Identification of a second rRNA gene unit in the Perkinsus andrewsi genome

A qPCR-Based Survey of Haplosporidium nelsoni and Perkinsus spp. in the Eastern Oyster, Crassostrea virginica in Maine, USA

Eastern oyster (Crassostrea virginica) aquaculture is increasingly playing a significant role in the state of Maine's (USA) coastal economy. Here, we conducted a qPCR-based survey for Haplosporidium nelsoni, Perkinsus marinus, and Perkinsus chesapeaki in C. virginica (n = 1440) from six Maine sites during the summer-fall of 2016 and 2017. In the absence of reported die-offs, our results indicated the continued presence of the three protozoan parasites in the six sites. The highest H. nelsoni qPCR-prevalence corresponded to Jack's Point and Prentiss Island (x=40 and 48% respectively), both located in the Damariscotta River Estuary. Jack's Point, Prentiss Island, New Meadows River, and Weskeag River recorded the highest qPCR-prevalence for P. marinus (32-39%). While the P. marinus qPCR-prevalence differed slightly for the years 2016 and 2017, P. chesapeaki qPCR-prevalence in 2016 was markedly lower than 2017 (<20% at all sites versus >60% at all sites for each of the years, respectively). Mean qPCR-prevalence values for P. chesapeaki over the two-year study were ≥40% for samples from Jack's Point (49%), Prentiss Island (44%), and New Meadows River (40%). This study highlights that large and sustained surveys for parasitic diseases are fundamental for decision making toward the management of the shellfish aquaculture industry, especially for having a baseline in the case that die-offs occur.

Perkinsus chesapeaki observed in a new host, the European common edible cockle Cerastoderma edule, in the Spanish Mediterranean coast

Histological observations showed the presence of a Perkinsus sp. parasite in Cerastoderma edule tissues for the first time in the Spanish Mediterranean coast. ITS molecular characterization by PCR-RFLP, in situ hybridization and sequencing, identified the parasite as Perkinsus chesapeaki, with a maximum identity of 99-100% with GenBank P. chesapeaki sequences from France and 97% with P. chesapeaki sequences of North American origin when BLAST analysis was carried out. Furthermore, phylogenetic studies placed the European cockle parasite in a well defined cluster together with the other European isolates. This is the first report of P. chesapeaki in the cockle C. edule.

One Perkinsus species may hide another: characterization of Perkinsus species present in clam production areas of France

Although clam populations in France are known to be infected with protozoans of the genus Perkinsus, no molecular characterization was previously performed on these parasites. Considering that several members of this genus have been associated with mortalities of molluscs worldwide, a study was undertaken in order to characterize these parasites in France. For that purpose, clams, Ruditapes philippinarum and R. decussatus, collected from different production areas and found to be infected with Perkinsus sp. in thioglycolate culture medium, were selected for PCR-RFLP tests and sequencing. Perkinsus olseni was detected in all the investigated areas and results also suggested the presence of P. chesapeaki in Leucate, a lagoon on the Mediterranean coast and in Bonne Anse in Charente Maritime, on the Atlantic coast. Clonal cultures from both detected species were produced in order to describe and compare in vitro stages. Differences in size between both Perkinsus spp. were noticed especially for schizonts and zoosporangia. Lastly, in situ hybridization tests allowed confirmation of the presence of both species in the same R. decussatus population and even in same clams. This is the first detection of P. chesapeaki in Ruditapes species and outside North America, which questions its introduction into Europe.

Using data-display networks for exploratory data analysis in phylogenetic studies

Exploratory data analysis (EDA) is a frequently undervalued part of data analysis in biology. It involves evaluating the characteristics of the data "before" proceeding to the definitive analysis in relation to the scientific question at hand. For phylogenetic analyses, a useful tool for EDA is a data-display network. This type of network is designed to display any character (or tree) conflict in a data set, without prior assumptions about the causes of those conflicts. The conflicts might be caused by 1) methodological issues in data collection or analysis, 2) homoplasy, or 3) horizontal gene flow of some sort. Here, I explore 13 published data sets using splits networks, as examples of using data-display networks for EDA. In each case, I performed an original EDA on the data provided, to highlight the aspects of the resulting network that will be important for an interpretation of the phylogeny. In each case, there is at least one important point (possibly missed by the original authors) that might affect the phylogenetic analysis. I conclude that EDA should play a greater role in phylogenetic analyses than it has done.

A survey of polymerase chain reaction (PCR) amplification studies of unicellular protists using single-cell PCR

We surveyed a variety of studies that have used single-cell polymerase chain reaction (SC-PCR) to examine the gene sequences of a diversity of unicellular protists. Representatives of all the Super-Groups of eukaryotes have been subjected to SC-PCR with ciliates and dinoflagellates being most commonly examined. The SC-PCR was carried out either by directly amplifying a single lysed cell or by first extracting DNA and following this with amplification of the DNA extract. Cell lysis methods included heating, freezing, mechanical rupture, and enzyme digestion. Cells fixed or preserved with ethanol, methanol, and Lugol's have also been used successfully. Heminested or seminested PCR might follow the initial PCR, whose products were then directly sequenced or cloned and then sequenced. The methods are not complicated. This should encourage protistologists to use SC-PCR in the description of new or revised taxa, especially rare and unculturable forms, and it should also enable the probing of gene expression in relation to life history stages.

Assessment of the northern distribution range of selected Perkinsus species in eastern oysters (Crassostrea virginica) and hard clams (Mercenaria mercenaria) with the use of PCR-based detection assays

Perkinsus species are protistan parasites of molluscs. In Chesapeake Bay, Perkinsus marinus, Perkinsus chesapeaki, and Perkinsus andrewsi are sympatric, infecting oysters and clams. Although P. marinus is a pathogen for Crassostrea virginica, it remains unknown whether P. andrewsi and P. chesapeaki are equally pathogenic. Perkinsus species have been reported in C. virginica as far north as Maine, sometimes associated with high prevalence, but low mortality. Thus, we hypothesized that, in addition to P. marinus, Perkinsus species with little or no pathogenicity for C. virginica may be present. Accordingly, we investigated the distribution of Perkinsus species in C. virginica and Mercenaria mercenaria, collected from Maine to Virginia, by applying PCR-based assays specific for P. marinus, P. andrewsi, and a Perkinsus sp. isolated from M. mercenaria. DNA samples of M. mercenaria possessed potent PCR inhibitory activity, which was overcome by the addition of 1 mg/ml BSA and 5% (v/v) DMSO to the PCR reaction mixture. All 3 Perkinsus species were found in both host species throughout the study area. Interestingly, the prevalence of P. marinus in M. mercenaria was significantly lower than in C. virginica, suggesting that M. mercenaria is not an optimal host for P. marinus.

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

Perkinsus marinus is a severe pathogen of the oyster Crassostrea virginica on the East Coast of the United States. Transmission dynamics of this parasite were investigated in situ for 2 consecutive years (May through October) at 2 lower Chesapeake Bay sites. Compared to previous studies where seasonal infection patterns in oysters were measured, this study also provided parasite water column abundance data measured using real-time PCR. As previously observed, salinity and temperature modulated parasite transmission dynamics. Using regression analysis, parasite prevalence, oyster mortalities and parasite water column abundance were significantly positively related to salinity. Perkinsus marinus weighted prevalence in wild oysters and parasite water column abundance both were significantly related to temperature, but the responses lagged 1 month behind temperature. Parasite water column abundance was the highest during August (up to 1,200 cells/l) and was significantly related to P. marinus weighted prevalence in wild oysters, and to wild oyster mortality suggesting that parasites are released in the environment via both moribund and live hosts (i.e. through feces). Incidence was not significantly related to parasite water column abundance, which seems to indicate the absence of a linear relationship or that infection acquisition is controlled by a more complex set of parameters.

Complete rRNA Gene Sequences Reveal that the MicrosporidiumNosema bombiInfects Diverse Bumblebee (Bombusspp.) Hosts and Contains Multiple Polymorphic Sites

Characterisation of microsporidian species and differentiation among genetic variants of the same species has typically relied on ribosomal RNA (rRNA) gene sequences. We characterised the entire rRNA gene of a microsporidium from 11 isolates representing eight different European bumblebee (Bombus) species. We demonstrate that the microsporidium Nosema bombi infected all hosts that originated from a wide geographic area. A total of 16 variable sites (all single nucleotid polymorphisms (SNPs)) was detected in the small subunit (SSU) rRNA gene and 42 (39 SNPs and 3 indels) in the large subunit (LSU) rRNA sequence. Direct sequencing of PCR-amplified DNA products of the internal transcribed spacer (ITS) region revealed identical sequences in all isolates. In contrast, ITS fragment length determined by PAGE and sequencing of cloned amplicons gave better resolution of sequences and revealed multiple SNPs across isolates and two fragment sizes in each isolate (six short and seven long amplicon variants). Genetic variants were not unique to individual host species. Moreover, two or more sequence variants were obtained from individual bumblebee hosts, suggesting the existence of multiple, variable copies of rRNA in the same microsporidium, and contrary to that expected for a class of multi-gene family under concerted evolution theory. Our data on within-genome rRNA variability call into question the usefulness of rRNA sequences to characterise intraspecific genetic variants in the Microsporidia and other groups of unicellular organisms.

Molecular, Morphological, and Experimental Evidence Support the Synonymy of Perkinsus chesapeaki and Perkinsus andrewsi

Diverse analytical and experimental results confirm that two protistan parasites, Perkinsus chesapeaki and Perkinsus andrewsi, described separately as parasites of Mya arenaria and Macoma balthica clams sympatric in Chesapeake Bay, USA, represent a single species. Ribosomal RNA (rRNA) internal transcribed spacer (ITS) regions, rRNA large subunit (LSU) gene, and actin gene sequences were obtained from clonal Perkinsus spp. cultured in vitro. Although multiple polymorphic sequences were found in DNA from clonal cultures at each locus, identical ITS region and actin gene sequences were found in the P. andrewsi holotype culture and in Perkinsus sp. clonal cultures from M. arenaria and Tagelus plebius. All sequences determined from cultures of P. chesapeaki and P. andrewsi at each locus grouped together in monophyletic clades with high support values in phylogenetic analyses. In vitro isolates of Perkinsus spp. from M. arenaria and M. balthica were reciprocally infective for each other's cognate host. Lesions and histozoic parasite cell morphologies were consistent with those described for the original host/parasite interactions. In vitro isolate cell cycles and cell types of both parasites were indistinguishable. In accordance with the International Code of Zoological Nomenclature rules of priority, P. andrewsi is declared a junior synonym of P. chesapeaki.

Real-time PCR for detection and quantification of the protistan parasite Perkinsus marinus in environmental waters

The protistan parasite Perkinsus marinus is a severe pathogen of the oyster Crassostrea virginica along the east coast of the United States. Very few data have been collected, however, on the abundance of the parasite in environmental waters, limiting our understanding of P. marinus transmission dynamics. Real-time PCR assays with SybrGreen I as a label for detection were developed in this study for quantification of P. marinus in environmental waters with P. marinus species-specific primers and of Perkinsus spp. with Perkinsus genus-specific primers. Detection of DNA concentrations as low as the equivalent of 3.3 x 10(-2) cell per 10-microl reaction mixture was obtained by targeting the multicopy internal transcribed spacer region of the genome. To obtain reliable target quantification from environmental water samples, removal of PCR inhibitors and efficient DNA recovery were two major concerns. A DNA extraction kit designed for tissues and another designed for stool samples were tested on environmental and artificial seawater (ASW) samples spiked with P. marinus cultured cells. The stool kit was significantly more efficient than the tissue kit at removing inhibitors from environmental water samples. With the stool kit, no significant difference in the quantified target concentrations was observed between the environmental and ASW samples. However, with the spiked ASW samples, the tissue kit demonstrated more efficient DNA recovery. Finally, by performing three elutions of DNA from the spin columns, which were combined prior to target quantification, variability of DNA recovery from different samples was minimized and more reliable real-time PCR quantification was accomplished.