Protist Interactions and Community Structure During Early Autumn in the Kerguelen Region (Southern Ocean)

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.

Predation has a significant impact on the complexity and stability of microbial food webs in subalpine lakes

IMPORTANCE

As an important part of microbial food webs, protists transfer organic carbon and nutrients to higher trophic levels in aquatic ecosystems. Protist predation often influences the abundance and composition of bacterial communities. However, we still do not understand whether and how predation affects the complexity and stability of microbial food webs. This study assessed the seasonal dynamic characteristics and driving factors of microbial food webs in terms of complexity and stability. Our findings have implications for future surveys to reveal the effects of climate and environmental changes.

Mesoscale oceanographic meanders influence protist community function and structure in the southern Indian Ocean

The interface between the nutrient-rich Southern Ocean and oligotrophic Indian Ocean creates unique environmental conditions that can strongly influence biological processes. We investigated protist communities across a mesoscale meander of the Subtropical Front within the Southern Indian Ocean. 18S V9 rDNA metabarcoding suggests a diverse protist community in which the dinoflagellates and parasitic Syndiniales were abundant. Diversity was highest in frontal waters of the mesoscale meander, with differences in community structure inside and outside the meander. While the overall community was dominated by mixotrophic taxa, the frontal boundary of the meander had increased abundances of heterotrophic taxa, with potential implications for net atmospheric CO2 drawdown. Pulse amplitude modulated (PAM) fluorimetry revealed significant differences in the photophysiology of phytoplankton communities inside and outside the meander. By using single-cell PAM microscopy, we identified physiological differences between dinoflagellate and coccolithophore taxa, which may have contributed to changes in photophysiology observed at community level. Overall, our results demonstrate that frontal areas have a strong impact on the composition of protist communities in the Southern Ocean with important implications for understanding biological processes in this region.

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.

Diversity and putative interactions of parasitic alveolates belonging to Syndiniales at a coastal Pacific site

The dinoflagellate lineage Syndiniales currently consists entirely of parasitic species that fall into five well-supported clades. Environmental sequencing studies worldwide have found an abundance of Syndiniales in a variety of marine ecosystems, but very little is known about the majority of Syndiniales species including two entire clades which have only been observed in sequence data. Syndiniales are known to have a wide range of hosts, but only a few dozen interactions have been confirmed through observation of actual infections. Here, we describe the diversity of Syndiniales found at the Scripps Institution of Oceanography pier over the course of a year based on 18S sequencing. We find Syndiniales to be the most species (amplicon sequence variant)-rich taxonomic group and for its members to be present and abundant throughout the year. We used several analytical techniques to identify potential parasite-host interactions which we were then able to visualize over time. Using mock communities and size fractionation of seawater, we suggest that the majority of Syndiniales sequences that are found in environmental studies belong to the free-living dinospore stage rather than representing active infections.

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.

Estuarine microbial networks and relationships vary between environmentally distinct communities

Microbial interactions have profound impacts on biodiversity, biogeochemistry, and ecosystem functioning, and yet, they remain poorly understood in the ocean and with respect to changing environmental conditions. We applied hierarchical clustering of an annual 16S and 18S amplicon dataset in the Skidaway River Estuary, which revealed two similar clusters for prokaryotes (Bacteria and Archaea) and protists: Cluster 1 (March-May and November-February) and Cluster 2 (June-October). We constructed co-occurrence networks from each cluster to explore how microbial networks and relationships vary between environmentally distinct periods in the estuary. Cluster 1 communities were exposed to significantly lower temperature, sunlight, NO₃, and SiO₄; only NH₄ was higher at this time. Several network properties (e.g., edge number, degree, and centrality) were elevated for networks constructed with Cluster 1 vs. 2 samples. There was also evidence that microbial nodes in Cluster 1 were more connected (e.g., higher edge density and lower path length) compared to Cluster 2, though opposite trends were observed when networks considered Prokaryote-Protist edges only. The number of Prokaryote-Prokaryote and Prokaryote-Protist edges increased by >100% in the Cluster 1 network, mainly involving Flavobacteriales, Rhodobacterales, Peridiniales, and Cryptomonadales associated with each other and other microbial groups (e.g., SAR11, Bacillariophyta, and Strombidiida). Several Protist-Protist associations, including Bacillariophyta correlated with Syndiniales (Dino-Groups I and II) and an Unassigned Dinophyceae group, were more prevalent in Cluster 2. Based on the type and sign of associations that increased in Cluster 1, our findings indicate that mutualistic, competitive, or predatory relationships may have been more representative among microbes when conditions were less favorable in the estuary; however, such relationships require further exploration and validation in the field and lab. Coastal networks may also be driven by shifts in the abundance of certain taxonomic or functional groups. Sustained monitoring of microbial communities over environmental gradients, both spatial and temporal, is critical to predict microbial dynamics and biogeochemistry in future marine ecosystems.

Monitoring harmful microalgal species and their appearance in Tokyo Bay, Japan, using metabarcoding

During the recent decade, high-throughput sequencing (HTS) techniques, in particular, DNA metabarcoding, have facilitated increased detection of biodiversity, including harmful algal bloom (HAB) species. In this study, the presence of HAB species and their appearance patterns were investigated by employing molecular and light microscopy-based monitoring in Tokyo Bay, Japan. The potential co-appearance patterns between the HAB species, as well as with other eukaryotes and prokaryotes were investigated using correlation and association rule-based time-series analysis. In total, 40 unique HAB species were detected, including 12 toxin-producing HAB species previously not reported from the area. More than half of the HAB species were present throughout the sampling season (summer to autumn) and no structuring or succession patterns associated with the environmental conditions could be detected. Statistically significant (p < 0.05, rS ranging from −0.88 to 0.90) associations were found amongst the HAB species and other eukaryotic and prokaryotic species, including genera containing growth-limiting bacteria. However, significant correlations between species differed amongst the years, indicating that variability in environmental conditions between the years may have a stronger influence on the microalgal community structure and interspecies interactions than the variability during the sampling season. The association rule-based time-series analysis allowed the detection of a previously reported negative relationship between Synechococcus sp. and Skeletonema sp. in nature. Overall, the results support the applicability of metabarcoding and HTS-based microalgae monitoring, as it facilitates more precise species identification compared to light microscopy, as well as provides input for investigating potential interactions amongst different species/groups through simultaneous detection of multiple species/genera.

Diversity of Microbial Eukaryotes Along the West Antarctic Peninsula in Austral Spring

During a cruise from October to November 2019, along the West Antarctic Peninsula, between 64.32 and 68.37°S, we assessed the diversity and composition of the active microbial eukaryotic community within three size fractions: micro- (> 20 μm), nano- (20-5 μm), and pico-size fractions (5-0.2 μm). The communities and the environmental parameters displayed latitudinal gradients, and we observed a strong similarity in the microbial eukaryotic communities as well as the environmental parameters between the sub-surface and the deep chlorophyll maximum (DCM) depths. Chlorophyll concentrations were low, and the mixed layer was shallow for most of the 17 stations sampled. The richness of the microplankton was higher in Marguerite Bay (our southernmost stations), compared to more northern stations, while the diversity for the nano- and pico-plankton was relatively stable across latitude. The microplankton communities were dominated by autotrophs, mostly diatoms, while mixotrophs (phototrophs-consuming bacteria and kleptoplastidic ciliates, mostly alveolates, and cryptophytes) were the most abundant and active members of the nano- and picoplankton communities. While phototrophy was the dominant trophic mode, heterotrophy (mixotrophy, phagotrophy, and parasitism) tended to increase southward. The samples from Marguerite Bay showed a distinct community with a high diversity of nanoplankton predators, including spirotrich ciliates, and dinoflagellates, while cryptophytes were observed elsewhere. Some lineages were significantly related-either positively or negatively-to ice coverage (e.g., positive for Pelagophyceae, negative for Spirotrichea) and temperature (e.g., positive for Cryptophyceae, negative for Spirotrichea). This suggests that climate changes will have a strong impact on the microbial eukaryotic community.

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.

Small phytoplankton contribute greatly to CO2-fixation after the diatom bloom in the Southern Ocean

Phytoplankton is composed of a broad-sized spectrum of phylogenetically diverse microorganisms. Assessing CO₂-fixation intra- and inter-group variability is crucial in understanding how the carbon pump functions, as each group of phytoplankton may be characterized by diverse efficiencies in carbon fixation and export to the deep ocean. We measured the CO₂-fixation of different groups of phytoplankton at the single-cell level around the naturally iron-fertilized Kerguelen plateau (Southern Ocean), known for intense diatoms blooms suspected to enhance CO₂ sequestration. After the bloom, small cells (<20 µm) composed of phylogenetically distant taxa (prymnesiophytes, prasinophytes, and small diatoms) were growing faster (0.37 ± 0.13 and 0.22 ± 0.09 division d^-1 on- and off-plateau, respectively) than larger diatoms (0.11 ± 0.14 and 0.09 ± 0.11 division d^-1 on- and off-plateau, respectively), which showed heterogeneous growth and a large proportion of inactive cells (19 ± 13%). As a result, small phytoplankton contributed to a large proportion of the CO₂ fixation (41-70%). The analysis of pigment vertical distribution indicated that grazing may be an important pathway of small phytoplankton export. Overall, this study highlights the need to further explore the role of small cells in CO₂-fixation and export in the Southern Ocean.

Response of protist community dynamics and co-occurrence patterns to the construction of artificial reefs: A case study in Daya Bay, China

Artificial reefs (ARs) are widely used for biodiversity conservation and coastal habitat restoration. Although protists play an important ecological role in marine ecosystems, the response of the protist community to ARs is still poorly understood. In the current study, an Illumina sequencing analysis of 18S rDNA was performed, and the diversity, community structure, and co-occurrence networks of protists in the ARs and open sea area (OW) in Daya Bay were described. The results indicated that significant seasonal differences occur in the seawater protists between the surface and bottom of the ARs and OW. However, the protists in the ARs and OW had different seasonal variations. The ARs always affected the alpha diversity of marine protists in different seasons, while the surface and bottom OW sites had different seasonal effects. The ARs sites had different effects on the community composition of the surface and bottom seawater in different seasons relative to the OW sites. The linear discriminant analysis (LDA) effect size (LEfSe) method showed that 85 biomarkers mainly belonging to 11 taxa, including Bacillariophyta, Chlorophyta, and Dinophyceae, were affected by the ARs (P < 0.05, LDA > 2.0). The ARs played an important role in the seasonal changes in the protist community composition and had different effects on the dominant species of protists in the surface and bottom seawater. A redundancy analysis (RDA) significance test showed that the structure of the protist community in Daya Bay was mainly affected by environmental factors, such as seawater temperature, salinity and dissolved oxygen. Compared with the OW group, the surface and bottom layers of the ARs had more complex protist interactions or more niches. The ARs increased the degree of spatial heterogeneity, which may lead to significant niche differentiation, indicating that ARs as habitat factors affect the complexity and stability of the symbiotic network of protists. The results could provide basic data on the response of the protist community to the ARs in Daya Bay and a reference for assessments of the impact of ARs on the ecological environment.

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

Syndiniales are a ubiquitous group of protist parasites that infect and kill a wide range of hosts, including harmful bloom-forming dinoflagellates. Despite the importance of parasitism as an agent of plankton mortality, parasite-host dynamics remain poorly understood, especially over time, hindering the inclusion of parasitism in food web and ecosystem models. For a full year in the Skidaway River Estuary (Georgia), we employed weekly 18S rRNA sampling and co-occurrence network analysis to characterize temporal parasite-host infection dynamics of Syndiniales. Over the year, Syndiniales exhibited strong temporal variability, with higher relative abundance from June to October (7 to 28%) than other months in the year (0.01% to 6%). Nonmetric dimensional scaling of Syndiniales composition revealed tight clustering in June to October that coincided with elevated temperatures (23 to 31°C), though in general, abiotic factors poorly explained composition (canonical correspondence analysis [CCA] and partial least-squares [PLS]) and were less important in the network than biotic relationships. Syndiniales amplicon sequence variants (ASVs) were well represented in the co-occurrence network (20% of edges) and had significant positive associations (Spearman r > 0.7), inferred to be putative parasite-host relationships, with known dinoflagellate hosts (e.g., Akashiwo and Gymnodinium) and other protist groups (e.g., ciliates, radiolarians, and diatoms). Positive associations rarely involved a single Syndiniales and dinoflagellate species, implying flexible parasite-host infection dynamics. These findings provide insight into the temporal dynamics of Syndiniales over a full year and reinforce the importance of single-celled parasites in driving plankton population dynamics. Further empirical work is needed to confirm network interactions and to incorporate parasitism within the context of ecosystem models.IMPORTANCE Protist parasites in the marine alveolate group, Syndiniales, have been observed within infected plankton host cells for decades, and recently, global-scale efforts (Tara Ocean exploration) have confirmed their importance within microbial communities. Yet, protist parasites remain enigmatic, particularly with respect to their temporal dynamics and parasite-host interactions. We employed weekly 18S amplicon surveys over a full year in a coastal estuary, revealing strong temporal shifts in Syndiniales parasites, with highest relative abundance during warmer summer to fall months. Though influenced by temperature, Syndiniales population dynamics were also driven by a high frequency of biological interactions with other protist groups, as determined through co-occurrence network analysis. Parasitic interactions implied by the network highlighted a range of confirmed (dinoflagellates) and putative (diatoms) interactions and suggests parasites may be less selective in their preferred hosts. Understanding parasite-host dynamics over space and time will improve our ability to include parasitism as a loss term in microbial food web models.