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The complex interactions between epiphytic bacteria and marine macroalgae are still poorly understood, with limited knowledge about their community structure, interactions, and functions. This study focuses on comparing epiphytic prokaryotes community structure between three seaweed phyla; Chlorophyta, Rhodophyta, and Heterokontophyta in an easternmost rocky intertidal site of the Mediterranean Sea. By taking a snapshot approach and simultaneously collecting seaweed samples from the same habitat, we minimize environmental variations that could affect epiphytic bacterial assembly, thereby emphasizing host specificity. Through 16S rRNA gene amplicon sequencing, we identified that the microbial community composition was more similar within the same seaweed phylum host compared to seaweed host from other phyla. Furthermore, exclusive Amplicon Sequence Variants (ASVs) were identified for each algal phyla despite sharing higher taxonomic classifications across the other phyla. Analysis of niche breadth indices uncovers distinctive affinities and potential specialization among seaweed host phyla, with 39% of all ASVs identified as phylum specialists and 13% as generalists. Using taxonomy function prediction, we observed that the taxonomic variability does not significantly impact functional redundancy, suggesting resilience to disturbance. The study concludes that epiphytic bacteria composition is connected to host taxonomy, possibly influenced by shared morphological and chemical traits among genetically related hosts, implying a potential coevolutionary relationship between specific bacteria and their host seaweeds. [ABSTRACT FROM AUTHOR]

Abstract The complex interactions between epiphytic bacteria and marine macroalgae are still poorly understood, with limited knowledge about their community structure, interactions, and functions. This study focuses on comparing epiphytic prokaryotes community structure between three seaweed phyla; Chlorophyta, Rhodophyta, and Heterokontophyta in an easternmost rocky intertidal site of the Mediterranean Sea. By taking a snapshot approach and simultaneously collecting seaweed samples from the same habitat, we minimize environmental variations that could affect epiphytic bacterial assembly, thereby emphasizing host specificity. Through 16S rRNA gene amplicon sequencing, we identified that the microbial community composition was more similar within the same seaweed phylum host compared to seaweed host from other phyla. Furthermore, exclusive Amplicon Sequence Variants (ASVs) were identified for each algal phyla despite sharing higher taxonomic classifications across the other phyla. Analysis of niche breadth indices uncovers distinctive affinities and potential specialization among seaweed host phyla, with 39% of all ASVs identified as phylum specialists and 13% as generalists. Using taxonomy function prediction, we observed that the taxonomic variability does not significantly impact functional redundancy, suggesting resilience to disturbance. The study concludes that epiphytic bacteria composition is connected to host taxonomy, possibly influenced by shared morphological and chemical traits among genetically related hosts, implying a potential coevolutionary relationship between specific bacteria and their host seaweeds.

The study of microalgal communities is critical for understanding aquatic ecosystems. These communities primarily comprise diatoms (Heterokontophyta), with two methods commonly used to study them: Microscopy and metabarcoding. However, these two methods often deliver different results; thus, their suitability for analyzing diatom communities is frequently debated and evaluated. This study used these two methods to analyze the diatom communities in identical water samples and compare the results. The taxonomy of the species constituting the diatom communities was confirmed, and both methods showed that species belonging to the orders Bacillariales and Naviculales (class Bacillariophyceae) are the most diverse. In the lower taxonomic levels (family, genus, and species), microscopy tended to show a bias toward detecting diatom species (Nitzschia frustulum, Nitzschia inconspicua, Nitzschia intermedia, Navicula gregaria, Navicula perminuta, Navicula recens, Navicula sp.) belonging to the Bacillariaceae and Naviculaceae families. The results of the two methods differed in identifying diatom species in the communities and analyzing their structural characteristics. These results are consistent with the fact that diatoms belonging to the genera Nitzschia and Navicula are abundant in the communities; furthermore, only the Illumina MiSeq data showed the abundance of the Melosira and Entomoneis genera. The results obtained from microscopy were superior to those of Illumina MiSeq regarding species-level identification. Based on the results obtained via microscopy and Illumina MiSeq, it was revealed that neither method is perfect and that each has clear strengths and weaknesses. Therefore, to analyze diatom communities effectively and accurately, these two methods should be combined. [ABSTRACT FROM AUTHOR]

Diatoms are widely dispersed single-celled eukaryotic microalgal species inhabiting every kind of aquatic ecosystem. Identification and isolation of diatoms have been the need of the hour for the sustainable development of environmental goals. The current study focuses on the isolation of various diatoms from the southern coastal region of Dhanushkodi, Rameshwaram and Mandapam in the Ramanathapuram district of Tamil Nadu, India, and their identification using scanning electron microscopy (SEM). The species were determined based on the girdle, striae, valves, and other crucial terms present on the frustules and identified as pennate diatoms Navicula sp., Amphora sp., and Gomphonema sp., respectively. The identified species were cultured in artificial saltwater that had been enhanced with a modified f/2-Si media composition. In addition to enhancing the local flora, the identified strains represent the diatoms diversity along India's southern coast. [ABSTRACT FROM AUTHOR]

The Opalinida comprise ciliated protists that live as intestinal endoparasites in poikilothermic vertebrates. They are classified as one group of colourless Stramenopiles, the Opalinata, along with Proteromonadida (Proteromonas and Karotomorpha). The validity of certain opalinid genera is questionable, and their genetic relationships remain unclear. In this study, we conducted complete ribosomal DNA gene sequencing of nine opalinid species (belonging to Opalina , Protoopalina , Zelleriella , and Cepedea) from China. We compared the primary sequences, secondary structures, and characteristics of short tandem repeats within the expansion segments of the sequences. Additionally, a TimeTree analysis was performed to estimate divergence times. Our findings suggest that opalinids diverged from proteromonads ~250–220 Mya, with Protoopalina being the ancient genus. There is no genetic evidence supporting the differentiation of Cepedea and Bezzenbergeria as distinct genera, and they have been synonymized: Opalina (= Cepedea) and Protoopalina (= Bezzenbergeria); new combinations of species names are listed. Opalinid rDNA sequences exhibit greater length compared with other groups owing to A-T insertions within the expansion segments. These insertions consist of short tandem repeats and appear to be associated with speciation events that led to genus differentiation. [ABSTRACT FROM AUTHOR]

Freshwater mussels (Mollusca: Unionidae) play a crucial role in freshwater river environments where they live in multi-species aggregations and often serve as long-lived benthic ecosystem engineers. Many of these species are imperiled and it is imperative that we understand their basic needs to aid in the reestablishment and maintenance of mussel beds in rivers. In an effort to expand our knowledge of the diet of these organisms, five species of mussel were introduced into enclosed systems in two experiments. In the first, mussels were incubated in water from the Clinch River (Virginia, USA) and in the second, water from a manmade pond at the Commonwealth of Virginia's Aquatic Wildlife Conservation Center in Marion, VA. Quantitative PCR and eDNA metabarcoding were used to determine which planktonic microbes were present before and after the introduction of mussels into each experimental system. It was found that all five species preferentially consumed microeukaryotes over bacteria. Most microeukaryotic taxa, including Stramenopiles and Chlorophytes were quickly consumed by all five mussel species. We also found that they consumed fungi but not as quickly as the microalgae, and that one species of mussel, Ortmanniana pectorosa, consumed bacteria but only after preferred food sources were depleted. Our results provide evidence that siphon feeding Unionid mussels can select preferred microbes from mixed plankton, and mussel species exhibit dietary niche differentiation. [ABSTRACT FROM AUTHOR]

Ciliates have been recognized as one of the major components of the microbial food web, especially in ultra-oligotrophic waters, such as the Eastern Mediterranean Sea, where nutrients are scarce and the microbial community is dominated by pico- and nano-sized organisms. For this reason, ciliates play an important role in these ecosystems since they are the main planktonic grazers. Regardless the importance of these organisms, little is known about the community structure of heterotrophic and mixotrophic ciliates and how they are associated to their potential prey. In this study, we used 18S V4 rRNA gene metabarcoding to analyze ciliate community dynamics and how the relationship with potential prey changes according to different seasons and depths. Samples were collected seasonally at two stations of the Eastern Mediterranean Sea (HCB: coastal, M3A: offshore) from the surface and deep chlorophyll maximum (DCM) layers. The ciliate community structure varied across depths in HCB and across seasons in M3A, and the network analysis showed that in both stations, mixotrophic oligotrichs were positively associated with diatoms and showed few negative associations with ASVs annotated as marine Stramenopiles (MAST). On the other hand, heterotrophic tintinnids showed negative relationships in both HCB and M3A stations, mostly with Ochrophyta and Chlorophyta. These results showed, in first place that, although the two stations are close to each other, the ciliate dynamics differed between them. Moreover, mixotrophic and heterotrophic ciliates may have different ecological niches since mixotrophic ciliates may be more selective compared to heterotrophic species regarding their prey. These findings are the first glimpse into an understanding of the dynamics between heterotrophic and mixotrophic ciliates and their role inmicrobial assemblages and dynamics of ultra-oligotrophic environments. [ABSTRACT FROM AUTHOR]

Eukaryotrophic protists are ecologically significant and possess characteristics key to understanding the evolution of eukaryotes; however, they remain poorly studied, due partly to the complexities of maintaining predator–prey cultures. Kaonashia insperata, gen. nov., et sp. nov., is a free‐swimming biflagellated eukaryotroph with a conspicuous ventral groove, a trait observed in distantly related lineages across eukaryote diversity. Di‐eukaryotic (predator–prey) cultures of K. insperata with three marine algae (Isochrysis galbana, Guillardia theta, and Phaeodactylum tricornutum) were established by single‐cell isolation. Growth trials showed that the studied K. insperata clone grew particularly well on G. theta, reaching a peak abundance of 1.0 × 105 ± 4.0 × 104 cells ml−1. Small‐subunit ribosomal DNA phylogenies infer that K. insperata is a stramenopile with moderate support; however, it does not fall within any well‐defined phylogenetic group, including environmental sequence clades (e.g. MASTs), and its specific placement remains unresolved. Electron microscopy shows traits consistent with stramenopile affinity, including mastigonemes on the anterior flagellum and tubular mitochondrial cristae. Kaonashia insperata may represent a novel major lineage within stramenopiles, and be important for understanding the evolutionary history of the group. While heterotrophic stramenopile flagellates are considered to be predominantly bacterivorous, eukaryotrophy may be relatively widespread amongst this assemblage. [ABSTRACT FROM AUTHOR]

The Bay of Bengal (BoB) is a 2,600,000 km2 expanse in the Indian Ocean upon which many humans rely. However, the primary producers underpinning food chains here remain poorly characterized. We examined phytoplankton abundance and diversity along strong BoB latitudinal and vertical salinity gradients—which have low temperature variation (27–29°C) between the surface and subsurface chlorophyll maximum (SCM). In surface waters, Prochlorococcus averaged 11.7 ± 4.4 × 104 cells ml−1, predominantly HLII, whereas LLII and 'rare' ecotypes, HLVI and LLVII, dominated in the SCM. Synechococcus averaged 8.4 ± 2.3 × 104 cells ml−1 in the surface, declined rapidly with depth, and population structure of dominant Clade II differed between surface and SCM; Clade X was notable at both depths. Across all sites, Ostreococcus Clade OII dominated SCM eukaryotes whereas communities differentiated strongly moving from Arabian Sea‐influenced high salinity (southerly; prasinophytes) to freshwater‐influenced low salinity (northerly; stramenopiles, specifically, diatoms, pelagophytes, and dictyochophytes, plus the prasinophyte Micromonas) surface waters. Eukaryotic phytoplankton peaked in the south (1.9 × 104 cells ml−1, surface) where a novel Ostreococcus was revealed, named here Ostreococcus bengalensis. We expose dominance of a single picoeukaryote and hitherto 'rare' picocyanobacteria at depth in this complex ecosystem where studies suggest picoplankton are replacing larger phytoplankton due to climate change. [ABSTRACT FROM AUTHOR]

In the age of genome sequencing, whole-genome data is readily and frequently generated, leading to a wealth of new information that can be used to advance various fields of research. New approaches, such as alignment-free phylogenetic methods that utilize k- mer-based distance scoring, are becoming increasingly popular given their ability to rapidly generate phylogenetic information from whole-genome data. However, these methods have not yet been tested using environmental data, which often tends to be highly fragmented and incomplete. Here, we compare the results of one alignment-free approach (which utilizes the D 2 statistic) to traditional multi-gene maximum likelihood trees in 3 algal groups that have high-quality genome data available. In addition, we simulate lower-quality, fragmented genome data using these algae to test method robustness to genome quality and completeness. Finally, we apply the alignment-free approach to environmental metagenome assembled genome data of unclassified Saccharibacteria and Trebouxiophyte algae, and single-cell amplified data from uncultured marine stramenopiles to demonstrate its utility with real datasets. We find that in all instances, the alignment-free method produces phylogenies that are comparable, and often more informative, than those created using the traditional multi-gene approach. The k -mer-based method performs well even when there are significant missing data that include marker genes traditionally used for tree reconstruction. Our results demonstrate the value of alignment-free approaches for classifying novel, often cryptic or rare, species, that may not be culturable or are difficult to access using single-cell methods, but fill important gaps in the tree of life. [ABSTRACT FROM AUTHOR]

A new freshwater microalgal isolate, CCALA 1135, was characterized using a polyphasic approach (morphology, ultrastructure, fatty acid composition, 18S rRNA gene and rbcL analyses). Non-motile vegetative cells were spherical with thick, smooth cell walls lacking ornamentation, with multiple overlapping chloroplasts and sometimes more than one red globule in the cytoplasm. The nuclear and chloroplast envelopes formed a continuous membrane and there was no pyrenoid. These morphological and ultrastructural features indicated assignment to the class Eustigmatophyceae. The strain was, however, unique in its mode of reproduction: only zoospores were formed, but no autospores were observed (i.e. obligate zoospory, which is rare in the Eustigmatophyceae). The zoospores were relatively fragile and their morphology was similar to those of other members of the clade Goniochloridales (a clade name under the PhyloCode) that have been studied, being uniflagellate and lacking an eyespot. A very high proportion of polyunsaturated fatty acids (up to 57% of total fatty acids) was found, dominated by nutritionally valuable arachidonic and eicosapentaenoic acids, the latter being the most abundant FA (up to 35%) in the total profile. Phylogenetic analysis based on 18S rDNA and rbcL sequences confirmed that CCALA 1135 represents a new member of Goniochloridales clade IIc. Based on cellular morphology, ultrastructure and molecular data we propose this strain as a new species and new genus of the Eustigmatophyceae, Trebonskia zoosporica gen. et sp. nov. Our work is a step toward clarifying the taxonomy of a group of the Eustigmatophyceae with many unnamed strains awaiting characterization. A new genus and species of Eustigmatophyceae is described using a polyphasic approach. This isolate reproduces only by zoospores, a mode rare within Eustigmatophyceae. It contained a high proportion of nutritionally valuable polyunsaturated fatty acids. [ABSTRACT FROM AUTHOR]

The pelagophytes, a morphologically diverse class of marine heterokont algae, have been historically united only by DNA sequences. Recently we described a novel perforated theca (PT) encasing cells from the Pelagophyceae and hypothesized it may be the first morphological feature to define the class. Here we consolidate that observation, describing a PT for the first time in an additional seven pelagophyte genera, including three genera new to science. We established clonal cultures of pelagophytes collected from intertidal pools located around Australia, and established phylogenetic trees based on nuclear 18S rDNA and plastid rbcL, psaA, psaB, psbA and psbC gene sequences that led to the discovery of three new species: Wyeophycus julieharrissiae and Chromopallida australis form a distinct lineage along with Ankylochrysis lutea within the Pelagomonadales, while Pituiglomerulus capricornicus is sister genus to Chrysocystis fragilis in the Chrysocystaceae (Sarcinochrysidales). Using fixation by high‐pressure freezing for electron microscope observations, a distinctive PT was observed in the three new genera described in this paper, as well as four genera not previously investigated: Chrysoreinhardia, Sargassococcus, Sungminbooa and Andersenia. The mechanism of PT formation is novel, being fabricated from rafts in Golgi‐derived vesicles before being inserted into an established PT. Extracellular wall and/or mucilage layers assemble exterior to the PT in most pelagophytes, the materials likewise secreted by Golgi‐derived vesicles, though the mechanism of secretion is novel. Secretory vesicles never fuse with the plasma membrane as in classic secretion and deposition, but rather relocate extracellularly beneath the PT and disintegrate, the contents having to pass through the PT prior to wall and/or mucilage synthesis. This study substantiates the diverse nature of pelagophytes, and provides further evidence that the PT is a sound morphological feature to define the Pelagophyceae, with all 14 of the 20 known genera studied to date by TEM possessing a PT. [ABSTRACT FROM AUTHOR]

Stomatocysts of the rare heterotrophic chrysophyte, Paraphysomonas caelifrica, were discovered from a shallow ephemeral pond Tavolgasai ("Orenburgskiy" State Nature Reserve, Orenburg Region, Russia). Morphology of stomatocysts was studied using scanning electron microscopy. Stomatocysts of P. caelifrica are spherical and smooth with a cylindrical collar surrounding the regular pore. So, they do not belong to the stomatocyst 1 Duff and Smol as previously thought. The description of a new stomatocyst morphotype is provided. [ABSTRACT FROM AUTHOR]

Brown algae are a group of multicellular, heterokont algae that have convergently evolved developmental complexity that rivals that of embryophytes, animals or fungi. Early in development, brown algal zygotes establish a basal and an apical pole, which will become respectively the basal system (holdfast) and the apical system (thallus) of the adult alga. Brown algae are interesting models for understanding the establishment of cell polarity in a broad evolutionary context, because they exhibit a large diversity of life cycles, reproductive strategies and, importantly, their zygotes are produced in large quantities free of parental tissue, with symmetry breaking and asymmetric division taking place in a highly synchronous manner. This review describes the current knowledge about the establishment of the apical-basal axis in the model brown seaweeds Ectocarpus , Dictyota , Fucus and Saccharina , highlighting the advantages and specific interests of each system. Ectocarpus is a genetic model system that allows access to the molecular basis of early development and life-cycle control over apical-basal polarity. The oogamous brown alga Fucus , together with emerging comparative models Dictyota and Saccharina, emphasize the diversity of strategies of symmetry breaking in determining a cell polarity vector in brown algae. A comparison with symmetry-breaking mechanisms in land plants, animals and fungi, reveals that the one-step zygote polarisation of Fucus compares well to Saccharomyces budding and Arabidopsis stomata development, while the two-phased symmetry breaking in the Dictyota zygote compares to Schizosaccharomyces fission, the Caenorhabditis anterior-posterior zygote polarisation and Arabidopsis prolate pollen polarisation. The apical-basal patterning in Saccharina zygotes on the other hand, may be seen as analogous to that of land plants. Overall, brown algae have the potential to bring exciting new information on how a single cell gives rise to an entire complex body plan. [ABSTRACT FROM AUTHOR]

Two autophagy-related (ATG) ubiquitin-like conjugation systems, the ATG12 and ATG8 systems, play important roles in macroautophagy. While multiple duplications and losses of the ATG conjugation system proteins are found in different lineages, the extent to which the underlying systems diversified across eukaryotes is not fully understood. Here, in order to understand the evolution of the ATG conjugation systems, we constructed a transcriptome database consisting of 94 eukaryotic species covering major eukaryotic clades and systematically identified ATG conjugation system components. Both ATG10 and the C-terminal glycine of ATG12 are essential for the canonical ubiquitin-like conjugation of ATG12 and ATG5. However, loss of ATG10 or the C-terminal glycine of ATG12 occurred at least 16 times in a wide range of lineages, suggesting that possible covalent-to-non-covalent transition is not limited to the species that we previously reported such as Alveolata and some yeast species. Some species have only the ATG8 system (with conjugation enzymes) or only ATG8 (without conjugation enzymes). More than 10 species have ATG8 homologs without the conserved C-terminal glycine, and Tetrahymena has an ATG8 homolog with a predicted transmembrane domain, which may be able to anchor to the membrane independent of the ATG conjugation systems. We discuss the possibility that the ancestor of the ATG12 and ATG8 systems is more similar to ATG8. Overall, our study offers a whole picture of the evolution and diversity of the ATG conjugation systems among eukaryotes, and provides evidence that functional diversifications of the systems are more common than previously thought. Abbreviations: APEAR: ATG8–PE association region; ATG: autophagy-related; LIR: LC3-interacting region; NEDD8: neural precursor cell expressed, developmentally down-regulated gene 8; PE: phosphatidylethanolamine; SAMP: small archaeal modifier protein; SAR: Stramenopiles, Alveolata, and Rhizaria; SMC: structural maintenance of chromosomes; SUMO: small ubiquitin like modifier; TACK: Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota; UBA: ubiquitin like modifier activating enzyme; UFM: ubiquitin fold modifier; URM: ubiquitin related modifier. [ABSTRACT FROM AUTHOR]

[Display omitted] • Generation of ten new ochrophyte transcriptomes, of under-represented lineages. • Recovered a robust relationship of previously contentious ochrophyte lineages. • Distinct gene properties affect various stramenopile lineages differently. • Genes with high phylogenetic signal recover more stable phylogenomic topologies. Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable groupings with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenetic relationships, and discrete gene properties affect lineages of stramenopiles differently. This is something which may be explored to further our understanding of the molecular evolution of stramenopiles. [ABSTRACT FROM AUTHOR]

The phylogeny of brown algae (Phaeophyceae) has undergone extensive changes in the recent past due to regular new scientific insights. We used nuclear 18S rDNA with an extensive dataset, aiming to increase the accuracy and robustness of the reconstructed phylogenetic trees using a simultaneous sequence-structure approach. Individual secondary structures were generated for all 18S rDNA sequences. The sequence-structure information was encoded and used for an automated simultaneous sequence-structure alignment. Neighbor-joining and profile neighbor-joining trees were calculated based on 186 phaeophycean sequence-structure pairs. Additionally, sequence-structure neighbor-joining, maximum parsimony and maximum likelihood trees were reconstructed on a representative subset. Using a similar approach, ITS2 rDNA sequence-structure information was used to reconstruct a neighbor-joining tree including 604 sequence-structure pairs of the Laminariales. Our study results are in significant agreement with previous single marker 18S and ITS2 rDNA analyses. Moreover, the 18S results are in wide agreement with recent multi-marker analyses. The bootstrap support was significantly higher for our sequence-structure analysis in comparison to sequence-only analyses in this study and the available literature. This study supports the simultaneous inclusion of sequence-structure data at least for 18S to obtain more accurate and robust phylogenetic trees compared to sequence-only analyses. [ABSTRACT FROM AUTHOR]

The silica-scaled chrysophyte flora from Indonesian Papua was investigated by means of electron microscopy. A total of twenty-four taxa were recorded, including five belonging to Paraphysomonas, one to Chrysosphaerella, one to Spiniferomonas, fifteen to Mallomonas and two to Synura. Thirteen taxa were recorded for the first time in Indonesia. Comparison of the species composition of silica-scaled chrysophytes from different parts of the Island of New Guinea shows significant differences. A "living fossil" was discovered, Mallomonas preisigii, which was described previously from Eocene deposits in Northern Canada. Although the scales from Papua slightly differ from those of the fossil one, we believe they belong to the same morphospecies. Mallomonas preisigii can be considered as a paleoendemic species. [ABSTRACT FROM AUTHOR]

Blastocystis is a genus of unicellular heterokont parasites belonging to a group of organisms known as Stramenopiles, which includes algae, diatoms, and water molds. Blastocystis includes several species that habitat in the gastrointestinal tracts of organisms as diverse as humans, farm animals, birds, rodents, reptiles, amphibians, fish, and cockroaches. It is important to public health and distributed globally, but its prevalence in dogs in Korea has not been reported to date. Here, we collected 787 canine fecal samples and assessed Blastocystis infection by age, sex, region, season, and diarrhea symptoms. We determined Blastocystis subtypes using phylogenetic analyses based on 18S rRNA gene sequences. We identified, 10 Blastocystis positive samples (1.3%). A higher proportion of infected dogs was asymptomatic; however, infection rates did not significantly differ according to region, age, sex, and season. Phylogenetic analysis showed that the Blastocystis sp. identified belonged to 4 subtypes (STs), ST1, ST5, ST10, and ST14, thus revealed the genetic diversity of Blastocystis sp. in dogs Korean. This is first report on the presence of Blastocystis sp. in dogs Korean. This study revealed a lower infection rate than expected and differed from previous studies in STs. Further studies are warranted to observe the national infection status of Blastocystis in dogs and the genetic characteristics of this genus. [ABSTRACT FROM AUTHOR]

MArine STramenopiles (MASTs) have been recognized as parts of heterotrophic protists and contribute substantially to protist abundances in the ocean. However, little is known about their spatiotemporal variations with respect to environmental and biological factors. The objectives of this study are to use canonical correspondence analysis to investigate how MASTs communities are shaped by environmental variables, and co-occurrence networks to examine their potential interactions with prokaryotic communities. Our dataset came from the southern East China Sea (sECS) in the subtropical northwestern Pacific, and involved 14 cruises along a coastal-oceanic transect, each of which sampled surface water from 4 to 7 stations. MASTs communities were revealed by metabarcoding of 18S rDNA V4 region. Most notably, MAST-9 had a high representation in warm waters in terms of read number and diversity. Subclades of MAST-9C and -9D showed slightly different niches, with MAST-9D dominating in more coastal waters where concentrations of nitrite and Synechococcus were higher. MAST-1C was a common component of colder water during spring. Overall, canonical correspondence analysis showed that MASTs communities were significantly influenced by temperature, nitrite and Synechococcus concentrations. The co-occurrence networks showed that certain other minor prokaryotic taxa can influence MAST communities. This study provides insight into how MASTs communities varied with environmental and biological variables. [ABSTRACT FROM AUTHOR]

Hermesinum adriaticum is a rare marine and brackish flagellate that is of considerable interest due to its markable and fossilizable siliceous skeleton. Based on this skeleton, Hermesinum was initially considered a microalga of the Dictyochophyceae (Ochrophyta, Stramenopiles). Later on, it was assigned to the Ebriida due to its similarity to Ebria tripartita. The taxonomic assignment of the Ebriida, however, changed several times until it was placed within the Thecofilosea (Cercozoa, Rhizaria), based on genetic data of E. tripartita. We sequenced the 18S marker gene sequence of Hermesinum and confirm the close relationship of Ebria and Hermesinum. [ABSTRACT FROM AUTHOR]

A plant-like cryptochrome of diatom microalgae, CryP, acts as a photoreceptor involved in transcriptional regulation. It contains FAD and 5,10-methenyltetrahydrofolate as chromophores. Here, we demonstrate that the unstructured C-terminal extension (CTE) of CryP has an influence on the redox state of the flavin. In CryP lacking the CTE, the flavin is in the oxidized state (FADox), whereas it is a neutral radical (FADH•) in the full-length protein. When the CTE of CryP is coupled to another diatom cryptochrome that naturally binds FADox, this chimera also binds FADH•. In full-length CryP, FADH• is the most stable redox state and oxidation to FADox is extremely slow, whereas reduction to FADH2 is reversible in the dark in approximately 1 h. We also identified novel interaction partners of this algal CRY and characterized two of them in depth regarding their binding activities. BolA, a putative transcription factor, binds to monomeric and to dimeric CryP via the CTE, independent of the redox state of the flavin. In contrast, an unknown protein, ID42612, which occurs solely in heterokont algae, binds only to CryP dimers. This binding is independent of the CTE and shows slight differences in strength depending on the flavin's redox state. [ABSTRACT FROM AUTHOR]

Ochrophyta is an algal group belonging to the Stramenopiles and comprises diverse lineages of algae which contribute significantly to the oceanic ecosystems as primary producers. However, early evolution of the plastid organelle in Ochrophyta is not fully understood. In this study, we provide a well-supported tree of the Stramenopiles inferred by the large-scale phylogenomic analysis that unveils the eukaryvorous (nonphotosynthetic) protist Actinophrys sol (Actinophryidae) is closely related to Ochrophyta. We used genomic and transcriptomic data generated from A. sol to detect molecular traits of its plastid and we found no evidence of plastid genome and plastid-mediated biosynthesis, consistent with previous ultrastructural studies that did not identify any plastids in Actinophryidae. Moreover, our phylogenetic analyses of particular biosynthetic pathways provide no evidence of a current and past plastid in A. sol. However, we found more than a dozen organellar aminoacyl-tRNA synthases (aaRSs) that are of algal origin. Close relationships between aaRS from A. sol and their ochrophyte homologs document gene transfer of algal genes that happened before the divergence of Actinophryidae and Ochrophyta lineages. We further showed experimentally that organellar aaRSs of A. sol are targeted exclusively to mitochondria, although organellar aaRSs in Ochrophyta are dually targeted to mitochondria and plastids. Together, our findings suggested that the last common ancestor of Actinophryidae and Ochrophyta had not yet completed the establishment of host–plastid partnership as seen in the current Ochrophyta species, but acquired at least certain nuclear-encoded genes for the plastid functions. [ABSTRACT FROM AUTHOR]

A review of algal (including cyanobacterial) symbionts associated with lichen-forming fungi is presented. General aspects of their biology relevant to lichen symbioses are summarized. The genera of algae currently believed to include lichen symbionts are outlined; approximately 50 can be recognized at present. References reporting algal taxa in lichen symbiosis are tabulated, with emphasis on those published since the 1988 review by Tschermak-Woess, and particularly those providing molecular evidence for their identifications. This review is dedicated in honour of Austrian phycologist Elisabeth Tschermak-Woess (1917–2001), for her numerous and significant contributions to our knowledge of lichen algae (some published under the names Elisabeth Tschermak and Liesl Tschermak). [ABSTRACT FROM AUTHOR]

Diatoms are unicellular organisms containing red algal‐derived plastids that probably originated as result of serial endosymbioses between an ancestral heterotrophic organism and a red alga or cryptophyta algae from which has only the chloroplast left. Diatom mitochondria are thus believed to derive from the exosymbiont. Unlike animals and fungi, diatoms seem to contain ancestral respiratory chains. In support of this, genes encoding gamma type carbonic anhydrases (CAs) whose products were shown to be intrinsic complex I subunits in plants, Euglena and Acanthamoeba were found in diatoms, a representative of Stramenopiles. In this work, we experimentally show that mitochondrial complex I in diatoms is a large complex containing gamma type CA subunits, supporting an ancestral origin. By using a bioinformatic approach, a complex I integrated CA domain with heterotrimeric subunit composition is proposed. [ABSTRACT FROM AUTHOR]

The filamentous microalga Tribonema sp. (Stramenopiles, Xanthophyceae) plays an important role in shallow water polar (streams and seepages) and seasonally cold habitats in temperate regions (ponds). In these habitats, freezing and desiccation, and thus freeze–thawing and drying–rewetting cycles, are frequent. These regions produce visible biomass and are important components of low temperature‐adapted communities. We characterized the annual cycles of a Tribonema cf. minus population in two habitats (seepage and stream) in the High Arctic, Svalbard. Seasonality, locality, and their combination (particularly changing environmental conditions) together with cultivation conditions of strains significantly affected their morphological characteristics. Morphological changes following hardening processes related to preparation for the winter period (transition from vegetative cells to akinete and/or pre‐akinete) were recorded. Over the year, positive water temperatures (warmest 13.3°C) occurred for 5 months while negative (lowest temperature was –17.4°C) lasted for 7 months. In winter, there were two melt periods. Vitality staining protocol showed a high number of viable (77.4% and 53.8%) and dormant cells (1.7% and 4.1%; capable of growth and reproduction once suitable conditions return) in the winter seepage and stream, respectively. NPQ and OJIP chlorophyll fluorescence parameters revealed several hours recovery of photosynthesis (both field and control samples). During recovery, only minor or mild stress on photosynthesis was detected. FV/FM values (the photosynthetic efficiency of photosystem II in a dark‐adapted state) in all field and control samples varied around 0.4. Tribonema cf. minus is capable of surviving winter Arctic conditions (perennial strategy). [ABSTRACT FROM AUTHOR]

• The first report of Rhizhochromulina sp. from the Arctic region. • Amoeboid cells of Rhizochromulina sp. B44 form meroplasmodia. • Mechanical stimulation triggers amoeba-to-flagellate transition in Rhizochromulina sp. B44. Rhizochromulina marina is a unicellular amoeboid alga capable of forming flagellate cells; it is a single validly named species in the genus. Besides, there are numerous environmental sequences and undescribed strains designated as Rhizochromulina sp. or R. marina. The biogeography of the genus is understudied: rhizochromulines from the Indian, Southern, and Arctic Oceans are unknown. Here, we present the description of Rhizochromulina sp. B44, which was for the first time isolated from an arctic habitat. Biofilms of this microalga grow at the bottom of a culture vessel, where neighbouring amoeboid cells form associations through a common network of pseudopodia, i.e. meroplasmodia. Pseudopodia branch, anastomose mainly during meroplasmodia formation, and are supported by microtubules that arise from the perinuclear zone. Actin filaments are localized in the cytoplasm and can be revealed only near the bases of pseudopodia. We succeeded in inducing the transformation of amoeboid cells into flagellates using a prolonged agitation of cultures. Morphological and molecular analyses revealed that the studied strain is most closely related to the type strain of R. marina. At the same time, 18S rDNA sequences of early branching-off rhizochromulinids differ significantly from Rhizochromulina sp. B44, suggesting a high divergence at the genus level. [ABSTRACT FROM AUTHOR]

The Heterokonta or Stramenopile phylum comprises clades of unicellular photosynthetic species, which are promising for a broad range of biotechnological applications, based on their capacity to capture atmospheric CO2 via photosynthesis and produce biomolecules of interest. These molecules include triacylglycerol (TAG) loaded inside specific cytosolic bodies, called the lipid droplets (LDs). Understanding TAG production and LD biogenesis and function in photosynthetic stramenopiles is therefore essential, and is mostly based on the study of a few emerging models, such as the pennate diatom Phaeodactylum tricornutum and eustigmatophytes, such as Nannochloropsis and Microchloropsis species. The biogenesis of cytosolic LD usually occurs at the level of the endoplasmic reticulum. However, stramenopile cells contain a complex plastid deriving from a secondary endosymbiosis, limited by four membranes, the outermost one being connected to the endomembrane system. Recent cell imaging and proteomic studies suggest that at least some cytosolic LDs might be associated to the surface of the complex plastid, via still uncharacterized contact sites. The carbon length and number of double bonds of the acyl groups contained in the TAG molecules depend on their origin. De novo synthesis produces long-chain saturated or monounsaturated fatty acids (SFA, MUFA), whereas subsequent maturation processes lead to very long-chain polyunsaturated FA (VLC-PUFA). TAG composition in SFA, MUFA, and VLC-PUFA reflects therefore the metabolic context that gave rise to the formation of the LD, either via an early partitioning of carbon following FA de novo synthesis and/or a recycling of FA from membrane lipids, e.g., plastid galactolipids or endomembrane phosphor- or betaine lipids. In this review, we address the relationship between cytosolic LDs and the complex membrane compartmentalization within stramenopile cells, the metabolic routes leading to TAG accumulation, and the physiological conditions that trigger LD production, in response to various environmental factors. [ABSTRACT FROM AUTHOR]

Phototrophic eukaryotes have evolved mainly by the primary or secondary uptake of photosynthetic organisms. A return to heterotrophy occurred multiple times in various protistan groups such as Chrysophyceae, despite the expected advantage of autotrophy. It is assumed that the evolutionary shift to mixotrophy and further to heterotrophy is triggered by a differential importance of nutrient and carbon limitation. We sequenced the genomes of 16 chrysophyte strains and compared them in terms of size, function, and sequence characteristics in relation to photo-, mixo- and heterotrophic nutrition. All strains were sequenced with Illumina and partly with PacBio. Heterotrophic taxa have reduced genomes and a higher GC content of up to 59% as compared to phototrophic taxa. Heterotrophs have a large pan genome, but a small core genome, indicating a differential specialization of the distinct lineages. The pan genome of mixotrophs and heterotrophs taken together but not the pan genome of the mixotrophs alone covers the complete functionality of the phototrophic strains indicating a random reduction of genes. The observed ploidy ranges from di- to tetraploidy and was found to be independent of taxonomy or trophic mode. Our results substantiate an evolution driven by nutrient and carbon limitation. Majda and colleagues employ a comparative genomic approach to investigate the effect of nutrient and carbon shortage on chrysophyte evolution. Their results indicate that heterotrophic taxa have reduced genome size and higher GC content compared to phototrophic taxa. [ABSTRACT FROM AUTHOR]

Eukaryotes most often synthesize storage polysaccharides in the cytosol or vacuoles in the form of either alpha (glycogen/starch)- or beta-glucosidic (chrysolaminarins and paramylon) linked glucan polymers. In both cases, the glucose can be packed either in water-soluble (glycogen and chrysolaminarins) or solid crystalline (starch and paramylon) forms with different impacts, respectively, on the osmotic pressure, the glucose accessibility, and the amounts stored. Glycogen or starch accumulation appears universal in all free-living unikonts (metazoa, fungi, amoebozoa, etc.), as well as Archaeplastida and alveolata, while other lineages offer a more complex picture featuring both alpha- and beta-glucan accumulators. We now infer the distribution of these polymers in stramenopiles through the bioinformatic detection of their suspected metabolic pathways. Detailed phylogenetic analysis of key enzymes of these pathways correlated to the phylogeny of Stramenopila enables us to retrace the evolution of storage polysaccharide metabolism in this diverse group of organisms. The possible ancestral nature of glycogen metabolism in eukaryotes and the underlying source of its replacement by beta-glucans are discussed. [ABSTRACT FROM AUTHOR]

A high degree of morphological variability is expressed between the ornately sculptured siliceous scales formed by species in the chrysophycean genus, Synura. In this study, we aimed to uncover the general principles and trends underlying the evolution of scale morphology in this genus. We assessed the relationships among thirty extant Synura species using a robust molecular analysis that included six genes, coupled with morphological characterization of the species‐specific scales. The analysis was further enriched with addition of morphological information from fossil specimens and by including the unique modern species, Synura punctulosa. We inferred the phylogenetic position of the morphologically unique S. punctulosa, to be an ancient Synura lineage related to S. splendida in the section Curtispinae. Some morphological traits, including development of a keel or a labyrinth ribbing pattern on the scale, appeared once in evolution, whereas other structures, such as a hexagonal meshwork pattern, originated independently several times over geologic time. We further uncovered numerous construction principles governing scale morphology and evolution, as follows: (i) scale roundness and pore diameter decreased during evolution; (ii) elongated scales became strengthened by a higher number of struts or ribs; (iii) as a consequence of scale biogenesis, scales with spines possessed smaller basal holes than scales with a keel and; and (iv) the keel area was proportional to scale area, indicating its potential value in strengthening the scale against breakage. [ABSTRACT FROM AUTHOR]

The stramenopiles are a large and diverse group of eukaryotes that possess various lifestyles required to thrive in a broad array of environments. The stramenopiles branch with the alveolates, rhizarians, and telonemids, forming the supergroup TSAR. Here, we present a new genus and species of aquatic nanoflagellated stramenopile: Mediocremonas mediterraneus, a free‐swimming heterotrophic predator. M. mediterraneus cell bodies measure between 2.0–4.0 μm in length and 1.2–3.7 μm in width, possessing two flagella and an oval body morphology. The growth and grazing rate of M. mediterraneus in batch cultures ranges from 0.68 to 1.83 d−1 and 1.99 to 5.38 bacteria/h, respectively. M. mediterraneus was found to be 93.9% phylogenetically similar with Developayella elegans and 94.7% with Develorapax marinus, two members within the class Developea. The phylogenetic position of the Developea and the ability of M. mediterraneus to remain in culture make it a good candidate for further genomic studies that could help us to better understand phagotrophy in marine systems as well as the transition from heterotrophy to phototrophy within the stramenopiles. [ABSTRACT FROM AUTHOR]

Xanthophyceae (Stramenopiles) are common microalgae in soil habitats, but not commonly known from maritime sandy habitats. Here we studied the genetic diversity of nine new isolates of Xanthophyceae from coastal habitats using two chloroplast-encoded markers. The isolates exhibited only three morphotypes. The sequence comparisons uncovered a respectable phylogenetic diversity, including novel infraspecific genotypes, among the isolates. The phylogenetic analyses of full rbcL gene sequences identified eight of the isolates to five named species based on monophyletic origins and short genetic distances with defined taxonomic reference strains. One strain, representing a coccoid species, was within a so far unrecognised lineage of Xanthophyceae. In four clades of the rbcL phylogeny, the coastal isolates were most closely related to strains from Antarctic soil habitats. Comparisons of the psbA/rbcL spacer region sequences, a highly variable molecular marker, uncovered a fine-scale structuring within a species which was consistent with habitat preferences. The new maritime isolates exhibited genotypes distinct from those of the same species from other habitats. It suggests that the environment selects for specific genotypes in these pioneering algae. [ABSTRACT FROM AUTHOR]

The brown algae (Phaeophyceae) are a group of multicellular heterokonts that are ubiquitous in today's oceans. Large brown algae from multiple orders are the foundation to temperate coastal ecosystems globally, a role that extends into arctic and tropical regions, providing services indirectly through increased coastal productivity and habitat provisioning, and directly as a source of food and commercially important extracts. Recent multi-locus and genome-scale analyses have revolutionized our understanding of the brown algal phylogeny, providing a robust framework to test evolutionary hypotheses and interpret genomic variation across diverse brown algal lineages. Here, we review recent developments in our understanding of brown algal evolution based on modern advances in phylogenetics and functional genomics. We begin by summarizing modern phylogenetic hypotheses, illuminating the timescales over which the various brown algal orders diversified. We then discuss key insights on our understanding of brown algal life cycle variation and sexual reproduction systems derived from modern genomic techniques. We also review brown algal speciation mechanisms and the associated biogeographic patterns that have emerged globally. We conclude our review by discussing promising avenues for future research opened by genomic datasets, directions that are expected to reveal critical insights into brown algal evolution in past, present, and future oceans. [ABSTRACT FROM AUTHOR]

We performed a comparison of molecular and morphological diversity in a freshwater colonial genus Synura (Chrysophyceae, Stramenopiles), using the island of Newfoundland (Canada) as a case study. We examined the morphological species diversity in collections from 79 localities, and compared these findings to diversity based on molecular characters for 150 strains isolated from the same sites. Of 27 species or species‐level lineages identified, only one third was recorded by both molecular and morphological techniques, showing both approaches are complementary in estimating species diversity within this genus. Eight taxa, each representing young evolutionary lineages, were recovered only by sequencing of isolated colonies, whereas ten species were recovered only microscopically. Our complex investigation, involving both morphological and molecular examinations, indicates that our knowledge of Synura diversity is still poor, limited only to a few well‐studied areas. We revealed considerable cryptic diversity within the core S. petersenii and S. leptorrhabda lineages. We further resolved the phylogenetic position of two previously described taxa, S. kristiansenii and S. petersenii f. praefracta, propose species‐level status for S. petersenii f. praefracta, and describe three new species, S. vinlandica, S. fluviatilis, and S. cornuta. Our findings add to the growing body of literature detailing distribution patterns observed in the genus, ranging from cosmopolitan species, to highly restricted taxa, to species such as S. hibernica found along coastal regions on multiple continents. Finally, our study illustrates the usefulness of combining detailed morphological information with gene sequence data to examine species diversity within chrysophyte algae. [ABSTRACT FROM AUTHOR]

We examined 12 strains representing eight species classified in the algal class Phaeothamniophyceae (Heterokontophyta). Based upon a five‐gene molecular phylogeny (nuclear‐encoded SSU rRNA and plastid‐encoded psaA, psbA, psbC, and rbcL) and light microscopic observations, we describe five new species: Phaeoschizochlamys santosii sp. nov., Phaeoschizochlamys siveri sp. nov., Phaeothamnion wetherbeei sp. nov., Stichogloea dopii sp. nov. and Stichogloea fawleyi sp. nov. The Phaeothamniophyceae, as delimited here, form a natural group that is sister to the Aurearenophyceae. Molecular phylogenetic analyses proved more reliable than morphological characters for distinguishing species. Evolutionary trends with the SI clade of the heterokont algae are discussed. [ABSTRACT FROM AUTHOR]

SUMMARY: The small phytoplankton genus Triparma belongs to the class Bolidophyceae and contains two distinct forms: silicified species and naked flagellated species (formerly Bolidomonas). Recent studies showed that four silicified species/strains (Triparma laevis f. inornata, T. laevis f. longispina, T. strigata, and T. aff. verrucosa) belong to a single clade that is paraphyletic, because it also contains an unclassified flagellated strain, and is sister to a flagellated species, T. eleuthera. In this study, we isolated and characterized two new strains of silicified species to test the phylogenetic unity of silicified bolidophytes. The isolates were identified as T. retinervis strains because they possessed fine areolation on the cell wall. 18S rDNA and rbcL phylogenetic analyses demonstrated that T. retinervis formed a new silicified clade that is sister to the flagellated species T. pacifica. This reveals that there are at least two distinct clades including both silicified and flagellated Triparma species. [ABSTRACT FROM AUTHOR]

The heterotrophic stramenopile Cafeteria roenbergensis is a globally distributed marine bacterivorous protist. This unicellular flagellate is host to the giant DNA virus CroV and the virophage mavirus. We sequenced the genomes of four cultured C. roenbergensis strains and generated 23.53 Gb of Illumina MiSeq data (99–282 × coverage per strain) and 5.09 Gb of PacBio RSII data (13–45 × coverage). Using the Canu assembler and customized curation procedures, we obtained high-quality draft genome assemblies with a total length of 34–36 Mbp per strain and contig N50 lengths of 148 kbp to 464 kbp. The C. roenbergensis genome has a GC content of ~70%, a repeat content of ~28%, and is predicted to contain approximately 7857–8483 protein-coding genes based on a combination of de novo, homology-based and transcriptome-supported annotation. These first high-quality genome assemblies of a bicosoecid fill an important gap in sequenced stramenopile representatives and enable a more detailed evolutionary analysis of heterotrophic protists. Measurement(s) DNA • mitochondrial_DNA • sequence_assembly • sequence feature annotation Technology Type(s) DNA sequencing • genome assembly • sequence annotation Sample Characteristic - Organism Cafeteria roenbergensis Sample Characteristic - Environment marine water body Sample Characteristic - Location Northwest Atlantic Ocean • Carribean Sea • Southeast Pacific Ocean • North East Pacific Ocean Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11419098 [ABSTRACT FROM AUTHOR]

The biotechnology in Latin America has had a substantial increase in scientific productions occupying 4.96% of the world production, being Brazil and México the countries that generate the highest production. Since 2004, the Latin American Congress of Algal Biotechnology (CLABA) has been held, bringing together different specialized branches in both micro and macro algae. The aim of this work is to get an approximation on the trends in algal biotechnology in Latin America using as data the researches presented in the VI CLABA carried out in October 2017 in Lima (Peru). The information was organized in a matrix where the species used were identified; likewise, it was classified according to the phylum and the groups of eukaryotes/bacteria. In the same way, the investigations were classified according to their application. Chlorophyta (47%), Cyanobacteria (16%) and Ochrophyta (13%) were among the most relevant groups in terms of phylum; on the other hand, the most outstanding group of eukaryote/bacteria were Archaeplastida (57%), Stramenopiles (24%) and Cyanobacteria (17%). It is interesting that, in spite of being a congress of algae, 16% of organisms used were cyanobacteria, probably due to the taxonomic tradition in this group of polyphyletic organisms. The most used applications in this congress are oriented to aquaculture and care of the environment. [ABSTRACT FROM AUTHOR]

Unicellular eukaryotes have pivotal ecological roles in aquatic ecosystems by participating in biogeochemical processes and structuring microbial food webs. However, revealing their biogeographical patterns remains challenging, as it is reflected in the rather limited available knowledge. In this study, two central patterns, the taxa–area and the distance–decay relationships, were tested for freshwater unicellular eukaryotes. Sampling was performed in 31 mountainous freshwater ecosystems in Thessaly (Greece). Sampling sites had different geohydromorphological characteristics (altitude, 124–704 m; depth, 0.3–1 m; surface area, 188–123 000 m2; geographical distances, 0.03–48.4 km). Unicellular eukaryote diversity was assessed by 18S rRNA gene diversity with high-throughput sequencing. Five supergroups (Stramenopiles, Alveolata, Rhizaria, Archaeplastida and Opisthokonta) were found with the most abundant taxa being Stramenopiles and Alveolata. Aquatic unicellular eukaryotes showed statistically significant but weak DDR and TAR. This can be attributed to the large proportion of specialists (91.9% of operational taxonomic units according to Levin's index). These results indicate that although mountainous pools and ponds can host high diversity of unicellular eukaryotes, the shaping of their communities is mainly regulated by niche-specific processes and environmental filtering and to a lesser extent by species dispersion processes. [ABSTRACT FROM AUTHOR]

[Display omitted] • Description of four new Bigyra species belonging to MAST-6 and Placididea. • Generation of six new Bigyra transcriptomes including that of two known Bikosia. • MAST-6 species are phylogenetically diverse and abundant in marine sediment. • The new Placididea species likely tolerates range of salinity. • Update on a stramenopile phylogenomic tree with six new Bigyra transcriptomes. Unlike morphologically conspicuous ochrophytes, many flagellates belonging to basally branching stramenopiles are small and often overlooked. As a result, many of these lineages are known only through molecular surveys and identified as MArine STramenopiles (MAST), and remain largely uncharacterized at the cellular or genomic level. These likely phagotrophic flagellates are not only phylogenetically diverse, but also extremely abundant in some environments, making their characterization all the more important. MAST-6 is one example of a phylogenetically distinct group that has been known to be associated with sediments, but little else is known about it. Indeed, until the present study, only a single species from this group, Pseudophyllomitus vesiculosus (Pseudophyllomitidae), has been both formally described and associated with genomic information. Here, we describe four new species including two new genera of sediment-dwelling MAST-6, Vomastramonas tehuelche gen. et sp. nov., Mastreximonas tlaamin gen. et sp. nov., one undescribed Pseudophyllomitus sp., BSC2, and a new species belonging to Placididea, the potentially halotolerant Haloplacidia sinai sp. nov. We also provide two additional bikosian transcriptomes from a public culture collection, to allow for better phylogenetic reconstructions of deep-branching stramenopiles. With the SSU rRNA sequences of the new MAST-6 species, we investigate the phylogenetic diversity of the MAST-6 group and show a high relative abundance of MAST-6 related to M. tlaamin in samples across various depths and geographical locations. Using the new MAST-6 species, we also update the phylogenomic tree of stramenopiles, particularly focusing on the paraphyly of Bigyra. [ABSTRACT FROM AUTHOR]

Taxonomic characterization of the diverse group of heterokont algae, scientifically documented since the 18th century, has been subject to many twists and turns. These results also demonstrated the need to obtain plastid genome sequences from more diverse, underrepresented lineages to fully understand plastid evolution in heterokont algae. The genus I Olisthodiscus i was described in 1937 by Nellie Carter using cells collected from the brackish Bembridge lagoon on the Isle of Wight, United Kingdom. [Extracted from the article]

Summary: Development of high‐throughput sequencing techniques has greatly benefited our understanding about microbial ecology, yet the methods producing short reads suffer from species‐level resolution and uncertainty of identification. Here, we optimize Pacific Biosciences‐based metabarcoding protocols covering the internal transcribed spacer (ITS region) and partial small subunit of the rRNA gene for species‐level identification of all eukaryotes, with a specific focus on Fungi (including Glomeromycota) and Stramenopila (particularly Oomycota). Based on tests on composite soil samples and mock communities, we propose best suitable degenerate primers, ITS9munngs + ITS4ngsUni for eukaryotes and selected groups therein and discuss the pros and cons of long read‐based identification of eukaryotes. [ABSTRACT FROM AUTHOR]

Summary: Elucidation of the potential roles of single‐celled eukaryotes (protists) in ecosystem function and trophodynamics in hydrothermal vent ecosystems is reliant on information regarding their abundance, distribution and preference for vent habitats. Using high‐throughput 18S rRNA gene sequencing on a diverse suite of hydrothermally influenced and background water samples, we assess the diversity and distribution of protists and identify potential vent endemics. We found that 95% of the recovered sequences belong to operational taxonomic units (OTUs) with a cosmopolitan distribution across vent and non‐vent habitats. Analysis of 'vent only' OTUs found in more than one vent sample and co‐occurrence network analysis comparing protist groups to extremophilic reference organisms suggest that the most likely vent endemics are infrequently encountered, potentially in low abundance, and belong to novel lineages, both at the phylum level and within defined clades of Rhizaria and Stramenopila. Potential endemism is inferred for relatives of known apusomonads, excavates and some clades of Syndiniales. Similarity in community composition among samples was low, indicating a strong stochastic component to protist community assembly and suggesting that rare endemics may serve as a reservoir poised to respond to changing environmental conditions in these dynamic systems. [ABSTRACT FROM AUTHOR]

Viruses are the most abundant biological entities on Earth and have fundamental ecological roles in controlling microbial communities. Yet, although their diversity is being increasingly explored, little is known about the extent of viral interactions with their protist hosts as most studies are limited to a few cultivated species. Here, we exploit the potential of single‐cell genomics to unveil viral associations in 65 individual cells of 11 essentially uncultured stramenopiles lineages sampled during the Tara Oceans expedition. We identified viral signals in 57% of the cells, covering nearly every lineage and with narrow host specificity signal. Only seven out of the 64 detected viruses displayed homologies to known viral sequences. A search for our viral sequences in global ocean metagenomes showed that they were preferentially found at the DCM and within the 0.2–3 µm size fraction. Some of the viral signals were widely distributed, while others geographically constrained. Among the viral signals we detected an endogenous mavirus virophage potentially integrated within the nuclear genome of two distant uncultured stramenopiles. Virophages have been previously reported as a cell's defence mechanism against other viruses, and may therefore play an important ecological role in regulating protist populations. Our results point to single‐cell genomics as a powerful tool to investigate viral associations in uncultured protists, suggesting a wide distribution of these relationships, and providing new insights into the global viral diversity. [ABSTRACT FROM AUTHOR]

Summary: Circadian clocks allow organisms to predict environmental changes caused by the rotation of the Earth. Although circadian rhythms are widespread among different taxa, the core components of circadian oscillators are not conserved and differ between bacteria, plants, animals and fungi. Stramenopiles are a large group of organisms in which circadian rhythms have been only poorly characterized and no clock components have been identified. We have investigated cell division and molecular rhythms in Nannochloropsis species. In the four strains tested, cell division occurred principally during the night period under diel conditions; however, these rhythms damped within 2–3 days after transfer to constant light. We developed firefly luciferase reporters for the long‐term monitoring of in vivo transcriptional rhythms in two Nannochlropsis species, Nannochloropsis oceanica CCMP1779 and Nannochloropsis salina CCMP537. The reporter lines express anticipatory behavior under light/dark cycles and free‐running bioluminescence rhythms with periods of ~21–31 h that damped within ~3–4 days under constant light. Using different entrainment regimes, we demonstrate that these rhythms are modulated by a circadian‐type oscillator. In addition, the phase of free‐running luminescence rhythms can be modulated pharmacologically using a CK1 ε/δ inhibitor, suggesting a role of this kinase in the Nannochloropsis clock. Together with the molecular and genomic tools available for Nannochloropsis species, these reporter lines represent an excellent system for future studies on the molecular mechanisms of stramenopile circadian oscillators. Significance Statement: Stramenopiles are a large and diverse line of eukaryotes in which circadian rhythms have been only poorly characterized and no clock components have been identified. We have developed bioluminescence reporter lines in Nannochloropsis species and provide evidence for the presence of a circadian oscillator in stramenopiles; these lines will serve as tools for future studies to uncover the molecular mechanisms of circadian oscillations in these species. [ABSTRACT FROM AUTHOR]