Search Results (24)

Kuibyshev Reservoir, the largest in the Volga basin, is poorly covered by modern molecular studies. The results of a metabarcoding study of pro- and eukaryotic microbial plankton in its lower section during the summer period are presented. Bacterioplankton composition was typical for most temperate freshwater bodies and characterized by the dominance of cyanobacteria, Pseudomonadota, Bacteroidota, Actinomycetota, and PVC superphylum (Verrucomicrobiota and Planctomycetota), with a somewhat increased proportion of the latter. The protist community was dominated by Cryptista, principally phototrophic, and various ciliates. Several picoeukaryotic groups were newly detected in the reservoir. A relationship between the composition of both bacterioplankton and protist communities and the stage of phytoplankton succession, including the cyanobacterial bloom, was observed. Some inconsistency between the cyanobacterial bloom phase and the structure of other parts of the microbial plankton is obviously due to some temporal delay, spatial station position, and inflow from tributaries. Heterotrophic bacterioplankton indicator species of the main bloom stage include OTUs representing both the phycosphere of colonial cyanobacteria and free-living species. Among the protists, sessile ciliates benefit most from plenty of substrates for colonization, while cyanobacterial grazers and parasites were minor. Overall, the cyanobacterial bloom creates new niches for the plankton community and significantly modifies its structure. Full article

Karst caves, formed by the erosion of soluble carbonate rocks, provide unique ecosystems characterized by stable temperatures and high humidity. These conditions support diverse microbial communities, including wall microbial fouling, aquatic biofilms, and planktonic communities. This study discloses the taxonomic diversity of protists in aquatic biotopes of Shulgan-Tash Cave, a culturally significant site and popular tourist destination, by 18S rRNA gene metabarcoding. Our findings reveal the rich protist communities in the cave’s aquatic biotopes, with the highest diversity observed in Blue Lake at the cave entrance. In contrast, Distant Lake in the depth of the cave was inhabited by specific communities of plankton, mats, and pool fingers, which exhibited lower richness and evenness, and were adapted to extreme conditions (cold, darkness, and limited nutrients). High-rank taxa including Opisthokonta, Stramenopiles, and Rhizaria dominated all biotopes, aligning with observations from other subterranean environments. Specific communities of biotopes inside the cave featured distinct dominant taxa: amoeboid stramenopile (Synchromophyceae) and flagellates (Choanoflagellatea and Sandona) in mats; flagellates (Choanoflagellatea, Bicoecaceae, Ancyromonadida) and amoeboid protists (Filasterea) in pool fingers; flagellates (Ochromonadales, Glissomonadida, Synchromophyceae), fungi-like protists (Peronosporomycetes), and fungi (Ustilaginomycotina) in plankton. The specificity of the communities was supported by LEfSe analysis, which revealed enriched or differentially abundant protist taxa in each type of biotope. The predominance of Choanoflagellatea in the communities of cave mats and pool fingers, as well as the predominance of Synchromophyceae in the cave mats, appears to be a unique feature of Shulgan-Tash Cave. The cold-tolerant yeast Malassezia recorded in other caves was present in both plankton and biofilm communities, suggesting its resilience to low temperatures. However, no potentially harmful fungi were detected, positioning this research as a baseline for future monitoring. Our results emphasize the need for ongoing surveillance and conservation efforts to protect the fragile ecosystems of Shulgan-Tash Cave from human-induced disturbances and microbial invasions. Full article

Plankton studies serve as a basis for marine ecosystem research, but knowledge of marine plankton is still incomplete due to its extreme taxonomic and functional complexity. The application of metabarcoding is very valuable for the characterisation of the plankton community. The plankton community of the Southern Adriatic is subject to strong environmental fluctuations and changes, which underlines the need for frequent, reliable and comprehensive characterisation of the plankton. The aim of this study was to determine the taxonomic composition and seasonal distribution of eukaryotic plankton in the Southern Adriatic. Plankton samples were collected monthly for one year at the coastal station of the Southern Adriatic and metabarcoding was used for taxonomic identification. The results showed a high taxonomic diversity and dynamic seasonal distribution patterns for both the protist and metazoan plankton communities. Metabarcoding revealed both the core, year-round plankton community and previously unrecorded plankton organisms in the Southern Adriatic. The results provide for the first time a comprehensive overview of the plankton community in this area by metabarcoding. The identified seasonal patterns of plankton genera and species in the Southern Adriatic will contribute to the understanding of plankton interactions and future changes in community diversity characterisation. Full article

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. Full article

Saline and hypersaline waters are one of the most peculiar ecosystems of our planet, characterized by extreme life conditions. Despite their worldwide distribution, the diversity and abundance of protist communities in these ecosystems remain poorly studied. Here, we analyze planktonic communities of protists sampled across 38 saline and hypersaline water environments (2–390‰) from arid climatic zones of the South Urals and Crimea in light of environmental data using high-throughput 18S rDNA amplicon sequencing. A total of 9 eukaryotic supergroups, 34 phyla, 104 classes, 184 orders, 315 families and 548 genera have been identified. We revealed significant differences in the taxonomic structure of protist communities depending on salinity, geographic location and pH. The protist communities demonstrated linear regression of richness and diversity and growth of the percentage of unclassified Eukaryota (up to 43%) with the increase in salinity. Centrohelids demonstrated the ability to inhabit a broad range of salinities, up to 320‰, which is four times higher than previously reported. Centrohelid species Pinjata ruminata and Yogsothoth sp. are assumed to be specifically adapted to salinity of 3–210‰. The obtained results provide insight into the taxonomy and diversity of protists in saline and hypersaline environments and highlight the great potential for the discovery of new taxa due to the large number of unclassified 18S rDNA sequences. Full article

Prorocentrum comprises dinophytes with several unique traits, including the presence of two large thecal plates and apical insertion of flagella. Species delimitation for many small and similar planktonic species is challenging, as SEM analyses and DNA sequence information of type material are rarely available. Based on a strain from the North Atlantic Prorocentrum spinulentum, sp. nov. is described here. Cells were small (9.0–12.8 µm long, 8.5–11.9 µm deep), oval to almost round in lateral view and moderately compressed. The ovoid nucleus was in median or slightly sub-median position on the cells ventral side. The plate surface appeared spiny in light microscopy with thecal pores visible in empty thecae. Electron microscopy revealed plates densely covered by relatively long spines and two size classes of thecal pores. The periflagellar area consisted of 8 platelets, and there was a prominent wing (ca. 1 µm wide and long) on platelet 1. The new species is distinct in DNA trees and embedded in the Prorocentrum shikokuense species group. It differs from the protologues of other small species of Prorocentrum by the unique combination of cell size and shape, the presence of long spines on the thecal plate surface and scattered thecal pores. The thorough morphological description of this species, representing a previously uncharacterised lineage within Prorocentrum, increases and improves our knowledge of the diversity within this important group of planktonic organisms. Full article

High-throughput sequencing technologies have revolutionized microbial diversity studies, shedding light on the oceans’ plankton evolution, distribution, and biological activity. Whereas marine prokaryotes have been more extensively studied and specific methods developed, the research on microbial eukaryotes (protists) is falling behind, with major groups still largely unknown regarding their ecology and function. Because of numerous anthropogenic pressures, it is increasingly important to highlight the functional roles of protists in marine ecosystems. This review outlines the practices, challenges, and opportunities of high-throughput sequencing approaches (i.e., metabarcoding, metagenomics, and metatranscriptomics) to disentangle evolutionary, ecological, and functional aspects of protists in the ocean. These multidimensional approaches allow us to move from the classic picture of microbial biogeography towards functional microbial biogeography, explicitly highlighting the role of protists therein. We provide resources for functional classification and reflect on the current and future potential. We outline aspects of detecting and describing ecosystem changes at the species, population, and community levels, advancing methodological approaches for studying taxonomic diversity towards functional and evolutionary biodiversity concepts, seeking a more complete understanding and monitoring of ocean ecosystems. Full article

Protist grazing pressure plays a major role in controlling aquatic bacterial populations, affecting energy flow through the microbial loop and biogeochemical cycles. Predator-escape mechanisms might play a crucial role in energy flow through the microbial loop, but are yet understudied. For example, some bacteria can use planktonic as well as surface-associated habitats, providing a potential escape mechanism to habitat-specific grazers. We investigated the escape response of the marine bacterium Marinobacter adhaerens in the presence of either planktonic (nanoflagellate: Cafeteria roenbergensis) or surface-associated (amoeba: Vannella anglica) protist predators, following population dynamics over time. In the presence of V. anglica, M. adhaerens cell density increased in the water, but decreased on solid surfaces, indicating an escape response towards the planktonic habitat. In contrast, the planktonic predator C. roenbergensis induced bacterial escape to the surface habitat. While C. roenbergensis cell numbers dropped substantially after a sharp initial increase, V. anglica exhibited a slow, but constant growth throughout the entire experiment. In the presence of C. roenbergensis, M. adhaerens rapidly formed cell clumps in the water habitat, which likely prevented consumption of the planktonic M. adhaerens by the flagellate, resulting in a strong decline in the predator population. Our results indicate an active escape of M. adhaerens via phenotypic plasticity (i.e., behavioral and morphological changes) against predator ingestion. This study highlights the potentially important role of behavioral escape mechanisms for community composition and energy flow in pelagic environments, especially with globally rising particle loads in aquatic systems through human activities and extreme weather events. Full article

Protists are a dominant group in marine microplankton communities and play important roles in energy flux and nutrient cycling in marine ecosystems. Environmental sequences produced by high-throughput sequencing (HTS) methods are increasingly used for inferring the diversity and distribution patterns of protists. However, studies testing whether methods disentangling biological variants affect the diversity and distribution patterns of protists using field samples are insufficient. Oligotrich (s.l.) ciliates are one group of the abundant and dominant planktonic protists in coastal waters and open oceans. Using oligotrich (s.l.) ciliates in field samples as an example, the present study indicates that DADA2 performs better than SWARM, UNOISE, UPARSE, and UCLUST for inferring diversity patterns of oligotrich (s.l.) ciliates in the Pearl River Estuary and surrounding regions. UPARSE and UNOISE might underestimate species richness. SWARM might not be suitable for the resolution of alpha diversity owing to its rigorous clustering and sensitivity to sequence variations. UCLUST with 99% clustering threshold overestimates species richness, and the beta diversity pattern inferred by DADA2 is more reasonable than that of the other methods. Additionally, salinity is shown to be one of the key factors responsible for variations in the community distribution of ciliates, but infrequent marine–freshwater transitions occurred during evolutionary terms of this group. Full article

Interpretations of sea-level changes over geological time are mainly based on analyses of sediments deposited within stable platforms. One of the criteria for recognizing these changes is the composition of skeleton-bearing protists living in environments close to the shoreline and on the continental shelf. It can be assumed that the source of information about sea-level changes may also be found in assemblages of microfossils redeposited from the shelf to the marginal ocean basin. With such an assumption, this article presents an interpretation of changes in marine plankton communities (radiolarians and planktonic foraminifera), which during late Albian–middle Cenomanian were redeposited with carbonate mud by gravity currents from the peri-Tethyan shelf to the northern, marginal Silesian Basin of the Western Tethys. Planktonic biota identified in sediments deposited by gravity flows and those found in hemipelagic shales separating them, indicate that their composition may be correlated with eustatic changes in the sea level from the late Albian (KAl8) to middle Cenomanian (KCe3). Full article

Various species of Alexandrium can produce a number of bioactive compounds, e.g., paralytic shellfish toxins (PSTs), spirolides, gymnodimines, goniodomins, and also uncharacterised bioactive extracellular compounds (BECs). The latter metabolites are released into the environment and affect a large range of organisms (from protists to fishes and mammalian cell lines). These compounds mediate allelochemical interactions, have anti-grazing and anti-parasitic activities, and have a potentially strong structuring role for the dynamic of Alexandrium blooms. In many studies evaluating the effects of Alexandrium on marine organisms, only the classical toxins were reported and the involvement of BECs was not considered. A lack of information on the presence/absence of BECs in experimental strains is likely the cause of contrasting results in the literature that render impossible a distinction between PSTs and BECs effects. We review the knowledge on Alexandrium BEC, (i.e., producing species, target cells, physiological effects, detection methods and molecular candidates). Overall, we highlight the need to identify the nature of Alexandrium BECs and urge further research on the chemical interactions according to their ecological importance in the planktonic chemical warfare and due to their potential collateral damage to a wide range of organisms. Full article

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. Full article

Since its existence, paleoceanography has relied on fossilized populations of planktonic foraminifera. Except for some extreme environments, this calcareous protist group composes most of the silty-to-sandy fraction of the marine sediments, i.e., the foraminiferal oozes, and its extraction is probably the simplest among the currently existing set of marine fossil proxies. This tool has provided significant insights in the building of knowledge on past climates based on marine archives, especially with the quantification of past hydrographical variables, which have been a turning point for major comprehensive studies and a step towards the essential junction of modelling and paleodata. In this article, using the modern analog technique and a database compiling modern analogs (n = 1007), we test the reliability of this proxy in reconstructing paleohydrographical data other than the classical sea-surface temperatures, taking advantage of an update regarding a set of extractions from the World Ocean Atlas for transfer functions. Our study focuses on the last glacial period and its high climatic variability, using a set of cores distributed along the European margin, from temperate to subpolar sites. We discuss the significance of the reconstructed parameters regarding abrupt and extreme climate events, such as the well-known Heinrich events. We tested the robustness of the newly obtained paleodata by comparing them with older published reconstructions, especially those based on the complementary dinoflagellate cyst proxy. This study shows that the potential of planktonic foraminifera permits going further in reconstructions, with a good degree of confidence; however, this implies considering ecological forcings in a more holistic perspective, with the corollary to integrate the message of this fossil protist group, i.e., the obtained parameters, in light of a cohort of other data. This article constitutes a first step in this direction. Full article

As a contribution to understanding the ecological framework of protistan seasonal succession patterns, we present the weekly-to-monthly (January–October) light microscopy-based study of nano- and microplanktonic protist communities of Adventfjorden waters in 2013. In general, protist dynamics corresponded to the classic paradigm for the Arctic ice-free waters with extremely low abundance and diversity in winter, with the main abundance and chlorophyll-a peak in April-May, followed by a diverse but low abundant community during summer/autumn. However, the reference of the obtained data to the previously conducted year-round research in 2012 allows us to observe substantial variability in seasonal patterns between the two consecutive years. The most striking difference concerned the spring bloom composition and abundance, with clear domination of Phaeocystis pouchetii in Atlantified fjord waters in 2012 and Bacillariophyceae-dominated (mainly Fragilariopsis, Thalassiosira nordenskioeldii, and, in a lesser extent, also Pseudo-nitzschia seriata) bloom in 2013 when local water prevailed. On the other hand, a surprisingly high share of spring bloom taxa persisted throughout the summer/autumn of 2013 when they co-occurred with typical summer taxa (dinoflagellates and other small flagellates). Their extended growth could, at least in part, result from scarce Ciliophora throughout the season, which, in turn, can be attributed to the high grazing pressure of very numerous meroplankton and mesozooplankton. In light of this, our results may be relevant in discussions proposed for the West Spitsbergen waters link between the Atlantic water inflow and the spring bloom composition, as well as its further progression in the productive season. They also highlight the strong need for further high-resolution monitoring of annual plankton cycles and great caution when looking for phenological patterns within a single year or when interpreting short-term data. Full article

Copepods have been known to be able to cause an increase in phytoplankton through trophic cascades, as copepods consume heterotrophic protists that feed on phytoplankton. However, how the intensity of copepod-induced trophic cascades varies with environmental conditions remains elusive. We hypothesized that a higher proportion of large phytoplankton in the phytoplankton size distribution, a higher stoichiometric quality of phytoplankton, and a higher temperature could mitigate the intensity of a trophic cascade through increasing direct grazing on phytoplankton by copepods. To explore this issue, we quantified the intensity of a trophic cascade as the difference in phytoplankton concentration reduction by grazing using in situ incubations with and without copepods in the East China Sea. We then investigated the relationship between the intensity of trophic cascades versus the slope of the normalized biomass size spectrum (NBSS) of the phytoplankton community, the C:N ratio of particulate organic matter (POM), and temperature. We found that the intensity of trophic cascades weakly decreased with the NBSS slope and increased with temperature; however, both relationships were not statistically significant. We did not find a clear relationship between the strength of the trophic cascades and the C:N ratio of POM. Our results do not support the hypothesis that the proportion of large phytoplankton, the stoichiometric quality of phytoplankton, and the temperature affect trophic cascades. Instead, we suggest that other critical factors, such as protist abundance, play a role in affecting trophic cascades in the plankton food web in the East China Sea. We further propose some issues which should be addressed when conducting in situ shipboard incubation. Full article