Host-parasitoid associations in marine planktonic time series: Can metabarcoding help reveal them?

Advanced genomic research in understanding fish-borne zoonotic parasitic infection

Fish-borne zoonotic parasites pose substantial risks to human health and global aquaculture, primarily through raw or undercooked fish consumption. The rapid expansion of aquaculture, increasing global fish trade, and rising human populations have amplified these concerns. Despite widespread awareness of meat-borne zoonoses, fish-borne parasitic infections remain underrecognized, especially in developed countries. Traditional morphological and molecular methods have provided critical foundations for studying these parasites, yet recent genomic advances have revolutionized our understanding of their genetic diversity, biology, and host-pathogen dynamics. This review underscores the significance of integrating genomic approaches with conventional methods to enhance disease surveillance, risk assessment, and control strategies. Harnessing genomic tools will enable the development of effective interventions to mitigate zoonotic parasite impacts, protect human health, and promote sustainable aquaculture. A comprehensive, genomics-driven approach is essential to overcoming the global challenges of fish-borne zoonotic infections.

Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes

Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North-East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments.

Morphology, phylogeny, and host range of the novel early-diverging oomycete Sirolpidium dinoletiferum sp. nov. parasitizing marine dinoflagellates

Oomycetes are fungus-like heterotrophic organisms with a broad environmental distribution, including marine, freshwater, and terrestrial habitats. They function as saprotrophs that use the remains of other organisms or as parasites of a variety of eukaryotes, including protists, diatoms, dinoflagellates, macroalgae, plants, fungi, animals, and even other oomycetes. Among the protist hosts, the taxonomy, morphology, and phylogenetic positions of the oomycete parasitoids of diatoms have been well studied; however, this information concerning the oomycete parasitoids of dinoflagellates is poorly understood. During intensive sampling along the east and west coasts of Korea in May and October 2019, a new species of oomycetes was discovered and two strains of the new parasitoid were successfully established in cultures. The new oomycete parasitoid penetrated the dinoflagellate host cell and developed to form a sporangium, which was very similar to the perkinsozoan parasitoids that infect marine dinoflagellates. The most distinctive morphological feature of the new parasitoid was a central large vacuole forming several long discharge tubes. The molecular phylogenetic tree inferred based on the small subunit (SSU) ribosomal DNA (rDNA) revealed that the new parasitoid forms a distinct branch unrelated to other described species belonging to early-diverging oomycetes. It clustered with species belonging to the genus Sirolpidium with strong support values in the cytochrome c oxidase subunit 2 (cox2) tree. Cross-infection experiments showed that infections by the new parasitoid occurred in only six genera belonging to dinoflagellates among the protists tested in this study. Based on the morphological and molecular data obtained in this study, we propose to introduce a new species, Sirolpidium dinoletiferum sp. nov., for this novel parasitoid, conservatively within the genus Sirolpidium.

A review of the taxonomic diversity, host-parasite interactions, and experimental research on chytrids that parasitize diatoms

Diatoms (Bacillariophyta) are a major source of primary production on Earth, generating between 1/4 to 1/2 of all oxygen. They are found in almost all bodies of water, the ice of mountains, the arctic and the antarctic, and soils. Diatoms are also a major source of food in aquatic systems, a key component of the silica cycle, and are carbon capturers in oceans. Recently, diatoms have been examined as sources of biofuels, food, and other economic boons. Chytrids are members of the Kingdom fungi comprising, at a minimum, Chytridiomycota, Blastocladiomycota, and Neocallimastigales. Most chytrids are saprobes, plant pathogens, or parasites, and play an important role in aquatic ecosystems. Chytrid parasitism of diatoms has been reported to cause epidemics of over 90% fatality, though most of the information regarding these epidemics is limited to interactions between just a few hosts and parasites. Given the ubiquity of diatoms, their importance in natural and economic systems, and the massive impact epidemics can have on populations, the relative lack of knowledge regarding parasitism by chytrids is alarming. Here we present a list of the firsthand accounts of diatoms reported parasitized by chytrids. The list includes 162 named parasitic chytrid-diatom interactions, with 63 unique chytrid taxa from 11 genera, and 74 unique diatom taxa from 28 genera. Prior to this review, no list of all documented diatom-chytrid interactions existed. We also synthesize the currently known methods of infection, defense, and experiments examining diatoms and chytrids, and we document the great need for work examining both a greater breadth of taxonomic diversity of parasites and hosts, and a greater depth of experiments probing their interactions. This resource is intended to serve as a building block for future researchers studying diatom-parasite interactions and global planktonic communities in both fresh and marine systems.

Interannual dynamics of putative parasites (Syndiniales Group II) in a coastal ecosystem

Temporal dynamics of Syndiniales Group II were investigated combining 18S rDNA amplicon sequencing and direct microscopy counts (fluorescence in situ hybridization-tyramide signal amplification [FISH-TSA]) during 5 years. The study was undertaken in meso-eutrophic coastal ecosystem, dominated by diatoms, the haptophyte Phaeocystis globosa and exhibiting relatively low dinoflagellate abundance (max. 18.6 × 10³  cells L^-1 ). Consistent temporal patterns of Syndiniales Group II were observed over consecutive years highlighting the existence of local populations. According to sequencing data, Syndiniales Group II showed increasing abundance and richness in summer and autumn. Dinospores counted by microscopy, were present at low abundances and were punctuated by transient peaks. In summer dinospore highest abundance (559 × 10³  L^-1 ) and prevalence (38.5%) coincided with the peak abundance of the dinoflagellate Prorocentrum minimum (13 × 10³  L^-1 ) while in autumn Syndiniales Group II likely had more diversified hosts. Although, several peaks of dinospore and read abundances coincided, there was no consistent relation between them. Ecological assembly processes at a seasonal scale revealed that stochastic processes were the main drivers (80%) of the Group II community assembly, though deterministic processes were noticeable (20%) in June and July. This latter observation may reflect the specific Syndiniales-dinoflagellate interactions in summer.

Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites

Marine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration of this uncharted protist diversity in oceanic communities relies essentially on studying genetic markers from the environment as taxonomic barcodes. Here we report that across 6 large scale spatio-temporal planktonic surveys, half of the genetic barcodes remain taxonomically unassigned at the genus level, preventing a fine ecological understanding for numerous protist lineages. Among them, parasitic Syndiniales (Dinoflagellata) appear as the least described protist group. We have developed a computational workflow, integrating diverse 18S rDNA gene metabarcoding datasets, in order to infer large-scale ecological patterns at 100% similarity of the genetic marker, overcoming the limitation of taxonomic assignment. From a spatial perspective, we identified 2171 unassigned clusters, i.e., Syndiniales sequences with 100% similarity, exclusively shared between the Tropical/Subtropical Ocean and the Mediterranean Sea among all Syndiniales orders and 25 ubiquitous clusters shared within all the studied marine regions. From a temporal perspective, over 3 time-series, we highlighted 39 unassigned clusters that follow rhythmic patterns of recurrence and are the best indicators of parasite community's variation. These clusters withhold potential as ecosystem change indicators, mirroring their associated host community responses. Our results underline the importance of Syndiniales in structuring planktonic communities through space and time, raising questions regarding host-parasite association specificity and the trophic mode of persistent Syndiniales, while providing an innovative framework for prioritizing unassigned protist taxa for further description.

Dinoflagellate hosts determine the community structure of marine Chytridiomycota: Demonstration of their prominent interactions

The interactions of parasitic fungi with their phytoplankton hosts in the marine environment are mostly unknown. In this study, we evaluated the diversity of Chytridiomycota in phytoplankton communities dominated by dinoflagellates at several coastal locations in the NW Mediterranean Sea and demonstrated the most prominent interactions of these parasites with their hosts. The protist community in seawater differed from that in sediment, with the latter characterized by a greater heterogeneity of putative hosts, such as dinoflagellates and diatoms, as well as a chytrid community more diverse in its composition and with a higher relative abundance. Chytrids accounted for 77 amplicon sequence variants, of which 70 were found exclusively among different blooming host species. The relative abundance of chytrids was highest in samples dominated by the dinoflagellate genera Ostreopsis and Alexandrium, clearly indicating the presence of specific chytrid communities. The establishment of parasitoid-host co-cultures of chytrids and dinoflagellates allowed the morphological identification and molecular characterization of three species of Chytridiomycota, including Dinomyces arenysensis, as one of the most abundant environmental sequences, and the discovery of two other species not yet described.

Parasite–copepod interactions in Svalbard: diversity, host specificity, and seasonal patterns

Copepods of the genera Calanus and Pseudocalanus are important components of Arctic marine ecosystems. Despite the key roles of these zooplankters, little is known about the organisms they interact with most intimately, their parasites and symbionts. We applied metabarcode sequencing to uncover eukaryotic parasites present within these two copepod genera from three areas around the high Arctic archipelago of Svalbard. Ten distinct parasite groups were observed: four different Apostome ciliates, four different dinoflagellates (Chytriodinium sp., Ellobiopsis sp., Thalassomyces sp., and Hematodinium sp.), a Paradinium sp., and a trematode. Apostome ciliates closely related to Pseudocollinia spp. were the most commonly observed parasite, with overall infection rates of 21.5% in Calanus and 12.5% in Pseudocalanus. Infection by these ciliates varied seasonally, with no infections observed in early winter, but infection rates exceeding 75% in spring. Host specificity varied between parasites, with significant differences in infection rate between the two host copepod genera for four parasites (two ciliates, Chytriodinium, and a trematode). The diverse assemblage of parasites observed in these copepods, and the frequency of infection, with over one in five copepod individuals infected, suggest parasites may be playing a greater role in Arctic plankton communities than generally acknowledged.

Basal Parasitic Fungi in Marine Food Webs-A Mystery Yet to Unravel

Although aquatic and parasitic fungi have been well known for more than 100 years, they have only recently received increased awareness due to their key roles in microbial food webs and biogeochemical cycles. There is growing evidence indicating that fungi inhabit a wide range of marine habitats, from the deep sea all the way to surface waters, and recent advances in molecular tools, in particular metagenome approaches, reveal that their diversity is much greater and their ecological roles more important than previously considered. Parasitism constitutes one of the most widespread ecological interactions in nature, occurring in almost all environments. Despite that, the diversity of fungal parasites, their ecological functions, and, in particular their interactions with other microorganisms remain largely speculative, unexplored and are often missing from current theoretical concepts in marine ecology and biogeochemistry. In this review, we summarize and discuss recent research avenues on parasitic fungi and their ecological potential in marine ecosystems, e.g., the fungal shunt, and emphasize the need for further research.

Eukaryotic Parasites Are Integral to a Productive Microbial Food Web in Oxygen-Depleted Waters

Oxygen-depleted water columns (ODWCs) host a diverse community of eukaryotic protists that change dramatically in composition over the oxic-anoxic gradient. In the permanently anoxic Cariaco Basin, peaks in eukaryotic diversity occurred in layers where dark microbial activity (chemoautotrophy and heterotrophy) were highest, suggesting a link between prokaryotic activity and trophic associations with protists. Using 18S rRNA gene sequencing, parasites and especially the obligate parasitic clade, Syndiniales, appear to be particularly abundant, suggesting parasitism is an important, but overlooked interaction in ODWC food webs. Syndiniales were also associated with certain prokaryotic groups that are often found in ODWCs, including Marinimicrobia and Marine Group II archaea, evocative of feedbacks between parasitic infection events, release of organic matter, and prokaryotic assimilative activity. In a network analysis that included all three domains of life, bacterial and archaeal taxa were putative bottleneck and hub species, while a large proportion of edges were connected to eukaryotic nodes. Inclusion of parasites resulted in a more complex network with longer path lengths between members. Together, these results suggest that protists, and especially protistan parasites, play an important role in maintaining microbial food web complexity, particularly in ODWCs, where protist diversity and microbial productivity are high, but energy resources are limited relative to euphotic waters.

Co-occurrence networks reveal the central role of temperature in structuring the plankton community of the Thau Lagoon

To identify the environmental factors that drive plankton community composition and structure in coastal waters, a shallow northwestern Mediterranean lagoon was monitored from winter to spring in two contrasting years. The campaign was based on high-frequency recordings of hydrological and meteorological parameters and weekly samplings of nutrients and the plankton community. The collected data allowed the construction of correlation networks, which revealed that water temperature was the most important factor governing community composition, structure and succession at different trophic levels, suggesting its ubiquitous food web control. Temperature favoured phytoplanktonic flagellates (Cryptophyceae, Chrysophyceae, and Chlorophyceae) and ciliates during winter and early spring. In contrast, it favoured Bacillariophyceae, dinoflagellates, phytoplankton < 6 µm and aloricate Choreotrichida during spring. The secondary factors were light, which influenced phytoplankton, and wind, which may regulate turbidity and the nutrient supply from land or sediment, thus affecting benthic species such as Nitzschia sp. and Uronema sp. or salinity-tolerant species such as Prorocentrum sp. The central role of temperature in structuring the co-occurrence network suggests that future global warming could deeply modify plankton communities in shallow coastal zones, affecting whole-food web functioning.