Temporal Variability and Ecological Interactions of Parasitic Marine Syndiniales in Coastal Protist Communities

Interaction patterns and assembly mechanisms of dinoflagellates and diatoms in a coastal bay suffering from long-term eutrophication

Dinoflagellates and diatoms are highly prevalent and ecologically important phytoplankton in coastal waters, greatly contributing to primary productivity in marine ecosystems. Although their composition and diversity have been extensively elucidated in the open ocean, their interaction patterns and community assembly in long-term eutrophic coastal waters remain poorly understood. This investigation aimed to elucidate the seasonal successional patterns of dinoflagellates and diatoms by 18S rRNA gene amplicon sequencing in a semi-enclosed bay. The results revealed that dinoflagellate and diatom communities have pronounced seasonal succession patterns, which are primarily associated with temperature. Furthermore, the most prevalent species throughout the year were Heterocapsa rotundata and Skeletonema costatum. Moreover, the assembly of dinoflagellate and diatom communities was mainly dominated by stochastic processes, with drift being the major factor. The co-occurrence of dinoflagellates and diatoms showed seasonal patterns, with the highest interactions observed in autumn. In addition, interactions of Syndiniales with dinoflagellates and diatoms highlighted the roles of parasites in eutrophic conditions. Flavobacteriaceae and Rhodobacteraceae are the bacterial taxa that most frequently interacted with dinoflagellates and diatoms, with interactions between dinoflagellates and bacteria being more complex than those between diatoms and bacteria. Overall, this study provides results that deepen our understanding of the phytoplankton dynamics in coastal eutrophic waters.IMPORTANCEDinoflagellates and diatoms are major phytoplankton groups in coastal waters. The composition and diversity of dinoflagellates and diatoms in the open ocean have been well documented; however, it remains uncertain to what extent their adaptation to long-term eutrophic conditions influences their response to environmental disturbances. Here, we investigated the interactions and assembly processes of dinoflagellates and diatoms in a eutrophic bay throughout the whole year. Our findings revealed that interactions between dinoflagellates and diatoms are primarily shaped by seasonal transitions, while prolonged eutrophic conditions tend to amplify stochastic processes in community assembly. These findings provide novel perspectives on the influence of long-term eutrophication on phytoplankton dynamics within eutrophic waters.

Biogeographical and biodiversity patterns of planktonic microeukaryotes along the tropical western to eastern Pacific Ocean transect revealed by metabarcoding

Microeukaryotic plankton (0.2-200 µm), which are morphologically and genetically highly diverse, play a crucial role in ocean productivity and carbon consumption. The Pacific Ocean (PO), one of the world's largest oligotrophic regions, remains largely unexplored in terms of the biogeography and biodiversity of microeukaryotes based on large-scale sampling. We investigated the horizontal distribution of microeukaryotes along a 16,000 km transect from the west to the east of the PO. The alpha diversity indices showed a distinct decreasing trend from west to east, which was highly correlated with water temperature. The microeukaryotic community, which was clustered into the western, central, and eastern PO groups, displayed a significant distance-decay relationship. Syndiniales, a lineage of parasitic dinoflagellates, was ubiquitously distributed along the transect and dominated the community in terms of both sequence and zero-radius operational taxonomic unit (ZOTU) proportions. The prevailing dominance of Syndiniales-affiliated ZOTUs and their close associations with dinoflagellates, diatoms, and radiolarians, as revealed by SparCC correlation analysis, suggested that parasitism may be an important trophic strategy in the surface waters of the PO. Geographical distance and temperature were the most important environmental factors that significantly correlated with community structure. Overall, our study sheds more light on the distribution pattern of both alpha and beta diversities of microeukaryotic communities and highlighted the importance of parasitisms by Syndiniales across the tropical PO.IMPORTANCEUnderstanding the biogeographical and biodiversity patterns of microeukaryotic communities is essential to comprehending their roles in biogeochemical cycling. In this study, planktonic microeukaryotes were collected along a west-to-east Pacific Ocean transect (ca. 16,000 km). Our study revealed that the alpha diversity indices were highly correlated with water temperature, and the microeukaryotic communities displayed a distinct geographical distance-driven pattern. The predominance of the parasitic dinoflagellate lineage Syndiniales and their close relationship with other microeukaryotic groups suggest that parasitism may be a crucial survival strategy for microeukaryotes in the surface waters of the Pacific Ocean. Our findings expand our understanding of the biodiversity and biogeographical pattern of microeukaryotes and highlight the significance of parasitic Syndiniales in the surface ocean.

Spring protistan communities in response to warming in the northeastern East China Sea

The northeastern East China Sea is a highly dynamic marine ecosystem influenced by seasonally varying water mass properties. However, despite being among the world's fastest-warming ocean, there has been limited investigation into the impacts of warming on protistan communities. We collected seawater from two stations (E42 and E46) with different natural protist communities and environmental attributes to investigate the acclimation of the two communities to artificially elevated temperatures (ambient T, +2, and +4 °C). Nutrient and Chl-a conditions reflected oceanographic differences, providing insights into protistan community dynamics. Notably, small-sized autotrophic protists prevailed in the phosphate-deficient E42 community, with mid-incubation heterotrophic conversions. Higher temperatures exacerbated the effects of the P deficiency on the E42 community. While the proportions of Bacillariophyta increased only in the nutrient-balanced E46 communities, those of mixotrophic dinoflagellates increased with elevated temperature, regardless of P deficiency, suggesting that mixotrophy likely aids adaptation in changing marine environments. In summary, the findings of this microcosm study illuminate the potential modulation of spring protistan communities in the northeastern East China Sea under anticipated future warming.

eDNA metabarcoding reveals biodiversity and depth stratification patterns of dinoflagellate assemblages within the epipelagic zone of the western Coral Sea

BACKGROUND

Dinoflagellates play critical roles in the functioning of marine ecosystems but also may pose a hazard to human and ecosystem health by causing harmful algal blooms (HABs). The Coral Sea is a biodiversity hotspot, but its dinoflagellate assemblages in pelagic waters have not been studied by modern sequencing methods. We used metabarcoding of the 18 S rRNA V4 amplicon to assess the diversity and structure of dinoflagellate assemblages throughout the water column to a depth of 150 m at three stations in the Western Coral Sea. Additionally, at one station we compared metabarcoding with morphological methods to optimise identification and detection of dinoflagellates.

RESULTS

Stratification of dinoflagellate assemblages was evident in depth-specific relative abundances of taxonomic groups; the greatest difference was between the 5-30 m assemblages and the 130-150 m assemblages. The relative abundance of Dinophyceae (photosynthetic and heterotrophic) decreased with increasing depth, whereas that of Syndiniales (parasitic) increased with increasing depth. The composition of major taxonomic groups was similar among stations. Taxonomic richness and diversity of amplicon sequence variants (ASVs) were similar among depths and stations; however, the abundance of dominant taxa was highest within 0-30 m, and the abundance of rare taxa was highest within 130-150 m, indicating adaptations to specific depth strata. The number of unclassified ASVs at the family and species levels was very high, particularly for Syndinian representatives.

CONCLUSIONS

Dinoflagellate assemblages in open water of the Coral Sea are highly diverse and taxonomically stratified by depth; patterns of relative abundance along the depth gradient reflect environmental factors and ecological processes. Metabarcoding detects more species richness than does traditional microscopical methods of sample analysis, yet the methods are complementary, with morphological analysis revealing additional richness. The large number of unclassified dinoflagellate-ASVs indicates a need for improved taxonomic reference databases and suggests presence of dinoflagellate-crypto and-morphospecies.

Insight into planktonic protistan and fungal communities across the nutrient-depleted environment of the South Pacific Subtropical Gyre

Ocean microorganisms constitute ~70% of the marine biomass, contribute to ~50% of the Earth's primary production, and play a vital role in global biogeochemical cycles. The marine heterotrophic and mixotrophic protistan and fungal communities have often been overlooked mainly due to limitations in morphological species identification. Despite the accumulation of studies on biogeographic patterns observed in microbial communities, our understanding of the abundance and distribution patterns within the microbial community of the largest subtropical gyre, the South Pacific Gyre (SPG), remains incomplete. Here, we investigated the diversity and vertical composition of protistan and fungal communities in the water column of the ultra-oligotrophic SPG. Our results showed apparent differences in protistan community diversity in the photic and aphotic regions. The entire protistan community diversity was significantly affected by temperature, salinity, oxygen, and nutrient concentrations, while the parasitic community diversity was also affected by chlorophyll a concentration. The parasitic protists were assigned to the class Syndiniales accounting for over 98% of the total parasitic protists, exhibiting higher relative sequence abundance along the water depth and displaying consistent patterns among different sampling stations. In contrast to the protistan community, the fungal community along the SPG primarily clustered based on the sampling station and pelagic zones. In particular, our study reveals a significant presence of parasitic protists and functionally diverse fungi in SPG and their potential impact on carbon cycling in the gyre.IMPORTANCEOur findings carry important implications for understanding the distribution patterns of the previously unrecognized occurrence of parasitic protists and functionally diverse fungi in the nutrient-limited South Pacific Gyre. In particular, our study reveals a significant presence of parasitic Syndiniales, predominantly abundant in the upper 300 m of the aphotic zone in the gyre, and a distinct presence of fungal communities in the aphotic zone at the central part of the gyre. These findings strongly suggest that these communities play a substantial role in yet insufficiently described microbial food web. Moreover, our research enhances our understanding of their contribution to the dynamics of the food webs in oligotrophic gyres and is valuable for projecting the ecological consequences of future climate warming.

Gazing into the abyss: A glimpse into the diversity, distribution, and behaviour of heterotrophic protists from the deep-sea floor

The benthic biome of the deep-sea floor, one of the largest biomes on Earth, is dominated by diverse and highly productive heterotrophic protists, second only to prokaryotes in terms of biomass. Recent evidence suggests that these protists play a significant role in ocean biogeochemistry, representing an untapped source of knowledge. DNA metabarcoding and environmental sample sequencing have revealed that deep-sea abyssal protists exhibit high levels of specificity and diversity across local regions. This review aims to provide a comprehensive summary of the known heterotrophic protists from the deep-sea floor, their geographic distribution, and their interactions in terms of parasitism and predation. We offer an overview of the most abundant groups and discuss their potential ecological roles. We argue that the exploration of the biodiversity and species-specific features of these protists should be integrated into broader deep-sea research and assessments of how benthic biomes may respond to future environmental changes.

Role of Syndiniales parasites in depth-specific networks and carbon flux in the oligotrophic ocean

Microbial associations that result in phytoplankton mortality are important for carbon transport in the ocean. This includes parasitism, which in microbial food webs is dominated by the marine alveolate group, Syndiniales. Parasites are expected to contribute to carbon recycling via host lysis; however, knowledge on host dynamics and correlation to carbon export remain unclear and limit the inclusion of parasitism in biogeochemical models. We analyzed a 4-year 18S rRNA gene metabarcoding dataset (2016-19), performing network analysis for 12 discrete depths (1-1000 m) to determine Syndiniales-host associations in the seasonally oligotrophic Sargasso Sea. Analogous water column and sediment trap data were included to define environmental drivers of Syndiniales and their correlation with particulate carbon flux (150 m). Syndiniales accounted for 48-74% of network edges, most often associated with Dinophyceae and Arthropoda (mainly copepods) at the surface and Rhizaria (Polycystinea, Acantharea, and RAD-B) in the aphotic zone. Syndiniales were the only eukaryote group to be significantly (and negatively) correlated with particulate carbon flux, indicating their contribution to flux attenuation via remineralization. Examination of Syndiniales amplicons revealed a range of depth patterns, including specific ecological niches and vertical connection among a subset (19%) of the community, the latter implying sinking of parasites (infected hosts or spores) on particles. Our findings elevate the critical role of Syndiniales in marine microbial systems and reveal their potential use as biomarkers for carbon export.

Increased contribution of parasites in microbial eukaryotic communities of different Aegean Sea coastal systems

Background-Aim

Protistan communities have a major contribution to biochemical processes and food webs in coastal ecosystems. However, related studies are scarce and usually limited in specific groups and/or sites. The present study examined the spatial structure of the entire protistan community in seven different gulfs and three different depths in a regional Mediterranean Sea, aiming to define taxa that are important for differences detected in the marine microbial network across the different gulfs studied as well as their trophic interactions.

Methods

Protistan community structure analysis was based on the diversity of the V2-V3 hypervariable region of the 18S rRNA gene. Operational taxonomic units (OTUs) were identified using a 97% sequence identity threshold and were characterized based on their taxonomy, trophic role, abundance and niche specialization level. The differentially abundant, between gulfs, OTUs were considered for all depths and interactions amongst them were calculated, with statistic and network analysis.

Results

It was shown that Dinophyceae, Bacillariophyta and Syndiniales were the most abundant groups, prevalent in all sites and depths. Gulfs separation was more striking at surface corroborating with changes in environmental factors, while it was less pronounced in higher depths. The study of differentially abundant, between gulfs, OTUs revealed that the strongest biotic interactions in all depths occurred between parasite species (mainly Syndiniales) and other trophic groups. Most of these species were generalists but not abundant highlighting the importance of rare species in protistan community assemblage.

Conclusion

Overall this study revealed the emergence of parasites as important contributors in protistan network regulation regardless of depth.

Food for all? Wildfire ash fuels growth of diverse eukaryotic plankton

In December 2017, one of the largest wildfires in California history, the Thomas Fire, created a large smoke and ash plume that extended over the northeastern Pacific Ocean. Here, we explore the impact of Thomas Fire ash deposition on seawater chemistry and the growth and composition of natural microbial communities. Experiments conducted in coastal California waters during the Thomas Fire revealed that leaching of ash in seawater resulted in significant additions of dissolved nutrients including inorganic nitrogen (nitrate, nitrite and ammonium), silicic acid, metals (iron, nickel, cobalt and copper), organic nitrogen and organic carbon. After exposure to ash leachate at high (0.25 g ash l-1) and low (0.08 g ash l-1) concentrations for 4 days, natural microbial communities had 59-154% higher particulate organic carbon concentrations than communities without ash leachate additions. Additionally, a diverse assemblage of eukaryotic microbes (protists) responded to the ash leachate with taxa from 11 different taxonomic divisions increasing in relative abundance compared with control treatments. Our results suggest that large fire events can be important atmospheric sources of nutrients (particularly nitrogen) to coastal marine systems, where, through leaching of various nutrients, ash may act as a 'food for all' in protist communities.

Integrated Biogeography and Assembly Mechanisms of Microeukaryotic Communities in Coastal Waters Near Shellfish Cultivation

The Lianjiang coast in the East China Sea is a typical subtropical marine ecosystem, and shellfish cultivation occupies almost all of the available tidal flats. Many studies have investigated the effects of shellfish cultivation on benthic organisms and sediments, while the impact of shellfish cultivation on plankton ecosystems is still poorly understood. This study investigated the biogeographical patterns of microeukaryotic communities from Lianjiang coastal waters in four seasons using 18S ribosomal RNA gene amplicon sequencing. Microeukaryotes were mainly comprised of Dinoflagellata, Diatomea, Arthropoda, Ciliophora, Chlorophyta, Protalveolata, Cryptophyceae, and Ochrophyta, and presented significant differences in three habitats (the aquaculture area, confluent area, and offshore area) and four seasons. Similarity percentage analysis revealed that Paracalanus parvus, Heterocapsa rotundata, Bestiolina similis, and five additional key taxa contributed to spatio-temporal differences. Seasonal environmental and spatial factors explained 27.47% of microeukaryotic community variation on average, with 11.11% of the variation shared. Environmental variables, particularly depth, pH, and nitrite concentration, were strongly associated with the microeukaryotic community compositions. The neutral community model further demonstrated that stochastic processes were sufficient in shaping substantial variation in microeukaryotic communities across four seasons, which may reveal the remaining unexplained microeukaryotic community variation. We further divided four seasons into the aquaculture stages and non-aquaculture stages, and speculated that aquaculture activities may increase the dispersal limitation of microeukaryotes in coastal waters, especially for the big bodied-microbes like Arthropoda. The results provide a better understanding of the biogeographical patterns, processes, and mechanisms of microeukaryotic communities near shellfish cultivation.

Contrasting Mechanisms Determine the Microeukaryotic and Syndiniales Community Assembly in a Eutrophic bay

Syndiniales is a diverse parasitic group, increasingly gaining attention owing to its high taxonomic diversity in marine ecosystems and inhibitory effects on the dinoflagellate blooms. However, their seasonal dynamics, host interactions, and mechanisms of community assembly are largely unknown, particularly in eutrophic waters. Here, using 18S rRNA gene amplicon sequencing, we intended to elucidate the interactions between Syndiniales and microeukaryotes, as well as community assembly processes in a eutrophic bay. The results showed that Syndiniales group II was dominating throughout the year, with substantially higher abundance in the winter and spring, whereas Syndiniales group I was more abundant in the summer and autumn. Temperature and Dinoflagellata were the most important abiotic and biotic factors driving variations of the Syndiniales community, respectively. The assembly processes of microeukaryotes and Syndiniales were completely different, with the former being controlled by a balance between homogeneous selection and drift and the latter being solely governed by drift. Network analysis revealed that Syndiniales group II had the largest number of interactions with microeukaryotes, and they primarily associated with Dinoflagellata in the winter, while interactions with Chlorophyta and Bacillariophyta increased dramatically in summer and autumn. These findings provide significant insights in understanding the interactions and assembly processes of Syndiniales throughout the year, which is critical in revealing the roles of single-celled parasites in driving protist dynamics in eutrophic waters.

Benthic Heterotrophic Protist Communities of the Southern Baltic Analyzed with the Help of Curated Metabarcoding Studies

Heterotrophic protists are key components of marine ecosystems. They act as controllers of bacterial and microphytobenthos production and contribute significantly to the carbon flux to higher trophic levels. Still, metabarcoding studies on benthic protist communities are much less frequent than for planktonic organisms. Especially in the Baltic Sea, representing the largest brackish water environment on earth, so far, no extensive metabarcoding studies have been conducted to assess the diversity of benthic protists in this unique and diverse habitat. This study aims to give first insights into the diversity of benthic protist communities in two different regions of the Baltic Sea, Fehmarnbelt, and Oderbank. Using amplicon sequencing of the 18S rDNA V9 region of over 100 individual sediment samples, we were able to show significant differences in the community composition between the two regions and to give insights into the vertical distribution of protists within the sediment (0-20 cm). The results indicate that the differences in community composition in the different regions might be explained by several abiotic factors such as salinity and water depth, but are also influenced by methodological aspects such as differences between DNA and RNA results.

Symbiotic UCYN-A strains co-occurred with El Niño, relaxed upwelling, and varied eukaryotes over 10 years off Southern California

Biological nitrogen fixation, the conversion of N2 gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A's presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by "universal primers" from monthly samples and resolved into Amplicon Sequence Variants, allowing us to observe multiple UCYN-A symbioses. UCYN-A1 relative abundances increased following the 2015-2016 El Niño event. This "open ocean ecotype" was present when coastal upwelling declined, and Ekman transport brought tropical waters into the region. Network analyses reveal all strains of UCYN-A co-occur with dinoflagellates including Lepidodinium, a potential predator, and parasitic Syndiniales. UCYN-A2 appeared to pair with multiple hosts and was not tightly coupled to its predominant host, while UCYN-A1 maintained a strong host-symbiont relationship. These biological relationships are particularly important to study in the context of climate change, which will alter UCYN-A distribution at regional and global scales.

RNA outperforms DNA-based metabarcoding in assessing the diversity and response of microeukaryotes to environmental variables in the Arctic Ocean

The Arctic Ocean (AO) has a harsh environment characterized by low temperatures, extensive ice coverage, and periodic freezing and melting of sea ice, which has provided diverse habitats for microorganisms. Prior studies primarily focused on microeukaryote communities in the upper water or sea ice based on environmental DNA, leaving the composition of active microeukaryotes in the diverse AO environments largely unknown. This study provided a vertical assessment of microeukaryote communities in the AO from snow and ice to sea water at a depth of 1670 m using high-throughput sequencing of co-extracted DNA and RNA. RNA extracts depicted microeukaryote community structure and intergroup correlations more accurately and responded more sensitively to environmental conditions than those derived from DNA. Using RNA:DNA ratios as a proxy for relative activity of major taxonomic groups, the metabolic activities of major microeukaryote groups were determined along depth. Analysis of co-occurrence networks showed that parasitism between Syndiniales and dinoflagellates/ciliates in the deep ocean may be significant. This study increased our knowledge of the diversity of active microeukaryote communities and highlighted the importance of using RNA-based sequencing over DNA-based sequencing to examine the relationship between microeukaryote assemblages and the responses of microeukaryotes to environmental variables in the AO.

Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy

Protists (microbial eukaryotes) are a critically important but understudied group of microorganisms. They are ubiquitous, represent most of the genetic and functional diversity among eukaryotes, and play essential roles in nutrient and energy cycling. Yet, protists remain a black box in marine sedimentary ecosystems like the intertidal mudflats in the Bay of Fundy. The harsh conditions of the intertidal zone and high energy nature of tides in the Bay of Fundy provide an ideal system for gaining insights into the major food web players, diversity patterns and potential structuring influences of protist communities. Our 18S rDNA metabarcoding study quantified seasonal variations and vertical stratification of protist communities in Bay of Fundy mudflat sediments. Three 'SAR' lineages were consistently dominant (in terms of abundance, richness, and prevalence), drove overall community dynamics and formed the core microbiome in sediments. They are Cercozoa (specifically thecate, benthic gliding forms), Bacillariophyta (mainly cosmopolitan, typically planktonic diatoms), and Dinophyceae (dominated by a toxigenic, bloom-forming species). Consumers were the dominant trophic functional group and were comprised mostly of eukaryvorous and bacterivorous Cercozoa, and omnivorous Ciliophora, while phototrophs were dominated by Bacillariophyta. The codominance of Apicomplexa (invertebrate parasites) and Syndiniales (protist parasites) in parasite assemblages, coupled with broader diversity patterns, highlighted the combined marine and terrestrial influences on microbial communities inhabiting intertidal sediments. Our findings, the most comprehensive in a hypertidal benthic system, suggest that synergistic interactions of both local and regional processes (notably benthic-pelagic coupling) may drive heterogenous microbial distribution in high-energy coastal 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.

Microbial food webs share similar biogeographic patterns and driving mechanisms with depths in oligotrophic tropical western Pacific Ocean

Microbial food web (MFW) dominates the energy flow in oligotrophic tropical open ocean pelagic ecosystems. Understanding biogeographic patterns and driving mechanisms of key components of the MFW is one of the central topics in current marine ecology. Investigations were conducted along an 1,100-km horizontal gradient and in the full-water column vertical gradient of the oligotrophic tropical western Pacific Ocean. High-throughput sequencing and association networking methods were used to analyze the community structure and interspecies interactions of MFW. The structure of MFW significantly differed with depths, but not across horizontal gradients. Bacteria and microeukaryotes were interconnected and had more predominantly positive and negative linkages in the aphotic layers. Key components of MFW exhibited similar biogeographic patterns and driving mechanisms. Geographic distance exerted minimal effects on the distribution patterns of the microbial food web, while environmental factors played more important roles, especially for temperature and inorganic nutrients. Stochastic processes were more important in the microbial food webs of the 5-200  m layer than the >500  m layer, and drift explained the majority of stochastic processes. Moreover, only a weak but not significant driving force for North Equatorial Current on the east-west connectivity of the microbial food web was found in the upper layers. This knowledge is a critical fundamental data for future planning of marine protected areas targeting the protection of tuna fishing in the western Pacific Ocean.

Methodological 'lenses' influence the characterization of phytoplankton dynamics in a coastal upwelling ecosystem

New technologies enable the opportunity to improve our monitoring and understanding of marine phytoplankton communities. However, careful consideration for how different methodological approaches, or 'lenses', influence our interpretation of phytoplankton ecology is important, particularly when drawing conclusions about change over time or space. Using both high-throughput 18S rRNA gene sequencing and microscopy, we explored how phytoplankton community structure varied over the course of a year within a nearshore semi-enclosed coastal embayment along the Central Coast of California. The seasonal shift in the relative community dominance (i.e., diatom vs. dinoflagellate dominance) was captured in the microscopy results but not effectively captured in the molecular-based findings. However, the molecular approach explained more of the variability in composition across seasons relative to the microscopy approach. Temporal dynamics of specific bloom-forming taxa also differed between the molecular and microscopy results. Overall, the observed differences between the molecular- and microscopy-derived characterization of phytoplankton dynamics suggest that the approaches are best suited to answer different research questions. Moreover, the approaches complement each other for a more comprehensive perspective of a coastal phytoplankton ecosystem. Therefore, identifying the biases of each approach within natural communities is necessary to effectively and accurately characterize phytoplankton communities.

Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral

Dinoflagellates are a diverse protist group possessing many unique traits. These include (but are not limited to) expansive genomes packaged into permanently condensed chromosomes, photosynthetic or cryptic plastids acquired vertically or horizontally in serial endosymbioses, and a ruffle-like transverse flagellum attached along its length to the cell. When reconstructing character evolution, early branching lineages with unusual features that distinguish them from the rest of the group have proven useful for inferring ancestral states. The Noctilucales are one such lineage, possessing relaxed chromosomes in some life stages and a trailing, thread-like transverse flagellum. However, most of the cellular and molecular data for the entire group come from a single cultured species, Noctiluca scintillans, and because its phylogenetic position is unresolved it remains unclear if these traits are ancestral or derived. Here, we use single cell transcriptomics to characterize three diverse Noctilucales genera: Spatulodinium, Kofoidinium, and a new lineage, Fabadinium gen. nov. We also provide transcriptomes for undescribed species in Amphidinium and Abediniales, critical taxa for clarifying the phylogenetic position of Noctilucales. Phylogenomic analyses suggests that the Noctilucales are sister to Amphidinium rather than an independent branch outside the core dinoflagellates. This topology is consistent with observations of shared characteristics between some members of Noctilucales and Amphidinium and provides the most compelling evidence to date that the unusual traits within this group are derived rather than ancestral. We also confirm that Spatulodinium plastids are photosynthetic and of ancestral origin, and show that all non-photosynthetic Noctilucales retain plastid genes indicating a cryptic organelle.

Parasitic infections by Group II Syndiniales target selected dinoflagellate host populations within diverse protist assemblages in a model coastal pond

Protists are integral to marine food webs and biogeochemical cycles; however, there is a paucity of data describing specific ecological niches for some of the most abundant taxa in marker gene libraries. Syndiniales are one such group, often representing the majority of sequence reads recovered from picoplankton samples across the global ocean. However, the prevalence and impacts of syndinian parasitism in marine environments remains unclear. We began to address these critical knowledge gaps by generating a high-resolution time series (March-October 2018) in a productive coastal pond. Seasonal shifts in protist populations, including parasitic Syndiniales, were documented during periods of higher primary productivity and increased summer temperature-driven stratification. Elevated concentrations of infected hosts and free-living parasite spores occurred at nearly monthly intervals in July, August, and September. We suggest intensifying stratification during this period correlated with the increased prevalence of dinoflagellates that were parasitized by Group II Syndiniales. Infections in some protist populations were comparable to previously reported large single-taxon dinoflagellate blooms. Infection dynamics in Salt Pond demonstrated the propagation of syndinian parasites through mixed protist assemblages and highlighted patterns of host/parasite interactions that better reflect many other marine environments where single taxon blooms are uncommon.

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.

Metabarcoding Analysis of Harmful Algal Bloom Species in the Western Pacific Seamount Regions

The Western Pacific is the most oligotrophic sea on Earth, with numerous seamounts. However, the plankton diversity and biogeography of the Western Pacific in general and the seamount regions in particular remains largely unexplored. In this project, we quantitatively analyzed the composition and distribution patterns of plankton species in the Western Pacific seamount regions by applying metabarcoding analysis. We identified 4601 amplicon sequence variants (ASVs) representing 34 classes in seven protist phyla/divisions in the Western Pacific seamount regions, among which Dinoflagellata was by far the most dominant division. Among the 336 annotated phytoplankton species (including species in Dinoflagellata), we identified 36 harmful algal bloom (HAB) species, many of which displayed unique spatial distribution patterns in the Western Pacific seamount regions. This study was the first attempt in applying ASV-based metabarcoding analysis in studying phytoplankton and HAB species in the Western Pacific seamount regions, which may facilitate further research on the potential correlation between HABs in the Western Pacific seamount regions and coastal regions.

Small pigmented eukaryote assemblages of the western tropical North Atlantic around the Amazon River plume during spring discharge

Small pigmented eukaryotes (⩽ 5 µm) are an important, but overlooked component of global marine phytoplankton. The Amazon River plume delivers nutrients into the oligotrophic western tropical North Atlantic, shades the deeper waters, and drives the structure of microphytoplankton (> 20 µm) communities. For small pigmented eukaryotes, however, diversity and distribution in the region remain unknown, despite their significant contribution to open ocean primary production and other biogeochemical processes. To investigate how habitats created by the Amazon river plume shape small pigmented eukaryote communities, we used high-throughput sequencing of the 18S ribosomal RNA genes from up to five distinct small pigmented eukaryote cell populations, identified and sorted by flow cytometry. Small pigmented eukaryotes dominated small phytoplankton biomass across all habitat types, but the population abundances varied among stations resulting in a random distribution. Small pigmented eukaryote communities were consistently dominated by Chloropicophyceae (0.8-2 µm) and Bacillariophyceae (0.8-3.5 µm), accompanied by MOCH-5 at the surface or by Dinophyceae at the chlorophyll maximum. Taxonomic composition only displayed differences in the old plume core and at one of the plume margin stations. Such results reflect the dynamic interactions of the plume and offshore oceanic waters and suggest that the resident small pigmented eukaryote diversity was not strongly affected by habitat types at this time of the year.

Dinophyceae can use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales)

Parasites in the genus Amoebophrya sp. infest dinoflagellate hosts in marine ecosystems and can be determining factors in the demise of blooms, including toxic red tides. These parasitic protists, however, rarely cause the total collapse of Dinophyceae blooms. Experimental addition of parasite-resistant Dinophyceae (Alexandrium minutum or Scrippsiella donghaienis) or exudates into a well-established host-parasite coculture (Scrippsiella acuminata-Amoebophrya sp.) mitigated parasite success and increased the survival of the sensitive host. This effect was mediated by waterborne molecules without the need for a physical contact. The strength of the parasite defenses varied between dinoflagellate species, and strains of A. minutum and was enhanced with increasing resistant host cell concentrations. The addition of resistant strains or exudates never prevented the parasite transmission entirely. Survival time of Amoebophrya sp. free-living stages (dinospores) decreased in presence of A. minutum but not of S. donghaienis. Parasite progeny drastically decreased with both species. Integrity of the dinospore membrane was altered by A. minutum, providing a first indication on the mode of action of anti-parasitic molecules. These results demonstrate that extracellular defenses can be an effective strategy against parasites that protects not only the resistant cells producing them, but also the surrounding community.

Parasite-mediated increase in prey edibility in the predator-prey interaction of marine planktonic protists

In planktonic predator-prey interactions, predation pressure could be affected by several factors associated with prey, including cell size, shape, nutritional quality, presence of chemical deterrents, and movement behaviors. In addition, parasitism may also play an important role in predator-prey interaction by infecting one or both partners involved in the biological interaction. In this study, parasite mediation in predator-prey interactions of planktonic protists was addressed using model organisms commonly observed in temperate coastal environments, namely, a phototrophic dinoflagellate Akashiwo sanguinea as a potential host and prey, a heterotrophic dinoflagellate predator Luciella masanensis, and a dinoflagellates-infecting parasitoid Parvilucifera infectans. Parasite mediation permitted L. masanensis to exploit the prey A. sanguinea that the predator was otherwise unable to use or did not prefer. However, parasite-mediated exploitation seems to be dependent on the infection cycle of P. infectans. Although zoospores and mature sporangium produced from infected A. sanguinea were not ingested by the predator L. masanensis, both newly infected (i.e., cells that zoospores had just penetrated) and infected (those containing early to late trophocytes) A. sanguinea cells attracted numerous L. masanensis cells and were rapidly ingested by the predator, leading to the predator's positive growth. The results from mixed culture experiments of the three protists showed that the presence of P. infectans at low density led to co-occurrence of the three protists. Thus, the parasitoid seems to play the role of a mediator in either inedible prey- or predator-dominated environments, leading to co-occurrence of the three protists.