Novel Widespread Marine Oomycetes Parasitising Diatoms, Including the Toxic Genus Pseudo-nitzschia: Genetic, Morphological, and Ecological Characterisation

Macroalgal eukaryotic microbiome composition indicates novel phylogenetic diversity and broad host spectrum of oomycete pathogens

Seaweeds are important components of marine ecosystems with emerging potential in aquaculture and as sources of biofuel, food products and pharmacological compounds. However, an increasingly recognised threat to natural and industrial seaweed populations is infection with parasitic single-celled eukaryotes from the relatively understudied oomycete lineage. Here we examine the eukaryomes of diverse brown, red and green marine macroalgae collected from polar (Baffin Island), cold-temperate (Falkland Islands) and tropical (Ascension Island) locations, with a focus on oomycete and closely related diatom taxa. Using 18S rRNA gene amplicon sequencing, we show unexpected genetic and taxonomic diversity of the eukaryomes, a strong broad-brush association between eukaryome composition and geographic location, and some evidence of association between eukaryome structure and macroalgal phylogenetic relationships (phylosymbiosis). However, the oomycete fraction of the eukaryome showed disparate patterns of diversity and structure, highlighting much weaker association with geography and no evidence of phylosymbiosis. We present several novel haplotypes of the most common oomycete Eurychasma dicksonii and report for the first time a cosmopolitan distribution and absence of host specificity of this important pathogen. This indicates rich diversity in macroalgal oomycete pathogens and highlights that these pathogens may be generalist and highly adaptable to diverse environmental conditions.

Miracula polaris - A New Species of Miracula from the East Fjords of Iceland

There is increasing evidence that holocarpic oomycetes, i.e., those converting their entire vegetative thallus into zoospores upon maturation, are a phylogenetically diverse group in both freshwater and marine ecosystems. Most of the known holocarpic oomycete species diverge before the main split of Peronosporomycetes and Saprolegniomycetes and are, thus, termed as early-diverging oomycetes. In environmental sequencing studies, it was revealed that of the early-diverging genera especially Sirolpidium, Miracula, and Diatomophthora are widespread. As in these studies especially the Arctic Ocean seemed to harbor many undiscovered species, sampling was conducted at the Blávík research station on Fáskrúðsfjörður in the East Fjords of Iceland, where there is both an influence from the Arctic Ocean and the North Atlantic. During the screening for infected diatoms, a parasitoid was found in the marine diatom genus Melosira, which is one of the most abundant genera in arctic ecosystems. Molecular phylogenetics and morphological characterization revealed that the parasitoid belonged to the genus Miracula and corresponded to one of the lineages previously found in single-cell sequencing. Thus, the current study both contributes to the knowledge of the genus Miracula and the increasing diversity of the genus suggests that the many linages found in environmental sequencing which can still not be associated with known species might represent actual species to be discovered in future studies.

Algal blooms in the ocean: hot spots for chemically mediated microbial interactions

The cycling of major nutrients in the ocean is affected by large-scale phytoplankton blooms, which are hot spots of microbial life. Diverse microbial interactions regulate bloom dynamics. At the single-cell level, interactions between microorganisms are mediated by small molecules in the chemical crosstalk that determines the type of interaction, ranging from mutualism to pathogenicity. Algae interact with viruses, bacteria, parasites, grazers and other algae to modulate algal cell fate, and these interactions are dependent on the environmental context. Recent advances in mass spectrometry and single-cell technologies have led to the discovery of a growing number of infochemicals - metabolites that convey information - revealing the ability of algal cells to govern biotic interactions in the ocean. The diversity of infochemicals seems to account for the specificity in cellular response during microbial communication. Given the immense impact of algal blooms on biogeochemical cycles and climate regulation, a major challenge is to elucidate how microscale interactions control the fate of carbon and the recycling of major elements in the ocean. In this Review, we discuss microbial interactions and the role of infochemicals in algal blooms. We further explore factors that can impact microbial interactions and the available tools to decipher them in the natural environment.

Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides

BACKGROUND

Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity, activity, and functional potential of such polysaccharide-degrading bacteria in different size fractions during a diverse spring phytoplankton bloom at Helgoland Roads (southern North Sea) at high temporal resolution using microscopic, physicochemical, biodiversity, metagenome, and metaproteome analyses.

RESULTS

Prominent active 0.2-3 µm free-living clades comprised Aurantivirga, "Formosa", Cd. Prosiliicoccus, NS4, NS5, Amylibacter, Planktomarina, SAR11 Ia, SAR92, and SAR86, whereas BD1-7, Stappiaceae, Nitrincolaceae, Methylophagaceae, Sulfitobacter, NS9, Polaribacter, Lentimonas, CL500-3, Algibacter, and Glaciecola dominated 3-10 µm and > 10 µm particles. Particle-attached bacteria were more diverse and exhibited more dynamic adaptive shifts over time in terms of taxonomic composition and repertoires of encoded polysaccharide-targeting enzymes. In total, 305 species-level metagenome-assembled genomes were obtained, including 152 particle-attached bacteria, 100 of which were novel for the sampling site with 76 representing new species. Compared to free-living bacteria, they featured on average larger metagenome-assembled genomes with higher proportions of polysaccharide utilization loci. The latter were predicted to target a broader spectrum of polysaccharide substrates, ranging from readily soluble, simple structured storage polysaccharides (e.g., laminarin, α-glucans) to less soluble, complex structural, or secreted polysaccharides (e.g., xylans, cellulose, pectins). In particular, the potential to target poorly soluble or complex polysaccharides was more widespread among abundant and active particle-attached bacteria.

CONCLUSIONS

Particle-attached bacteria represented only 1% of all bloom-associated bacteria, yet our data suggest that many abundant active clades played a pivotal gatekeeping role in the solubilization and subsequent degradation of numerous important classes of algal glycans. The high diversity of polysaccharide niches among the most active particle-attached clades therefore is a determining factor for the proportion of algal polysaccharides that can be rapidly remineralized during generally short-lived phytoplankton bloom events. Video Abstract.

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.

The Reemergence of Phycopathology: When Algal Biology Meets Ecology and Biosecurity

Viruses, bacteria, and eukaryotic symbionts interact with algae in a variety of ways to cause disease complexes, often shaping marine and freshwater ecosystems. The advent of phyconomy (a.k.a. seaweed agronomy) represents a need for a greater understanding of algal disease interactions, where underestimated cryptic diversity and lack of phycopathological basis are prospective constraints for algal domestication. Here, we highlight the limited yet increasing knowledge of algal pathogen biodiversity and the ecological interaction with their algal hosts. Finally, we discuss how ecology and cultivation experience contribute to and reinforce aquaculture practice, with the potential to reshape biosecurity policies of seaweed cultivation worldwide.

Intercomparison of Two Fluorescent Dyes to Visualize Parasitic Fungi (Chytridiomycota) on Phytoplankton

Fungal microparasites (here chytrids) are widely distributed and yet, they are often overlooked in aquatic environments. To facilitate the detection of microparasites, we revisited the applicability of two fungal cell wall markers, Calcofluor White (CFW) and wheat germ agglutinin (WGA), for the direct visualization of chytrid infections on phytoplankton in laboratory-maintained isolates and field-sampled communities. Using a comprehensive set of chytrid-phytoplankton model pathosystems, we verified the staining pattern on diverse morphological structures of chytrids via fluorescence microscopy. Empty sporangia were stained most effectively, followed by encysted zoospores and im-/mature sporangia, while the staining success was more variable for rhizoids, stalks, and resting spores. In a few instances, the staining was unsuccessful (mostly with WGA), presumably due to insufficient cell fixation, gelatinous cell coatings, and multilayered cell walls. CFW and WGA staining could be done in Utermöhl chambers or on polycarbonate filters, but CFW staining on filters seemed less advisable due to high background fluorescence. To visualize chytrids, 1 µg dye mL-1 was sufficient (but 5 µg mL-1 are recommended). Using a dual CFW-WGA staining protocol, we detected multiple, mostly undescribed chytrids in two natural systems (freshwater and coastal), while falsely positive or negative stained cells were well detectable. As a proof-of-concept, we moreover conducted imaging flow cytometry, as a potential high-throughput technology for quantifying chytrid infections. Our guidelines and recommendations are expected to facilitate the detection of chytrid epidemics and to unveil their ecological and economical imprint in natural and engineered aquatic systems.

Miracula blauvikensis: a new species of Miracula from Iceland, and report of a co-cultivation system for studying oomycete-diatom interactions

The genus Miracula represents an early-diverging lineage of diatom-parasitic Oomycota, straminipilous eukaryotes that have evolved fungal features independent from the opisthokont Fungi. Recent studies have revealed that diatom parasitoids are much more species-rich than previously thought and may play an important role in limnic and marine ecosystems. Of the different diatom-parasitic lineages, the genus Miracula is one of the most abundant in marine ecosystems. Here a species of Miracula parasitising Fragilaria capucina s.l. from Iceland is described as Miracula blauvikensis. In addition, its phylogenetic position is clarified and its life-cycle documented. The species has been brought into co-cultivation with its host, and due to the ease of cultivation and the convenient microscopy of the diatom threads, this co-culture might be a useful tool to study oomycete-diatom interactions in the future. Citation: Buaya A, Thines M (2022). Miracula blauvikensis: a new species of Miracula from Iceland, and report of a co-cultivation system for studying oomycete-diatom interactions. Fungal Systematics and Evolution 10: 169-175. doi: 10.3114/fuse.2022.10.07.

Lagena—an overlooked oomycete genus with a wide range of hosts

Lagena has so far only been known from the scarcely reported but widespread species Lagena radicicola, which is a parasite of root epidermal cells. While it was mostly reported from a wide range of cereals and other grasses, it has been shown to affect some dicot species under, e.g. tobacco and sugar beet. Due to the wide host spectrum under laboratory conditions, there were no attempts to subdivide the genus into several species, even though some morphological differentiation was reported and the species had been found in several continents. During a survey of diatoms, we came across some parasitoids that would have previously been assumed to be members of the genus Lagenidium. The species exhibited rather narrow host specificity in nature. One species was brought into dual culture with host diatoms of the genus Ulnaria, but could not be transferred to other host genera. Surprisingly, phylogenetic analyses revealed that Lagena radicicola was in a sister clade to that formed by the diatom parasitoids, suggesting a versatile pathogenicity of the genus. Interestingly, several phylogenetic lineages only known from environmental sequencing were clustered with the species found in this study, hinting an undiscovered diversity in the genus Lagena.

Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi

Microbial glycan degradation is essential to global carbon cycling. The marine bacterium Salegentibacter sp. Hel_I_6 (Bacteroidota) isolated from seawater off Helgoland island (North Sea) contains an α-mannan inducible gene cluster with a GH76 family endo-α-1,6-mannanase (ShGH76). This cluster is related to genetic loci employed by human gut bacteria to digest fungal α-mannan. Metagenomes from the Hel_I_6 isolation site revealed increasing GH76 gene frequencies in free-living bacteria during microalgae blooms, suggesting degradation of α-1,6-mannans from fungi. Recombinant ShGH76 protein activity assays with yeast α-mannan and synthetic oligomannans showed endo-α-1,6-mannanase activity. Resolved structures of apo-ShGH76 (2.0 Å) and of mutants co-crystalized with fungal mannan-mimicking α-1,6-mannotetrose (1.90 Å) and α-1,6-mannotriose (1.47 Å) retained the canonical (α/α)6 fold, despite low identities with sequences of known GH76 structures (GH76s from gut bacteria: <27%). The apo-form active site differed from those known from gut bacteria, and co-crystallizations revealed a kinked oligomannan conformation. Co-crystallizations also revealed precise molecular-scale interactions of ShGH76 with fungal mannan-mimicking oligomannans, indicating adaptation to this particular type of substrate. Our data hence suggest presence of yet unknown fungal α-1,6-mannans in marine ecosystems, in particular during microalgal blooms.

Miracula einbuarlaekurica sp. nov., a new holocarpic endoparasitoid species from pennate freshwater diatoms in Iceland

Holocarpic oomycetes infecting freshwater diatoms are obligate endobiotic parasites reported from a wide range of habitats. So far, the taxonomy of and phylogeny of most species remains unresolved, since most have not been reported throughout the past decades and sequence data are available for only the four species, Aphanomycopsis bacillariacearum, Diatomophthora gillii, Ectrogella bacillariacearum, and the recently-discovered species Miracula moenusica. In the current study, a new freshwater diatom parasite resembling Ectrogella bacillariacearum in the sense of Scherffel was discovered from pennate diatoms (Ulnaria acus, Ulnaria ulna) collected from the small stream Einbúalækur on Víkurskarð, North Iceland and investigated for its life cycle and phylogenetic placement. In contrast to the original description, Scherffel reports an achlya-like spore discharge for Ectrogella bacillariacearum. The phylogenetic reconstruction and morphological characterisation in this study revealed that Scherffel’s E. bacillariacearum is largely unrelated to the epitype of the species and is a member of the early-diverging genus Miracula. Consequently, the new species is described as M. einbuarlaekurica in the present study. This adds a second freshwater member to the genus, demonstrating the high ecological adaptability of the genus, which thrives in both freshwater and marine ecosystems.

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.

High-Throughput Sequencing of Environmental DNA as a Tool for Monitoring Eukaryotic Communities and Potential Pathogens in a Coastal Upwelling Ecosystem

The marine environment includes diverse microeukaryotic organisms that play important functional roles in the ecosystem. With molecular approaches, eukaryotic taxonomy has been improved, complementing classical analysis. In this study, DNA metabarcoding was performed to describe putative pathogenic eukaryotic microorganisms in sediment and marine water fractions collected in Galicia (NW Spain) from 2016 to 2018. The composition of eukaryotic communities was distinct between sediment and water fractions. Protists were the most diverse group, with the clade TSAR (Stramenopiles, Alveolata, Rhizaria, and Telonemida) as the primary representative organisms in the environment. Harmful algae and invasive species were frequently detected. Potential pathogens, invasive pathogenic organisms as well as the causative agents of harmful phytoplanktonic blooms were identified in this marine ecosystem. Most of the identified pathogens have a crucial impact on the aquacultural sector or affect to relevant species in the marine ecosystem, such as diatoms. Moreover, pathogens with medical and veterinary importance worldwide were also found, as well as pathogens that affect diatoms. The evaluation of the health of a marine ecosystem that directly affects the aquacultural sector with a zoonotic concern was performed with the metabarcoding assay.

A New Marine Species of Miracula (Oomycota) Parasitic to Minidiscus sp. in Iceland†

Obligate endoparasitic oomycetes are known to ubiquitously occur in marine and freshwater diatoms, but their diversity is still largely unexplored. Many of these parasitoids are members of the early-diverging oomycete lineages (Miracula, Diatomophthora), others are within the Leptomitales of the Saprolegniomycetes (Ectrogella, Lagenisma) and some have been described in the Peronosporomycetes (Aphanomycopsis, Lagenidium). Even though some species have been recently described and two new genera were introduced (Miracula and Diatomophthora), the phylogeny and taxonomy of most of these organisms remain unresolved. This is contrasted by the high number of sequences from unclassified species, as recently revealed from environmental sequencing, suggesting the presence of several undiscovered species. In this study, a new species of Miracula is reported from a marine centric diatom (Minidiscus sp.) isolated from Skagaströnd harbor in Northwest Iceland. The morphology and life cycle traits of this novel oomycete parasite are described herein, and its taxonomic placement within the genus Miracula is confirmed by molecular phylogeny. As it cannot be assigned to any previously described species, it is introduced as Miracula islandica in this study. The genus Miracula thus contains three described holocarpic species (M. helgolandica, M. islandica, M. moenusica) to which likely additional species will need to be added in the future, considering the presence of several lineages known only from environmental sequencing that clustered within the Miracula clade.

Cox2 community barcoding at Prince Edward Island reveals long-distance dispersal of a downy mildew species and potentially marine members of the Saprolegniaceae

Marine oomycetes are highly diverse, globally distributed, and play key roles in marine food webs as decomposers, food source, and parasites. Despite their potential importance in global ocean ecosystems, marine oomycetes are comparatively little studied. Here, we tested if the primer pair cox2F_Hud and cox2-RC4, which is already well-established for phylogenetic investigations of terrestrial oomycetes, can also be used for high-throughput community barcoding. Community barcoding of a plankton sample from Brudenell River (Prince Edward Island, Canada), revealed six distinct oomycete OTU clusters. Two of these clusters corresponded to members of the Peronosporaceae—one could be assigned to Peronospora verna, an obligate biotrophic pathogen of the terrestrial plant Veronica serpyllifolia and related species, the other was closely related to Globisporangium rostratum. While the detection of the former in the sample is likely due to long-distance dispersal from the island, the latter might be a bona fide marine species, as several cultivable species of the Peronosporaceae are known to withstand high salt concentrations. Two OTU lineages could be assigned to the Saprolegniaceae. While these might represent marine species of the otherwise terrestrial genus, it is also conceivable that they were introduced on detritus from the island. Two additional OTU clusters were grouped with the early-diverging oomycete lineages but could not be assigned to a specific family. This reflects the current underrepresentation of cox2 sequence data which will hopefully improve with the increasing interest in marine oomycetes.

Host preferences of coexisting Perkinsea parasitoids during coastal dinoflagellate blooms

Parasites in aquatic systems are highly diverse and ubiquitous. In marine environments, parasite-host interactions contribute substantially to shaping microbial communities, but their nature and complexity remain poorly understood. In this study, we examined the relationship between Perkinsea parasitoids and bloom-forming dinoflagellate species. Our aim was to determine whether parasite-host species interactions are specific and whether the diversity and distribution of parasitoids are shaped by their dinoflagellate hosts. Several locations along the Catalan coast (NW Mediterranean Sea) were sampled during the blooms of five dinoflagellate species and the diversity of Perkinsea was determined by combining cultivation-based methods with metabarcoding of the V4 region of 18S rDNA. Most known species of Parviluciferaceae, and others not yet described, were detected, some of them coexisting in the same coastal location, and with a wide distribution. The specific parasite-host interactions determined for each of the studied blooms demonstrated the host preferences exhibited by parasitoids in nature. The dominance of a species within the parasitoid community is driven by the presence and abundances of its preferred host(s). The absence of parasitoid species, often associated with a low abundance of their preferred hosts, suggested that high infection rates are reached only under conditions that favour parasitoid propagation, especially dinoflagellate blooms.

Sirolpidium bryopsidis, a parasite of green algae, is probably conspecific with Pontisma lagenidioides, a parasite of red algae

The genus Sirolpidium (Sirolpidiaceae) of the Oomycota includes several species of holocarpic obligate aquatic parasites. These organisms are widely occurring in marine and freshwater habitats, mostly infecting filamentous green algae. Presently, all species are only known from their morphology and descriptive life cycle traits. None of the seven species classified in Sirolpidium, including the type species, S. bryopsidis, has been rediscovered and studied for their molecular phylogeny, so far. Originally, the genus was established to accommodate all parasites of filamentous marine green algae. In the past few decades, however, Sirolpidium has undergone multiple taxonomic revisions and several species parasitic in other host groups were added to the genus. While the phylogeny of the marine rhodophyte- and phaeophyte-infecting genera Pontisma and Eurychasma, respectively, has only been resolved recently, the taxonomic placement of the chlorophyte-infecting genus Sirolpidium remained unresolved. In the present study, we report the phylogenetic placement of Sirolpidium bryopsidis infecting the filamentous marine green algae Capsosiphon fulvescens sampled from Skagaströnd in Northwest Iceland. Phylogenetic reconstructions revealed that S. bryopsidis is either conspecific or at least very closely related to the type species of Pontisma, Po. lagenidioides. Consequently, the type species of genus Sirolpidium, S. bryopsidis, is reclassified to Pontisma. Further infection trials are needed to determine if Po. bryopsidis and Po. lagenidioides are conspecific or closely related. In either case, the apparently recent host jump from red to green algae is remarkable, as it opens the possibility for radiation in a largely divergent eukaryotic lineage.

Citation: Buaya AT, Scholz B, Thines M (2021). Sirolpidium bryopsidis, a parasite of green algae, is probably conspecific with Pontisma lagenidioides, a parasite of red algae. Fungal Systematics and Evolution7: 223–231. doi: 10.3114/fuse.2021.07.11

Taxonomy and phylogeny of Aphanomycopsis bacillariacearum, a holocarpic oomycete parasitoid of the freshwater diatom genus Pinnularia

Investigations into simple holocarpic oomycetes are challenging, because of the obligate biotrophic nature of many lineages and the periodic presence in their hosts. Thus, despite recent efforts, still, the majority of species described remains to be investigated for their phylogenetic relationships. One of these species is Aphanomycopsis bacillariacearum, the type species of the genus Aphanomycopsis. Species of Aphanomycopsis are endobiotic holocarpic parasites of diverse hosts (e.g., diatoms, desmids, dinoflagellates). All species classified in this genus were assigned to it based on the presence of branching hyphae and the formation of two generations of zoospores, of which the first one is not motile. Originally, Aphanomycopsis with its type species, A. bacillariacearum, had been classified in the Saprolegniaceae. However, the genus has undergone multiple taxonomic reassignments (to Ectrogellaceae, Lagenidiaceae, and Leptolegniellaceae) in the past. To settle the taxonomy and investigate the phylogenetic placement of Aphanomycopsis, efforts were undertaken to isolate A. bacillariacearum from its original host, Pinnularia viridis and infer its phylogenetic placement based on nrSSU (18S) sequences. By targeted isolation, the diatom parasitoid was rediscovered from Heiðarvatn lake, Höskuldsstaðir, Iceland. Phylogenetic reconstruction shows that A. bacillariacearum from Pinnularia viridis is embedded within the Saprolegniales, and largely unrelated to both diatom-infecting oomycetes in the Leptomitales (Ectrogella, Lagenisma) and those placed within the early-diverging lineages (Miracula, Diatomophthora) of the Oomycota.

Current distribution and potential expansion of the harmful benthic dinoflagellate Ostreopsis cf. siamensis towards the warming waters of the Bay of Biscay, North-East Atlantic

In a future scenario of increasing temperatures in North-Atlantic waters, the risk associated with the expansion of the harmful, benthic dinoflagellate Ostreopsis cf. siamensis has to be evaluated and monitored. Microscopy observations and spatio-temporal surveys of environmental DNA (eDNA) were associated with Lagrangian particle dispersal simulations to: (i) establish the current colonization of the species in the Bay of Biscay, (ii) assess the spatial connectivity among sampling zones that explain this distribution, and (iii) identify the sentinel zones to monitor future expansion. Throughout a sampling campaign carried out in August to September 2018, microscope analysis showed that the species develops in the south-east of the bay where optimal temperatures foster blooms. Quantitative PCR analyses revealed its presence across almost the whole bay to the western English Channel. An eDNA time-series collected on plastic samplers showed that the species occurs in the bay from April to September. Due to the water circulation, colonization of the whole bay from the southern blooming zones is explained by inter-site connectivity. Key areas in the middle of the bay permit continuous dispersal connectivity towards the north. These key areas are proposed as sentinel zones to monitor O. cf. siamensis invasions towards the presumably warming water of the North-East Atlantic.

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

In this study, we created a dataset of a continuous three-year 18S metabarcoding survey to identify eukaryotic parasitoids, and potential connections to hosts at the Long-Term Ecological Research station Helgoland Roads. The importance of parasites and parasitoids for food web dynamics has previously been recognized mostly in terrestrial and freshwater systems, while marine planktonic parasitoids have been understudied in comparison to those. Therefore, the occurrence and role of parasites and parasitoids remains mostly unconsidered in the marine environment. We observed high abundances and diversity of parasitoid operational taxonomic units in our dataset all year round. While some parasitoid groups were present throughout the year and merely fluctuated in abundances, we also detected a succession of parasitoid groups with peaks of individual species only during certain seasons. Using co-occurrence and patterns of seasonal occurrence, we were able to identify known host-parasitoid dynamics, however identification of new potential host-parasitoid interactions was not possible due to their high dynamics and variability in the dataset.

Diatomophthoraceae - a new family of olpidiopsis-like diatom parasitoids largely unrelated to Ectrogella

The oomycete genus Ectrogella currently comprises a rather heterogeneous group of obligate endoparasitoids, mostly of diatoms and algae. Despite their widespread occurrence, little is known regarding the phylogenetic affinities of these bizarre organisms. Traditionally, the genus was included within the Saprolegniales, based on zoospore diplanetism and a saprolegnia/achlya-like zoospore discharge. The genus has undergone multiple re-definitions in the past, and has often been used largely indiscriminately for oomycetes forming sausage-like thalli in diatoms. While the phylogenetic affinity of the polyphyletic genus Olpidiopsis has recently been partially resolved, taxonomic placement of the genus Ectrogella remained unresolved, as no sequence data were available for species of this genus. In this study, we report the phylogenetic placement of Ectrogella bacillariacearum infecting the freshwater diatom Nitzschia sigmoidea. The phylogenetic reconstruction shows that Ectrogella bacillariacearum is grouped among the early diverging lineages of the Saprolegniomycetes with high support, and is unrelated to the monophyletic diatom-infecting olpidiopsis-like species. As these species are neither related to Ectrogella, nor to the early diverging lineages of Olpidiopsis s. str. and Miracula, they are placed in a new genus, Diatomophthora, in the present study.

Host and pathogen autophagy are central to the inducible local defences and systemic response of the giant kelp Macrocystis pyrifera against the oomycete pathogen Anisolpidium ectocarpii

Kelps are key primary producers of cold and temperate marine coastal ecosystems and exhibit systemic defences against pathogens. Yet, the cellular mechanisms underpinning their immunity remain to be elucidated. We investigated the time course of infection of the kelp Macrocystis pyrifera by the oomycete Anisolpidium ectocarpii using TEM, in vivo autophagy markers and autophagy inhibitors. Over several infection cycles, A. ectocarpii undergoes sequential physiological shifts sensitive to autophagy inhibitors. Initially lipid-rich, pathogen thalli become increasingly lipid-depleted; they subsequently tend to become entirely abortive, irrespective of their lipid content. Moreover, infected algal cells mount local defences and can directly eliminate the pathogen by xenophagy. Finally, autophagy-dependent plastid recycling is induced in uninfected host cells. We demonstrate the existence of local, inducible autophagic processes both in the pathogen and infected host cells, which result in the restriction of pathogen propagation. We also show the existence of a systemic algal response mediated by autophagy. We propose a working model accounting for all our observations, whereby the outcome of the algal-pathogen interaction (i.e. completion or not of the pathogen life cycle) is dictated by the induction, and possibly the mutual hijacking, of the host and pathogen autophagy machineries.

Phylogeny and cultivation of the holocarpic oomycete Diatomophthora perforans comb. nov., an endoparasitoid of marine diatoms

Oomycetes infecting diatoms are biotrophic parasitoids and live in both marine and freshwater environments. They are ubiquitous, but the taxonomic affinity of many species remains unclear and the majority of them have not been studied for their molecular phylogeny. Only recently, the phylogenetic and taxonomic placement of some diatom-infecting, early-diverging oomycetes was resolved, including the genera Ectrogella, Miracula, Olpidiopsis, and Pontisma. A group of holocarpic diatom parasitoids with zoospores swarming within the sporangium before release were found to be unrelated to the known genera with diatom-infecting species, and were re-classified to a new genus, Diatomophthora. However, about a dozen species of holocarpic diatom parasitoids with unclear affinity remained unsequenced, which includes a commonly occurring species so far identified as Ectrogella perforans. However, this assignment to Ectrogella is doubtful, as the species was not reported to feature a clear-cut diplanetism, a hallmark of Ectrogella s. str. and the whole class Saprolegniomycetes. It was the aim of the current study to clarify the phylogenetic affinities of the species and if the rather broad host range reported is correct or a reflection of cryptic species. By targeted screening, the parasitoid was rediscovered from Helgoland Roads, North Sea and Oslo Fjord, Southern Norway and investigated for its phylogenetic placement using small ribosomal subunit (18S) sequences. Stages of its life cycle on different marine diatoms were described and its phylogenetic placement in the genus Diatomophthora revealed. A stable host-parasite axenic culture from single spore strains of the parasitoid were established on several strains of Pleurosigma intermedium and Coscinodiscus concinnus. These have been continuously cultivated along with their hosts for more than 2 years, and cultural characteristics are reported. Cross-infection trials revealed the transferability of the strains between hosts under laboratory conditions, despite some genetic distance between the pathogen strains. Thus, we hypothesise that D. perforans might be in the process of active radiation to new host species.

Bolbea parasitica gen. et sp. nov., a cultivable holocarpic parasitoid of the early-diverging Saprolegniomycetes

Holocarpic oomycetes convert their entire cytoplasm into zoospores and thus do not form dedicated sporangia or hyphal compartments for asexual reproduction. The majority of holocarpic oomycetes are obligate parasites and parasitoids of a diverse suite of organisms, among them green and red algae, brown seaweeds, diatoms, fungi, oomycetes and invertebrates. Most of them are found among the early diverging oomycetes or the Peronosporomycetes, and some in the early-diverging Saprolegniomycetes (Leptomitales). The obligate parasitism renders it difficult to study some of these organisms. Only a few members of the genus Haliphthoross. l. have been cultured without their hosts, and of the parasitoid Leptomitales, some transient cultures have been established, which are difficult to maintain. Here, the cultivation of a new holocarpic oomycete genus of the Leptomitales, Bolbea, is presented. Bolbea is parasitic to ostracods, is readily cultivable on malt extract agar, and upon contact with water converts its cytoplasm into zoospores. Its morphology and phylogenetic relationships are reported. Due to the ease of cultivation and the ready triggering of zoospore development, similar to some lagenidiaceous oomycetes, the species could be a promising model to study sporulation processes in detail.

Analysis of interdomain taxonomic patterns in urban street mats

Streets are constantly crossed by billions of vehicles and pedestrians. Their gutters, which convey stormwater and contribute to waste management, and are important for human health and well-being, probably play a number of ecological roles. Street surfaces may also represent an important part of city surface areas. To better characterize the ecology of this yet poorly explored compartment, we used filtration and DNA metabarcoding to address microbial community composition and assembly across the city of Paris, France. Diverse bacterial and eukaryotic taxonomic groups were identified, including members involved in key biogeochemical processes, along with a number of parasites and putative pathogens of human, animals and plants. We showed that the beta diversity patterns between bacterial and eukaryotic communities were correlated, suggesting interdomain associations. Beta diversity analyses revealed the significance of biotic factors (cohesion metrics) in shaping gutter microbial community assembly and, to a lesser extent, the contribution of abiotic factors (pH and conductivity). Co-occurrences analysis confirmed contrasting non-random patterns both within and between domains of life, specifically when comparing diatoms and fungi. Our results highlight microbial coexistence patterns in streets and reinforce the need to further explore biodiversity in urban ground transportation infrastructures.

"Ectrogella" Parasitoids of the Diatom Licmophora sp. are Polyphyletic

The diatom genera Licmophora and Fragilaria are frequent epiphytes on marine macroalgae and can be infected by intracellular parasitoids traditionally assigned to the oomycete genus Ectrogella. Much debate and uncertainty remains about the taxonomy of these oomycetes, not least due to their morphological and developmental plasticity. Here, we used single-cell techniques to obtain partial sequences of the parasitoids 18S and cox2 genes. The former falls into two recently identified clades of Pseudo-nitzschia parasites temporarily named OOM_1_2 and OOM_2, closely related to the genera of brown and red algal pathogens Anisolpidium and Olpidiopsis. A third group of sequences falls at the base of the red algal parasites assigned to Olpidiopsis. In one instance, two oomycete parasitoids seemed to co-exist in a single diatom cell; this co-occurrence of distinct parasitoid taxa not only within a population of diatom epiphytes, but also within the same host cell, possibly explains the ongoing confusion in the taxonomy of these parasitoids. We demonstrate the polyphyly of Licmophora parasitoids previously assigned to Ectrogella (sensu Sparrow, 1960) and show that parasites of red algae assigned to the genus Olpidiopsis are most likely not monophyletic. We conclude that combining single-cell microscopy and molecular methods is necessary for their full characterisation.