A new phylogeny and environmental DNA insight into paramyxids: an increasingly important but enigmatic clade of protistan parasites of marine invertebrates

Marteilia pararefringens infections are more frequent than revealed by the Norwegian surveillance programme, highlighting the need for its improvement

Norway had historically been considered free of marteiliosis in bivalves since the disease surveillance programme began in 1995. However, in 2016, Marteilia pararefringens, a protistan parasite of mussels Mytilus spp., was described in a heliothermic lagoon-a poll-previously used to produce flat oyster spat. To study whether the parasite was introduced, and possibly spread, via the historical flat oyster networks on the south and west coast, we sampled aquaculture polls that were part of different networks of farmers and wild, natural polls with no aquaculture activity. Additionally, we sampled mussel banks influenced by polls and sheltered bays that could have a similar environment to that of polls. We identified 7 sites with M. pararefringens-infected mussel populations: 5 were polls used in flat oyster production and 2 were in fjord areas with no known connection to any bivalve aquaculture. Prevalence ranged between 2 and 88%. At one site, Trysfjorden, we found M. pararefringens in atypical organs, including the gills, mantle, and intestine. Marteilia-like cells were also observed in the epithelium, lumen, and surrounding connective tissue of metanephridia and in the sinus of the anterior retractor muscle. Our results demonstrate that the parasite is more widespread than previously thought and is neither isolated to polls nor connected directly to aquaculture activity. Lastly, our findings highlight the need for an improved sampling strategy in surveillance programmes to detect marteiliosis in mussels.

Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria

BACKGROUND

Ascetosporea (Endomyxa, Rhizaria) is a group of unicellular parasites infecting aquatic invertebrates. They are increasingly being recognized as widespread and important in marine environments, causing large annual losses in invertebrate aquaculture. Despite their importance, little molecular data of Ascetosporea exist, with only two genome assemblies published to date. Accordingly, the evolutionary origin of these parasites is unclear, including their phylogenetic position and the genomic adaptations that accompanied the transition from a free-living lifestyle to parasitism. Here, we sequenced and assembled three new ascetosporean genomes, as well as the genome of a closely related amphizoic species, to investigate the phylogeny, origin, and genomic adaptations to parasitism in Ascetosporea.

RESULTS

Using a phylogenomic approach, we confirm the monophyly of Ascetosporea and show that Paramyxida group with Mikrocytida, with Haplosporida being sister to both groups. We report that the genomes of these parasites are relatively small (12-36 Mb) and gene-sparse (~ 2300-5200 genes), while containing surprisingly high amounts of non-coding sequence (~ 70-90% of the genomes). Performing gene-tree aware ancestral reconstruction of gene families, we demonstrate extensive gene losses at the origin of parasitism in Ascetosporea, primarily of metabolic functions, and little gene gain except on terminal branches. Finally, we highlight some functional gene classes that have undergone expansions during evolution of the group.

CONCLUSIONS

We present important new genomic information from a lineage of enigmatic but important parasites of invertebrates and illuminate some of the genomic innovations accompanying the evolutionary transition to parasitism in this lineage. Our results and data provide a genetic basis for the development of control measures against these parasites.

Variation in Paramarteilia canceri infections in velvet crab Necora puber

Sustainable management of crustacean populations requires an understanding of the range of factors affecting different crustacean species. Recently, a high prevalence of a paramyxid parasite, Paramarteilia canceri, was reported in velvet crabs Necora puber in Ireland. Similar parasites have been known to cause mass mortalities in bivalves and, as velvet crabs are an important commercial species, these parasite infections are cause for concern. The main objective of this study was to examine variation in P. canceri infections in relation to host biology and season over a 2 yr period. In addition, we tested a range of host tissues and organs to gain more information on the host-parasite interaction. The parasite was present in all tissues and organs investigated, including the gonad and eggs of a berried female. Parasite prevalence was highest in the cuticular epithelium and hepatopancreas. Both annual and seasonal variation was found in parasite prevalence and parasite load. No difference was found in parasite prevalence or parasite load with either crab size or crab sex. Granulomas as a response to infection were significantly more abundant in infected velvet crab individuals. The results of this study provide important information on the host-parasite interaction between P. canceri and the velvet crab and highlight the importance of including parasite monitoring in the management of crustacean fisheries.

Long-term survey discloses a shift in the dynamics pattern of an emerging disease of cockles Cerastoderma edule, marteiliosis, and raises hypotheses to explain it

Drivers of marine disease outbreaks are poorly understood in spite of their growing impact. We present here results from a unique case study examining how cockles Cerastoderma edule have responded to the introduction of the novel protistan Marteilia cochillia, which led in 2012 to cockle fishery collapse in Galician rias. Based on intensive survey for eight years (2011-2019) of two affected shellfish beds, inner and outer in the Ría de Arousa, involving monthly evaluation of cockle health status and estimation of mortality, detailed information is provided of the declining impact of marteiliosis over a wild cockle population with evidence suggesting its increasing resistance. Disease dynamics involved an annual "breaking wave" of prevalence and subsequent cockle mass mortality, causing the near extinction of every recruited cohort. A shift in this pattern, from a severe epidemic towards an endemic profile, was observed in the inner shellfish bed since the cohort that was recruited in 2016, suggesting the hypothesis of increasing marteiliosis resistance through natural selection. Risk factors that may contribute to trigger marteiliosis outbreaks were analysed. Host age and sex did not influence susceptibility to marteiliosis. No clear relationships between environmental conditions (temperature, salinity and upwelling index) or cockle density and disease dynamics were found. Spatial differences in disease dynamics could be due to differences in the abundance of infective stages hypothetically linked to spatial differences in the population dynamics of a putative planktonic intermediate host. All these findings have potential implications for the management of diseased populations.

Integration of transcriptomic and metabolomic analyses reveal the molecular responses of the mud crab Scylla paramamosain to infection by an undescribed endoparasite Portunion sp

Portunion is a rare endoparasitic isopod genus, recently observed inhabiting the hemocoel of the commercially important mud crab, Scylla paramamosain. For better understanding of the host-parasite interaction between S. paramamosain and Portunion sp., the metabolomic and transcriptomic changes in the hemolymph of the S. paramamosain were analyzed. We detected a total of 143 and 126 differentially accumulated metabolites in the positive and negative modes, respectively. Pathways related to amino acids and vitamin synthesis, such as Aminoacyl-tRNA biosynthesis, Tyrosine metabolism, Cysteine and methionine metabolism, Vitamin B6 metabolism, and Biotin metabolism were significantly enriched. Based on the transcriptomic data, a total of 942 differentially expressed genes were identified, of which 25 and 36 were significantly related to the immune system and metabolic pathways, respectively. Based on the metabolomic and transcriptomic data, 90 correlated metabolite-gene pairs were selected to build a regulatory network. Common significantly enriched pathways, including Starch and sucrose metabolism, Metabolism of xenobiotics by cytochrome P450, Aminoacyl-tRNA biosynthesis, Nitrogen metabolism, and Galactose metabolism were detected. On the basis of our analysis, the endoparasite Portunion sp. places a heavy metabolic burden on the host, particularly with respect to fundamental resources, such as amino acids, vitamins, carbohydrates, and lipids. In summary, these data provide an overview of the global metabolic and transcriptomic changes of the S. paramamosain resulting from Portunion sp. infection.

Histopathological survey of putative parasites and pathogens in non-native slipper limpets Crepidula fornicata

Two populations of the invasive slipper limpet Crepidula fornicata were sampled in Swansea Bay and Milford Haven, Wales, UK, to determine the presence of putative pathogens and parasites known to affect co-located commercially important shellfish (e.g. oysters). A multi-resource screen, including molecular and histological diagnoses, was used to assess 1800 individuals over 12 mo for microparasites, notably haplosporidians, microsporidians and paramyxids. Although initial PCR-based methods suggested the presence of these microparasites, there was no evidence of infection when assessed histologically, or when all PCR amplicons (n = 294) were sequenced. Whole tissue histology of 305 individuals revealed turbellarians in the lumen of the alimentary canal, in addition to unusual cells of unknown origin in the epithelial lining. In total, 6% of C. fornicata screened histologically harboured turbellarians, and approximately 33% contained the abnormal cells-so named due to their altered cytoplasm and condensed chromatin. A small number of limpets (~1%) also had pathologies in the digestive gland including tubule necrosis, haemocytic infiltration and sloughed cells in the tubule lumen. Overall, these data suggest that C. fornicata are not susceptible to substantive infections by microparasites outside of their native range, which may contribute in part to their invasion success.

Molecular and microscopic identification of Eomarteilia granula infection in Manila clam Ruditapes philippinarum off the south coast of Korea

A report on the new species Eomarteilia (=Marteilia) granula infecting Manila clam Ruditapes philippinarum from Japan in 2014 suggests the possibility of E. granula infecting other Manila clam populations in the Northwest Pacific region, including Korea. In this study, we report the first infections by E. granula in Manila clams off the south coast of Korea. Histology revealed Marteilia-like plasmodia in the digestive tubule epithelia. Tissue imprints demonstrated that each parasite sporangium enclosed 4 spores and transmission electron microscopy (TEM) revealed ultrastructure of primary cells enclosing secondary cells, which contained spores. Mature spores consisted of 3 sporoplasms: outermost, intermediate, and innermost. The outermost sporoplasm showed a peripheral electron-dense monolayer characteristic of E. granula. The 18S rDNA amplified from the Marteilia-like parasite yielded 1784-bp PCR amplicon sequences which were 99.8% similar to that of E. granula previously reported (as M. granula) from Japan. In the molecular phylogenetic analysis, the novel Marteilia-like organism formed a well-supported clade with E. granula. Accordingly, we concluded that the novel Marteilia-like parasite that we found infecting some Korean Manila clams is Eomarteilia granula. Field surveys revealed that the infection was limited to clams of the south coast of Korea, with the prevalence ranging from 3.3 to 5.0%.

Discovery of the parasite Marteilia cocosarum sp. nov. In common cockle (Cerastoderma edule) fisheries in Wales, UK and its comparison with Marteilia cochillia

Diseases of bivalve molluscs caused by paramyxid parasites of the genus Marteilia have been linked to mass mortalities and the collapse of commercially important shellfish populations. Until recently, no Marteilia spp. have been detected in common cockle (Cerastoderma edule) populations in the British Isles. Molecular screening of cockles from ten sites on the Welsh coast indicates that a Marteilia parasite is widespread in Welsh C. edule populations, including major fisheries. Phylogenetic analysis of ribosomal DNA (rDNA) gene sequences from this parasite indicates that it is a closely related but different species to Marteilia cochillia, a parasite linked to mass mortality of C. edule fisheries in Spain, and that both are related to Marteilia octospora, for which we provide new rDNA sequence data. Preliminary light and transmission electron microscope (TEM) observations support this conclusion, indicating that the parasite from Wales is located primarily within areas of inflammation in the gills and the connective tissue of the digestive gland, whereas M. cochillia is found mainly within the epithelium of the digestive gland. The impact of infection by the new species, here described as Marteilia cocosarum n. sp., upon Welsh fisheries is currently unknown.

Infection cycle of Marteilia pararefringens in blue mussels Mytilus edulis in a heliothermic marine oyster lagoon in Norway

Agapollen is a traditional heliothermic marine oyster lagoon in western Norway, representing the northernmost site of any Marteilia sp. protists detected in Europe. The semi-closed lagoon is a unique site to study the life cycle and development of M. pararefringens in naïve mussels. Two baskets with uninfected mussels were deployed in the lagoon outlet in May and October 2018, respectively, and sampled every 6 wk. The parasite was first detected in the mussels by PCR in early July and by histology in late August. By then, M. pararefringens had developed into mature stages, indicating a rapid development during mid-summer. Sporulation occurred during autumn. Mussels deployed in October never became infected, indicating that transmission was restricted to the warmest period of the year. Pronounced pathology was observed in infected mussels, including degenerated digestive tubules and infiltration of haemocytes. Mussel mortality was observed in the baskets, but whether this was due to infections of M. pararefringens or other environmental factors could not be determined. Plankton samples from the lagoon were also collected for PCR analysis. These samples, dominated by copepods, were positive for M. pararefringens in summer. In sorted samples, M. pararefringens was detected in the Acartia spp. and Paracartia grani fractions between July and October. These plankton copepods are therefore potentially involved in the life cycle of M. pararefringens.

High prevalence of Paramarteilia canceri infecting velvet swimming crabs Necora puber in Ireland

The velvet swimming crab Necora puber has been fished in Ireland since the early 1980s and contributes significant income to smaller fishing vessels. From 2016 onwards, reduced landings have been reported. We undertook a full pathological investigation of crabs from fishing grounds at 3 sites on the west (Galway), southwest (Castletownbere) and east (Howth) coasts of Ireland. Histopathology, transmission electron microscopy and molecular taxonomic and phylogenetic analyses showed high prevalence and infection level of Paramarteilia canceri, previously only reported from the edible crab Cancer pagurus. This study provides the first molecular data for P. canceri, and shows its phylogenetic position in the order Paramyxida (Rhizaria). Other parasites and symbionts detected in the crabs were also noted, including widespread but low co-infection with Hematodinium sp. and a microsporidian consistent with the Ameson and Nadelspora genera. This is the first histological record of Hematodinium sp. in velvet crabs from Ireland. Four N. puber individuals across 2 sites were co-infected by P. canceri and Hematodinium sp. At one site, 3 velvet crabs infected with P. canceri were co-infected with the first microsporidian recorded from this host; the microsporidian 18S sequence was almost identical to Ameson pulvis, known to infect European shore crabs Carcinus maenas. The study provides a comprehensive phylogenetic analysis of this and all other available Ameson and Nadelspora 18S sequences. Together, these findings provide a baseline for further investigations of N. puber populations along the coast of Ireland.

Hematodinium sp. infection does not drive collateral disease contraction in a crustacean host

Host, pathogen, and environment are determinants of the disease triangle, the latter being a key driver of disease outcomes and persistence within a community. The dinoflagellate genus Hematodinium is detrimental to crustaceans globally - considered to suppress the innate defences of hosts, making them more susceptible to co-infections. Evidence supporting immune suppression is largely anecdotal and sourced from diffuse accounts of compromised decapods. We used a population of shore crabs (Carcinus maenas), where Hematodinium sp. is endemic, to determine the extent of collateral infections across two distinct environments (open-water, semi-closed dock). Using a multi-resource approach (PCR, histology, haematology, population genetics, eDNA), we identified 162 Hematodinium-positive crabs and size/sex-matched these to 162 Hematodinium-free crabs out of 1191 analysed. Crabs were interrogated for known additional disease-causing agents; haplosporidians, microsporidians, mikrocytids, Vibrio spp., fungi, Sacculina, trematodes, and haemolymph bacterial loads. We found no significant differences in occurrence, severity, or composition of collateral infections between Hematodinium-positive and Hematodinium-free crabs at either site, but crucially, we recorded site-restricted blends of pathogens. We found no gross signs of host cell immune reactivity towards Hematodinium in the presence or absence of other pathogens. We contend Hematodinium sp. is not the proximal driver of co-infections in shore crabs, which suggests an evolutionary drive towards latency in this environmentally plastic host.

Advances and Discoveries in Myxozoan Genomics

Myxozoans are highly diverse and globally distributed cnidarian endoparasites in freshwater and marine habitats. They have adopted a heteroxenous life cycle, including invertebrate and fish hosts, and have been associated with diseases in aquaculture and wild fish stocks. Despite their importance, genomic resources of myxozoans have proven difficult to obtain due to their miniaturized and derived genome character and close associations with fish tissues. The first 'omic' datasets have now become the main resource for a better understanding of host-parasite interactions, virulence, and diversity, but also the evolutionary history of myxozoans. In this review, we discuss recent genomic advances in the field and outline outstanding questions to be answered with continuous and improved efforts of generating myxozoan genomic data.

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

Phytomyxea (phytomyxids) is a group of obligate biotrophic pathogens belonging to the Rhizaria. Some phytomyxids are well studied and include known plant pathogens such as Plasmodiophora brassicae, the causal agent of clubroot disease. Despite this economic importance, the taxonomy and biodiversity of this group are largely cryptic, with many species described in the premolecular area. Some of these species were key for establishing the morphotaxonomic concepts that define most genera to this day, but systematic efforts to include and integrate those species into molecular studies are still lacking. The aim of this study was to expand our understanding of phytomyxid biodiversity in terrestrial environments. Thirty-eight environmental samples from habitats in which novel and known diversity of Phytomyxea was expected were analysed. We were able to generate 18S rRNA sequences from Ligniera verrucosa, a species which is well defined based on ultrastructure. Phylogenetic analyses of the collected sequences rendered the genera Lignera, Plasmodiophora and Spongospora polyphyletic, and identified two novel and apparently diverse lineages (clade 17, clade 18). Based on these findings and on data from previous studies, we formally establish the new genera Pseudoligniera n. gen. for L. verrucosa,Hillenburgia n. gen. for Spongospora nasturtii and revert Plasmodiophora diplantherae to its original name Ostenfeldiella diplantherae.

An eDNA/eRNA-based approach to investigate the life cycle of non-cultivable shellfish micro-parasites: the case of Bonamia ostreae, a parasite of the European flat oyster Ostrea edulis

Environmental DNA approaches are increasingly used to detect microorganisms in environmental compartments, including water. They show considerable advantages to study non-cultivable microorganisms like Bonamia ostreae, a protozoan parasite inducing significant mortality in populations of flat oyster Ostrea edulis. Although B. ostreae development within the host has been well described, questions remain about its behaviour in the environment. As B. ostreae transmission is direct, seawater appears as an interesting target to develop early detection tools and improve our understanding of disease transmission mechanisms. In this context, we have developed an eDNA/eRNA approach allowing detecting and quantifying B. ostreae 18S rDNA/rRNA as well as monitoring its presence in seawater by real-time PCR. B. ostreae DNA could be detected up to 4 days while RNA could be detected up to 30 days, suggesting a higher sensitivity of the eRNA-based tool. Additionally, more than 90% of shed parasites were no longer detected after 2 days outside the oysters. By allowing B. ostreae detection in seawater, this approach would not only be useful to monitor the presence of the parasite in oyster production areas but also to evaluate the effect of changing environmental factors on parasite survival and transmission.

Cosmopolitan Distribution of Endozoicomonas-Like Organisms and Other Intracellular Microcolonies of Bacteria Causing Infection in Marine Mollusks

Intracellular microcolonies of bacteria (IMC), in some cases developing large extracellular cysts (bacterial aggregates), infecting primarily gill and digestive gland, have been historically reported in a wide diversity of economically important mollusk species worldwide, sometimes associated with severe lesions and mass mortality events. As an effort to characterize those organisms, traditionally named as Rickettsia or Chlamydia-like organisms, 1950 specimens comprising 22 mollusk species were collected over 10 countries and after histology examination, a selection of 99 samples involving 20 species were subjected to 16S rRNA gene amplicon sequencing. Phylogenetic analysis showed Endozoicomonadaceae sequences in all the mollusk species analyzed. Geographical differences in the distribution of Operational Taxonomic Units (OTUs) and a particular OTU associated with pathology in king scallop (OTU_2) were observed. The presence of Endozoicomonadaceae sequences in the IMC was visually confirmed by in situ hybridization (ISH) in eight selected samples. Sequencing data also indicated other symbiotic bacteria. Subsequent phylogenetic analysis of those OTUs revealed a novel microbial diversity associated with molluskan IMC infection distributed among different taxa, including the phylum Spirochetes, the families Anaplasmataceae and Simkaniaceae, the genera Mycoplasma and Francisella, and sulfur-oxidizing endosymbionts. Sequences like Francisella halioticida/philomiragia and Candidatus Brownia rhizoecola were also obtained, however, in the absence of ISH studies, the association between those organisms and the IMCs were not confirmed. The sequences identified in this study will allow for further molecular characterization of the microbial community associated with IMC infection in marine mollusks and their correlation with severity of the lesions to clarify their role as endosymbionts, commensals or true pathogens.

Haplosporosomes, sporoplasmosomes and their putative taxonomic relationships in rhizarians and myxozoans

This paper reviews current knowledge of the structure, genesis, cytochemistry and putative functions of the haplosporosomes of haplosporidians (Urosporidium, Haplosporidium, Bonamia, Minchinia) and paramyxids (Paramyxa, Paramyxoides, Marteilia, Marteilioides, Paramarteilia), and the sporoplasmosomes of myxozoans (Myxozoa - Malacosporea, Myxosporea). In all 3 groups, these bodies occur in plasmodial trophic stages, disappear at the onset of sporogony, and reappear in the spore. Some haplosporidian haplosporosomes lack the internal membrane regarded as characteristic of these bodies and that phylum. Haplosporidian haplosporogenesis is through the Golgi (spherulosome in the spore), either to form haplosporosomes at the trans-Golgi network, or for the Golgi to produce formative bodies from which membranous vesicles bud, thus acquiring the external membrane. The former method also forms sporoplasmosomes in malacosporeans, while the latter is the common method of haplosporogenesis in paramyxids. Sporoplasmogenesis in myxosporeans is largely unknown. The haplosporosomes of Haplosporidium nelsoni and sporoplasmosomes of malacosporeans are similar in arraying themselves beneath the plasmodial plasma membrane with their internal membranes pointing to the exterior, possibly to secrete their contents to lyse host cells or repel haemocytes. It is concluded that these bodies are probably multifunctional within and between groups, their internal membranes separating different functional compartments, and their origin may be from common ancestors in the Neoproterozoic.

Microeukaryotes in animal and plant microbiomes: Ecologies of disease?

Studies of animal and plant microbiomes are burgeoning, but the majority of these focus on bacteria and rarely include microeukaryotes other than fungi. However, there is growing evidence that microeukaryotes living on and in larger organisms (e.g. plants, animals, macroalgae) are diverse and in many cases abundant. We present here a new combination of 'anti-metazoan' primers: 574*f-UNonMet_DB that amplify a wide diversity of microeukaryotes including some groups that are difficult to amplify using other primer combinations. While many groups of microeukaryotic parasites are recognised, myriad other microeukaryotes are associated with hosts as previously unknown parasites (often genetically divergent so difficult to amplify using standard PCR primers), opportunistic parasites, commensals, and other ecto- and endo-symbionts, across the 'symbiotic continuum'. These fulfil a wide range of roles from pathogenesis to mutually beneficial symbioses, but mostly their roles are unknown and likely fall somewhere along this spectrum, with the potential to switch the nature of their interactions with the host under different conditions. The composition and dynamics of host-associated microbial communities are also increasingly recognised as important moderators of host health. This 'pathobiome' approach to understanding disease is beginning to supercede a one-pathogen-one-disease paradigm, which cannot sufficiently explain many disease scenarios.

Diversity and microhabitat associations of Labyrinthula spp. in the Indian River Lagoon System

Seagrasses create foundational habitats in coastal ecosystems. One contributing factor to their global decline is disease, primarily caused by parasites in the genus Labyrinthula. To explore the relationship between seagrass and Labyrinthula spp. diversity in coastal waters, we examined the diversity and microhabitat association of Labyrinthula spp. in 2 inlets on Florida's Atlantic Coast, the Indian River Lagoon (IRL) and Banana River. We used amplicon-based high throughput sequencing with 2 newly designed primers to amplify Labyrinthula spp. from 5 seagrass species, water, and sediments to determine their spatial distribution and microhabitat associations. The SSU primer set identified 12 Labyrinthula zero-radius operational taxonomic units (ZOTUs), corresponding to at least 8 putative species. The ITS1 primer set identified 2 ZOTUs, corresponding to at least 2 putative species. Based on our phylogenetic analyses, which include sequences from previous studies that assigned seagrass-related pathogenicity to Labyrinthula clades, all but one of the ZOTUs that we recovered with the SSU primers were from non-pathogenic species, while the 2 ZOTUs recovered with the ITS1 primers were from pathogenic species. Some of the ZOTUs were widespread across the sampling sites and microhabitats (e.g. SSU ZOTU_10), and most were present in more than one site. Our results demonstrate that targeted metabarcoding is a useful tool for examining the relationships between seagrass and Labyrinthula diversity in coastal waters.

The planktonic protist interactome: where do we stand after a century of research?

Microbial interactions are crucial for Earth ecosystem function, but our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2500 ecological interactions from ~500 publications, spanning the last 150 years. All major protistan lineages were involved in interactions as hosts, symbionts (mutualists and commensalists), parasites, predators, and/or prey. Predation was the most common interaction (39% of all records), followed by symbiosis (29%), parasitism (18%), and ‘unresolved interactions’ (14%, where it is uncertain whether the interaction is beneficial or antagonistic). Using bipartite networks, we found that protist predators seem to be ‘multivorous’ while parasite–host and symbiont–host interactions appear to have moderate degrees of specialization. The SAR supergroup (i.e., Stramenopiles, Alveolata, and Rhizaria) heavily dominated PIDA, and comparisons against a global-ocean molecular survey (TARA Oceans) indicated that several SAR lineages, which are abundant and diverse in the marine realm, were underrepresented among the recorded interactions. Despite historical biases, our work not only unveils large-scale eco-evolutionary trends in the protist interactome, but it also constitutes an expandable resource to investigate protist interactions and to test hypotheses deriving from omics tools.

Pathogens and other symbionts of the Amphipoda: taxonomic diversity and pathological significance

With over 10000 species of Amphipoda currently described, this order is one of the most diverse groups of freshwater and marine Crustacea. Members of this group are globally distributed, and many are keystone species and ecosystem engineers within their respective ecologies. As with most organisms, disease is a key factor that can alter population size, behaviour, survival, invasion potential and physiology of amphipod hosts. This review explores symbiont diversity and pathology in amphipods by coalescing a range of current and historical literature to provide the first full review of our understanding of amphipod disease. The review is broken into 2 parts. The first half explores amphipod microparasites, which include data pertaining to viruses, bacteria, fungi, oomycetes, microsporidians, dinoflagellates, myxozoans, ascetosporeans, mesomycetozoeans, apicomplexans and ciliophorans. The second half reports the metazoan macroparasites of Amphipoda, including rotifers, trematodes, acanthocephalans, nematodes, cestodes and parasitic Crustacea. In all cases we have endeavoured to provide a complete list of known species that cause disease in amphipods, while also exploring the effects of parasitism. Although our understanding of disease in amphipods requires greater research efforts to better define taxonomic diversity and host effects of amphipod symbionts, research to date has made huge progress in cataloguing and experimentally determining the effects of disease upon amphipods. For the future, we suggest a greater focus on developing model systems that use readily available amphipods and diseases, which can be comparable to the diseases in other Crustacea that are endangered, economically important or difficult to house.

The Pathobiome in Animal and Plant Diseases

A growing awareness of the diversity and ubiquity of microbes (eukaryotes, prokaryotes, and viruses) associated with larger 'host' organisms has led to the realisation that many diseases thought to be caused by one primary agent are the result of interactions between multiple taxa and the host. Even where a primary agent can be identified, its effect is often moderated by other symbionts. Therefore, the one pathogen-one disease paradigm is shifting towards the pathobiome concept, integrating the interaction of multiple symbionts, host, and environment in a new understanding of disease aetiology. Taxonomically, pathobiomes are variable across host species, ecology, tissue type, and time. Therefore, a more functionally driven understanding of pathobiotic systems is necessary, based on gene expression, metabolic interactions, and ecological processes.

The joint evolution of the Myxozoa and their alternate hosts: A cnidarian recipe for success and vast biodiversity

The relationships between parasites and their hosts are intimate, dynamic and complex; the evolution of one is inevitably linked to the other. Despite multiple origins of parasitism in the Cnidaria, only parasites belonging to the Myxozoa are characterized by a complex life cycle, alternating between fish and invertebrate hosts, as well as by high species diversity. This inspired us to examine the history of adaptive radiations in myxozoans and their hosts by determining the degree of congruence between their phylogenies and by timing the emergence of myxozoan lineages in relation to their hosts. Recent genomic analyses suggested a common origin of Polypodium hydriforme, a cnidarian parasite of acipenseriform fishes, and the Myxozoa, and proposed fish as original hosts for both sister lineages. We demonstrate that the Myxozoa emerged long before fish populated Earth and that phylogenetic congruence with their invertebrate hosts is evident down to the most basal branches of the tree, indicating bryozoans and annelids as original hosts and challenging previous evolutionary hypotheses. We provide evidence that, following invertebrate invasion, fish hosts were acquired multiple times, leading to parallel cospeciation patterns in all major phylogenetic lineages. We identify the acquisition of vertebrate hosts that facilitate alternative transmission and dispersion strategies as reason for the distinct success of the Myxozoa, and identify massive host specification-linked parasite diversification events. The results of this study transform our understanding of the origins and evolution of parasitism in the most basal metazoan parasites known.

Detection and characterisation of haplosporidian parasites of the blue mussel Mytilus edulis, including description of the novel parasite Minchinia mytili n. sp

The edible mussel Mytilus edulis is a major aquaculture commodity in Europe, with 168000 t produced in 2015. A number of abundant, well characterised parasites of the species are known, though none are considered to cause significant mortality. Haplosporida (Rhizaria, Endomyxa) is an order of protistan parasites of aquatic invertebrates, the best studied of which are the oyster pathogens Haplosporidium nelsoni and Bonamia ostreae. While these species are well characterised within their hosts, the diversity, life-cycle and modes of transmission of haplosporidians are very poorly understood. Haplosporidian parasites have previously been reported from Mytilus spp., however the majority of these remain uncharacterised, and no molecular data exist for any species. In this study, we identified 2 novel haplosporidian parasites of M. edulis present in the UK. The first of these, observed by light microscopy and in situ hybridisation infecting the gills, mantle, gonadal tubules and digestive connective tissues of mussels in the Tamar estuary, England, we describe as Minchinia mytili on the basis of 18S sequence data. The second, observed infecting a single archive specimen collected in Loch Spelve, Mull, Scotland, infects the foot muscle, gills and connective tissue of the digestive gland. Sequence data places this parasite in an uncharacterised clade of sequences amplified from tropical bivalve guts and water samples, sister to H. nelsoni. Screening of water and sediment samples collected at the sample site in the Tamar estuary revealed the presence of both sequence types in the water column, suggesting host-free or planktonic life stages.

Marteilia refringens and Marteilia pararefringens sp. nov. are distinct parasites of bivalves and have different European distributions

Marteilia refringens causes marteiliosis in oysters, mussels and other bivalve molluscs. This parasite previously comprised two species, M. refringens and Marteilia maurini, which were synonymized in 2007 and subsequently referred to as M. refringens ‘O-type’ and ‘M-type’. O-type has caused mass mortalities of the flat oyster Ostrea edulis. We used high throughput sequencing and histology to intensively screen flat oysters and mussels (Mytilus edulis) from the UK, Sweden and Norway for infection by both types and to generate multi-gene datasets to clarify their genetic distinctiveness. Mussels from the UK, Norway and Sweden were more frequently polymerase chain reaction (PCR)-positive for M-type (75/849) than oysters (11/542). We did not detect O-type in any northern European samples, and no histology-confirmed Marteilia-infected oysters were found in the UK, Norway and Sweden, even where co-habiting mussels were infected by the M-type. The two genetic lineages within ‘M. refringens’ are robustly distinguishable at species level. We therefore formally define them as separate species: M. refringens (previously O-type) and Marteilia pararefringens sp. nov. (M-type). We designed and tested new Marteilia-specific PCR primers amplifying from the 3’ end of the 18S rRNA gene through to the 5.8S gene, which specifically amplified the target region from both tissue and environmental samples.

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

Rhizarian ‘Novel Clade 10’ (NC10) is frequently detected by 18S rRNA gene sequencing studies in freshwater planktonic samples. We describe a new genus and two species of eukaryovorous biflagellate protists, Aquavolon hoantrani n. gen. n. sp. and A. dientrani n. gen. n. sp., which represent the first morphologically characterized members of NC10, here named Aquavolonida ord. nov. The slightly metabolic cells possess naked heterodynamic flagella, whose kinetosomes lie at a right angle to each other and are connected by at least one fibril. Unlike their closest known relative Tremula longifila, they rotate around their longitudinal axis when swimming and only very rarely glide on surfaces. Screening of a wide range of environmental DNA extractions with lineage‐specific PCR primers reveals that Aquavolonida consists of a large radiation of protists, which are most diversified in freshwater planktonic habitats and as yet undetected in marine environments. Earlier‐branching lineages in Aquavolonida include less frequently detected organisms from soils and freshwater sediments. The 18S rRNA gene phylogeny suggests that Aquavolonida forms a common evolutionary lineage with tremulids and uncharacterized ‘Novel Clade 12’, which likely represents one of the deepest lineages in the Rhizaria, separate from Cercozoa (Filosa), Endomyxa, and Retaria.

Phytocercomonas venanatans, a New Species of Cercozoa Associated with Chlorotic Streak of Sugarcane

Chlorotic streak is a global disease of commercial sugarcane (Saccharum spp. hybrids). The disease is transmitted by wet soil, water, as well as in diseased planting material. Although first recognized almost 90 years ago and despite significant research effort, the identity of the causal agent has been elusive. Metagenomic high throughput sequencing (HTS) facilitated the discovery of novel protistan ribosomal and nuclear genes in chlorotic streak-infected sugarcane. These sequences suggest a possible causal agent belonging to the order Cercomonadida (Rhizaria, phylum Cercozoa). An organism with morphological features similar to cercomonads (=Cercomonadida) was isolated into pure axenic culture from internal stalk tissues of infected sugarcane. The isolated organism contained DNA sequences identical to those identified in infected plants by HTS. The DNA sequences and the morphology of the organism did not match any known species. Here we present a new genus and species, Phytocercomonas venanatans, which is associated with chlorotic streak of sugarcane. Amplicon sequencing also supports that P. venanatans is associated with this disease. This is the first reported member from Cercomonadida showing a probable pathogenic association with higher plants.

Population screening and transmission experiments indicate paramyxid-microsporidian co-infection in Echinogammarus marinus represents a non-hyperparasitic relationship between specific parasite strains

Phylogenetically distant parasites often infect the same host. Indeed, co-infections can occur at levels greater than expected by chance and are sometimes hyperparasitic. The amphipod Echinogammarus marinus presents high levels of co-infection by two intracellular and vertically transmitted parasites, a paramyxid (Paramarteilia sp. Em) and a microsporidian strain (Dictyocoela duebenum Em). This co-infection may be hyperparasitic and result from an exploitative ‘hitchhiking’ or a symbiotic relationship between the parasites. However, the best-studied amphipod species are often collected from contaminated environments and may be immune-compromised. Immune-challenged animals frequently present co-infections and contaminant-exposed amphipods present significantly higher levels of microsporidian infection. This suggests the co-infections in E. marinus may result from contaminant-associated compromised immunity. Inconsistent with hyperparasitism, we find that artificial infections transmit Paramarteilia without microsporidian. Our population surveys reveal the co-infection relationship is geographically widespread but find only chance co-infection between the Paramarteilia and another species of microsporidian, Dictyocoela berillonum. Furthermore, we identify a haplotype of the Paramarteilia that presents no co-infection, even in populations with otherwise high co-infection levels. Overall, our results do not support the compromised-immunity hypothesis but rather that the co-infection of E. marinus, although non-hyperparasitic, results from a relationship between specific Paramarteilia and Dictyocoela duebenum strains.

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

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.

Multiple origins of parasitic feminization: thelygeny and intersexuality in beach-hoppers are caused by paramyxid parasites, not microsporidia

Within populations of the amphipod crustaceans Orchestia gammarellus and Orchestia aestuarensis, a proportion of females produce thelygenic (female-only) broods, which often contain intersexual individuals. This phenomenon is associated with the presence of two putative feminizing parasites, the paramyxid Paramarteilia orchestiae and the microsporidian Dictyocoela cavimanum, which frequently co-infect the same host. In order to determine which of the parasites causes feminization, Orchestia were resampled from the type locality of P. orchestiae in France and from another population in the UK. Breeding experiments indicated that female O. gammarellus infected with P. orchestiae produced a significantly higher proportion of female and intersex offspring than uninfected females, even in the absence of D. cavimanum. There was no difference in mortality between infected and uninfected broods, indicating that the paramyxid alters the sex ratio through feminization rather than male-killing. Although D. cavimanum also displays a female-biased prevalence in Orchestia populations, this is due to co-infection with P. orchestiae, indicating that the paramyxid, rather than the microsporidian, is the cause of feminization in these Orchestia populations.

Hyperspora aquatica n.gn., n.sp. (Microsporidia), hyperparasitic in Marteilia cochillia (Paramyxida), is closely related to crustacean-infecting microspordian taxa

The Paramyxida, closely related to haplosporidians, paradinids, and mikrocytids, is an obscure order of parasitic protists within the class Ascetosporea. All characterized ascetosporeans are parasites of invertebrate hosts, including molluscs, crustaceans and polychaetes. Representatives of the genus Marteilia are the best studied paramyxids, largely due to their impact on cultured oyster stocks, and their listing in international legislative frameworks. Although several examples of microsporidian hyperparasitism of paramyxids have been reported, phylogenetic data for these taxa are lacking. Recently, a microsporidian parasite was described infecting the paramyxid Marteilia cochillia, a serious pathogen of European cockles. In the current study, we investigated the phylogeny of the microsporidian hyperparasite infecting M. cochillia in cockles and, a further hyperparasite, Unikaryon legeri infecting the digenean Meiogymnophallus minutus, also in cockles. We show that rather than representing basally branching taxa in the increasingly replete Cryptomycota/Rozellomycota outgroup (containing taxa such as Mitosporidium and Paramicrosoridium), these hyperparasites instead group with other known microsporidian parasites infecting aquatic crustaceans. In doing so, we erect a new genus and species (Hyperspora aquatica n. gn., n.sp.) to contain the hyperparasite of M. cochillia and clarify the phylogenetic position of U. legeri. We propose that in both cases, hyperparasitism may provide a strategy for the vectoring of microsporidians between hosts of different trophic status (e.g. molluscs to crustaceans) within aquatic systems. In particular, we propose that the paramyxid hyperparasite H. aquatica may eventually be detected as a parasite of marine crustaceans. The potential route of transmission of the microsporidian between the paramyxid (in its host cockle) to crustaceans, and, the 'hitch-hiking' strategy employed by H. aquatica is discussed.