Real-time PCR investigation of parasite ecology: in situ determination of oyster parasite Perkinsus marinus transmission dynamics in lower Chesapeake Bay

Haplosporidium nelsoni and Perkinsus marinus occurrence in waters of Great Bay Estuary, New Hampshire

In Great Bay Estuary, New Hampshire, USA, Haplosporidium nelsoni and Perkinsus marinus are 2 active pathogens of the eastern oyster Crassostrea virginica (Gmelin), that cause MSX (multinucleated sphere with unknown affinity 'X') and dermo mortalities, respectively. Whereas studies have quantified infection intensities in oyster populations and determined whether these parasites exist in certain planktonic organisms, no studies thus far have examined both infectious agents simultaneously in water associated with areas that do and do not have oyster populations. As in other estuaries, both organisms are present in estuarine waters throughout the Bay, especially during June through November, when oysters are most active. Waters associated with oyster habitats had higher, more variable DNA concentrations from these pathogenic organisms than waters at a non-oyster site. This finding allows for enhanced understanding of disease-causing organisms in New England estuaries, where oyster restoration is a priority.

Anthropogenic Vector Ecology and Management to Combat Disease Spread in Aquaculture

Anthropogenic vectors (transfer mechanisms) can facilitate the introduction and spread of aquatic disease in marine farming regions. Preventing or interrupting pathogen transfers associated with movements of these vectors is key to ensuring productivity and profitability of aquaculture operations. However, practical methods to identify and manage vector risks are lacking. We developed a risk analysis framework to identify disease risks and management gaps associated with anthropogenic vector movements in New Zealand's main aquaculture sectors - Chinook salmon (Oncorhynchus tshawytscha), green-lipped mussels (Perna canaliculus), and Pacific oysters (Crassostrea gigas). Vectors within each sector were identified and assigned categorical risk scores for (i) movement characteristics (size, frequency, likelihood of return to sea), (ii) biological association with pathogens (entrainment potential, contribution to previous aquaculture disease outbreaks) and (iii) available best practice biosecurity methods and tools, to inform unmitigated and mitigated risk rankings. Thirty-one vectors were identified to operate within the national network and association with livestock was found to be a primary driver of vector risk rankings. Movements of live growing stock and culture substrates (e.g., mussel ropes) in shellfish farming had high-risk vector profiles that are logistically challenging to address, while vessel vectors were identified as the salmon farming sector's priority. The framework and rankings can be used to inform both research and management priorities in aquaculture and other primary production systems, including risk validation, vector roles in disease epidemiology, compliance with permit conditions, policy development, and treatment options.

Application of a Quantitative PCR to Investigate the Distribution and Dynamics of Two Morphologically Similar Species, Karenia mikimotoi and K. papilionacea (Dinophyceae) in Korean Coastal Waters

Species of the marine dinoflagellate genus Karenia are known to produce various potent biotoxins and can form noxious blooms that cause mass mortalities of fish and shellfish. To date, harmful blooms of the species K. mikimotoi have been reported in Korea, but K. papilionacea was recently recorded off the southern coast of Korea. Here, we developed a quantitative real-time PCR (qRT-PCR) assay with specific primer pairs for the accurate detection and quantification of these two similar-looking unarmored species, K. mikimotoi and K. papilionacea, and investigated their distribution and dynamics in Korean coastal waters. Overall, K. papilionacea had not only a wider distribution, but also higher cell abundances (15-2553 cells L-1) than K. mikimotoi (3-122 cells L-1) in surface waters. Of 18 sampling sites, the two Karenia species were found to coexist at two sites. During monitoring at a fixed station (S5), K. papilionacea was generally predominant over K. mikimotoi; however, the two species exhibited similar dynamics and occasionally co-occurred. Both Karenia species showed similar physiological responses to temperature and salinity, requiring similar conditions for optimum growth. These results suggest that blooms of the two species may co-occur and induce a synergistic adverse effect on marine environments.

Development of duplex TaqMan-based real-time PCR assay for the simultaneous detection of Perkinsus olseni and P. chesapeaki in host Manila clam tissue samples

The aetiological agent Perkinsus olseni is globally recognised as a major threat for shellfish production considering its wide geographical distribution across Asia, Europe, Australia and South America. Another species, Perkinsus chesapeaki, which has never been known to be associated with significant mortality events, was recently detected along French coasts infecting clam populations sporadically in association with P. olseni. Identifying potential cryptic infections affecting Ruditapes philippinarum is essential to develop appropriate host resource management strategies. Here, we developed a molecular method based on duplex real-time quantitative PCR for the simultaneous detection of these two parasites, P. olseni and P. chesapeaki, in the different clam tissues: gills, digestive gland, foot, mantle, adductor muscle and the rest of the soft body. We firstly checked the presence of possible PCR inhibitors in host tissue samples. The qPCR reactions were inhibited depending on the nature of the host organ. The mantle and the rest of the soft body have a high inhibitory effect from threshold of host gDNA concentration of 2 ng.µL^-1, the adductor muscle and the foot have an intermediate inhibition of 5 ng.µL^-1, and the gills and digestive gland do not show any inhibition of the qPCR reaction even at the highest host gDNA concentration of 20 ng.µL^-1. Then, using the gills as a template, the suitability of the molecular technique was checked in comparison with the Ray's Fluid Thioglycolate Medium methodology recommended by the World Organisation for Animal Health. The duplex qPCR method brought new insights and unveiled cryptic infections as the co-occurrence of P. olseni and P. chesapeaki from in situ tissue samples in contrast to the RFTM diagnosis. The development of this duplex qPCR method is a fundamental work to monitor in situ co-infections that will lead to optimised resource management and conservation strategies to deal with emerging diseases.

Environmental factors drive the release of Perkinsus marinus from infected oysters

Since the discovery of Perkinsus marinus as the cause of dermo disease in Crassostrea virginica, salinity and temperature have been identified as the main environmental drivers of parasite prevalence. However, little is known about how these variables affect the movement of the parasite from host to water column. In order to elucidate how environmental factors can influence the abundance of this parasite in the water column, we conducted a series of experiments testing the effects of time of day, temperature and salinity on the release of P. marinus cells from infected oysters. We found that P. marinus cells were released on a diurnal cycle, with most cells released during the hottest and brightest period of the day (12:00-18:00). Temperature also had a strong and immediate effect on the number of cells released, but salinity did not, only influencing the intensity of infection over the course of several months. Taken together, our results demonstrate that (1) the number of parasites in the water column fluctuates according to a diurnal cycle, (2) temperature and salinity act on different timescales to influence parasite abundance, and (3) live infected oysters may substantially contribute to the abundance of transmissive parasites in the water column under particular environmental conditions.

A Dual Omics Approach to Evaluate Transcriptional and Metabolic Responses During Lipid Deprivation in an Oyster Parasite, Perkinsus marinus

Perkinsus marinus, a protozoan and the causative agent of perkinsosis (dermo disease) is a prevalent parasite found within the eastern oyster (Crassostrea virginica). In this study, we explore metabolic processes of P. marinus cells under lipid-depleted medium conditions to elucidate the interchanging flux of lipid and carbohydrate metabolism. Although P. marinus can synthesize their own lipids from available nutrients, they display a slower growth in medium not supplemented with lipids as opposed to medium with lipids. Under these conditions, using transcriptomics, we surprisingly observed evidence of stimulated lipid degradation through increased transcription of two core β-oxidation pathway enzymes. Simultaneously, phospholipid biosynthetic pathways were downregulated. Metabolomic analysis supported the transcriptomic results. Most fatty acids were decreased in lipid-deplete medium as opposed to lipid-replete medium, and available glucose was fermented to lactate. A significant increase in the cholesterol derivative zymosterol further supported a downregulation of membrane synthesis under the experimental conditions. A robust tricarboxylic acid (TCA) cycle was apparent by enhanced citrate synthase transcription, and a simultaneous reduction in branched chain amino acids. It is concluded that although P. marinus has the capacity for synthesizing its own lipids, it can respond to lipid deprivation in medium by oxidizing readily available stores, and likely transitioning into a resting stage.

Dynamics of Amoebophrya parasites during recurrent blooms of the ichthyotoxic dinoflagellate Cochlodinium polykrikoides in Korean coastal waters

During the bloom events of the harmful dinoflagellate Cochlodinium polykrikoides in August and October, 2012, infections by two different Amoebophrya species were observed in Korean coastal waters. To investigate the dynamics of the two parasites and their relative impact on the host populations, a quantitative real-time PCR (qPCR) method was applied to detect and quantify the parasites in the free-living and parasitic stages. Each specific primer set of the target species, Amoebophrya sp. 1 and sp. 2 was designed on the large subunit (LSU) and the first internal transcribed spacer (ITS1) of ribosomal RNA (rRNA) gene, respectively. Dynamics of the two Amoebophrya species via qPCR assay showed distinct patterns during the C. polykrikoides bloom events. Amoebophrya sp. 1 showed peaks during both bloom events in August and October with relatively low copies (10⁶ to 10⁷ copies L^-1), while Amoebophrya sp. 2 appeared only during the bloom event in October with very high copies (10⁹ to 10¹⁰ copies L^-1). Overall, the qPCR measurements for the dynamics of two Amoebophrya species in the parasitic stage (> 5 μm fractions) were consistent with parasite prevalence through microscopic observations. Amoebophrya sp. 1 infections were observed during both bloom events in August and October with relatively low parasite prevalence (0.1-1.5%), while Amoebophrya sp. 2 infections were detected only during the bloom event in October with high prevalence (up to 45%). Taken together, Amoebophrya sp. 1 may be a generalist and C. polykrikoides may not be its primary host, while Amoebophrya sp. 2 may be a specialist which can substantially impact host population dynamics.

Tetracapsuloides bryosalmonae abundance in river water

Tetracapsuloides bryosalmonae is a myxozoan parasite of freshwater bryozoans and salmonids, causing proliferative kidney disease in the latter. To date, detection of the parasite has required collection of hosts and subsequent molecular or histological examination. The release of infectious spores from both hosts offers an opportunity to detect the parasite in water samples. We developed a novel SYBR® Green quantitative real-time PCR (qPCR) assay for T. bryosalmonae in water samples which provides an estimation of bryozoan malacospore numbers and tested the assay in 3 rivers in southern England (UK) over a period of 5 wk. The assay proved to be both highly sensitive and specific to the parasite, detecting low levels of spores throughout the study period. Larger-volume samples afforded greater detection likelihood, but did not increase the number of spores detected, possibly as a result of low and patchy spore distributions and lack of within-site replication of large-volume samples. Based on point-measurements, temperature was positively associated with the likelihood of detecting spores, possibly reflecting the temperature dependence of spore shedding from bryozoan hosts. The presence of T. bryosalmonae in water samples was predominantly influenced by spatial (sites within rivers, amongst rivers) and temporal (sampling dates) factors, while the latter also influenced quantification cycle (Cq) values and spore abundance. Environmental monitoring for infectious stages can complement traditional methods, providing faster and easier detection and avoiding potentially prolonged searching, collecting and destructive sampling of invertebrate and vertebrate hosts.

Landscape-level variation in disease susceptibility related to shallow-water hypoxia

Diel-cycling hypoxia is widespread in shallow portions of estuaries and lagoons, especially in systems with high nutrient loads resulting from human activities. Far less is known about the effects of this form of hypoxia than deeper-water seasonal or persistent low dissolved oxygen. We examined field patterns of diel-cycling hypoxia and used field and laboratory experiments to test its effects on acquisition and progression of Perkinsus marinus infections in the eastern oyster, Crassostrea virginica, as well as on oyster growth and filtration. P. marinus infections cause the disease known as Dermo, have been responsible for declines in oyster populations, and have limited success of oyster restoration efforts. The severity of diel-cycling hypoxia varied among shallow monitored sites in Chesapeake Bay, and average daily minimum dissolved oxygen was positively correlated with average daily minimum pH. In both field and laboratory experiments, diel-cycling hypoxia increased acquisition and progression of infections, with stronger results found for younger (1-year-old) than older (2-3-year-old) oysters, and more pronounced effects on both infections and growth found in the field than in the laboratory. Filtration by oysters was reduced during brief periods of exposure to severe hypoxia. This should have reduced exposure to waterborne P. marinus, and contributed to the negative relationship found between hypoxia frequency and oyster growth. Negative effects of hypoxia on the host immune response is, therefore, the likely mechanism leading to elevated infections in oysters exposed to hypoxia relative to control treatments. Because there is considerable spatial variation in the frequency and severity of hypoxia, diel-cycling hypoxia may contribute to landscape-level spatial variation in disease dynamics within and among estuarine systems.

Quantitative PCR assay to determine prevalence and intensity of MSX (Haplosporidium nelsoni) in North Carolina and Rhode Island oysters Crassostrea virginica

The continuing challenges to the management of both wild and cultured eastern oyster Crassostrea virginica populations resulting from protozoan parasites has stimulated interest in the development of molecular assays for their detection and quantification. For Haplosporidium nelsoni, the causative agent of multinucleated sphere unknown (MSX) disease, diagnostic evaluations depend extensively on traditional but laborious histological approaches and more recently on rapid and sensitive (but not quantitative) end-point polymerase chain reaction (PCR) assays. Here, we describe the development and application of a quantitative PCR (qPCR) assay for H. nelsoni using an Applied Biosystems TaqMan® assay designed with minor groove binder (MGB) probes. The assay was highly sensitive, detecting as few as 20 copies of cloned target DNA. Histologically evaluated parasite density was significantly correlated with the quantification cycle (Cq), regardless of whether quantification was categorical (r2 = 0.696, p < 0.0001) or quantitative (r2 = 0.797, p < 0.0001). Application in field studies conducted in North Carolina, USA (7 locations), revealed widespread occurrence of the parasite with moderate to high intensities noted in some locations. In Rhode Island, USA, application of the assay on oysters from 2 locations resulted in no positives.

Quantitative real-time PCR assay for QPX (Thraustochytriidae), a parasite of the hard clam (Mercenaria mercenaria)

We developed a real-time quantitative PCR (qPCR) assay targeting the rRNA internal transcribed spacer region of the hard clam pathogen QPX. The qPCR assay was more sensitive than was histology in detecting clams with light QPX infections. QPX was detected in 4 of 43 sediment samples but in none of 40 seawater samples.