VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center.

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.

Since 2005, the Pathogen-Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.

The Phylogenetic Position of Spironucleus sp. (Diplomonadida: Hexamitidae) from the Intestine of Chinese Sleeper Perccottus glenii Dybowski, 1877 (Actinopterygii: Odontobutidae).

INTRODUCTION: The Chinese (Amur) sleeper (Perccottus glenii Dybowski, 1877) (Actinopterygii: Odontobutidae) is a freshwater fish species with high invasive potential. Diplomonads have been detected in the intestines of Chinese sleepers using light microscopy. AIM: The aim of this study was to identify the diplomonads in Chinese sleepers using molecular-genetic methods. MATERIALS AND METHODS: The fish used in this analysis were caught in the following bodies of water in Russia between 2014 and 2016: Lake Dolgoe, the floodplain of the Ingoda River (Amur River basin), the Tsna River (the Oka River basin), and the littoral of the Kotlin Island (Gulf of Finland). Partial sequences of small subunit rRNA genes were obtained for the intestinal diplomonads of Chinese sleeper. RESULTS: The analysis of all sequenced samples revealed the presence of Spironucleus salmonis Moore, 1922; other Spironucleus species were not found in the sampled fish. With 82% probability, the sampled sequences of diplomonads from Chinese sleeper formed a separate cluster in the clade of S. salmonis on the phylogenetic tree. CONCLUSION: This is the first record of S. salmonis in fish in the family Odontobutidae.

Comparative Ultrastructure of Fornicate Excavates, Including a Novel Free-living Relative of Diplomonads: Aduncisulcus paluster gen. et sp. nov.

The Fornicata (Excavata) is a group of microbial eukaryotes consisting of both free-living lineages (e.g., Carpediemonas) and parasitic lineages (e.g. Giardia and Retortamonas) that share several molecular and ultrastructural traits. Carpediemonas-like organisms (CLOs) are free-living lineages that diverged early within the Fornicata, making them important for inferring the early evolutionary history of the group. Molecular phylogenetic analyses of free-living fornicates, including sequences from environmental PCR surveys, have demonstrated that CLOs form six different lineages. Representatives from five of these lineages have been studied at the ultrastructural level. The sixth lineage has been labeled "CL2" but has yet to be described with ultrastructural data. Improved understanding of CL2 is expected to help elucidate character evolution within the Fornicata. Therefore, we comprehensively characterized CL2 (NY0171) in order to understand the ultrastructural traits in this lineage, especially the organization of the microtubular root system (i.e., the flagellar apparatus). CL2 shared several morphological features with other fornicates, including reduced mitochondria and an arched B fiber bridging flagellar roots 1 and 2. The molecular phylogenetic position combined with some distinctive ultrastructural traits (e.g., a curved ventral groove) in CL2 required us to establish a new genus and species, Aduncisulcus paluster gen. et sp. nov.

Genetic diversity of Diplomonadida in fish of the genus Coregonus from Southeastern Siberia.

Diplomonadida are primitive flagellate protozoa, among which both commensals and pathogens have been recorded. To date, members of the genera Hexamita and Spironucleus have been reported in the digestive system of fish in the Baikal region. We determined the genetic diversity of Diplomonadida in fish of the genus Coregonus from south-eastern Siberia using molecular-genetic methods. Fish for analysis were caught in Lake Baikal and in the Barguzin, Nepa, Chechuy, and Kirenga rivers from 2010 to 2013. Gall bladders, hindguts and foreguts of 120 specimens of Coregonus migratorius representing three morpho-ecological groups, 25 specimens of Coregonus lavaretus baicalensis, 25 specimens of Coregonus tugun and 30 specimens of Coregonus lavaretus pidschian were analysed via amplification with primers specifically designed for eukaryotes. Amplicons positive for Diplomonadida were sequenced. A phylogenetic analysis revealed that diplomonad flagellates of whitefish from Southeastern Siberia belong to Spironucleus barkhanus. Positive Diplomonadida DNA samples were analysed with primers designed in the present study for the amplification of small subunits of ribosomal DNA fragments of S. barkhanus (about 1,430 bp) and sequenced. Phylogenetic analysis revealed inside the clade of S. barkhanus besides the cosmopolitan genotype from European salmon that was detected earlier in Baikalian grayling, a new genotype unique to the fish of the genus Coregonus from Lake Baikal.

Comparative biochemistry of Giardia, Hexamita and Spironucleus: Enigmatic diplomonads.

The diplomonad genera are here represented by three highly diverse species, both free-living (Hexamita inflata), and parasitic (Spironucleus vortens and Giardia intestinalis). All three are moderately aerotolerant flagellates, inhabiting environments where O2 tensions are low and fluctuating. Many diplomonads are opportunistic pathogens of avian, terrestrial and aquatic animals. Hexamitids inhabit deep waters and sediments of lakes and marine basins, S. vortens commonly infects the intestinal tract of ornamental fish, particularly of cichlids and cyprinids, and G. intestinalis, the upper intestinal tracts of humans as well as domestic and farm animals. Despite these very different habitats, their known physiological and biochemical characteristics are similar, but they do differ in significant respects as their lifestyles and life cycles demand. They have efficient O2 scavenging systems, and are highly effective at countering rapid O2 fluctuations, or clustering away from its source (except for G. intestinalis when attached to the jejunal villi). Their core metabolic pathways (glycolysis using pyrophosphate), incomplete tricarboxylic acid cycle (lacking α-ketoglutarate dehydrogenase), and amino acid metabolism (with an alternative energy-generating arginine dihydrolase pathway as a possibility in some cases), largely conform to those of other protists inhabiting low-O2 environments. Mitochondrial evolutionary reduction to give hydrogenosomes as seen in Spironucleus spp. has proceeded further to its minimal state in the mitosomes of G. intestinalis. Understanding of essential redox reactions and the maintentence of redox state, especially in the infective encysted stage of G. intestinalis provide increasing possibilities for parasite control. To this aim a plethora of new synthetic chemicals and natural products (especially those from garlic, Allium sativum) show promise as replacements for the highly effective (but potentially toxic to higher organisms) 5-nitroimidazoles (e.g., metronidazole) in the treatment and/or prevention of dimplomonad infection in humans and animals.

Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochondriate' diplomonads and retortamonads.

Diplomonads, retortamonads, and "Carpediemonas-like" organisms (CLOs) are a monophyletic group of protists that are microaerophilic/anaerobic and lack typical mitochondria. Most diplomonads and retortamonads are parasites, and the pathogen Giardia intestinalis is known to possess reduced mitochondrion-related organelles (mitosomes) that do not synthesize ATP. By contrast, free-living CLOs have larger organelles that superficially resemble some hydrogenosomes, organelles that in other protists are known to synthesize ATP anaerobically. This group represents an excellent system for studying the evolution of parasitism and anaerobic, mitochondrion-related organelles. Understanding these evolutionary transitions requires a well-resolved phylogeny of diplomonads, retortamonads and CLOs. Unfortunately, until now the deep relationships amongst these taxa were unresolved due to limited data for almost all of the CLO lineages. To address this, we assembled a dataset of up to six protein-coding genes that includes representatives from all six CLO lineages, and complements existing rRNA datasets. Multigene phylogenetic analyses place CLOs as well as the retortamonad Chilomastix as a paraphyletic basal assemblage to the lineage comprising diplomonads and the retortamonad Retortamonas. In particular, the CLO Dysnectes was shown to be the closest relative of the diplomonads + Retortamonas clade, with strong support. This phylogeny is consistent with a drastic degeneration of mitochondrion-related organelles during the evolution from a free-living organism resembling extant CLOs to a probable parasite/commensal common ancestor of diplomonads and Retortamonas.

Risk factors and control of intestinal parasite infections in sled dogs in Poland.

Training and racing constitute serious challenges for working sled dogs. Attainment of the highest levels of stamina and speed are possible only by completely healthy dogs. Infections with nematodes as whipworm Trichuris sp. or hookworms Uncinaria/Ancylostoma can significantly reduce the fitness of working dogs leading to anemia or even to death. In the middle of the racing season, between December 2009 and April 2010, 108 individual fecal samples were collected from 25 sled dog kennels situated in different regions of Poland. Saturated salt flotation was performed for helminth egg detection. The immunofluorescent assay MeriFluor Cryptosporidium/Giardia and nested PCRs on 18S rRNA (Cryptosporidium spp.) and TPI gene (Giardia spp.) were carried out for detection of intestinal protozoa. Overall prevalence of 6 species of intestinal parasites was 68% in sled dogs (73/108). In 51 samples the eggs of a single species of helminth were detected (47%), two nematode species were detected in 13%, three species of nematodes were found in two dogs. The most prevalent helminths were the hookworms Uncinaria/Ancylostoma-identified in 36% of kennels, and in 34% of sled dogs. Toxocara eggs were detected in 36% of kennels, in 17% of dogs. Trichuris sp. eggs were found in 20% of kennels (5/25), in 13% of dogs. Cysts/oocysts of intestinal protozoa were detected in 31% of sled dogs. The most prevalent was Giardia spp. infection-in 54% of kennels [13/24], in 28% of dogs. Cryptosporidium spp. infections were identified in 37.5% of kennels [9/24], in 13% of dogs. Two sequenced Giardia isolates presented 100% homology with G. intestinalis Assemblage C isolate (AY228641.1), specific for dogs. A range of factors was shown to affect the prevalence of intestinal parasites in sled dogs. The highest prevalence of parasites was found among dogs from large kennels (housing >3 dogs), in dogs less than 2 years old, and in kennels, where prophylactic treatment was carried out 1-4 times a year. The present study has demonstrated a high prevalence of intestinal parasites in working sled dogs in Poland, including the zoonotic human pathogens Toxocara or Cryptosporidium.

Cell morphology and formal description of Ergobibamus cyprinoides n. g., n. sp., another Carpediemonas-like relative of diplomonads.

About 20 new isolates of Carpediemonas-like organisms (CLOs) have been reported since 2006. Small subunit rRNA gene phylogenies divide CLOs into six major clades: four contain described exemplars (i.e. Carpediemonas, Dysnectes, Hicanonectes, and Kipferlia), but two include only undescribed organisms. Here we describe a representative of one of these latter clades as Ergobibamus cyprinoides n. g., n. sp., and catalogue its ultrastructure. Ergobibamus cyprinoides is a bean-shaped biflagellated cell, 7-11.5 µm long, with a conspicuous groove. Instead of classical mitochondria there are cristae-lacking rounded organelles 300-400 nm in diameter. The posterior flagellum has a broad ventral vane and small dorsal vane. There are normally four basal bodies, two non-flagellated. There is one anterior root (AR), containing six microtubules. The posterior flagellar apparatus follows the "typical excavate" pattern of a splitting right root supported by fibres "I,""B," and "A," a "composite" fibre, a singlet root, and a left root (LR) with a "C" fibre. The B fibre originates against the LR--a synapomorphy of the taxon Fornicata--supporting the assignation of Ergobibamus to Fornicata, along with diplomonads, retortamonads, and other CLOs. Distinctive features of E. cyprinoides include the complexity of the AR, which is intermediate between Hicanonectes, and Carpediemonas and Dysnectes, and a dorsal extension of the C fibre.

A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats.

Over the last 15 years classical culturing and environmental PCR techniques have revealed a modest number of genuinely new major lineages of protists; however, some new groups have greatly influenced our understanding of eukaryote evolution. We used culturing techniques to examine the diversity of free-living protists that are relatives of diplomonads and retortamonads, a group of evolutionary and parasitological importance. Until recently, a single organism, Carpediemonas membranifera, was the only representative of this region of the tree. We report 18 new isolates of Carpediemonas-like organisms (CLOs) from anoxic marine sediments. Only one is a previously cultured species. Eleven isolates are conspecific and were classified within a new genus, Kipferlia n. gen. The remaining isolates include representatives of three other lineages that likely represent additional undescribed genera (at least). Small-subunit ribosomal RNA gene phylogenies show that CLOs form a cloud of six major clades basal to the diplomonad-retortamonad grouping (i.e. each of the six CLO clades is potentially as phylogenetically distinct as diplomonads and retortamonads). CLOs will be valuable for tracing the evolution of diplomonad cellular features, for example, their extremely reduced mitochondrial organelles. It is striking that the majority of CLO diversity was undetected by previous light microscopy surveys and environmental PCR studies, even though they inhabit a commonly sampled environment. There is no reason to assume this is a unique situation - it is likely that undersampling at the level of major lineages is still widespread for protists.

Large genomic differences between the morphologically indistinguishable diplomonads Spironucleus barkhanus and Spironucleus salmonicida.

BACKGROUND: Microbial eukaryotes show large variations in genome structure and content between lineages, indicating extensive flexibility over evolutionary timescales. Here we address the tempo and mode of such changes within diplomonads, flagellated protists with two nuclei found in oxygen-poor environments. Approximately 5,000 expressed sequence tag (EST) sequences were generated from the fish commensal Spironucleus barkhanus and compared to sequences from the morphologically indistinguishable fish parasite Spironucleus salmonicida, and other diplomonads. The ESTs were complemented with sequence variation studies in selected genes and genome size determinations. RESULTS: Many genes detected in S. barkhanus and S. salmonicida are absent in the human parasite Giardia intestinalis, the most intensively studied diplomonad. For example, these fish diplomonads show an extended metabolic repertoire and are able to incorporate selenocysteine into proteins. The codon usage is altered in S. barkhanus compared to S. salmonicida. Sequence variations were found between individual S. barkhanus ESTs for many, but not all, protein coding genes. Conversely, no allelic variation was found in a previous genome survey of S. salmonicida. This difference was confirmed by sequencing of genomic DNA. Up to five alleles were identified for the cloned S. barkhanus genes, and at least nineteen highly expressed S. barkhanus genes are represented by more than four alleles in the EST dataset. This could be explained by the presence of a non-clonal S. barkhanus population in the culture, by a ploidy above four, or by duplications of parts of the genome. Indeed, genome size estimations using flow cytometry indicated similar haploid genome sizes in S. salmonicida and G. intestinalis (approximately 12 Mb), whereas the S. barkhanus genome is larger (approximately 18 Mb). CONCLUSIONS: This study indicates extensive divergent genome evolution within diplomonads. Genomic traits such as codon usage, frequency of allelic sequence variation, and genome size have changed considerably between S. barkhanus and S. salmonicida. These observations suggest that large genomic differences may accumulate in morphologically indistinguishable eukaryotic microbes.

Systemic spironucleosis in 2 immunodeficient rhesus macaques (Macaca mulatta).

Spironucleus spp are parasites of fish and terrestrial vertebrates, including mice and turkeys, that rarely cause extraintestinal disease. Two rhesus macaques (Macaca mulatta) were experimentally inoculated with simian immunodeficiency virus mac251. Both progressed to simian acquired immune deficiency syndrome within 1 year of inoculation and developed systemic protozoal infections in addition to common opportunistic infections, including rhesus cytomegalovirus, rhesus lymphocryptovirus, and rhesus adenovirus. In the first case, the protozoa were associated with colitis, multifocal abdominal abscessation, and lymphadenitis. In the second case, they were one of a number of organisms associated with extensive pyogranulomatous pneumonia and colitis. Ultrastructural, molecular, and phylogenetic analysis revealed the causative organism to be a species of Spironucleus closely related to Spironucleus meleagridis of turkeys. This report is the first of extraintestinal infection with Spironucleus sp in higher mammals and expands the list of opportunistic infections found in immunocompromised rhesus macaques.

Light microscopic observations, ultrastructure, and molecular phylogeny of Hicanonectes teleskopos n. g., n. sp., a deep-branching relative of diplomonads.

We describe Hicanonectes teleskopos n. g., n. sp., a heterotrophic flagellate isolated from low-oxygen marine sediment. Hicanonectes teleskopos has a ventral groove and two unequal flagella, and rapidly rotates during swimming. At the ultrastructural level H. teleskopos is a "typical excavate": it displays flagellar vanes, a split right microtubular root, "I,""B," and "C" fibres, a singlet microtubular root, and a possible composite fibre. Small subunit rRNA (SSU rRNA) gene phylogenies and an "arched" B fibre demonstrate that H. teleskopos belongs to Fornicata (i.e. diplomonads, retortamonads, and relatives). It forms a clade with the deep-branching fornicate Carpediemonas, with moderate-to-strong bootstrap support, although their SSU rRNA gene sequences are quite dissimilar. Hicanonectes differs from Carpediemonas in cell shape, swimming behaviour, number of basal bodies (i.e. 4 vs. 3), number of flagellar vanes (i.e. 2 vs. 3), anterior root organization, and by having a cytopharynx. Like Carpediemonas and Dysnectes, Hicanonectes has conspicuous mitochondrion-like organelles that lack cristae and superficially resemble the hydrogenosomes of parabasalids, rather than the mitosomes of their closer relatives the diplomonads (e.g. Giardia).

Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, alpha-tubulin and HSP90 genes: implications for the evolutionary history of the double karyomastigont of diplomonads.

BACKGROUND: Fornicata is a relatively recently established group of protists that includes the diplokaryotic diplomonads (which have two similar nuclei per cell), and the monokaryotic enteromonads, retortamonads and Carpediemonas, with the more typical one nucleus per cell. The monophyly of the group was confirmed by molecular phylogenetic studies, but neither the internal phylogeny nor its position on the eukaryotic tree has been clearly resolved. RESULTS: Here we have introduced data for three genes (SSU rRNA, alpha-tubulin and HSP90) with a wide taxonomic sampling of Fornicata, including ten isolates of enteromonads, representing the genera Trimitus and Enteromonas, and a new undescribed enteromonad genus. The diplomonad sequences formed two main clades in individual gene and combined gene analyses, with Giardia (and Octomitus) on one side of the basal divergence and Spironucleus, Hexamita and Trepomonas on the other. Contrary to earlier evolutionary scenarios, none of the studied enteromonads appeared basal to diplokaryotic diplomonads. Instead, the enteromonad isolates were all robustly situated within the second of the two diplomonad clades. Furthermore, our analyses suggested that enteromonads do not constitute a monophyletic group, and enteromonad monophyly was statistically rejected in 'approximately unbiased' tests of the combined gene data. CONCLUSION: We suggest that all higher taxa intended to unite multiple enteromonad genera be abandoned, that Trimitus and Enteromonas be considered as part of Hexamitinae, and that the term 'enteromonads' be used in a strictly utilitarian sense. Our result suggests either that the diplokaryotic condition characteristic of diplomonads arose several times independently, or that the monokaryotic cell of enteromonads originated several times independently by secondary reduction from the diplokaryotic state. Both scenarios are evolutionarily complex. More comparative data on the similarity of the genomes of the two nuclei of diplomonads will be necessary to resolve which evolutionary scenario is more probable.

A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution.

BACKGROUND: Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have performed a sequence survey project resulting in 2341 expressed sequence tags (EST) corresponding to 853 unique clones, 5275 genome survey sequences (GSS), and eleven finished contigs from the diplomonad fish parasite Spironucleus salmonicida (previously described as S. barkhanus). RESULTS: The analyses revealed a compact genome with few, if any, introns and very short 3' untranslated regions. Strikingly different patterns of codon usage were observed in genes corresponding to frequently sampled ESTs versus genes poorly sampled, indicating that translational selection is influencing the codon usage of highly expressed genes. Rigorous phylogenomic analyses identified 84 genes--mostly encoding metabolic proteins--that have been acquired by diplomonads or their relatively close ancestors via lateral gene transfer (LGT). Although most acquisitions were from prokaryotes, more than a dozen represent likely transfers of genes between eukaryotic lineages. Many genes that provide novel insights into the genetic basis of the biology and pathogenicity of this parasitic protist were identified including 149 that putatively encode variant-surface cysteine-rich proteins which are candidate virulence factors. A number of genomic properties that distinguish S. salmonicida from its human parasitic relative G. lamblia were identified such as nineteen putative lineage-specific gene acquisitions, distinct mutational biases and codon usage and distinct polyadenylation signals. CONCLUSION: Our results highlight the power of comparative genomic studies to yield insights into the biology of parasitic protists and the evolution of their genomes, and suggest that genetic exchange between distantly-related protist lineages may be occurring at an appreciable rate in eukaryote genome evolution.

Phylogeny of spironucleus (eopharyngia: diplomonadida: hexamitinae).

Diplomonad flagellates from the genera Spironucleus and Hexamita (Hexamitinae) inhabit the digestive tract of a variety of animal hosts, some as important pathogens, and others as commensals. Species descriptions of many diplomonads have been based on light microscopy only, causing many taxa to be misidentified. Presently, electron microscopy is considered the appropriate tool for description of diplomonads. The existence of morphologically very similar genotypes/species has in addition prompted the need for molecular tools to resolve the true identity of many diplomonad taxa. To further explore the relationship within the Hexamitinae we have sequenced most of the SSU rRNA gene from Spironucleus torosa isolated from Atlantic cod, Spironucleus meleagridis isolated from turkey, Spironucleus vortens isolated from ide and Hexamita nelsoni isolated from oyster. Phylogenetic analyses recovered three non-monophyletic Spironucleus clades that may have originated separately in the sea, in freshwater or on land. Spironucleus torosa was identified as a sister taxon to Spironucleus barkhanus and Spironucleus salmonicida. Spironucleus vortens from ide appeared to be genetically very different from Spironucleus vortens isolated from angelfish.

The marine pathogenic genotype of Spironucleus barkhanus from farmed salmonids redescribed as Spironucleus salmonicida n. sp.

There are two genotypes of the diplomonad Spironucleus barkhanus. Based on sequence data from the small subunit ribosomal RNA gene the conspecificity of these two genotypes has been questioned. Therefore, we have sampled Spironucleus from 27 fish, representing 14 populations, five species, and four genera. Partial nucleotide sequences from the three genes; small subunit ribosomal DNA, glutamate dehydrogenase 1 and alpha-tubulin were compared. The pathogenic isolates of S. barkhanus, which causes systemic spironucleosis in Atlantic salmon, Chinook salmon, and Arctic charr, all farmed in sea water, were genetically very different from the commensal isolate found in wild freshwater populations of Arctic charr and grayling. The genetic distances between the genotypes were of the same magnitude as those separating species of Giardia. Based on these genetic and ecological data, the pathogenic genotype from farmed salmonids is described as a new species, Spironucleus salmonicida n. sp. Scanning and transmission electron microscopy showed no specific morphological or ultrastructural features distinguishing S. salmonicida n. sp. from S. barkhanus. The present study clearly demonstrates the value of applying genetics in identification of Spironucleus species. Phylogenetic analyses that included the isolates of S. salmonicida n. sp. did not change the phylogenetic relationship within the genus Spironucleus.

Evidence from SSU rRNA phylogeny that Octomitus is a sister lineage to Giardia.

Octomitus intestinalis is a diplomonad flagellate inhabiting the digestive tract of rodents and amphibians. Octomitus is of evolutionary interest because, based on ultrastructural characteristics, it is thought to be closely related to the morphologically derived genus Giardia, and together they have been proposed to make up the Giardiinae. In molecular trees of diplomonads, Giardia is the deepest branching lineage, so identifying a sister group to Giardia that is less derived would be informative. Octomitus is a logical candidate for this position, but unfortunately there are no molecular data from it, and it is not available in culture. To determine the position of Octomitus, and specifically test whether it is more closely related to Giardia than other diplomonads, we have isolated it directly from the caecum of wild mice and characterized its small subunit ribosomal RNA (SSU rRNA) gene. Phylogenetic analysis showed Octomitus to be the sister to Giardia with strong support, together occupying one side of the deepest split in the diplomonad tree.

The phylogenetic position of enteromonads: a challenge for the present models of diplomonad evolution.

Unikaryotic enteromonads and diplokaryotic diplomonads have been regarded as closely related protozoan groups. It has been proposed that diplomonads originated within enteromonads in a single event of karyomastigont duplication. This paper presents the first study to address these questions using molecular phylogenetics. The sequences of the small-subunit rRNA genes for three isolates of enteromonads were determined and a tree constructed with available diplomonad, retortamonad and Carpediemonas sequences. The diplomonad sequences formed two main groups, with the genus Giardia on one side and the genera Spironucleus, Hexamita and Trepomonas on the other. The three enteromonad sequences formed a clade robustly situated within the diplomonads, a position inconsistent with the original evolutionary proposal. The topology of the tree indicates either that the diplokaryotic cell of diplomonads arose several times independently, or that the monokaryotic cell of enteromonads originated by secondary reduction from the diplokaryotic state.

Ultrastructure of Spironucleus salmonis n. comb. (formerly Octomitus salmonis sensu Moore 1922, Davis 1926, and Hexamita salmonis sensu Ferguson 1979), with a guide to spironucleus species.

Diplomonad flagellates can be associated with significant morbidity and mortality in fishes, particularly in farmed salmonids. Diagnosis using only light microscopy is limited, and species cannot be confirmed. We therefore undertook a comprehensive transmission electron microscopy study of 20 trophozoites from the intestine of farmed juvenile rainbow trout Oncorhynchus mykiss from Northern Ireland (reported as Hexamita salmonis by Ferguson in 1979). Re-assignment to the genus Spironucleus was determined based on the anteriorly tapering and intertwined elongate nuclei, anterior-medial kinetosomes, and the presence of a flagellar pocket. At the species level we observed a tri-radiate pattern of microtubules in the opening of the asymetrical striated lamina, comprising 3 to 5 microtubules following the edge of the flagellar pocket, 3 radiating away from the opening of the striated lamina, and 4 to 5 curving over the striated lamina. We observed electron-dense plaques adjacent to the kinetosomes, electron-dense bodies, numerous free ribosomes, aggregations of glycogen, bowl-shaped membranous structures, rough endoplasmic reticulum, and a novel distinctive pyriform sac of densely packed free ribosomes at the posterior of the cell (8-shaped in transverse section, and delineated by furrowed endoplasmic reticulum). We now propose to rename H. salmonis sensu Ferguson (1979) Spironucleus salmonis. Our review of the morphology of Octomitus salmonis illustrated by Moore (1922a,b) and Davis (1926), has shown that this organism also belongs to the genus Spironucleus. We synonymise H. salmonis sensu Ferguson (1979) with O. salmonis sensu Moore (1922) and Davis (1926), and rename them S. salmonis. An expanded diagnostic guide, including new cytoplasmic elements, is presented for the 4 species of Spironucleus from fishes (S. barkhanus, S. salmonis, S. torosa and S. vortens). We recommend that type descriptions of diplomonads be based on organisms taken directly from the host rather than from in vitro culture in order to reliably include the cytoplasmic organelles.