High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans

Heterotrophic protists (unicellular eukaryotes) form a major link from bacteria and algae to higher trophic levels in the sunlit ocean. Their role on the deep seafloor, however, is only fragmentarily understood, despite their potential key function for global carbon cycling. Using the approach of combined DNA metabarcoding and cultivation-based surveys of 11 deep-sea regions, we show that protist communities, mostly overlooked in current deep-sea foodweb models, are highly specific, locally diverse and have little overlap to pelagic communities. Besides traditionally considered foraminiferans, tiny protists including diplonemids, kinetoplastids and ciliates were genetically highly diverse considerably exceeding the diversity of metazoans. Deep-sea protists, including many parasitic species, represent thus one of the most diverse biodiversity compartments of the Earth system, forming an essential link to metazoans.

First investigation of pathogenic bacteria, protozoa and viruses in rodents and shrews in context of forest-savannah-urban areas interface in the city of Franceville (Gabon)

Rodents are reservoirs of numerous zoonotic diseases caused by bacteria, protozoans, or viruses. In Gabon, the circulation and maintenance of rodent-borne zoonotic infectious agents are poorly studied and are often limited to one type of pathogen. Among the three existing studies on this topic, two are focused on a zoonotic virus, and the third is focused on rodent Plasmodium. In this study, we searched for a wide range of bacteria, protozoa and viruses in different organs of rodents from the town of Franceville in Gabon. Samples from one hundred and ninety-eight (198) small mammals captured, including two invasive rodent species, five native rodent species and 19 shrews belonging to the Soricidae family, were screened. The investigated pathogens were bacteria from the Rickettsiaceae and Anaplasmataceae families, Mycoplasma spp., Bartonella spp., Borrelia spp., Orientia spp., Occidentia spp., Leptospira spp., Streptobacillus moniliformis, Coxiella burnetii, and Yersinia pestis; parasites from class Kinetoplastida spp. (Leishmania spp., Trypanosoma spp.), Piroplasmidae spp., and Toxoplasma gondii; and viruses from Paramyxoviridae, Hantaviridae, Flaviviridae and Mammarenavirus spp. We identified the following pathogenic bacteria: Anaplasma spp. (8.1%; 16/198), Bartonella spp. (6.6%; 13/198), Coxiella spp. (5.1%; 10/198) and Leptospira spp. (3.5%; 7/198); and protozoans: Piroplasma sp. (1%; 2/198), Toxoplasma gondii (0.5%; 1/198), and Trypanosoma sp. (7%; 14/198). None of the targeted viral genes were detected. These pathogens were found in Gabonese rodents, mainly Lophuromys sp., Lemniscomys striatus and Praomys sp. We also identified new genotypes: Candidatus Bartonella gabonensis and Uncultured Anaplasma spp. This study shows that rodents in Gabon harbor some human pathogenic bacteria and protozoans. It is necessary to determine whether the identified microorganisms are capable of undergoing zoonotic transmission from rodents to humans and if they may be responsible for human cases of febrile disease of unknown etiology in Gabon.

Isolation of Novel Trypanosomatid, Zelonia australiensis sp. nov. (Kinetoplastida: Trypanosomatidae) Provides Support for a Gondwanan Origin of Dixenous Parasitism in the Leishmaniinae

The genus Leishmania includes approximately 53 species, 20 of which cause human leishmaniais; a significant albeit neglected tropical disease. Leishmaniasis has afflicted humans for millennia, but how ancient is Leishmania and where did it arise? These questions have been hotly debated for decades and several theories have been proposed. One theory suggests Leishmania originated in the Palearctic, and dispersed to the New World via the Bering land bridge. Others propose that Leishmania evolved in the Neotropics. The Multiple Origins theory suggests that separation of certain Old World and New World species occurred due to the opening of the Atlantic Ocean. Some suggest that the ancestor of the dixenous genera Leishmania, Endotrypanum and Porcisia evolved on Gondwana between 90 and 140 million years ago. In the present study a detailed molecular and morphological characterisation was performed on a novel Australian trypanosomatid following its isolation in Australia’s tropics from the native black fly, Simulium (Morops) dycei Colbo, 1976. Phylogenetic analyses were conducted and confirmed this parasite as a sibling to Zelonia costaricensis, a close relative of Leishmania previously isolated from a reduviid bug in Costa Rica. Consequently, this parasite was assigned the name Zelonia australiensis sp. nov. Assuming Z. costaricensis and Z. australiensis diverged when Australia and South America became completely separated, their divergence occurred between 36 and 41 million years ago at least. Using this vicariance event as a calibration point for a phylogenetic time tree, the common ancestor of the dixenous genera Leishmania, Endotrypanum and Porcisia appeared in Gondwana approximately 91 million years ago. Ultimately, this study contributes to our understanding of trypanosomatid diversity, and of Leishmania origins by providing support for a Gondwanan origin of dixenous parasitism in the Leishmaniinae.

The genus Leishmania includes approximately 53 species, 20 of which cause human leishmaniais, a significant disease that has afflicted humans for millennia. But how ancient is Leishmania and where did it arise? Some suggest Leishmania originated in the Palearctic. Others suggest it appeared in the Neotropics. The Multiple Origins theory proposes that separation of certain Old World and Neotropical species occurred following the opening of the Atlantic. Others suggest that an ancestor to the Euleishmania and Paraleishmania appeared on Gondwana 90 to 140 million years ago (MYA). We performed a detailed molecular and morphological characterisation of a novel Australian trypanosomatid. This parasite is a sibling to the Neotropical Zelonia costaricensis, a close relative of Leishmania, and designated as Zelonia australiensis sp. nov. Assuming Z. costaricensis and Z. australiensis split when Australia and South America separated, their divergence occurred between 36 and 41 MYA. Using this event as a calibration point for a phylogenetic time tree, an ancestor of the dixenous Leishmaniinae appeared in Gondwana ~ 91 MYA. This study contributes to our understanding of trypanosomatid diversity by describing a unique Australian trypanosomatid and to our understanding of Leishmania evolution by inferring a Gondwanan origin for dixenous parasitism in the Leishmaniinae.

Detection of the kinetoplastid Azumiobodo hoyamushi, the causative agent of soft tunic syndrome, in wild ascidians Halocynthia roretzi

The occurrence of soft tunic syndrome in wild populations of the ascidian Halocynthia roretzi was monitored by diving at 5 to 6 sites in Miyagi Prefecture in Japan in summer 2010 and 2011. These sites were located at varying distances from farming sites at which the disease had previously been detected. All dead ascidians were collected, and their tunics were examined for Azumiobodo hoyamushi, the causative agent of soft tunic syndrome, using 18S rRNA PCR. In both years, <1% of wild ascidians we observed (18 out of 2100 in 2010, and 30 out of 3100 in 2011) were dead. The flagellates were only detected in 8 out of 18 dead ascidians from 3 sites in 2010, and 4 out of 30 from 2 sites in 2011. Healthy ascidians were successfully experimentally infected with the disease by immersing tunic samples from diseased wild ascidians into the rearing water. When apparently healthy ascidians collected from the wild population were reared for 40 d using pathogen-free water, the tunics of some ascidians became softened. The flagellates were detected in these individuals, which were diagnosed with soft tunic syndrome. Our results suggest that soft tunic syndrome affects the wild population of ascidians in Japan.

Patterns of Ichthyobodo necator sensu stricto infections on hatchery-reared Atlantic salmon Salmo salar in Norway

Infection patterns with ectoparasitic flagellates belonging to the genus Ichthyobodo were studied in an Atlantic salmon Salmo salar (L.) hatchery in western Norway during an 11 mo period, from eyed eggs to smoltification. Since the earlier species designation Ichthyobodo necator (sensu lato, s.l.) has been shown to represent a complex of several species, the epizootiology of different Ichthyobodo spp. is poorly known. Therefore, we employed molecular methods to ascertain the specific identity of the parasites detected in our study. Only I. necator in the recently redefined and restricted sense occurred (I. necator sensu stricto, s.s.). We observed a 2-peak pattern of infection; the first peak occurred among fry in March and the second peak among fingerlings and pre-smolt in August and September. Skin lesions observed on fingerlings and pre-smolt were significantly associated with Ichthyobodo infections. Also, these infections were negatively correlated with both haematocrit values (Hct) and the condition factor (K) of the fish. The patterns of infection on the farmed salmon suggest that I. necator s.s. is an opportunistic parasite of salmon, flourishing in periods when susceptible hosts are present and the environment favours parasite proliferation. Our study is the first to detect and identify I. necator s.s. on wild-caught adult salmonids (brown trout S. trutta L.). Wild salmonids and sticklebacks Gasterosteus aculeatus (L.) caught in the lakes serving as a water supply to the hatchery were found infected with I. necator s.s., hence these are the likely sources of parasites entering the hatchery via the inlet water.

[Occurrence of the flagellated protozoan, Cryptobia helicis Leidy, 1846 (Kinetoplasta: Bodonea: Cryptobiidae) in the garden snail, Helix aspersa]

In this survey, the prevalence and cytological features of the flagellated protozoan, Cryptobia helicis living in the bursa copulatrix of the garden snail, Helix aspersa Müller 1774 found in the vicinity of Izmir, Turkey was investigated. The prevalence of Cryptobia helicis in garden snails collected in the spring of 2005 was found to be 68.65%. This study is the first record of the occurrence of Cryptobia helicis in the garden snail Helix aspersa found in Turkey.

Ichthyobodo hippoglossi n. sp. (Kinetoplastea: Prokinetoplastida: Ichthyobodonidae fam. nov.), an ectoparasitic flagellate infecting farmed Atlantic halibut Hippoglossus hippoglossus

Diseased Atlantic halibut Hippoglossus hippoglossus juveniles from a hatchery in western Norway showed gill and skin infections with an Ichthyobodo species. Genus Ichthyobodo contains a single valid species, I. necator, a parasite originally described from the skin and fins of a salmonid fish in freshwater. Many studies have identified this species from other hosts, but recent molecular evidence suggests that many Ichthyobodo spp. occur in both fresh- and seawater. We redescribe I. necator from Atlantic salmon Salmo salar skin infections in Norway and compare the morphology of I. necator with the form from halibut. A scheme to standardise the measurements of Ichthyobodo cells is presented. Morphologically, the Ichthyobodo species from the skin and gills of halibut differs from I. necator from salmon skin by shape (in air dried stained smears), by a low number of variably sized kinetoplasts and by a long flagellar pocket. There is also a clear increase in the number of kinetoplasts in L necator with increasing cell size (area), a pattern absent from Ichthyobodo sp. from halibut. The 2 forms are also clearly separated by their small subunit (ssu) rDNA sequences; alignments of partial ssu sequences showed 93.5 % similarity. Consequently, Ichthyobodo sp. from halibut is considered a new species, and is named I. hippoglossi n. sp. Its closest relative is Ichthyobodo sp. IV from another marine fish, the Atlantic cod Gadus morhua. A family, Ichthyobodonidae fam. nov. in the order Prokinetoplastida Vickerman, 2004, is erected to encompass Ichthyobodo spp.

Cellular identity of an 18S rRNA gene sequence clade within the class Kinetoplastea: the novel genus Actuariola gen. nov. (Neobodonida) with description of the type species Actuariola framvarensis sp. nov

Environmental molecular surveys of microbial diversity have uncovered a vast number of novel taxonomic units in the eukaryotic tree of life that are exclusively known by their small-subunit (SSU) rRNA gene signatures. In this study, we reveal the cellular and taxonomic identity of a novel eukaryote SSU rRNA gene sequence clade within the Kinetoplastea. Kinetoplastea are ubiquitously distributed flagellated protists of high ecological and medical importance. We isolated an organism from the oxic-anoxic interface of the anoxic Framvaren Fjord (Norway), which branches within an unidentified kinetoplastean sequence clade. Ultrastructural studies revealed a typical cellular organization that characterized the flagellated isolate as a member of the order Neobodonida Vickerman 2004, which contains five genera. The isolate differed in several distinctive characters from Dimastigella, Cruzella, Rhynchobodo and Rhynchomonas. The arrangement of the microtubular rod that supports the apical cytostome and the cytopharynx differed from the diagnosis of the fifth described genus (Neobodo Vickerman 2004) within the order Neobodonida. On the basis of both molecular and microscopical data, a novel genus within the order Neobodonida, Actuariola gen. nov., is proposed. Here, we characterize its type species, Actuariola framvarensis sp. nov., and provide an in situ tool to access the organism in nature and study its ecology.

Culturing and environmental DNA sequencing uncover hidden kinetoplastid biodiversity and a major marine clade within ancestrally freshwater Neobodo designis

Bodonid flagellates (class Kinetoplastea) are abundant, free-living protozoa in freshwater, soil and marine habitats, with undersampled global biodiversity. To investigate overall bodonid diversity, kinetoplastid-specific PCR primers were used to amplify and sequence 18S rRNA genes from DNA extracted from 16 diverse environmental samples; of 39 different kinetoplastid sequences, 35 belong to the subclass Metakinetoplastina, where most group with the genus Neobodo or the species Bodo saltans, whilst four group with the subclass Prokinetoplastina (Ichthyobodo). To study divergence between freshwater and marine members of the genus Neobodo, 26 new Neobodo designis strains were cultured and their 18S rRNA genes were sequenced. It is shown that the morphospecies N. designis is a remarkably ancient species complex with a major marine clade nested among older freshwater clades, suggesting that these lineages were constrained physiologically from moving between these environments for most of their long history. Other major bodonid clades show less-deep separation between marine and freshwater strains, but have extensive genetic diversity within all lineages and an apparently biogeographically distinct distribution of B. saltans subclades. Clade-specific 18S rRNA gene primers were used for two N. designis subclades to test their global distribution and genetic diversity. The non-overlap between environmental DNA sequences and those from cultures suggests that there are hundreds, possibly thousands, of different rRNA gene sequences of free-living bodonids globally.

An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea

Given their ecological and medical importance, the classification of the kinetoplastid protists (class Kinetoplastea) has attracted much scientific attention for a long time. Morphology-based taxonomic schemes distinguished two major kinetoplastid groups: the strictly parasitic, uniflagellate trypanosomatids and the biflagellate bodonids. Molecular phylogenetic analyses based on 18S rRNA sequence comparison suggested that the trypanosomatids emerged from within the bodonids. However, these analyses revealed a huge evolutionary distance between the kinetoplastids and their closest relatives (euglenids and diplonemids) that makes very difficult the correct inference of the phylogenetic relationships between the different kinetoplastid groups. Using direct PCR amplification of 18S rRNA genes from hydrothermal vent samples, several new kinetoplastid-like sequences have been reported recently. Three of them emerge robustly at the base of the kinetoplastids, breaking the long branch leading to the euglenids and diplonemids. One of these sequences belongs to a close relative of Ichthyobodo necator (a fish parasite) and of the 'Perkinsiella amoebae'-like endosymbiont of Neoparamoeba spp. amoebae. The authors have studied the reliability of their basal position and used all these slow-evolving basal-emerging sequences as a close outgroup to analyse the phylogeny of the apical kinetoplastids. They thus find a much more stable and resolved kinetoplastid phylogeny, which supports the monophyly of groups that very often emerged as polyphyletic in the trees rooted using the traditional, distant outgroup sequences. A new classification of the class Kinetoplastea is proposed based on the results of the phylogenetic analysis presented. This class is now subdivided into two new subclasses, Prokinetoplastina (accommodating the basal species I. necator and 'Perkinsiella amoebae') and Metakinetoplastina (containing the Trypanosomatida together with three additional new orders: Eubodonida, Parabodonida and Neobodonida). The classification of the species formerly included in the genus Bodo is also revised, with the amendment of this genus and the genus Parabodo and the creation of a new genus, Neobodo.

Cryptobia iubilans infection in juvenile discus

Four commercial producers of discus (Symphysodon aequifasciatus) were found to have fish infested with the flagellate Cryptobia iubilans. Affected fish had granulomatous gastritis, and many also had granulomatous disease of other organs. The parasite had to be differentiated from the related flagellates Spironucleus spp, which induce different lesions. Transmission electron microscopy was found to be useful in detecting and identifying the parasite. Morbidity and mortality rates in the various fish populations appeared to be linked to a number of variables, including water quality, presence of other parasites and bacteria, diet, species, size, and age of the fish, and optimization of husbandry appeared to be important in alleviating the severity of disease. Metronidazole was not effective for treatment of C iubilans, but bath treatments with dimetridazole (80 mg/L for 24 hours, repeated daily for 3 days) or 2-amino-5-nitrothiazol (10 mg/L for 24 hours, repeated daily for 3 days) may be useful in decreasing the prevalence of infestation.

Flow cytometric detection and quantification of heterotrophic nanoflagellates in enriched seawater and cultures

A flow cytometric protocol to detect and enumerate heterotrophic nanoflagellates (HNF) in enriched waters is reported. At present, the cytometric protocols that allow accurate quantification of bacterioplankton cannot be used to quantify protozoa for the following reasons: i) the background produced by the bacterial acquisitions does not allow the discrimination of protozoa at low abundance, ii) since the final protozoan fluorescence is much higher than the bacterioplankton fluorescence (more than 35 fold) the protozoa acquisitions lie outside the range. With an increase in the fluorescence threshold and a reduction of the fluorescence detector voltage, low fluorescence particles (bacteria) are beneath the detection limits and only higher fluorescence particles (most of them heterotrophic nanoflagellates) are detected. The main limitation for the application of the cytometric protocol developed is that a ratio of bacteria/HNF below 1000 is needed. At higher ratios, the background of larger cells of bacterioplankton makes it difficult to discriminate protozoa. The proposed protocol has been validated by epifluorescence microscopy analyzing both a mixed community and two single species of HFN: Rhynchomonas nasuta and Jakoba libera. Taking into account the required bacteria/HNF ratio cited above, the results provide evidence that the flow cytometric protocol reported here is valid for counting mixed communities of HNF in enriched seawater and in experimental micro or mesocosms. In the case of single species of HNF previous knowledge of the biological characteristics of the protist and how they can affect the effectiveness of the flow cytometric count is necessary.

[Cryptobia udonellae sp. n. (Kinetoplastidea: Cryptobiida) - parasites of the excretory system of Udonella murmanica (Udonellida)]

A new cryptobiid flagellates, Cryptobia udonellae sp. n., is described from the excretory channels of Udonella murmanica. The body of flagellates is spindle-shaped. The flagellar pocket is subapical. Two flagella emerge from the pocket. One flagellum turns anterior and is forward-directed; the other flagellum is directed posterior and close to the ventral cell surface. The ventral groove is well developed. The cytostome opens just anterior to the flagellar pocket. The cytostome leads to the short cytopharynx. In the excretory channel of worms the flagellates C. udonellae sp. n. are attached to microvilli of epithelium or lay free in the lumen. Both flagellates have been studied with TEM. The unusual parasite system which involves organisms of four different phylums of animals has been described for the first time.

Relations between histopathology and parasitaemias in Oncorhynchus mykiss infected with Cryptobia salmositica, a pathogenic haemoflagellate

One group (n = 50) of juvenile rainbow trout Oncorhynchus mykiss was inoculated intraperitoneally with 2000 (low dose [LD]) and another group (n = 50) with 20,000 (high dose [HD]) Cryptobia salmositica fish(-1). The histopathology was a generalised inflammatory reaction, and lesions were in connective tissues and in the reticulo-endothelial system. In the LD group, the first lesions were observed in the liver, gills and spleen at 2 wk post infection (pi) while in the HD group they were in the liver and gills at 1 wk pi. Endovasculitis and mononuclear cell infiltration were observed at 3 wk pi in the HD group. These were followed by tissue necrosis and extravascular infiltration of parasites at 4 wk pi. The severity of lesions was directly related to parasitaemias in the blood and extravascular location of parasites. In the HD group, the most extensive tissue necrosis was at 4 wk pi and in the LD group it was 6 to 7 wk pi. Necrosis in the vital organs (liver, kidney and depletion of the haematopoeitic tissues) and anaemia were probably in part responsible for mortality of fish during acute disease. Regeneration and replacement of necrotic tissues were seen at 7 to 9 wk pi in the HD group, and it was most noticeable in haematopoietic and reticular tissues. These occurred during the recovery phase of the disease and were associated with significant reduction in blood parasitaemia.

A novel trypanoplasm-like flagellate Jarrellia atramenti n. g., n. sp. (Kinetoplastida: Bodonidae) and ciliates from the blowhole of a stranded pygmy sperm whale Kogia breviceps (Physeteridae): morphology, life cycle and potential pathogenicity

The successful 6 mo rehabilitation of a stranded juvenile pygmy sperm whale Kogia breviceps afforded the opportunity to study the poorly known protozoan fauna of the upper respiratory tract of cetaceans. Mucus samples were collected by holding either a petri dish or glass slides over the blowhole for 3 to 5 exhalations; preparations were examined as wet mounts, and then stained with Wrights-Giemsa or Gram stain. Blood smears were stained with Wrights-Giemsa. Unidentified spindle-shaped and unidentified broad ciliates, reported from the blowhole of the pygmy sperm whale for the first time, were seen only initially, while yeast-like organisms and bacteria were seen intermittently. Epithelial cells and white blood cells were often present in the blowhole mucus, but red blood cells were never seen. A novel trypanoplasm-like bodonid kinetoplastid biflagellate (Order Kinetoplastida) was commonly encountered in the blowhole mucus, but never in the blood. Both mature flagellates and those undergoing longitudinal binary fission were present. The elongate flagellate had a long whiplash anterior flagellum; the recurrent flagellum was attached along at least two-thirds of the body length, forming a prominent undulating membrane, and the trailing portion was short. The kinetoplast was irregularly fragmented. The flagellates were either free-swimming, or attached to host material via the free portion of the posterior flagellum. The prominent undulating membrane was characteristic of Trypanoplasma, while the fragmented kinetoplast was characteristic of some species of Cryptobia. For the novel bodonid kinetoplastid, with its unique combination of morphological features (prominent undulating membrane and fragmented kinetoplast), we propose the creation of a new genus Jarrellia. We believe this to be the first published description of a flagellate from a marine mammal, and among the first reports of a trypanoplasm-like flagellate from a warm-blooded host. We expect that a diversity of flagellates and ciliates are commonly present in the blowhole of cetaceans. Future studies on the identity of the protozoans and the health of their cetacean hosts, which are readily studied in captivity, are necessary to establish their status as commensals or parasites.

In vitro cultivation of Trypanoplasma borreli (protozoa: kinetoplastida), a parasite from the blood of common carp Cyprinus carpio

An in vitro culture system was developed for Trypanoplasma borreli, a pathogenic flagellate from the blood of European cyprinids. Trypanoplasms multiplied rapidly in a mixture of Hanks' balanced salt solution (HBSS, 45%), L15 (22.5%), Earle's minimum essential medium (MEM, 22.5%) and 10% distilled water, which was supplemented with 5 to 10% heat-inactivated pooled carp serum. In medium supplemented with fetal bovine serum, multiplication of T. borreli seemed to be inhibited. Cultures initiated with less than 100 000 T. borreli per ml culture medium did not survive, and a substantial multiplication of trypanoplasms was found at inocula beginning with 630 000 flagellates ml(-1). Trypanoplasms multiplied at 15, 20 and 25 degrees C. In cultures incubated at 4 degrees C the trypanoplasms remained viable but the number of flagellates did not increase. Trypanoplasms from in vitro cultures retained their infectivity for carp for at least 90 d (5 passages). The trypanoplasms survived in culture over a period of up to 5 mo (10 passages). The established culture system allows the propagation of high numbers of fish-infective trypanoplasms, which are required to study parasite-host relationships in carp.