Planktonic Protists Research Articles

A meta-barcoding census of freshwater planktonic protists in Appalachia – Natural Tunnel State Park, Virginia, USA

The purpose of our study was to survey the freshwater planktonic protists within an inland natural preserve in the Ridge and Valley physiographic province of the Appalachian Region using metabarcoding. Microbial eukaryotes are essential primary producers and predators in small freshwater ecosystems, yet they are often overlooked due to the difficulty of identification. This has been remedied, in part, by the cost reduction of high throughput DNA sequencing and the growth of barcode databases, making the identification and analysis of microorganisms by way of metabarcoding surveys in complex ecosystems increasingly feasible. Water samples were collected from five sites at the Natural Tunnel State Park in Scott County, VA (USA), representing three common bodies of water found in this region. Samples were initially collected during a Bioblitz event in April 2016 and then seven and fourteen weeks afterwards. Metabarcode analysis of the 23S and 18S genes identified 3663 OTUs representing 213 family level and 332 genus level taxa. This study provides an initial barcode census within a region that has a reputation as a temperate biodiversity “hotspot”. The overall protist diversity was comparably high to other temperate systems, but not unusually high; the microalgal diversity, however, was higher than that reported for other temperate regions. The three types of water bodies had their own distinctive protist biomes despite close proximity.

Characterization of protistan plankton diversity in ancient salt evaporation ponds located in a volcanic crater on the island Sal, Cape Verde.

Salinity is an important factor when exploring the limits known for life. Therefore, hypersaline systems have attracted much attention in recent years. In this study, we investigated the protistan diversity and community composition in two natural salt evaporation ponds (27-30% salinity) located in an ancient volcanic crater on the Cape Verde island Sal using high-throughput DNA sequencing. Our study revealed a broad range of protistan taxa and a high taxonomic diversity within the Ciliophora, Dinophyceae, and Chlorophyta. We detected a total of 23 Dinophyceae families, although Dinophyceae were generally considered to be only this diverse in aquatic environments of less than 10% salinity. Moreover, we uncovered a high degree of genetic novelty in this habitat. The mean similarity of all detected OTUs to previously described sequences was only 93.6%. These findings strongly dispute the traditional view that extreme hypersaline environments generally maintain low protistan diversity. A meta-analysis covering our and previously published data from other inland and coastal salt ponds clearly showed that our samples clustered according to salinity and not biogeography. This result further supports the claim that salinity is a major transition boundary for protistan communities, regardless of their biogeographic origin.

Behavioral and mechanistic characteristics of the predator-prey interaction between the dinoflagellate Dinophysis acuminata and the ciliate Mesodinium rubrum

Predator-prey interactions of planktonic protists are fundamental to plankton dynamics and include prey selection, detection, and capture as well as predator detection and avoidance. Propulsive, morphology-specific behaviors modulate these interactions and therefore bloom dynamics. Here, interactions between the mixotrophic, harmful algal bloom (HAB) dinoflagellate Dinophysis acuminata and its ciliate prey Mesodinium rubrum were investigated through quantitative microvideography using a high-speed microscale imaging system (HSMIS). The dinoflagellate D. acuminata is shown to detect its M. rubrum prey via chemoreception while M. rubrum is alerted to D. acuminata via mechanoreception at much shorter distances (89 ± 39 μm versus 41 ± 32 μm). On detection, D. acuminata approaches M. rubrum with reduced speed. The ciliate M. rubrum responds through escape jumps that are long enough to detach its chemical trail from its surface, thereby disorienting the predator. To prevail, D. acuminata uses capture filaments and/or releases mucus to slow and eventually immobilize M. rubrum cells for easier capture. Mechanistically, results support the notion that the desmokont flagellar arrangement of D. acuminata lends itself to phagotrophy. In particular, the longitudinal flagellum plays a dominant role in generating thrust for the cell to swim forward, while at other times, it beats to supply a tethering or anchoring force to aid the generation of a posteriorly-directed, cone-shaped scanning current by the transverse flagellum. The latter is strategically positioned to generate flow for enhanced chemoreception and hydrodynamic camouflage, such that D. acuminata can detect and stealthily approach resting M. rubrum cells in the water column.

Seasonal succession, distribution, and diversity of planktonic protists in relation to hydrography of the Godthåbsfjord system (SW Greenland)

High-latitude fjord environments are undergoing dynamic seasonal changes, affecting spatio-temporal patterns in planktonic abundances. To investigate how physical gradients impact sub-Arctic planktonic protists (> 20 μm), a seasonal transect study was performed in 2013 during three periods of planktonic succession: spring, summer, and autumn. The samples were collected from the glacier-fjord-ocean transect in SW Greenland using two complementary sampling methods, i.e. net hauls (20-μm net) and Niskin bottles. The key drivers of the distribution of planktonic groups and dominant taxa were hydrographic properties (defined as ‘time’, salinity, and temperature) reflecting the area’s seasonally changing circulation system. Cold and relatively saline waters in spring favoured the single haptophyte species Phaeocystis cf. pouchetii, while in summer, fresher waters influenced by glacial discharge favoured diatoms, followed by dinoflagellates and predatory ciliates in autumn. Our findings reveal a monodominant structure among the planktonic protists observed in each key sub-region and in each season. (1) Gedaniella boltonii (spring) was associated with inner fjord upwelling, (2) Chaetoceros sp. (summer) and Chaetoceros cf. socialis (autumn) were linked to ‘glacial meltwater’ circulation in the main fjord, and (3) Thalassiosira poroseriata (summer) and Skeletonema sp. (autumn) characterized warm and relatively saline offshore waters influenced by the West Greenland Current. The observed spatio-temporal patterns were linked to changes in hydrographic regimes driven by the interplay between the melting of the Greenland Ice Sheet and inflows of offshore, Atlantic-sourced waters.

Phylogeny and Morphology of New Diplonemids from Japan

Diplonemids were recently found to be the most species-rich group of marine planktonic protists. Based on phylogenetic analysis of 18S rRNA gene sequences and morphological observations, we report the description of new members of the genus Rhynchopus - R. humris sp. n. and R. serpens sp. n., and the establishment of two new genera - Lacrimia gen. n. and Sulcionema gen. n., represented by L. lanifica sp. n. and S. specki sp. n., respectively. In addition, we describe the organism formerly designated as Diplonema sp. 2 (ATCC 50224) as Flectonema neradi gen. n., sp. n. The newly described diplonemids share a common set of traits. Cells are sac-like but variable in shape and size, highly metabolic, and surrounded by a naked cell membrane, which is supported by a tightly packed corset of microtubules. They carry a single highly reticulated peripheral mitochondrion containing a large amount of mitochondrial DNA, with lamellar cristae. The cytopharyngeal complex and flagellar pocket are contiguous and have separate openings. Two parallel flagella are inserted sub-apically into a pronounced flagellar pocket. Rhynchopus species have their flagella concealed in trophic stages and fully developed in swimming stages, while they permanently protrude in all other known diplonemid species.

Inorganic mercury (Hg2+) accumulation in autotrophic and mixotrophic planktonic protists: Implications for Hg trophodynamics in ultraoligotrophic Andean Patagonian lakes

Microbial assemblages are typical of deep ultraoligotrophic Andean Patagonian lakes and comprise picoplankton and protists (phytoflagellates and mixotrophic ciliates), having a central role in the C cycle, primary production and in the incorporation of dissolved inorganic mercury (Hg2+) into lake food webs. In this study we evaluated the mechanisms of Hg2+ incorporation in hetero- and autotrophic bacteria, in the autotrophic dinoflagellate (Gymnodinium paradoxum) and in two mixotrophic ciliates (Stentor araucanus and Ophrydium naumanni) dominating the planktonic microbial assemblage. The radioisotope 197Hg was used to trace the Hg2+ incorporation in microbiota. Hg uptake was analyzed as a function of cell abundance (BCF: bioconcentration factor), cell surface (SCF: surface concentration factor) and cell volume (VCF: volume concentration factor). Overall, the results obtained showed that these organisms incorporate substantial amounts of dissolved Hg2+ passively (adsorption) and actively (bacteria consumption or attachment), displaying different Hg internalization and therefore, varying potential for Hg transfer. Surface area and quality, and surface:volume ratio (S:V) control the passive uptake in all the organisms. Active incorporation depends on bacteria consumption in the mixotrophic ciliates, or on bacteria association to surface in the autotrophic dinoflagellate. Hg bioaccumulated by pelagic protists can be transferred to higher trophic levels through plankton and fish feeding, regenerated to the dissolved phase by excretion, and/or transferred to the sediments by particle sinking. In ultraoligotrophic Andean Patagonian lakes, picoplankton and planktonic protists are key components of lake food webs, linking the pelagic and benthic Hg pathways, and thereby playing a central role in Hg trophodynamics.

Abundance and size structure of planktonic protist communities in a Neotropical floodplain: effects of top-down and bottom-up controls

Abstract: Aim: We aimed to assess the influence of bottom-up and top-down control mechanisms on the abundance and size structure of protist communities (heterotrophic flagellates and ciliates). We formulated the following hypothesis: bottom-up control mechanisms, related to the availability of resources in the environment, are responsible for structuring the abundance of these communities, whereas top-down control mechanisms, related to predation effects, determine the size pattern of these organisms. Methods Samples for planktonic organisms were taken in 20 shallow lakes belonging to the upper Paraná River floodplain. We evaluated linear regression models to select the best model which predicts the patterns observed according to Akaike Information Criterion. Results The best models selected to explain the abundance of heterotrophic flagellates included negative relations with picophytoplankton abundance and positive with rotifers abundance, while for their size structure, negative relationships were found with heterotrophic bacteria, ciliates and rotifers biovolumes. In relation to the ciliates, their abundances were positively related to the rotifers and picophytoplankton abundances and negatively with the heterotrophic bacteria abundance. On the other hand, for the size structure, the best models selected strong negative relations with the microcrustaceans biovolumes, in addition to relations with the different fractions of the phytoplankton. Conclusion For both flagellates and ciliates, their abundance is being mainly regulated by a bottom up control mechanism, whereas for the size structure the results showed that both food resources and predators were important, indicating that bottom-up and top-down mechanisms act simultaneously in determining the size of these microorganisms.

Unravel the hidden protistan diversity: application of blocking primers to suppress PCR amplification of metazoan DNA.

Planktonic protists, including both autotroph and heterotroph, have been recognized as a major contributor to primary production and consumers of bacteria, archaea and picophytoplankton. However, the understanding of protistan diversity is typically impeded by the large amount of metazoans when employing universal primers to environmental samples. In this study, we developed 3 blocking primers to inhibit the amplification of metazoan DNA in PCR. First, we optimized the design and concentration of blocking primers by using 2 metazoans and 3 protists in quantitative PCR. No significant difference (q>0.05) was found in protistan community structure at phylum, family or OTU levels and genetic diversity between samples amplified with and without adding blocking primers, indicating that the blocking primer does not alter the composition of protistan community. An application to samples with a high abundance of metazoans showed that the blocking primer can reduce 42.1-72.4% of metazoan sequences, resulting the retrieval of a higher protistan richness and diversity. The use of the blocking primer helped to identify protistan community composition from a large size fraction, which is usually dominated by metazoans. Protistan community from the small (0.2-10μm) and large (>10μm) size fractions exhibited a low similarity of 36.6% and shared 14.7% OTUs. About 63.8% of the OTUs were unique to the large fraction. Species from groups, such as Lepidodinium, Warnowia, Kareniaceae, Torodiniales, Phaeocystis, Chrysochromulina and Chrysophyceae, were enriched in the large fraction, indicating that they could be largely underestimated in studies that exclude the large-sized cells. Blocking primers are a promising tool to increase the efficiency for the characterization of protistan diversity in aquatic planktonic ecosystems.

Introducing mixotrophy into a biogeochemical model describing an eutrophied coastal ecosystem: The Southern North Sea

Most biogeochemical/ecological models divide planktonic protists between phototrophs (phytoplankton) and heterotrophs (zooplankton). However, a large number of planktonic protists are able to combine several mechanisms of carbon and nutrient acquisition. Not representing these multiple mechanisms in biogeochemical/ecological models describing eutrophied coastal ecosystems can potentially lead to different conclusions regarding ecosystem functioning, especially regarding the success of harmful algae, which are often reported as mixotrophic. This modelling study investigates the implications for trophic dynamics of including 3 contrasting forms of mixotrophy, namely osmotrophy (using alkaline phosphatase activity, APA), non-constitutive mixotrophy (acquired phototrophy by microzooplankton) and also constitutive mixotrophy. The application is in the Southern North Sea, an ecosystem that faced, between 1985 and 2005, a significant increase in the nutrient supply N:P ratio (from 31 to 81molN:P). The comparison with a traditional model shows that, when the winter N:P ratio in the Southern North Sea is above 22molN molP−1 (as occurred from mid-1990s), APA allows a 3–32% increase of annual gross primary production (GPP). In result of the higher GPP, the annual sedimentation increases as well as the bacterial production. By contrast, APA does not affect the export of matter to higher trophic levels because the increased GPP is mainly due to Phaeocystis colonies, which are not grazed by copepods. Under high irradiance, non-constitutive mixotrophy appreciably increases annual GPP, transfer to higher trophic levels, sedimentation, and nutrient remineralisation. In this ecosystem, non-constitutive mixotrophy is also observed to have an indirect stimulating effect on diatoms. Constitutive mixotrophy in nanoflagellates appears to have little influence on this ecosystem functioning. An important conclusion from this work is that contrasting forms of mixotrophy have different impacts on system dynamics and, due to the complex interactions in the ecosystem, their combined effect is not exactly the addition of the effects individually observed. It is thus important to describe such contrasting forms in an appropriate fashion.

Oceanic protists with different forms of acquired phototrophy display contrasting biogeographies and abundance.

This first comprehensive analysis of the global biogeography of marine protistan plankton with acquired phototrophy shows these mixotrophic organisms to be ubiquitous and abundant; however, their biogeography differs markedly between different functional groups. These mixotrophs, lacking a constitutive capacity for photosynthesis (i.e. non-constitutive mixotrophs, NCMs), acquire their phototrophic potential through either integration of prey-plastids or through endosymbiotic associations with photosynthetic microbes. Analysis of field data reveals that 40-60% of plankton traditionally labelled as (non-phototrophic) microzooplankton are actually NCMs, employing acquired phototrophy in addition to phagotrophy. Specialist NCMs acquire chloroplasts or endosymbionts from specific prey, while generalist NCMs obtain chloroplasts from a variety of prey. These contrasting functional types of NCMs exhibit distinct seasonal and spatial global distribution patterns. Mixotrophs reliant on 'stolen' chloroplasts, controlled by prey diversity and abundance, dominate in high-biomass areas. Mixotrophs harbouring intact symbionts are present in all waters and dominate particularly in oligotrophic open ocean systems. The contrasting temporal and spatial patterns of distribution of different mixotroph functional types across the oceanic provinces, as revealed in this study, challenges traditional interpretations of marine food web structures. Mixotrophs with acquired phototrophy (NCMs) warrant greater recognition in marine research.

Seasonal succession in zooplankton feeding traits reveals trophic trait coupling

AbstractThe seasonal forcing of pelagic communities invokes a succession of the dominant phytoplankton and zooplankton species. Here, we characterize the seasonal succession of the plankton traits and their interactions using observations and model simulations of the plankton community in the western English Channel. We focus on activity traits that characterize the defensive and feeding abilities of zooplankton and distinguish between low risk, low return ambush feeders and high risk, high return feeding‐current feeders. While the phytoplankton succession depends on traits related to nutrient acquisition and photosynthesis, it also depends on grazing which couples feeding and motility traits across trophic guilds. Despite interannual variations in the species dominating the protist plankton community, the seasonal trait distribution reveals robust and repeatable seasonal patterns, changing between non‐motile cells flourishing in spring and motile community dominating during summer. The zooplankton community is dominated by active feeding‐current feeders with peak biomass in the late spring declining during summer. The model reveals how zooplankton grazing reinforces protist plankton seasonal succession and shows how the physical environment controls the vertical structure of plankton communities, where ambush feeders exhibit a preference for greater depths during summer. We characterize the seasonal succession as trophic trait coupling and conjecture that this coupling leads to a trophic trait cascade where successive trophic levels alternate in their expression of activity traits further up in the food chain.

Environmental impact on diversity and distribution of tintinnid (Ciliata: Protozoa) along Hooghly Estuary, India: A multivariate approach

The spatiotemporal distribution, diversity and biomass of the choreotrich ciliate tintinnid, the ubiquitous planktonic protist, were analysed from nine sampling sites (n=252) of diverse environmental stresses along the Hooghly Estuary, eastern part of India during March 2012 to August 2014. Among 32 identified tintinnid species, the agglomerated genera Tintinnopsis (20 sp), dominated the community (∼62%) followed by Tintinnidium (2 sp), Leprotintinnus (2 sp), Codonellopsis, Stenosemella, Helicostomella, Favella, Eutintinnus, Metacylis, Dadayiellaand Wangiella (each comprising single species). A wide range of seasonal variations in tintinnid abundance was recorded maximum (2067±893 ind. l−1) for Tintinnopsis beroidea and minimum (11±4 ind. l−1) for Metacylis sp. during the investigation period. The biomass and daily production rate of tintinnid ranged from 0.004–2.764 μg C l−1 and 0.04–3.54 μg C l−1 day−1 respectively. An overall dominance and diversity of the small-sized tintinnid (lorica length <76 μm) belonging to the genera Tintinnopsis sp., Tintinnidium sp., Codonellopsis sp., Wangiella sp., Eutintinnus sp., Metacylis sp. and Helicostomella sp. was pronounced, accounting ∼66% of the total tintinnid abundance. K-dominance curves were plotted against log rank k, showed species dominance over the investigated sites. The multidimensional scaling (MDS) Canonical Analysis of Principal coordinates (CAP) highlighting a significantly different spatial distribution of tintinnid. Principal Component Analysis (PCA) map showed clustering of core species with chl a and nitrate and could be considered as the crucial factors controlling the distribution and seasonal patterns of tintinnid. Biota-environment (BIOENV) analyses also reveal that these two parameters were the significant causative factors, suggesting that tintinnid may be used as a bioindicator for discriminating water quality in this estuarine system. The study provided detailed information of microzooplankton which enhances our understanding regarding its crucial role in marine ecosystem and complex biotic interactions for maintaining the ecological and economic stability.

Dimethylated sulfur compounds in symbiotic protists: A potentially significant source for marine DMS(P)

AbstractSymbiosis with micro‐algae (photosymbiosis) is a common feature among marine planktonic protists, but very little is known about the physiology and ecological significance of these associations. High concentrations of dimethylsulfoniopropionate (DMSP), a metabolite produced by marine microalgae, are commonly observed in coral‐microalgae symbiosis, where DMS(P) is involved in multiple physiological functions. Knowledge on concentration and role of DMSP in analogous photosymbiosis in plankton is lacking. Here, we assess the total DMSP (DMSPt = DMSP + DMS) concentration and natural stable isotopes of sulfur across ecologically relevant symbiotic plankton groups, the Radiolaria and Foraminifera. We found that intracellular DMSPt concentrations in microalgal symbionts were among the highest recorded (range = 170–702 mmol L−1), while lower concentrations (range = 0.1–23 mmol L−1) were characteristic of the holobiont (i.e., host‐microalgae). The contribution of symbiotic Radiolaria to the water column particulate DMSPt concentration ranged 0.1–8%. Sulfur isotopic composition (34S) of DMSPt in the Collodaria holobionts was significantly higher than their symbiotic microalgae isolated in culture. Despite their high intracellular DMSPt content, uptake in these holobionts throughout 3‐d incubations was not detected. We observed a systematic 34S depletion (∼ 1.5‰) of DMS relative to DMSP in experimental incubations containing filtered seawater, which we hypothesize is related to the bacterial preference for the uptake of 34S‐depleted DMS. Overall, the results indicate that plankton symbiosis can, at times, represent a potentially important source of DMS(P). Specific differences in 34S provided new insights into sulfur isotopic fractionation associated with DMS(P) biotransformation processes, with potential implications for current interpretations of isotopically tracked biogenic sources of marine aerosols.

The annual planktonic protist community structure in an ice-free high Arctic fjord (Adventfjorden, West Spitsbergen)

We investigated the size and trophic structure of the annual planktonic protist community structure in the ice-free Adventfjorden in relation to environmental factors. Our high-resolution (weekly to monthly) study was conducted in 2012, when warm Atlantic water was advected into the fjord in winter and summer. We observed a distinct seasonality in the protist communities. The winter protist community was characterised by extremely low levels of protist abundance and biomass (primarily Dinophyceae, Ciliophora and Bacillariophyceae) in a homogenous water column. In the second half of April, the total protist abundance and biomass rapidly increased, thus initiating the spring bloom in a still well-mixed water column. The spring bloom was initially dominated by the prymnesiophyte Phaeocystis pouchetii and Bacillariophyceae (primarily from the genera Thalassiosira, Fragilariopsis and Chaetoceros) and was later strictly dominated by Phaeocystis colonies. When the bloom terminated in mid-June, the community shifted towards flagellates (Dinophyceae, Ciliophora, Cryptophyceae and nanoflagellates 3–7μm in size) in a stratified, nutrient-depleted water column. Decreases in the light intensity decreased the protist abundance and biomass, and the fall community (Dinophyceae, Cryptophyceae and Bacillariophyceae) was followed by the winter community.

Amino acid utilization by eukaryotic picophytoplankton in a coastal upwelling system

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 588:43-57 (2018) - DOI: https://doi.org/10.3354/meps12435 Amino acid utilization by eukaryotic picophytoplankton in a coastal upwelling system Marta Hernández-Ruiz1,2,*, Antero Prieto1,2, Esther Barber-Lluch1,2, Eva Teira1,2 1Grupo de Oceanografía Biológica, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310 Vigo, Spain 2Estación de Ciencias Marinas de Toralla (ECIMAT), Universidad de Vigo, 36331 Vigo, Spain *Corresponding author: mhernandez@uvigo.es ABSTRACT: The ability to combine autotrophic and heterotrophic nutritional modes by planktonic protists may significantly influence nutrient dynamics in the surface ocean. The extent and significance of organic resource utilization by small photosynthetic eukaryotes remain poorly explored. In order to evaluate the importance of autotrophy and heterotrophy within the most abundant pico-nanoeukaryotic phytoplankton groups in surface waters of a coastal upwelling area of NW of Spain, we combined catalyzed reported deposition-fluorescence in situ hybridization and microautoradiography with radiolabeled bicarbonate or amino acids. Over an annual cycle in 2015, picoplanktonic taxa represented more than 55% of the pico-nanoeukaryotic cells. The genus Ostreococcus dominated both in terms of abundance and activity during the nutrient-limiting spring to summer stratification period, when the utilization of amino acids was confirmed for dinoflagellates (22 to 33% of total dinoflagellate cells), Haptophyta (23 to 88% of total Haptophyta cells) and the picoeukaryotic genera Micromonas (9 to 38% of total Micromonas cells), Ostreococcus (10 to 38% of total Ostreococcus cells) and Bathycoccus (19 to 22% of total Bathycoccus cells). Our data suggest the adoption of different nutritional strategies among the smallest plastidic protists, which likely implies contrasting functional roles and competitive abilities within the picoeukaryotic phytoplankton. KEY WORDS: Eukaryotic picophytoplankton · Autotrophy · Heterotrophy · CARD-FISH · Microautoradiography Full text in pdf format PreviousNextCite this article as: Hernández-Ruiz M, Prieto A, Barber-Lluch E, Teira E (2018) Amino acid utilization by eukaryotic picophytoplankton in a coastal upwelling system. Mar Ecol Prog Ser 588:43-57. https://doi.org/10.3354/meps12435 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 588. Online publication date: February 08, 2018 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2018 Inter-Research.

Diversity and temporal patterns of planktonic protist assemblages at a Mediterranean Long Term Ecological Research site.

We tracked temporal changes in protist diversity at the Long Term Ecological Research (LTER) station MareChiara in the Gulf of Naples (Mediterranean Sea) on eight dates in 2011 using a metabarcoding approach. Illumina analysis of the V4 and V9 fragments of the 18S rDNA produced 869522 and 1410071 sequences resulting in 6517 and 6519 OTUs, respectively. Marked compositional variations were recorded across the year, with less than 2% of OTUs shared among all samples and similar patterns for the two marker tags. Alveolata, Stramenopiles and Rhizaria were the most represented groups. A comparison with light microscopy data indicated an over-representation of Dinophyta in the sequence dataset, whereas Bacillariophyta showed comparable taxonomic patterns between sequence and light microscopy data. Shannon diversity values were stable from February to September, increasing thereafter with a peak in December. Community variance was mainly explained by seasonality (as temperature), trophic status (as chlorophyll a), and influence of coastal waters (as salinity). Overall, the background knowledge of the system provided a sound context for the result interpretation, showing that LTER sites provide an ideal setting for high-throughput sequencing (HTS) metabarcoding characterisation of protist assemblages and their relationships with environmental variations.

The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates.

Illumina reads of the SSU-rDNA-V9 region obtained from the circumglobal Tara Oceans expedition allow the investigation of protistan plankton diversity patterns on a global scale. We analyzed 6,137,350 V9-amplicons from ocean surface waters and the deep chlorophyll maximum, which were taxonomically assigned to the phylum Ciliophora. For open ocean samples global planktonic ciliate diversity is relatively low (ca. 1,300 observed and predicted ciliate OTUs). We found that 17% of all detected ciliate OTUs occurred in all oceanic regions under study. On average, local ciliate OTU richness represented 27% of the global ciliate OTU richness, indicating that a large proportion of ciliates is widely distributed. Yet, more than half of these OTUs shared <90% sequence similarity with reference sequences of described ciliates. While alpha-diversity measures (richness and exp(Shannon H)) are hardly affected by contemporary environmental conditions, species (OTU) turnover and community similarity (β-diversity) across taxonomic groups showed strong correlation to environmental parameters. Logistic regression models predicted significant correlations between the occurrence of specific ciliate genera and individual nutrients, the oceanic carbonate system and temperature. Planktonic ciliates displayed distinct vertical distributions relative to chlorophyll a. In contrast, the Tara Oceans dataset did not reveal any evidence that latitude is structuring ciliate communities.

Benthic protists: the under-charted majority.

Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.

Defining Planktonic Protist Functional Groups on Mechanisms for Energy and Nutrient Acquisition: Incorporation of Diverse Mixotrophic Strategies

Arranging organisms into functional groups aids ecological research by grouping organisms (irrespective of phylogenetic origin) that interact with environmental factors in similar ways. Planktonic protists traditionally have been split between photoautotrophic "phytoplankton" and phagotrophic "microzooplankton". However, there is a growing recognition of the importance of mixotrophy in euphotic aquatic systems, where many protists often combine photoautotrophic and phagotrophic modes of nutrition. Such organisms do not align with the traditional dichotomy of phytoplankton and microzooplankton. To reflect this understanding, we propose a new functional grouping of planktonic protists in an eco-physiological context: (i) phagoheterotrophs lacking phototrophic capacity, (ii) photoautotrophs lacking phagotrophic capacity, (iii) constitutive mixotrophs (CMs) as phagotrophs with an inherent capacity for phototrophy, and (iv) non-constitutive mixotrophs (NCMs) that acquire their phototrophic capacity by ingesting specific (SNCM) or general non-specific (GNCM) prey. For the first time, we incorporate these functional groups within a foodweb structure and show, using model outputs, that there is scope for significant changes in trophic dynamics depending on the protist functional type description. Accordingly, to better reflect the role of mixotrophy, we recommend that as important tools for explanatory and predictive research, aquatic food-web and biogeochemical models need to redefine the protist groups within their frameworks.

Spatial and temporal distribution of planktonic protists in the East Greenland fjord and offshore waters

Spatial and temporal distribution of planktonic protists in the East Greenland fjord and offshore waters