Haplosporidium littoralis sp. nov.: a crustacean pathogen within the Haplosporida (Cercozoa, Ascetosporea)

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.

A health survey of the reef forming scleractinian cold-water corals Lophelia pertusa and Madrepora oculata in a remote submarine canyon on the European continental margin, NE Atlantic

Monitoring of cold-water corals (CWCs) for pathogens and diseases is limited due to the environment, protected nature of the corals and their habitat and as well as the challenging and sampling effort required. It is recognised that environmental factors such as temperature and pH can expedite the ability of pathogens to cause diseases in cold-water corals therefore the characterisation of pathogen diversity, prevalence and associated pathologies is essential. The present study combined histology and polymerase chain reaction (PCR) diagnostic techniques to screen for two significant pathogen groups (bacteria of the genus Vibrio and the protozoan Haplosporidia) in the dominant NE Atlantic deep-water framework corals Lophelia pertusa (13 colonies) and Madrepora oculata (2 colonies) at three sampling locations (canyon head, south branch and the flank) in the Porcupine Bank Canyon (PBC), NE Atlantic. One M. oculata colony and four L. pertusa colonies were collected from both the canyon flank and the south branch whilst five L. pertusa colonies were collected from the canyon head. No pathogens were detected in the M. oculata samples. Neither histology nor PCR detected Vibrio spp. in L. pertusa, although Illumina technology used in this study to profile the CWCs microbiome, detected V. shilonii (0.03%) in a single L. pertusa individual, from the canyon head, that had also been screened in this study. A macroborer was observed at a prevalence of 0.07% at the canyon head only. Rickettsiales-like organisms (RLOs) were visualised with an overall prevalence of 40% and with a low intensity of 1 to 4 (RLO) colonies per individual polyp by histology. L. pertusa from the PBC canyon head had an RLO prevalence of 13.3% with the highest detection of 26.7% recorded in the south branch corals. Similarly, unidentified cells observed in L. pertusa from the south branch (20%) were more common than those observed in L. pertusa from the canyon head (6.7%). No RLOs or unidentified cells were observed in corals from the flank. Mean particulate organic matter concentration is highest in the south branch (2,612 μg l^-1) followed by the canyon head (1,065 μg l^-1) and lowest at the canyon flank (494 μg l^-1). Although the route of pathogen entry and the impact of RLO infection on L. pertusa is unclear, particulate availability and the feeding strategies employed by the scleractinian corals may be influencing their exposure to pathogens. The absence of a pathogen in M. oculata may be attributed to the smaller number of colonies screened or the narrower diet in M. oculata compared to the unrestricted diet exhibited in L. pertusa, if ingestion is a route of entry for pathogen groups. The findings of this study also shed some light on how environmental conditions experienced by deep sea organisms and their life strategies may be limiting pathogen diversity and prevalence.

Invasive Non-Native Crustacean Symbionts: Diversity and Impact

Invasive non-native species (INNS) pose a risk as vectors of parasitic organisms (Invasive Parasites). Introducing invasive parasites can result in ecological disturbances, leading to biodiversity loss and native species illness/mortality, but occasionally can control INNS limiting their impact. Risks to human health and the economy are also associated with INNS and invasive parasites; however, we understand little about the diversity of symbiotic organisms co-invading alongside INNS. This lack of clarity is an important aspect of the 'One Health' prerogative, which aims to bridge the gap between human, wildlife, and ecosystem health. To explore symbiont diversity associated with the invasive crustacean group (including: crab, lobster, crayfish, shrimp, amphipod, isopod, copepod, barnacle, other) (n = 323) derived from 1054 aquatic invertebrates classed as INNS across databases, we compile literature (year range 1800-2017) from the native and invasive range to provide a cumulative symbiont profile for each species. Our search indicated that 31.2% of INN crustaceans were known to hold at least one symbiont, whereby the remaining 68.8% had no documented symbionts. The symbiont list mostly consisted of helminths (27% of the known diversity) and protists (23% of the known diversity), followed by bacteria (12%) and microsporidians (12%). Carcinus maenas, the globally invasive and extremely well-studied green crab, harboured the greatest number of symbionts (n = 72). Additional screening is imperative to become more informed on invasive symbiont threats. We reveal that few studies provide truly empirical data that connect biodiversity loss with invasive parasites and suggest that dedicated studies on available systems will help to provide vital case studies. Despite the lack of empirical data, co-invasive parasites of invasive invertebrates appear capable of lowering local biodiversity, especially by causing behavioural change and mortality in native species. Alternatively, several invasive parasites appear to protect ecosystems by controlling the impact and population size of their invasive host. We provide a protocol that could be followed to explore symbiont diversity in invasive groups as part of our case studies. The consequence of limited parasite screening of INNS, in addition to the impacts invasive parasites impart on local ecologies, are explored throughout the review. We conclude in strong support of the 'One Health' prerogative and further identify a need to better explore disease in invasion systems, many of which are accountable for economic, human health and ecological diversity impacts.

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.

Diagnosis and prevalence of two new species of haplosporidians infecting shore crabs Carcinus maenas: Haplosporidium carcini n. sp., and H. cranc n. sp

This study provides a morphological and phylogenetic characterization of two novel species of the order Haplosporida (Haplosporidium carcini n. sp., and H. cranc n. sp.) infecting the common shore crab Carcinus maenas collected at one location in Swansea Bay, South Wales, UK. Both parasites were observed in the haemolymph, gills and hepatopancreas. The prevalence of clinical infections (i.e. parasites seen directly in fresh haemolymph preparations) was low, at ~1%, whereas subclinical levels, detected by polymerase chain reaction, were slightly higher at ~2%. Although no spores were found in any of the infected crabs examined histologically (n = 334), the morphology of monokaryotic and dikaryotic unicellular stages of the parasites enabled differentiation between the two new species. Phylogenetic analyses of the new species based on the small subunit (SSU) rDNA gene placed H. cranc in a clade of otherwise uncharacterized environmental sequences from marine samples, and H. carcini in a clade with other crustacean-associated lineages.

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

This study provides morphological, ultrastructural and phylogenetic characterization of 2 novel species of Haplosporidia (Haplosporidium echinogammari n. sp. and H. orchestiae n. sp.) infecting amphipods of the genera Echinogammarus and Orchestia collected in southwestern England. Both parasites infect the connective tissues associated with the digestive gland and the tegument, and eventually infect other organs causing disruption of host tissues with associated motor impairment and fitness reduction. Prevalence of infection varied with host species, provenance and season, being as high as 75% for individuals of E. marinus infected with H. echinogammari in June (n = 50). Although no spores were found in any of the infected amphipods examined (n = 82), the morphology of monokaryotic and dikaryotic unicellular stages of the parasites enabled differentiation between the 2 new species. Phylogenetic analysis of the new species based on the small subunit (SSU) rDNA gene placed H. echinogammari close to H. diporeiae in haplosporidian lineage C, and H. orchestiae in a novel branch within Haplosporidium. Genetic diversity of the haplosporidians infecting these and other amphipod species was evaluated and compared to morphological and ultrastructural changes to host tissues. The phylogenetic relationship of haplosporidian infections in other crustacean hosts is discussed after inclusion into the analysis of 25 novel SSU rDNA sequences obtained from crabs, isopods and crayfish.

Green crab Carcinus maenas symbiont profiles along a North Atlantic invasion route

The green crab Carcinus maenas is an invader on the Atlantic coast of Canada and the USA. In these locations, crab populations have facilitated the development of a legal fishery in which C. maenas is caught and sold, mainly for use as bait to capture economically important crustaceans such as American lobster Homarus americanus. The paucity of knowledge on the symbionts of invasive C. maenas in Canada and their potential for transfer to lobsters poses a potential risk of unintended transmission. We carried out a histological survey for symbionts of C. maenas from their native range in Northern Europe (in the UK and Faroe Islands), and invasive range in Atlantic Canada. In total, 19 separate symbiotic associations were identified from C. maenas collected from 27 sites. These included metazoan parasites (nematodes, Profilicollis botulus, Sacculina carcini, Microphallidae, ectoparasitic crustaceans), microbial eukaryotes (ciliates, Hematodinium sp., Haplosporidium littoralis, Ameson pulvis, Parahepatospora carcini, gregarines, amoebae), bacteria (Rickettsia-like organism, milky disease), and viral pathogens (parvo-like virus, herpes-like virus, iridovirus, Carcinus maenas bacilliform virus and a haemocyte-infecting rod-shaped virus). Hematodinium sp. were not observed in the Canadian population; however, parasites such as Trematoda and Acanthocephala were present in all countries despite their complex, multi-species lifecycles. Some pathogens may pose a risk of transmission to other decapods and native fauna via the use of this host in the bait industry, such as the discovery of a virus resembling the previously described white spot syndrome virus (WSSV), B-virus and 'rod-shaped virus' (RV-CM) and amoebae, which have previously been found to cause disease in aquaculture (e.g. Salmo salar) and fisheries species (e.g. H. americanus).

Managing marine mollusc diseases in the context of regional and international commerce: policy issues and emerging concerns

Marine mollusc production contributes to food and economic security worldwide and provides valuable ecological services, yet diseases threaten these industries and wild populations. Although the infrastructure for mollusc aquaculture health management is well characterized, its foundations are not without flaws. Use of notifiable pathogen lists can leave blind spots with regard to detection of unlisted and emerging pathogens. Increased reliance on molecular tools has come without similar attention to diagnostic validation, raising questions about assay performance, and has been accompanied by a reduced emphasis on microscopic diagnostic expertise that could weaken pathogen detection capabilities. Persistent questions concerning pathogen biology and ecology promote regulatory paralysis that impedes trade and which could weaken biosecurity by driving commerce to surreptitious channels. Solutions that might be pursued to improve shellfish aquaculture health management include the establishment of more broad-based surveillance programmes, wider training and use of general methods like histopathology to ensure alertness to emerging diseases, an increased focus on assay assessment and validation as fundamental to assay development, investment in basic research, and application of risk analyses to improve regulation. A continual sharpening of diagnostic tools and approaches and deepening of scientific knowledge is necessary to manage diseases and promote sustainable molluscan shellfish industries.

Pathology of Haplosporidium patagon affecting siphonariid gastropods in Patagonia

Haplosporidium patagon was found parasitizing Siphonaria lessonii and S. lateralis, 2 siphonariid gastropods co-occurring on the littoral rocky shore at Puerto Deseado, Santa Cruz, Argentina. Gastropods from 2 habitats representing 2 different levels of environmental harshness were studied. In both cases, S. lessonii showed a higher prevalence of infection (3.78%) over the entire 14 mo study period than S. lateralis (0.13%). Very different values of prevalence of infection were observed at the different sampling sites: Site 1, the more restrictive habitat (exposed for long periods to desiccation during low tides, higher ultraviolet exposure, and high ranges of temperature variation) showed a higher prevalence value (5.99%) than Site 2 (1.46%). Statistical differences in prevalence were also found between values corresponding to the austral spring (3.35% at Site 1 and 0.74% at Site 2) and winter (13.79% at Site 1 and 2.13% at Site 2). The presence/absence of H. patagon did not vary significantly with gastropod shell length. Infection affected the digestive gland, whose normal histology was greatly modified. The hermaphroditic gonads were also affected; the female germinal cells disappeared or only a few primary or previtellogenic oocytes were present, and vitellogenesis was inhibited. The function of the male germinal epithelium, as well as spermatogenesis and spermiogenesis processes and associated organs (seminal vesicles and seminal receptacles), were not affected. However, the glandular pallial complex of the reproductive systemwas affected, and we observed a significant reduction in development in parasitized gastropods. H. patagon sporocysts also invaded the supporting connective tissues of both the kidney and pseudobranch.

Overview on the European green crab Carcinus spp. (Portunidae, Decapoda), one of the most famous marine invaders and ecotoxicological models

Green crabs (Carcinus, Portunidae) include two species native to Europe--Carcinus aestuarii (Mediterranean species) and Carcinus maenas (Atlantic species). These small shore crabs (maximal length carapace, approximately 10 cm) show rapid growth, high fecundity, and long planktonic larval stages that facilitate broad dispersion. Carcinus spp. have a high tolerance to fluctuations of environmental factors including oxygen, salinity, temperature, xenobiotic compounds, and others. Shipping of Carcinus spp. over the past centuries has resulted in its invasions of America, Asia, and Australia. Classified as one of the world's 100 worst invaders by the International Union for Conservation of Nature, Carcinus spp. are the most widely distributed intertidal crabs in the world. Their voracious predatory activity makes them strong interactors in local communities, and they are recognized as a model for invasiveness in marine systems as well as a sentinel species in ecotoxicology. This review shows an exhaustive analysis of the literature on the life cycle, diversity, physiological tolerance, genomic investigations, ecotoxicological use, historical invasion, control programs, and putative economical valorization of shore crabs.

Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians

Haplosporidians are rhizarian parasites of mostly marine invertebrates. They include the causative agents of diseases of commercially important molluscs, including MSX disease in oysters. Despite their importance for food security, their diversity and distributions are poorly known. We used a combination of group-specific PCR primers to probe environmental DNA samples from planktonic and benthic environments in Europe, South Africa and Panama. This revealed several highly distinct novel clades, novel lineages within known clades and seasonal (spring vs autumn) and habitat-related (brackish vs littoral) variation in assemblage composition. High frequencies of haplosporidian lineages in the water column provide the first evidence for life cycles involving planktonic hosts, host-free stages or both. The general absence of haplosporidian lineages from all large online sequence data sets emphasises the importance of lineage-specific approaches for studying these highly divergent and diverse lineages. Combined with host-based field surveys, environmental sampling for pathogens will enhance future detection of known and novel pathogens and the assessment of disease risk.