Developing an Apicomplexan DNA Barcoding System to Detect Blood Parasites of Small Coral Reef Fishes

A new and widespread group of fish apicomplexan parasites

Apicomplexans are obligate intracellular parasites that have evolved from a free-living, phototrophic ancestor. They have been reported from marine environmental samples in high numbers,1 with several clades of apicomplexan-related lineages (ARLs) having been described from environmental sequencing data (16S rRNA gene metabarcoding).2 The most notable of these are the corallicolids (previously ARL-V), which possess chlorophyll-biosynthesis genes in their relic chloroplast (apicoplast) and are geographically widespread and abundant symbionts of anthozoans.3 Corallicolids are related to the Eimeriorina, a suborder of apicomplexan coccidians that include other notable members such as Toxoplasma gondii.4Ophioblennius macclurei, the redlip blenny, along with other tropical reef fishes, is known to be infected by Haemogregarina-like and Haemohormidium-like parasites5 supposedly belonging to the Adeleorina; however, phylogenetics shows that these parasites are instead related to the Eimeriorina.6,7 Hybrid genomic sequencing of apicomplexan-infected O. macclurei blood recovered the entire rRNA operon of this apicomplexan parasite along with the complete mitochondrion and apicoplast genomes. Phylogenetic analyses using this new genomic information consistently place these fish-infecting apicomplexans, hereby informally named ichthyocolids, sister to the corallicolids within Coccidia. The apicoplast genome did not contain chlorophyll biosynthesis genes, providing evidence for another independent loss of this pathway within Apicomplexa. Based on the 16S rRNA gene found in the apicoplast, this group corresponds to the previously described ARL-VI. Screening of fish microbiome studies using the plastid 16S rRNA gene shows these parasites to be geographically and taxonomically widespread in fish species across the globe with implications for commercial fisheries and oceanic food webs.

First Molecular Identification of a Goussia Parasite from a New World Invasive Blenny

PURPOSE

Introduced or invasive fish are susceptible to new parasites but can simultaneously carry infectious parasites from their native range towards new hosts. Screening these parasites is key to address the health of fish populations and spread of diseases.

METHODS

In this study, we sequenced a Coccidia parasite, for the first time from the blenny Omobranchus sewalli, introduced in the northern coast of Brazil with an Indo-Pacific origin.

RESULTS

Only one individual was infected, its genetic sequence matched (over 99%) with two lineages of undetermined species, belonging to the genus Goussia, sequenced from three marine fish species (Mulloidichthys flavolineatus, Lutjanus kasmira, and Selar crumenophthalmus) in Hawaii.

CONCLUSIONS

Phylogenetic analysis suggests considerable differentiation between the Goussia detected and other Goussia spp. sequenced from North Atlantic marine fish, thus we cannot exclude the possibly that this parasite was carried by O. sewalli from its native Indo-Pacific range.

APOLOCYSTIS BOSANQUETI N. SP. (APICOMPLEXA: EUGREGARINORIDA) FROM THE INVASIVE EARTHWORM AMYNTHAS AGRESTIS (ANNELIDA: MEGASCOLECIDAE), WITH SIGNIFICANCE FOR THE MONOPHYLY OF THE FAMILY MONOCYSTIDAE

Apolocystis bosanqueti n. sp., a parasite of an important invasive earthworm in North America, Amynthas agrestis, is described from a site in northern Vermont. The earthworm host follows an annual life cycle in Vermont, so the entire life cycle of the parasite can be observed in 7 mo. In spring, the parasites were first seen in juvenile worms as paired gamonts (suggesting precocious association). These paired gamonts mature into gametocytes that form an opaque structure, with a thick gelatinous envelope (epicyst), that becomes full of zygotes. The resulting gametocyst becomes packed with ∼105 fusiform oocysts. The mature orbicular gametocysts are large (∼1 mm in diameter) and visible to the naked eye through the body wall of the host's anterior segments. The new species most resembles Apolocystis herculea described from many lumbricid earthworm species in Europe but differs from that parasite because Ap. herculea infects the intestinal wall in the posterior of the host rather than the anterior segments. A survey of 9 other earthworm species sympatric with Am. agrestis revealed that only Amynthas tokioensis, also an invasive species, was infected with Ap. bosanqueti, albeit much less commonly. Diagnosis for the family Monocystidae is problematic because cardinal characters are lacking, and the commonly cited character, a trophozoite with no anterior differentiation, is violated in most genera placed in the family. For the first time, a molecular phylogeny is presented that includes 3 genera of monocystids with diverse cell morphology (including the new species) and supports the monophyly of the family. The only morphological character that may be used to diagnose the Monocystidae is the morphology of oocysts, which are fusiform with extended terminal tips. A comparison of oocysts from 7 parasites recovered from local earthworms, including from 3 monocystid species in the phylogeny, confirms the utility of this diagnostic trait. The 2 hosts of the new species were most likely introduced from Japan, so the range of Apolocystis likely extends into East Asia.

Using RDNA sequences to define dinoflagellate species

Dinoflagellate species are traditionally defined using morphological characters, but molecular evidence accumulated over the past several decades indicates many morphologically-based descriptions are inaccurate. This recognition led to an increasing reliance on DNA sequence data, particularly rDNA gene segments, in defining species. The validity of this approach assumes the divergence in rDNA or other selected genes parallels speciation events. Another concern is whether single gene rDNA phylogenies by themselves are adequate for delineating species or if multigene phylogenies are required instead. Currently, few studies have directly assessed the relative utility of multigene versus rDNA-based phylogenies for distinguishing species. To address this, the current study examined D1-D3 and ITS/5.8S rDNA gene regions, a multi-gene phylogeny, and morphological characters in Gambierdiscus and other related dinoflagellate genera to determine if they produce congruent phylogenies and identify the same species. Data for the analyses were obtained from previous sequencing efforts and publicly available dinoflagellate transcriptomic libraries as well from the additional nine well-characterized Gambierdiscus species transcriptomic libraries generated in this study. The D1-D3 and ITS/5.8S phylogenies successfully identified the described Gambierdiscus and Alexandrium species. Additionally, the data showed that the D1-D3 and multigene phylogenies were equally capable of identifying the same species. The multigene phylogenies, however, showed different relationships among species and are likely to prove more accurate at determining phylogenetic relationships above the species level. These data indicated that D1-D3 and ITS/5.8S rDNA region phylogenies are generally successful for identifying species of Gambierdiscus, and likely those of other dinoflagellates. To assess how broadly general this finding is likely to be, rDNA molecular phylogenies from over 473 manuscripts representing 232 genera and 863 described species of dinoflagellates were reviewed. Results showed the D1-D3 rDNA and ITS phylogenies in combination are capable of identifying 97% of dinoflagellate species including all the species belonging to the genera Alexandrium, Ostreopsis and Gambierdiscus, although it should be noted that multi-gene phylogenies are preferred for inferring relationships among these species. A protocol is presented for determining when D1-D3, confirmed by ITS/5.8S rDNA sequence data, would take precedence over morphological features when describing new dinoflagellate species. This protocol addresses situations such as: a) when a new species is both morphologically and molecularly distinct from other known species; b) when a new species and closely related species are morphologically indistinguishable, but genetically distinct; and c) how to handle potentially cryptic species and cases where morphotypes are clearly distinct but have the same rDNA sequence. The protocol also addresses other molecular, morphological, and genetic approaches required to resolve species boundaries in the small minority of species where the D1-D3/ITS region phylogenies fail.

A New Species of Monocystis (Apicomplexa: Gregarina: Monocystidae) from the Asian Invasive Earthworm Amynthas agrestis (Megascolecidae), with an Improved Standard for Monocystis Species Descriptions

Monocystis perplexa n. sp., a parasite of an important invasive Japanese earthworm in North America, Amynthas agrestis, is described from a site in Vermont. An improved standard for Monocystis species descriptions is proposed including a standard nomenclature to reduce synonymies, a standard set of biometrics and shape descriptions for living cells, and a DNA genomic sequence for the 18S rRNA (∼1,700 base pairs). Comparing morphologies of Monocystis parasites in sympatric earthworm species indicates that M. perplexa is specific to A. agrestis in the study region. Also, polymerase chain reaction primers specific to M. perplexa amplified samples of A. agrestis earthworms taken from several sites in Japan. This suggests the parasite entered North America from Japan, the origin of the invasive Amynthas earthworm, and thus M. perplexa would be the first Monocystis described from the diverse Japanese Amynthas earthworms and the first from East Asia. Monocystis perplexa was found in every population of A. agrestis surveyed in Vermont, always reaching 100% prevalence by late summer (the host has an annual life cycle in Vermont). The 18S gene sequence differed from that of Monocystis agilis from the sympatric earthworm Lumbricus terrestris (the only other sequence available for Monocystis), and a genetic similarity tree places them closest among other gregarines. Many of the 95 described species of Monocystis are very similar in morphology (based on species descriptions), so the 18S gene can act as a barcode for Monocystis species and thus will help to eliminate both synonymies and reveal cryptic species.

Molecular detection of apicomplexan blood parasites of coral reef fishes from free-living stages of ectoparasitic gnathiid isopods

Gnathiid isopods are marine ectoparasites that feed on the blood of fishes that have been implicated as vectors of blood parasites, with transmission possibly occurring through biting during their parasitic life-stages, or through ingestion by fishes. However, evidence for their role as vectors is limited, reflecting the small number of research groups working on them. Here, we used a molecular barcode approach to identify fish hosts and apicomplexan parasites in free-living gnathiids from the eastern Caribbean Sea, with the goal of further evaluating their potential role as reservoirs and/or vectors for these parasites. Apicomplexa were only identified in 8% of the Gnathia analyzed, and in four cases we could identify both Apicomplexa and fish host DNA. The results further suggest that Gnathia spp. in this region may serve as reservoirs for Apicomplexa, but whether they are vectors for this parasite remains uncertain.

Molecular insights into the identification and phylogenetics of the cosmopolitan marine fish blood parasite, Haemogregarina bigemina (Adeleorina: Haemogregarinidae)

Haemogregarina bigemina is one of the most prevalent haemogregarines of marine fishes and has long been considered an enigmatic and cosmopolitan species. However, to determine whether H. bigemina truly represents a single global species, or whether it should be partitioned into several species or subspecies, and to confirm its taxonomic status among the Haemogregarina, molecular analysis is required. Here, we provide the first molecular characterisation of H. bigemina from one of its type hosts, Lipophrys pholis, in the UK using 18S rDNA sequences. Phylogenetic and p-distance comparisons of the newly generated H. bigemina sequences with those published from other haemogregarine taxa and related apicomplexans suggest that H. bigemina falls outside of the "Haemogregarina" clade as well as the Adeleorina altogether, forming a separate apicomplexan marine clade, and appears to be in fact more closely related to other non-haemogregarine Apicomplexa genera. Further work including sequences of H. bigemina and H. bigemina-like parasites observed from fishes in other localities is now needed to investigate this further.

PCR and histology identify new bivalve hosts of Apicomplexan-X (APX), a common parasite of the New Zealand flat oyster Ostrea chilensis

Apicomplexan-X (APX) is a significant pathogen of the flat oyster Ostrea chilensis in New Zealand. The life cycle and host range of this species are poorly known, with only the zoite stage identified. Here, we report the use of molecular approaches and histology to confirm the presence of APX in samples of green-lipped mussels Perna canaliculus, Mediterranean mussels Mytilus galloprovincialis and hairy mussels Modiolus areolatus collected from widely distributed locations in New Zealand. The prevalence of APX infection estimated by PCR was 22.2% (n = 99) and 50% (n = 30) in cultured green-lipped mussels from Nelson and Coromandel, respectively; 0.8% (n = 258), 3.3% (n = 150) and 35.3% (n = 17) in wild Mediterranean mussels from Nelson, Foveaux Strait and Golden Bay, respectively; and 46.7% (n = 30) in wild hairy mussels from Foveaux Strait. Histology detected all cases of PCR that were positive with APX and appeared to be more sensitive. The prevalence of APX estimated by histology in green-lipped mussels from Coromandel was 60% versus 50% by PCR, and 4.3%, 10.7% and 52.9% by histology versus 0.8%, 3.3% and 35.3% by PCR in wild Mediterranean mussels from Nelson, Foveaux Strait and Golden Bay, respectively. The specific identity of the parasite found in mussels was determined by sequencing PCR products for a portion (676 bp) of the 18S rRNA gene; the resulting sequences were 99-100% similar to APX found in flat oysters. Phylogenetic analyses also confirmed that all isolates from green-lipped, Mediterranean and hairy mussels grouped with APX isolates previously identified from flat oysters. This study indicates the wide geographical distribution of APX and highlights the potentially multi-host specific distribution of the parasite in commercially important bivalve shellfish.

The distribution and host-association of a haemoparasite of damselfishes (Pomacentridae) from the eastern Caribbean based on a combination of morphology and 18S rDNA sequences

Coral reefs harbor the greatest biodiversity per unit area of any ecosystem on earth. While parasites constitute the majority of this biodiversity, they remain poorly studied due to the cryptic nature of many parasites and the lack of appropriate training among coral reef ecologists. Damselfishes (Pomacentridae) are among the most abundant and diverse fishes on coral reefs. In a recent study of blood parasites of Caribbean reef fishes, the first ever apicomplexan blood parasites discovered in damselfishes were reported for members of the genus Stegastes. While these blood parasites were characterized as “Haemohormidium-like”, they appear to be distinct from any other known apicomplexan. In this study, we examined host associations, geographic distributions, and provide further insights on the phylogenetic affiliation of this parasite. A combination of morphological characteristics and 18S rDNA sequences suggest that this parasite may be the same species at multiple sites and occurs from the southern to the northern extreme of the eastern Caribbean, although it appears rare in the north. At present it appears to be limited to members of the genus Stegastes and infects all life history stages. It is most common in benthophagous species that occur in high population densities and appears basal to a major monophyletic clade containing species of coccidia, distinct from the Piroplasmida, the order to which Haemohormidium spp. have been assigned. These findings suggest a possible fecal-oral mode of transmission.

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A new species of Haemorhormidium-like apicomplexan blood parasite has recently been discovered in Caribbean damselfishes.

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Morphological and molecular data indicate that it is widespread in the eastern Caribbean.

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This parasite is limited to damselfish species of the genus Stegastes and infects juveniles and adults.

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It is most common in benthophagous species that occur in high population densities.

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This parasite resembles coccidia but 18S rDNA show it to be distinct from known genera, as well as genera of piroplasms.

Phylogenetic analysis of apicomplexan parasites infecting commercially valuable species from the North-East Atlantic reveals high levels of diversity and insights into the evolution of the group

Background

The Apicomplexa from aquatic environments are understudied relative to their terrestrial counterparts, and the seminal work assessing the phylogenetic relations of fish-infecting lineages is mostly based on freshwater hosts. The taxonomic uncertainty of some apicomplexan groups, such as the coccidia, is high and many genera were recently shown to be paraphyletic, questioning the value of strict morphological and ecological traits for parasite classification. Here, we surveyed the genetic diversity of the Apicomplexa in several commercially valuable vertebrates from the North-East Atlantic, including farmed fish.

Results

Most of the sequences retrieved were closely related to common fish coccidia of Eimeria, Goussia and Calyptospora. However, some lineages from the shark Scyliorhinus canicula were placed as sister taxa to the Isospora, Caryospora and Schellakia group. Additionally, others from Pagrus caeruleostictus and Solea senegalensis belonged to an unknown apicomplexan group previously found in the Caribbean Sea, where it was sequenced from the water column, corals, and fish. Four distinct parasite lineages were found infecting farmed Dicentrarchus labrax or Sparus aurata. One of the lineages from farmed D. labrax was also found infecting wild counterparts, and another was also recovered from farmed S. aurata and farm-associated Diplodus sargus.

Conclusions

Our results show that marine fish apicomplexans are diverse, and we highlight the need for a more extensive assessment of parasite diversity in this phylum. Additionally, parasites recovered from S. canicula were recovered as basal to their piscine counterparts reflecting hosts phylogeny.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-2645-7) contains supplementary material, which is available to authorized users.