positions of the microturbellarian hosts and their parasites. Multiple lines of evidence, including morphological and molecular data, show that at least nine new species of Rhytidocystis infect the microturbellarian hosts collected in this study, more than doubling the number of previously recognized species of Rhytidocystis, all of which infect polychaete hosts. A cophylogenetic analysis examining patterns of phylosymbiosis between hosts and parasites suggests a complex picture of overall incongruence between host and parasite phylogenies, and varying degrees of geographic signals and taxon specificity.

Droplet digital PCR as a tool for investigating dynamics of cryptic symbionts

Interactions among symbiotic organisms and their hosts are major drivers of ecological and evolutionary processes. Monitoring the infection patterns among natural populations and identifying factors affecting these interactions are critical for understanding symbiont-host relationships. However, many of these interactions remain understudied since the knowledge about the symbiont species is lacking, which hinders the development of appropriate tools. In this study, we developed a digital droplet PCR (ddPCR) assay based on apicomplexan COX1 gene to detect an undescribed agamococcidian symbiont. We show that the method gives precise and reproducible results and enables detecting cryptic symbionts in low target concentration. We further exemplify the assay's use to survey seasonally sampled natural host (Pygospio elegans) populations for symbiont infection dynamics. We found that symbiont prevalence differs spatially but does not show seasonal changes. Infection load differed between populations and was low in spring and significantly increased towards fall in all populations. We also found that the symbiont prevalence is affected by host length and population density. Larger hosts were more likely to be infected, and high host densities were found to have a lower probability of infection. The observed variations could be due to characteristics of both symbiont and host biology, especially the seasonal variation in encounter rates. Our findings show that the developed ddPCR assay is a robust tool for detecting undescribed symbionts that are otherwise difficult to quantify, enabling further insight into the impact cryptic symbionts have on their hosts.

Nutrient Acquisition and Attachment Strategies in Basal Lineages: A Tough Nut to Crack in the Evolutionary Puzzle of Apicomplexa

Apicomplexa are unicellular eukaryotes that parasitise a wide spectrum of invertebrates and vertebrates, including humans. In their hosts, they occupy a variety of niches, from extracellular cavities (intestine, coelom) to epicellular and intracellular locations, depending on the species and/or developmental stages. During their evolution, Apicomplexa thus developed an exceptionally wide range of unique features to reach these diversified parasitic niches and to survive there, at least long enough to ensure their own transmission or that of their progeny. This review summarises the current state of knowledge on the attachment/invasive and nutrient uptake strategies displayed by apicomplexan parasites, focusing on trophozoite stages of their so far poorly studied basal representatives, which mostly parasitise invertebrate hosts. We describe their most important morphofunctional features, and where applicable, discuss existing major similarities and/or differences in the corresponding mechanisms, incomparably better described at the molecular level in the more advanced Apicomplexa species, of medical and veterinary significance, which mainly occupy intracellular niches in vertebrate hosts.

Taxonomy of the Apicomplexan Symbionts of Coral, including Corallicolida ord. nov., Reassignment of the Genus Gemmocystis, and Description of New Species Corallicola aquarius gen. nov. sp. nov. and Anthozoaphila gnarlus gen. nov. sp. nov

Corals (Metazoa; Cnidaria; Anthozoa) have recently been shown to play host to a widespread and diverse group of intracellular symbionts of the phylum Apicomplexa. These symbionts, colloquially called "corallicolids", are mostly known through molecular analyses, and no formal taxonomy has been proposed. Another apicomplexan, Gemmocystis cylindrus (described from the coral Dendrogyra cylindrus), may be related to corallicolids, but lacks molecular data. Here, we isolate and describe motile trophozoite (feeding) corallicolids cells using microscopic (light, SEM, and TEM) and molecular phylogenetic analysis to provide the basis for a formal description. Phylogenetic analyses using nuclear and plastid rRNA operons, and three mitochondrial protein sequences derived from single cell transcriptomes, all confirm that these organisms fall into a discrete deep-branching clade within the Apicomplexa not closely related to any known species or major subgroup. As a result, we assign this clade to a new order, Corallicolida ord. nov., and family, Corallicolidae fam. nov. We describe a type species, Corallicola aquarius gen. nov. sp. nov. from its Rhodactis sp. host, and also describe a second species, Anthozoaphila gnarlus gen. nov. sp. nov., from the coral host Madracis mirabilis. Finally, we propose reassigning the incertae sedis taxon G. cylindrus from the order Agamococcidiorida to the Corallicolida, based on similarities in morphology and host localization to that of the corallicolids.

Phylogenomics Identifies a New Major Subgroup of Apicomplexans, Marosporida class nov., with Extreme Apicoplast Genome Reduction

The phylum Apicomplexa consists largely of obligate animal parasites that include the causative agents of human diseases such as malaria. Apicomplexans have also emerged as models to study the evolution of nonphotosynthetic plastids, as they contain a relict chloroplast known as the apicoplast. The apicoplast offers important clues into how apicomplexan parasites evolved from free-living ancestors and can provide insights into reductive organelle evolution. Here, we sequenced the transcriptomes and apicoplast genomes of three deep-branching apicomplexans, Margolisiella islandica, Aggregata octopiana, and Merocystis kathae. Phylogenomic analyses show that these taxa, together with Rhytidocystis, form a new lineage of apicomplexans that is sister to the Coccidia and Hematozoa (the lineages including most medically significant taxa). Members of this clade retain plastid genomes and the canonical apicomplexan plastid metabolism. However, the apicoplast genomes of Margolisiella and Rhytidocystis are the most reduced of any apicoplast, are extremely GC-poor, and have even lost genes for the canonical plastidial RNA polymerase. This new lineage of apicomplexans, for which we propose the class Marosporida class nov., occupies a key intermediate position in the apicomplexan phylogeny, and adds a new complexity to the models of stepwise reductive evolution of genome structure and organelle function in these parasites.

Polyphyletic origin, intracellular invasion, and meiotic genes in the putatively asexual agamococcidians (Apicomplexa incertae sedis)

Agamococcidians are enigmatic and poorly studied parasites of marine invertebrates with unexplored diversity and unclear relationships to other sporozoans such as the human pathogens Plasmodium and Toxoplasma. It is believed that agamococcidians are not capable of sexual reproduction, which is essential for life cycle completion in all well studied parasitic apicomplexans. Here, we describe three new species of agamococcidians belonging to the genus Rhytidocystis. We examined their cell morphology and ultrastructure, resolved their phylogenetic position by using near-complete rRNA operon sequences, and searched for genes associated with meiosis and oocyst wall formation in two rhytidocystid transcriptomes. Phylogenetic analyses consistently recovered rhytidocystids as basal coccidiomorphs and away from the corallicolids, demonstrating that the order Agamococcidiorida Levine, 1979 is polyphyletic. Light and transmission electron microscopy revealed that the development of rhytidocystids begins inside the gut epithelial cells, a characteristic which links them specifically with other coccidiomorphs to the exclusion of gregarines and suggests that intracellular invasion evolved early in the coccidiomorphs. We propose a new superorder Eococcidia for early coccidiomorphs. Transcriptomic analysis demonstrated that both the meiotic machinery and oocyst wall proteins are preserved in rhytidocystids. The conservation of meiotic genes and ultrastructural similarity of rhytidocystid trophozoites to macrogamonts of true coccidians point to an undescribed, cryptic sexual process in the group.

Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation

Sarcocystis scandentiborneensis sp. nov. was discovered in histological sections of striated musculature of treeshrews (Tupaia minor, T. tana) from Northern Borneo. Sarcocysts were cigar-shaped, 102 μm–545 μm long, and on average 53 μm in diameter. The striated cyst wall varied in thickness (2–10 μm), depending on whether the finger-like, villous protrusions (VP) were bent. Ultrastructurally, sarcocysts were similar to wall type 12 but basal microtubules extended into VPs that tapered off with a unique U-shaped, electron-dense apical structure. In phylogenetic trees of the nuclear 18S rRNA gene, S. scandentiborneensis formed a distinct branch within a monophyletic subclade of Sarcocystis spp. with (colubrid) snake-rodent life cycle. We mapped all intraspecific (two haplotypes) and interspecific nucleotide substitutions to the secondary structure of the 18S rRNA gene: in both cases, the highest variability occurred within helices V2 and V4 but intraspecific variability mostly related to transitions, while transition/transversion ratios between S. scandentiborneensis, S. zuoi, and S. clethrionomyelaphis were skewed towards transversions. Lack of relevant sequences restricted phylogenetic analysis of the mitochondrial Cytochrome C oxidase subunit I (COI) gene to include only one species of Sarcocystis recovered from a snake host (S. pantherophisi) with which the new species formed a sister relationship. We confirm the presence of the functionally important elements of the COI barcode amino acid sequence of S. scandentiborneensis, whereby the frequency of functionally important amino acids (Alanine, Serine) was markedly different to other taxa of the Sarcocystidae. We regard S. scandentiborneensis a new species, highlighting that structurally or functionally important aspects of the 18S rRNA and COI could expand their utility for delineation of species. We also address the question why treeshrews, believed to be close to primates, carry a parasite that is genetically close to a Sarcocystis lineage preferably developing in the Rodentia as intermediate hosts.

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Sarcocystis scandentiborneensis sp. nov. identified from Tupaia tana and T. minor.

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Putative snake-treeshrew life cycle.

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Unique brush-like cyst wall with an electron-dense apical structure.

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Transition/transversion ratios of 18S rDNA improve species discrimination.

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COI: Interspecific differences of functionally important amino acids of barcode area.

Apicomplexan-like parasites are polyphyletic and widely but selectively dependent on cryptic plastid organelles

The phylum Apicomplexa comprises human pathogens such as Plasmodium but is also an under-explored hotspot of evolutionary diversity central to understanding the origins of parasitism and non-photosynthetic plastids. We generated single-cell transcriptomes for all major apicomplexan groups lacking large-scale sequence data. Phylogenetic analysis reveals that apicomplexan-like parasites are polyphyletic and their similar morphologies emerged convergently at least three times. Gregarines and eugregarines are monophyletic, against most expectations, and rhytidocystids and Eleutheroschizon are sister lineages to medically important taxa. Although previously unrecognized, plastids in deep-branching apicomplexans are common, and they contain some of the most divergent and AT-rich genomes ever found. In eugregarines, however, plastids are either abnormally reduced or absent, thus increasing known plastid losses in eukaryotes from two to four. Environmental sequences of ten novel plastid lineages and structural innovations in plastid proteins confirm that plastids in apicomplexans and their relatives are widespread and share a common, photosynthetic origin.

Microscopic parasites known collectively as apicomplexans are responsible for several infectious diseases in humans including malaria and toxoplasmosis. The cells of the malaria parasite and many other apicomplexans contain compartments known as cryptic chloroplasts that produce molecules the parasites need to survive. Cryptic chloroplasts are similar to the chloroplasts found in plant cells, but unlike plants the compartments in apicomplexans are unable to harvest energy from sunlight.

Since the cells of humans and other animals do not contain chloroplasts, cryptic chloroplasts are a potential target for new drugs to treat diseases caused by apicomplexans. However, it remains unclear how widespread cryptic chloroplasts are in these parasites, largely because few apicomplexans have been successfully grown in the laboratory.

To address this question, Janouškovec et al. used an approach called single-cell transcriptomics to study ten different apicomplexans. This provided new data about the genetic make-up of each parasite that the team analysed to find out how they are related to one another. The analysis revealed that, unexpectedly, apicomplexan parasites do not share a close common ancestor and are therefore not a natural grouping from an evolutionary perspective. Instead, their similar physical appearances and lifestyles evolved independently on at least three separate occasions.

Further analysis demonstrated that cryptic chloroplasts are common in apicomplexan parasites, including in lineages where they were not previously known to exist. However, at least three lineages of apicomplexans have independently lost their cryptic chloroplasts.

The findings of Janouškovec et al. shed new light on the importance of chloroplasts in the evolution of life and may help develop new treatments for diseases caused by apicomplexan parasites. Several drugs targeting the cryptic chloroplasts in malaria parasites are currently in clinical trials, and this work suggests that these drugs may also have the potential to be used against other apicomplexan parasites in the future.

Electron microscopic observation of the early stages of Cryptosporidium parvum asexual multiplication and development in in vitro axenic culture

The stages of Cryptosporidium parvum asexual exogenous development were investigated at high ultra-structural resolution in cell-free culture using transmission electron microscopy (TEM). Early C. parvum trophozoites were ovoid in shape, 1.07 × 1.47 μm(2) in size, and contained a large nucleus and adjacent Golgi complex. Dividing and mature meronts containing four to eight developing merozoites, 2.34 × 2.7 μm(2) in size, were observed within the first 24h of cultivation. An obvious peculiarity was found within the merozoite pellicle, as it was composed of the outer plasma membrane with underlying middle and inner membrane complexes. Further novel findings were vacuolization of the meront's residuum and extension of its outer pellicle, as parasitophorous vacuole-like membranes were also evident. The asexual reproduction of C. parvum was consistent with the developmental pattern of both eimerian coccidia and Arthrogregarinida (formerly Neogregarinida). The unique cell-free development of C. parvum described here, along with the establishment of meronts and merozoite formation, is the first such evidence obtained from in vitro cell-free culture at the ultrastructural level.

Comparative ultrastructure and molecular phylogeny of Selenidium melongena n. sp. and S. terebellae Ray 1930 demonstrate niche partitioning in marine gregarine parasites (apicomplexa)

Gregarine apicomplexans are a diverse group of single-celled parasites that have feeding stages (trophozoites) and gamonts that generally inhabit the extracellular spaces of invertebrate hosts living in marine, freshwater, and terrestrial environments. Inferences about the evolutionary morphology of gregarine apicomplexans are being incrementally refined by molecular phylogenetic data, which suggest that several traits associated with the feeding cells of gregarines arose by convergent evolution. The study reported here supports these inferences by showing how molecular data reveals traits that are phylogenetically misleading within the context of comparative morphology alone. We examined the ultrastructure and molecular phylogenetic positions of two gregarine species isolated from the spaghetti worm Thelepus japonicus: Selenidium terebellaeRay 1930 and S. melongena n. sp. The ultrastructural traits of S. terebellae were very similar to other species of Selenidium sensu stricto, such as having vermiform trophozoites with an apical complex, few epicytic folds, and a dense array of microtubules underlying the trilayered pellicle. By contrast, S. melongena n. sp. lacked a comparably discrete assembly of subpellicular microtubules, instead employing a system of fibrils beneath the cell surface that supported a relatively dense array of helically arranged epicytic folds. Molecular phylogenetic analyses of small subunit rDNA sequences derived from single-cell PCR unexpectedly demonstrated that these two gregarines are close sister species. The ultrastructural differences between these two species were consistent with the fact that S. terebellae infects the inner lining of the host intestines, and S. melongena n. sp. primarily inhabits the coelom, infecting the outside wall of the host intestine. Altogether, these data demonstrate a compelling case of niche partitioning and associated morphological divergence in marine gregarine apicomplexans.

Molecular systematics of marine gregarines (Apicomplexa) from North-eastern Pacific polychaetes and nemerteans, with descriptions of three novel species: Lecudina phyllochaetopteri sp. nov., Difficilina tubulani sp. nov. and Difficilina paranemertis sp. nov

Most eugregarine apicomplexans infecting the intestines of marine invertebrates have been described within the family Lecudinidae and the type genus Lecudina. The diversity of these parasites is vast and poorly understood and only a tiny number of species has been characterized at the molecular phylogenetic level. DNA sequences coupled with high-resolution micrographs of trophozoites provide an efficient and precise approach for delimiting gregarine lineages from one another and also facilitate our overall understanding of gregarine biodiversity. In this study, phylogenetic analyses of small subunit (SSU) rDNA sequences from five (uncultivated) gregarines isolated from polychaetes and nemerteans in the North-eastern Pacific Ocean are presented. Lecudina phyllochaetopteri sp. nov. was isolated from the intestines of the parchment tubeworm Phyllochaetopterus prolifica (Polychaeta). Lecudina longissima and Lecudina polymorpha were both isolated from the intestines of Lumbrineris japonica (Polychaeta). Difficilina tubulani sp. nov. was isolated from the nemertean Tubulanus polymorpha and Difficilina paranemertis sp. nov. was isolated from the nemertean Paranemertes peregrina. This is the first report of molecular sequence data from gregarines that infect nemerteans. The two novel species of the genus Difficilina described in this study formed a strongly supported clade in the phylogenetic analyses. This Difficilina clade formed the sister group to a robust subclade of lecudinids consisting of Lecudina longissima, Lecudina phyllochaetopteri sp. nov. (which lacked epicytic folds), Lecudina tuzetae, species of the genus Lankesteria and several sequences derived from previous environmental DNA surveys of marine biodiversity.

Marine gregarines: evolutionary prelude to the apicomplexan radiation?

Gregarine apicomplexans inhabit the intestines, coeloms and reproductive vesicles of invertebrates. An emphasis on specific ancestral characteristics in marine gregarines has given the group a reputation of being 'primitive.' Although some lineages have retained characteristics inferred to be ancestral for the group, and perhaps apicomplexans as a whole, most gregarines represent highly derived parasites with novel ultrastructural and behavioral adaptations. Many marine gregarines have become giants among single-celled organisms and have evolved ornate surface structures. A comparison of gregarine morphology, placed in a modern phylogenetic context, helps clarify the earliest stages of apicomplexan evolution, the origin of Cryptosporidium, and specific cases of convergent evolution within the group and beyond.