Sequence homogeneity of internal transcribed spacer rDNA in Mikrocytos mackini and detection of Mikrocytos sp. in a new location

Evaluation of histopathology, PCR, and qPCR to detect Mikrocytos mackini in oysters Crassostrea gigas using Bayesian latent class analysis

Latent class analysis (LCA) is a common method to evaluate the diagnostic sensitivity (DSe) and specificity (DSp) for pathogen detection assays in the absence of a perfect reference standard. Here we used LCA to evaluate the diagnostic accuracy of 3 tests for the detection of Mikrocytos mackini in Pacific oysters Crassostrea gigas: conventional polymerase chain reaction (PCR), real-time quantitative PCR (qPCR), and histopathology. A total of 802 Pacific oysters collected over 12 sampling events from 9 locations were assessed. Preliminary investigations indicated that standard LCA assumptions of test independence and constant detection accuracy across locations were likely unrealistic. This was mitigated by restructuring the LCA in a Bayesian framework to include test-derived knowledge about pathogen prevalence and load for categorizing populations into 2 classes of infection severity (low or high) and assessing separate DSe and DSp estimates for each class. Median DSp estimates were high (>96%) for all 3 tests in both population classes. DSe estimates varied between tests and population classes but were consistently highest for qPCR (87-99%) and lowest for histopathology (21-51%). Acknowledging that detection of M. mackini may be fitted to multiple diagnostic and management purposes, qPCR had the highest DSe while maintaining similar DSp to both conventional PCR and histopathology and thus is generally well-suited to most applications.

Mikrocytos mytilicoli n.sp. (Cercozoa, Mikrocytida, Mikrocytiidae) infecting the copepod Mytilicola intestinalis (Arthropoda, Cyclopoida, Mytilicolidae), a symbiont of Mytilus galloprovincialis in Galicia (NW Spain)

During a histopathological survey of Mytilus galloprovincialis in Galicia (NW Spain), microcells were observed infecting several organs of the symbiont copepod Mytilicola intestinalis. Positive results of PCR assay with specific primers for genus Mikrocytos and a clear signal of in situ hybridization with MACKINI-1 digoxigenin- labelled DNA probe (DIG-ISH) indicated a protozoan parasite of Mikrocytos genus. The ultrastructural study revealed intra and extracellular locations, polymorphic nuclei, intracellular round vesicles in the cytoplasm and absence of mitochondria. The present paper reports the characterization of the Mikrocytos sp. infecting M. intestinalis and proposes a novel species in the genus: Mikrocytos mytilicoli n. sp. A sequence of 18S-28S rDNA was obtained with 95.6% maximum identity (query cover 100%) with Mikrocytos mackini. Phylogenetic analysis showed that M. mytilicoli n. sp. and M. mackini share a common ancestor. However, comparison of the ITS1 rDNA region showed low similarity (75.8%) with M. mackini, which, combined with differences in ultrastructural details, host and geographic location, support the designation of a new species. This is the first description of a microcytid parasite of the genus Mikrocytos from a non-bivalve host.

Low internal transcribed spacer rDNA variation in New Zealand Bonamia ostreae: evidence for a recent arrival

Bonamia ostreae is a haplosporidian parasite of oysters that was first reported to occur in the Southern Hemisphere in 2015 in the New Zealand flat oyster Ostrea chilensis. Until that report, B. ostreae had been restricted to populations of O. edulis within the Northern Hemisphere. This large range extension raised questions regarding B. ostreae dispersal, including whether B. ostreae is a recent introduction and from where it originated. The whole 18S rRNA gene of New Zealand B. ostreae revealed 99.9-100% sequence homology to other published B. ostreae 18S rDNA sequences. Internal transcribed spacer (ITS) rDNA sequences (n = 29) were generated from New Zealand B. ostreae and compared to published B. ostreae sequences from 3 Northern Hemisphere sites: California, USA (n = 18), Maine, USA (n = 7), and the Netherlands (n = 6) to investigate intraspecific variation. Low ITS rDNA variation was observed from New Zealand B. ostreae isolates, and high levels of variation were observed from Northern Hemisphere B. ostreae sequences. We hypothesise that the low ITS rDNA diversity found in New Zealand B. ostreae is the result of a founder effect resulting from a single introduction from a limited number of propagules. The high level of ITS rDNA variation from the Northern Hemisphere prevented inferences of dispersal origins. New Zealand B. ostreae were genetically differentiated from all sites, and additional genetic data are required to better determine the origin of B. ostreae in New Zealand.

Microbial Diversity of Hypersaline Sediments from Lake Lucero Playa in White Sands National Monument, New Mexico, USA

Lake Lucero is a gypsum-rich, hypersaline, ephemeral playa located on the southern part of the Alkali Flat at the White Sands National Monument (WSNM), New Mexico, USA. This modern playa setting provides a dynamic extreme environment that changes from a freshwater lake to a hypersaline dry desert during the year. We investigated the microbial diversity (bacteria, archaea, and microbial eukaryotes) of the Lake Lucero sediments using 16S- and 18S-based amplicon sequencing approach and explored the diversity patterns in different geochemical microenvironments. Our results indicated that similar microbial communities, in particular bacterial communities colonized, were remarkably consistent across our depth profiles. Therefore, these communities show a first-order relevance on the environmental conditions (moisture content, oxygen content, and mineral composition). We found that Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Gemmatimonadetes were the major bacterial phyla, while Cyanobacteria were present in relatively low abundances and appeared only at the surface. Genus level assessment reflected that Truepera, Delftia, and Pseudomonas were the predominant bacterial genera across all samples. Euryarchaeota was the major archaeal phylum in all the samples, while Candidatus Halobonum and Candidatus Nitrososphaera were the main genera. Diatoms were the dominant eukaryotic group in surface samples and Fungi, Ciliophora, Metazoa, and Nematodes were the other major groups. As expected, metabolic inference indicated that aerobic microbial communities were near surface colonizers, with anaerobic communities dominating with increasing depth. We demonstrated that these microbial communities could be used to characterize unique geochemical microenvironments enabling us to extrapolate these results into other terrestrial and possibly extraterrestrial environments with comparable geochemical characteristics.

Descriptions of Mikrocytos veneroïdes n. sp. and Mikrocytos donaxi n. sp. (Ascetosporea: Mikrocytida: Mikrocytiidae), detected during important mortality events of the wedge clam Donax trunculus Linnaeus (Veneroida: Donacidae), in France between 2008 and 2011

BACKGROUND

Microcell parasites are small intracellular protozoans mostly detected in molluscs and can be associated with mortalities. In 2010 and 2011, strong increases in mortality events were reported in different wild beds of the wedge clam Donax trunculus Linnaeus, along the Atlantic coast of France and the presence of potential pathogens, including microcells, was investigated.

METHODS

Clams collected in different beds showing mortality were examined by histology. Based on histological observations, confirmatory analyses were carried out, including transmission electron microscopy (TEM) and molecular characterization.

RESULTS

Histological analyses revealed the presence of small protozoans similar to microcell parasites in different tissues of Donax trunculus, particularly in muscular and connective tissues. TEM examination confirmed the intracellular localization of the protozoans. Moreover, the lack of haplosporosomes and mitochondria suggested that the observed parasites belong to the genus Mikrocytos Farley, Wolf & Elston, 1988. Mikrocytos genus-specific PCR and in situ hybridization results supported the microscopic observations. Sequence fragments of the 18S rRNA gene shared 75-83% identity with the different Mikrocytos spp. described previously, including Mikrocytos mackini Farley, Wolf & Elston, 1988 and M. boweri Abbott, Meyer, Lowe, Kim & Johnson, 2014. Phylogenetic analyses confirmed that the microcell parasites observed in Donax trunculus in France belong to the genus Mikrocytos and suggest the existence of two distinct species.

CONCLUSIONS

Based on morphological, ultrastructural, molecular data and host information, the two microcell parasites detected in Donax trunculus belong to the genus Mikrocytos and are distinct from previously described members of this genus. This is the first report of Mikrocytos spp. found in France and infecting the clam Donax trunculus. Mikrocytos veneroïdes n. sp. was detected in different wild beds and Mikrocytos donaxi n. sp. was detected only in Audierne Bay.

Legislative and regulatory aspects of molluscan health management

The world population is growing quickly and there is a need to make sustainable protein available through an integrated approach that includes marine aquaculture. Seafood is already a highly traded commodity but the production from capture fisheries is rarely sustainable, which makes mollusc culture more important. However, an important constraint to its continued expansion is the potential for trade movements to disseminate pathogens that can cause disease problems and loss of production. Therefore, this review considers legislative and regulatory aspects of molluscan health management that have historically attempted to control the spread of mollusc pathogens. It is argued that the legislation has been slow to react to emerging diseases and the appearance of exotic pathogens in new areas. In addition, illegal trade movements are taken into account and possible future developments related to improvements in areas such as data collection and diagnostic techniques, as well as epidemiology, traceability and risk analysis, are outlined.

Denman Island disease in Washington State, USA: distribution and prevalence in Pacific and Olympia oysters

We sampled over 2400 wild, feral, and cultured Pacific oysters Crassostrea gigas and Olympia oysters Ostrea lurida in Washington State, USA, from 2002 to 2006 to estimate the prevalence of infection with Mikrocytos mackini, the causative agent of Denman Island disease. Both histology and qualitative PCR methods were used. Estimates of true prevalence of M. mackini infection in C. gigas, after accounting for imperfect test sensitivity, ranged from mean values of 0 to 10.0% by histology and 0 to 8.4% based on pooled PCR samples. M. mackini was not detected in any of the O. lurida samples. Results suggest a lower prevalence of the pathogen and severity of this oyster disease in Washington than that indicated in previous reports from British Columbia, Canada, potentially attributable to higher seawater temperatures in the Washington sample locations.

Molecular detection of Mikrocytos mackini in Pacific oysters using quantitative PCR

Mikrocytos mackini is an internationally regulated pathogen and causative agent of Denman Island disease in Pacific oysters Crassostrea gigas. Recent phylogenetic breakthroughs have placed this parasite within a highly divergent and globally distributed eukaryotic lineage that has been designated a new taxonomic order, Mikrocytida. The discovery of this new radiation of parasites is accompanied by a heightened awareness of the many knowledge gaps that exist with respect to the general biology, epizootiology, and potential impact of mikrocytid parasites on hosts, ecosystems, and commercial fisheries. It has also highlighted current shortcomings regarding our ability to detect these organisms. In this study, we developed a species-specific, sensitive, and quantitative method for detecting M. mackini DNA from host tissues using probe-based real-time qPCR technology. A limit of sensitivity between 2 and 5 genome copy equivalents was achieved in a reaction matrix containing ≥ 40 ng/μL host gDNA without inhibition. This detection proved superior to existing methods based on conventional PCR, histology or gross pathology and is the first species-specific diagnostic test for M. mackini. Quantitative assessment of parasite DNA using this assay remained accurate to between 10 and 50 copies identifying that during infection, M. mackini DNA was significantly more prevalent in hemolymph, labial palp, and mid-body cross-sections compared to mantle or adductor muscle. DNA extracted from a mid-body cross-section also provided the highest likelihood for detection during diagnostic screening of infected oysters. Taken together, these findings provide strong analytical evidence for the adoption of qPCR as the new reference standard for detecting M. mackini and give preliminary insight into the distribution of the parasite within host tissues. Standardised operating methodologies for sample collection and qPCR testing are provided to aid in the international regulatory diagnosis of M. mackini and serve as a useful platform for the future development of multiplexed or alternate mikrocytid species detection.

Molecular taxonomy of Mikrocytos boweri sp. nov. from Olympia oysters Ostrea lurida in British Columbia, Canada

Mikrocytos mackini is a microcell parasite that usually infects Crassostrea gigas distributed along the Pacific Northwest coast of North America. For many years, M. mackini was the only known species in the genus, but there have been multiple recent findings of genetically divergent forms of Mikrocytos in different hosts and in distantly located geographic locations. This note describes M. boweri sp. nov. found in Olympia oysters Ostrea lurida collected from and native to British Columbia, Canada, primarily using a molecular taxonomic approach.

Infection of Manila clams Ruditapes philippinarum from Galicia (NW Spain) with a Mikrocytos-like parasite

The name 'microcells' is frequently used to refer to small-sized unicellular stages of molluscan parasites of the genera Bonamia (Rhizaria, Haplosporidia) and Mikrocytos (Rhizaria). Histological examination of Manila clams Ruditapes philippinarum revealed microcells in the connective tissue of adductor muscle, foot, mantle, gills, siphon and visceral mass. The clams had been collected from 4 beds on the coast of Galicia, Spain. The prevalence of these microcells ranged from 73 to 93% in surface clams and from 3 to 33% in buried clams. However, the detection of brown ring disease signs in clams from every bed prevented us from making the assumption that the microcells alone were responsible for clam mortality. PCR assays using primer pairs designed to detect Bonamia spp. and haplosporidians gave negative results, whereas positive results were obtained with primers for the genus Mikrocytos. A consensus sequence of 1670 bp of the ribosomal gene complex of the microcells was obtained. It contained a section of the 18S region, the whole first internal transcribed spacer, the 5.8S region, the second internal transcribed spacer and a section of the 28S region. Comparison of this sequence with those of M. mackini infecting Crassostrea gigas and Mikrocytos sp. infecting Ostrea edulis showed that the microcells of Galician clams were the most divergent among the compared parasites. This is the first report of a Mikrocytos-like parasite infecting Manila clams. Care must be taken to avoid the spread of this parasite through Manila clam transfers.

Review of Mikrocytos microcell parasites at the dawn of a new age of scientific discovery

The genus Mikrocytos is traditionally known for Mikrocytos mackini, the microcell parasite that typically infects Pacific oysters along the west coast of North America. Multiple factors have conspired to create difficulty for scientific research on Mikrocytos parasites. These include their tiny cell size, infections that are often of light intensity, lack of suitable cell lines and techniques for in vitro culture, and the seasonal nature of infections. The extreme rate of molecular evolution in Mikrocytos stymied new species discovery and confounded attempts to resolve its phylogenetic position for many years. Fortunately, 2 recent landmark studies have paved the way forward for future research by drastically changing our understanding of the evolution and diversity of these parasites. No longer an orphan eukaryotic lineage, the phylogenetic placement of Mikrocytos has been confidently resolved within Rhizaria and as sister taxon to Haplosporidia. The genus has also found a taxonomic home within the newly-discovered order, Mikrocytida - a globally distributed lineage of parasites infecting a wide range of invertebrate hosts. Here we review available scientific information on Mikrocytos parasites including their evolution and diversity, host and geographic ranges, epizootiology, and detection of the regulated pathogen, M. mackini. We also make recommendations towards a consistent taxonomic framework for this genus by minimally suggesting the use of 18S rDNA sequence, host species information, and histopathological presentation in new species descriptions. This is timely given that we are likely embarking on a new era of scientific advancements, including species discovery, in this genus and its relatives.

Evolution: hidden at the end of a very long branch

DNA-based methods continue to unveil the diversity and evolutionary origins of life on Earth. 'Next generation' methods have just solved a long-standing puzzle by uncovering previously unseen yet globally distributed diversity within a lineage of amitochondriate parasites affecting commercially exploited aquatic hosts. This discovery will impact both pure and applied research fields.