Journal of Phycology

John Raven pioneered the field of algae ecophysiology, advancing our understanding of cellular resource economics, carbon acquisition, and energy allocation. His work laid the foundation for investigating integrative physiology, linking growth-survival trade-offs across diverse environments. The sea ice habitat provides an excellent framework to continue the research John championed. With steep temperature-salinity gradients, algae survival requires a shift in physiology that we are only beginning to understand. We developed two small scale, reproducible icecosms to investigate physiological changes associated with incorporation into sea ice and survival potential post-melt. Fragilariopsis cylindrus and Nitzschia frigida, known for their association with the ice environment, and Porosira glacialis, known for its association with the ice edge, were used to mechanistically link physical properties with algal physiology and post-melt survival. We observe incorporation into the ice of F. cylindrus and N. frigida alongside vertical photophysiological profiles of F. cylindrus revealing inhospitable conditions in the top compared to the bottom layers of ice. N. frigida and P. glacialis remain viable within the ice and retain the capacity to seed populations following melt. Our results establish icecosms as experimental framework to investigate ecophysiological responses of sea ice algae and provide a foundation toward ecological and evolutionary questions.

Diatom mating activity contributes to their enormous phenotypic and genetic diversity, yet little is known about patterns in diatom reproductive compatibility across genetically diverse strains, nor the effects on offspring phenotypes that may confer adaptive evolution, niche partitioning, or trait improvement. Here a panel of 38 Arctic Cylindrotheca sp. isolates were crossed pairwise to detect mating compatibility. Positive mating patterns were identified in multiple clades, including amongst crosses of different parental rbcL genotypes. F1 isolated from three different crosses presented phenotypic variation in growth rate, plastid traits, and associated photo-physiological responses to blue and green actinic light. Offspring gliding speed and behaviour also varied, providing insights into complex motility traits that link cell morphology, bioenergetics and sensory adaptation with emergent movement patterns. Exploratory analysis of the F1 trait landscape identified a varaible mixture of individual-level and cross-dependent effects, including substantial variation in growth rate between individuals and strong effects of different crosses on morphology and motility. Experimental diatom breeding may offer a unique strategy to study ocean protist evolution and phenotypic diversification and could complement other biotechnological innovations to enhance cultivation yields and crop resilience in mass cultivation.

Primary production in the Southern Ocean (SO) plays a critical role in regulating the global carbon cycle, yet the physiological mechanisms governing phytoplankton responses to iron (Fe) limitation and variable light remain poorly constrained. Using a custom made incubation system that simulated natural diel solar variability, we examined the interactive effects of Fe availability, light intensity, and photoperiod (continuous vs. variable) on three ecologically important SO phytoplankton: Fragilariopsis cylindrus, Phaeocystis antarctica, and Thalassiosira antarctica. Physiological, photophysiological, and proteomic measurements revealed that Fe availability was the dominant factor regulating growth, carbon production, photosynthetic performance and protein expression across all species. Distinct acclimation strategies emerged: F. cylindrus exhibited marked trade-offs between productivity and photoprotection under Fe stress, consistent with adaptation to stable, low-light, Fe-poor environments; P. antarctica maintained growth by flexibly modulating photoprotective and photosynthetic capacity, reflecting high plasticity suited to dynamic, open-ocean conditions; and T. antarctica expressed a balanced strategy, sustaining productivity and photoprotection simultaneously, characteristic of coastal bloom formers with higher Fe demand. Dynamic light regimes produced smaller, species-specific effects, influencing chlorophyll content and carbon storage primarily in T. antarctica. Correlation and z-score analyses demonstrated that Fe-rich photosynthetic proteins co-varied with biomass production, whereas photoprotective traits clustered independently, underscoring divergent energy-allocation strategies. Together, these results reveal how SO phytoplankton partition resources between productivity and photoprotection under shifting Fe-light regimes, providing mechanistic insight into their ecological niches.

Algae require specific acclimation strategies to cope with spectral variability in shallow marine habitats. We investigated how the siphonous green alga Derbesia alters its photosynthetic and metabolic processes under white (WL), blue (BL), green (GL), red (RL), and far-red light (FL) by conducting photobiological and transcriptomic sampling over a 10-day period. Our results show two contrasting photoacclimation strategies: BL and GL promoted metabolic activity associated with growth, whereas FL and RL induced a low-light-like survival strategy characterized by reduced growth and suppression of the core metabolism. Photosynthetic acclimation across all conditions primarily occurs within the light dependent reactions. BL and GL promoted early acclimation marked by the immediate activation of light-harvesting complexes (LHCs) and a key transcriptional regulator MYB, and showed better acclimation marked by the sustained activation of ATPases, ATP transporters, and hormone-signaling components. BL induced a distinct transcriptional shift during the transition to prolonged exposure, including enhanced cyclic electron transport, and key regulators of protein synthesis, DNA replication, and transcriptional regulation. In contrast, FL, and to a lesser extent RL, triggered responses resembling low light acclimation with constrained growth, characterized by inefficient energy utilization, enlarged antenna systems, chloroplast proliferation with aggregations, and reduced growth rates. This study suggests high accumulation of core photopigments and reduction in chlorophyll a/b is an acclimatory response to FL, and consistently higher activation of core metabolic processes under WL likely indicates the evolutionary adaptation of Derbesia to shallow coastal environments where broad-spectrum light predominates. Additionally, our newly sequenced draft genome of the Derbesia strain for this study could serve as a genomic resource for future molecular photobiology research in Bryopsidales algae.

We present a genome assembly of Aiptasia strain F003, a broadly used laboratory strain of the sea anemone and coral model organism Exaiptasia diaphana (Cnidaria; Anthozoa; Hexacorallia; Actiniaria; Aiptasiidae; Exaiptasia). The genome assembly spans 237.34 Mb across 12,480 contigs with a contig N50 of 76.47 kb (12,423 scaffolds with a scaffold N50 of 77.93 kb), including a single-contig mitochondrial genome with a length of 19.79 kb. The assembly is highly complete with a BUSCO completeness of 96.50% based on the metazoa dataset, including 94.80% single-copy, 1.70% duplicated, 1.70% fragmented, and 1.80% missing BUSCO genes. Genome annotation identified 29,589 protein-coding genes (including 2 pseudogenes) and a repeat content of 32.89%. The genome of the female Aiptasia strain F003 enhances the utility of a key cnidarian model organism by enabling comparisons among Aiptasia strains in studies of symbiosis, microbiomes, and thermal stress. It thereby strengthens the value of Aiptasia as a model for investigating the mechanisms underlying coral holobiont function, response, and resilience to environmental change.

The impacts of a changing abiotic environment on fitness and performance arise not only from low tolerance to new environmental conditions, but also from changes in the abundance and interaction intensity with other species. The strength of the interaction may itself depend on how well each species performs across environments, but there is a dearth of studies investigating how intrinsic fitness and interaction intensity covary across an abiotic environmental gradient. We addressed this question in a hypersaline consumer-resource system: the microalga Dunaliella spp. grazed by the brine shrimp Artemia franciscana. We exposed four Dunaliella strains to a range of salinities above seawater, with or without brine shrimps, and tracked their population sizes over time and the survival of their predators, to estimate basic parameters of a Lotka-Volterra model. We found that the intrinsic growth rate of algae, the survival rate of predators, and the per-capita predation rate, all varied with salinity and algal strain. Significant interactions between strain and salinity further revealed that these ecological responses to salinity are evolvable. Together with correlations between demographic parameters across salinity, this suggests that predation may influence the evolution of salinity tolerance curves, blurring the line between the fundamental and realized niches.

Many dinoflagellates are mixotrophic and regulate their vertical position to navigate dynamic gradients in light, nutrients, and prey. Here, it is shown that the obligate kleptoplastidic mixotroph, Dinophysis acuminata, transitions from diel vertical migration to formation of a stationary, sub-surface thin layer in response to prolonged prey deprivation. An inshore bloom within a salt marsh kettle pond was recorded through continuous in-situ imaging, automated oxygen and fluorescence depth profiling, and targeted water chemistry measurements. During the blooms initial development, D. acuminata cells were photosynthetically active and divided vegetatively while vertically migrating. As photosynthesis and growth slowed, vertical migration ceased and cells formed a stable thin layer that promoted conditions for local acidification and nitrogen remineralization. Surface avoidance by the thin layer drove selective retention of cells within the relatively deep kettle hole. Together, these findings illustrate linkage of metabolic state and swimming behavior in D. acuminata and show how swimming behavior can drive development of toxic blooms within inshore systems. They also illustrate how D. acuminata and other eurytolerant bloom-forming species can exploit and shape physicochemical gradients associated with coastal eutrophication.

The picocyanobacterium Prochlorococcus is a fundamental contributor to ocean primary productivity. While its free-living population has been extensively studied, primarily using flow cytometric analyses, the size and distribution of its particle-associated population is not well understood. Using filter fractionated samples from cruises in the Pacific Ocean, Atlantic Ocean, and Mediterranean Sea, we generated metagenomic data using internal standards, yielding absolute genome equivalent counts of Prochlorococcus cells in different size fractions. We used these data to model a relationship between relative and absolute genome equivalent counts, yielding a correction factor that we validated using published datasets. We then applied the correction factor to size-fractionated global metagenomic data from the TARA Oceans Project, which has widespread Prochlorococcus cells in size fractions >1.6 m throughout the transects, to calculate the fraction of the total Prochlorococcus population in large size fractions. The ''particle-associated'' population fraction increased with net primary productivity. Dissolved inorganic carbon was also directly correlated with increased particle association, which, combined with other evidence, could indicate an association with upwelling. We also examined the relationship between particle-associated population and carbon export at 150 m by incorporating published estimates of carbon flux based on TARA optical scattering data. This study highlights the potential importance of particle-associated Prochlorococcus to carbon flux in marine ecosystems and offers a way to convert relative to absolute genome equivalents of microorganisms in archival metagenomic datasets.

The non-indigenous brown macroalga Rugulopteryx okamurae has emerged as one of the most aggressive marine invaders in European waters, deeply altering benthic communities and causing severe socioeconomic impacts. While its expansion has been extensively documented along the southern Iberian Peninsula, understanding the dynamics of its northward range expansion along the Spanish Mediterranean coast remains critical for coastal management. This study documents the first formal record of R. okamurae in Calpe (Alicante), representing its current northernmost distribution limit within the Comunitat Valenciana. Sampling was conducted through an initial opportunistic scuba diving observation along the surrounding waters of the Penyal dIfac Natural Park, followed by targeted underwater surveys and an ad hoc inspection of commercial bottom-trawling nets drying at the port of Calpe during June 2026. Morphological and anatomical identification was confirmed through cross-sections of the thallus under optical microscopy, revealing the presence of both the thick and intermediate morphotypes of the species. The collected specimens were found either entangled within a native photophilic algal canopy in shallow waters or recovered from deeper offshore fishing grounds. Given the absence of records in the area during 2023-2025 surveys, these findings suggest either a very recent front-wave colonization event or a contribution from nearby, yet undetected, established patches, driven by secondary local dispersal mechanisms such as drifting fragments and explicitly highlighting commercial fishing activities as an active vector. Furthermore, considering that the species was recorded within a marine protected area and deeper environments, these results highlight a potential ecological threat to local benthic ecosystems, emphasizing the urgent need f or competent authorities to implement spatiotemporal monitoring and public awareness campaigns to prevent the definitive establishment of this invader.

Marine diatoms contribute to about 20% of global primary production. We present the first basin-scale, multiyear assessment of diatom communities in the North Pacific, combining taxonomically high-resolution RuBisCO large subunit gene (rbcL) metabarcoding with concurrent environmental measurements. Using a nine-year time series of daily samples resolved at the species level via ~500 bp rbcL fragments, we performed multivariate analyses across biogeographic provinces, identifying significant correlations between community structure and environmental drivers such as temperature and macronutrient availability. We report the prevalence of a previously overlooked centric diatom species in the North Pacific, Eunotogramma lunatum, which appears to be near-dominant even in subarctic high-nitrate, low-chlorophyll waters where pennate diatoms are typically favored. These results demonstrate the power of rbcL for large-scale ocean monitoring and provide a critical baseline for future studies of diatom population dynamics, climate change impacts, and ecosystem resilience in a key marine region.

Quantitative stable isotope probing (qSIP) allows researchers to calculate taxon-specific carbon incorporation from sequencing of natural microbial communities, which can be used as a proxy for metabolic activity rates and subsequently as an input for biogeochemical modeling. While qSIP is widely utilized in soils to investigate the identity and metabolic activity of largely unculturable microbes, the application of qSIP in marine and aquatic ecosystems is more recent. Here, we investigated how bioreactor type (batch vs. chemostat) and carbon substrate complexity (single vs. multiple substrates) affect the incorporation of {superscript 1}3C-labeled glucose into rRNA after 24 hours using excess atomic fraction (EAF) as a proxy for metabolic activity rate. We found that the growth dynamics and community composition of the {superscript 1}3C-incorporating bacteria differed significantly for each treatment. EAF was positively correlated with both 16S gene copy number and a genomic index of copiotrophy in both batch treatments, but not in the chemostat, suggesting that chemostats dampen the competitive advantage of fast-growing copiotrophic taxa. Our results demonstrate that both substrate complexity and experimental regime influence qSIP-derived metabolic activity estimates and provide guidance for future applications of qSIP in aquatic environments.

Giant clams are some of the largest bivalve molluscs. They form a vital partnership with Symbiodiniaceae dinoflagellates that supply most of their energetic requirements. However, the factors that shape giant clam-associated photosymbiont communities remain unknown. Here, we profiled Symbiodiniaceae communities using ITS2 metabarcoding in eight giant clam species (Hippopus hippopus, H. porcellanus, Tridacna crocea, T. derasa, T. gigas, T. maxima, T. noae and T. squamosa) from 11 sites across the Philippine archipelago. Symbiodiniaceae community structure was shaped by an interplay between giant clam host and environment. Most giant clams were dominated by members of a single symbiont genus, with Cladocopium as the most prevalent, followed by Durusdinium and Symbiodinium. However, giant clam hosts also exhibited flexibility in their symbiotic partners that was evident across sites. Differences in giant clam-associated symbiont communities may contribute to differences in holobiont function and adaptability to variable environments. These findings deepen our understanding of giant clam-Symbiodiniaceae associations, offering a framework for predicting how giant clams may be affected by increasingly stressful reef conditions and, more importantly, informing strategies to improve mariculture and conservation practices.

Environmental DNA (eDNA) has the potential to be a powerful tool in blue carbon science for characterizing and quantifying the contribution of marine macrophytes; but its complex, dynamic relationship with bulk biomass is poorly understood. Here, we used eDNA to examine the degradation dynamics of sugar kelp (Saccharina latissima) in muddy, anaerobic marine sediment. This involved three 16-week incubations; with additions of lyophilized sugar kelp alone, a mix of lyophilized marine macrophytes including sugar kelp, and sugar kelp holdfasts buried in sediment. We used species-specific digital polymerase chain reaction assays for mitochondrial, chloroplast and nuclear markers, and metabarcoding for the 16S and 18S ribosomal RNA genes. In the former two incubations, all sugar kelp eDNA markers showed rapid log exponential declines (up to 98-99%) to asymptotes greater than the unamended controls, even as part of a more complex mix of macrophytes. In contrast, for the buried kelp holdfasts, sugar kelp eDNA increased to an asymptote (by up to [~]15X), which may be reflective of the different nature of added biomass. Overall, we demonstrate substantial preservation of environmental DNA and total organic carbon under anaerobic conditions, and the potential to use environmental DNA to quantify biomass in a blue carbon context.

Freshwater salinization is of increasing concern for integrity and functioning of freshwater habitats worldwide. Experiments so far often have studied drastic salt additions, while gradient designs have been performed less commonly. We tested the effect of freshwater salinization in a mesocosm exposing the plankton community of the oligotrophic Lake Lunz, Austria, to a four-fold salinization gradient (control, 0.2, 1, a 5 ppt salt). Salinity was manipulated in a factorial design with enrichment, with 10 g L-1 and 30 g L-1 phosphorus, resulting in 8 treatments with 3 replicates each. We followed the effects of salinization on diversity, community composition and resource use over 36 days. Community composition was assessed by amplicon sequencing, Diversity loss and community turnover followed upon salt addition. All levels of salinization caused pronounced changes in community composition, with 5 ppt causing the most drastic changes. Salinization caused trophic downgrading by kicking out especially protistan consumers and rotifers, while some green algae and chrysophytes were especially tolerant, resulting in reduced phylogenetic and functional diversity with increasing salinization. In line with reduced top down control, salinization affected temporal variability in chlorophyll-a (chl-a) and resource use (RUE), with higher salinity causing more extreme fluctuations in chl-a and RUE. Enrichment overall aggravated salinization, enhancing temporal turnover and temporal fluctuations in resource use.

The cyanobacterium Trichodesmium is important in ocean nitrogen (N) and carbon (C) biogeochemistry through fixation of N2 gas and CO2 into NH3, amino acids, and carbohydrates. These essential compounds then fuel primary productivity, bacterial and grazing communities, and upper trophic levels. In the oligotrophic surface oceans, they are one of few taxa capable of utilizing both atmospheric C and N. Trichodesmium fall into 2 diazotrophic phylogenomic clades named "Thieb" and "Tery" after the most well characterized botanical species, Trichodesmium thiebautii and Trichodesmium erythraeum. Thieb is commonly the most abundant clade in all major ocean regions and paradoxically, is also the least characterized in terms of morphology, genomics, and ecophysiology due to underrepresentation in culture collections. In this study, 25 novel strains of Thieb were enriched in culture from the Sargasso Sea, phenotypically characterized, and whole genome sequenced. Cultures were found to belong to four well-supported subclades (i.e., ThiebA, ThiebB, ThiebC, and ThiebD). Trichodesmium subclades were found to have environmentally relevant differences in colony shape, gene content, cell dimensions, and inferred temperature range. Specifically, ThiebD and ThiebC had the largest biovolumes whereas ThiebA and ThiebB had the smallest. Importantly ThiebB also became relatively more abundant only in bulk seawater metagenomes collected at high temperature (>28{degrees}C). This finding indicates that as ocean warming continues, there may be shifts in Trichodesmium community structure towards smaller cells, which would affect overall C+N standing stocks.

Trichodesmium is an important oceanic N2 fixing cyanobacterial genus that has been shown to provide up to 50% of new N to oligotrophic regimes. Despite its importance, we know relatively little about the genomic potential and functional diversity of the two major clades of Trichodesmium (Clade I and Clade III, hereafter Thieb and Tery, respectively). With the expanded collection of Trichodesmium isolates in the USCTCC (University of Southern California Trichodesmium Culture Collection), we sequenced genomes from seven cultivated strains to further characterize the genomic diversity within the genus. For example, sequencing the genome of the "gigantic", red Trichodesmium contortum surprisingly shows that they are closely related to the smallest Trichodesmium clade, TeryA. The high genomic identity between TeryA and T. contortum (>98.5% ANI) and lack of implicated auxiliary genes suggests their large biovolume differences might be transcriptional or epigenetic in origin. Furthermore, these data show that using Tery-subclades are a more accurate designation than the classical Trichodesmium species delineation. Finally, we placed the analysis of these genomes in an ecological context via read mapping with globally distributed RNA and DNA datasets. Our data show that Tery clades (A&B) are both lower in relative abundance compared to Thieb in global oceans, generally co-occur when detected in the field, and are highly linked to decreased salinity and increased temperatures, especially for sampling locations in the Bay of Bengal. Lastly, even though TeryA members are undersaturated with respect to current CO2 concentrations, our phenotypic and biogeography data suggests that salinity/ocean color could limit their predicted global impact as climate changes.

The nutritional symbiosis between corals and their photosynthetic dinoflagellate partners underpins the ecological success of reef-building corals in nutrient-poor environments. Although coral holobionts can assimilate the abundant yet highly variable environmental nitrate, direct insight into how nitrate reductase is regulated in these symbiotic algae has been lacking. Here, we provide the first characterization of nitrate reductase protein and gene expression in cultured Symbiodiniaceae exposed to different nitrogen sources and light regimes, revealing the multifactorial nature of its regulation. We demonstrate that nitrate reductase operates as a substrate-induced enzyme: nitrate stimulates protein synthesis in nitrogen-starved cultures, whereas ammonium actively suppresses its expression in a concentration-dependent manner. Light availability and photosynthetic electron transport further modulate protein abundance, suggesting that while nitrate reductase synthesis depends on nitrate availability, its stability may rely on photosynthesis. We also show that nitrate reductase is synthesized within hours of nitrate exposure by symbionts from nitrogen-starved corals, demonstrating that nitrate reduction can occur within the host environment. However, this response is transient and diminished relative to free-living cells, indicating that nitrate reduction is a facultative pathway activated when preferred nitrogen sources are limited. Finally, gene expression measurements and pharmacological inhibition confirm that nitrate reductase regulation is predominantly post-transcriptional, enabling this rapid and reversible control of nitrate assimilation. Together, these findings reveal a tightly regulated and responsive nitrate reduction system in coral symbionts that provides a flexible mechanism contributing to nitrogen homeostasis under fluctuating nutrient regimes.

Compared with bacterial and archaeal extremophiles, single-celled eukaryotes living in extreme habitats are understudied and underrepresented in genomic databases. An exception is the obligately halophilic stramenopile Halocafeteria seosinensis strain EHF34. A transcriptome-focused analysis of this extremophilic protists revealed the importance of organic osmolyte regulation and transport in its adaptation to hypersaline environments. However, genomic resources for H. seosinensis are currently limited to a highly fragmented assembly generated by short-read sequencing, which has hindered further investigation of the genome biology and evolution of this fascinating organism. Here, we used long-read Oxford Nanopore sequencing to generate a highly contiguous, chromosome-scale genome assembly for H. seosinensis. The assembly is 38.8 megabase pairs (Mbp) in size and contains 60 nuclear contigs, making it the most contiguous genome for a member of the order Bicosoecida. Approximately 19% of the genome is comprised of transposable elements. Of the 11,684 predicted protein-coding genes, many appear to be associated with DNA mobility-related functions, and several may be linked to adaptation to a hypersaline environment. Analysis of the H. seosinensis long-read genome assembly presented herein will facilitate our understanding of the ways in which protists have adapted to extreme environments. SignificanceHalocafeteria seosinensis is an extremophilic protist adapted to hypersaline environments. Previous analyses of a transcriptome and short-read draft genome assembly for this organism provided insights into the molecular mechanisms underlying osmotic regulation, which facilitate its adaptation to high-salt conditions. However, the lack of contiguity and quality of the draft assembly prevented the characterization of complex genomic regions, including transposable elements and viral insertions, as well as genomic comparisons with related species. Here we present a highly contiguous, chromosome-scale genome assembly for H. seosinensis that enables accurate gene prediction, detailed analysis of repeat content, and comparative genomic analysis. This long-read genome assembly will serve as a valuable resource for studying one of the few tractable halophilic protists sequenced to date.

The Upside-Down Jellyfish, Cassiopea, has become a mainstay of cnidarian photosymbiosis research. Two nominal sister species, C. xamachana and the globally introduced C. andromeda, supply most of the medusae used in American and European laboratory research within this genus. As founder identity can shape experimental outcomes, here we utilize whole genome resequencing of 21 Cassiopea medusae spanning the Florida Keys, Bocas del Toro (Panama), and a European laboratory line, to ask whether mitochondrial species assignment predicts nuclear genome identity. Across multiple population structure analyses using the nuclear genome, Floridian Cassiopea carrying C. xamachana or C. andromeda mitotypes are indistinguishable, and geography is the dominant axis of nuclear genetic structure. A population tree that groups the two Floridian mitotypes as a single interbreeding unit is strongly supported (Patterson's D {approx} 0.0, Z = 0.02), whereas a tree that respects mitochondrial species boundaries is rejected (D = 0.42, Z = 20.8). Strikingly, the European "true" C. andromeda line clusters with Panamanian C. xamachana rather than with Floridian C. andromeda-mitotype animals. From the same sequencing effort, we recover evidence of symbiont community variability (Cladocopium) in Panama and assemble two near-complete Tenacibaculum and Endozoicomonas metagenomically-assembled genomes from Floridian host tissue. Together these results indicate that the C. andromeda/C. xamachana hybridization zone may extend across ocean basins, and that a "pure" original of either species may be difficult to find. We urge Cassiopea researchers to establish new European laboratory lines with described genomes.

Holomycota, together with Holozoa, represents one of the two main branches of the supergroup Opisthokonta. Fungi, as well as three basal protist lineages Nuclearida, Rosellida, and Aphelida belong to Holomycota. Surprisingly, among all these holomycotan groups, only the most basal lineage, Nuclearida, lacks any traces of flagella in its life cycle and is represented by free-living amoebae, in contrast to the obligately parasitic and flagellated Rosellida and Aphelida, which evolved later. As the earliest-branching lineage, nucleariids play a key role in understanding the origin and diversification of Opisthokonta, which is presumed to have evolved from a uniflagellated ancestor. In this study, we describe the first known nucleariid that is parasitic on algae and possesses a flagellated stage in its life cycle. We studied the life cycle, and showed the ultrastructure of main life cycle stages of this parasite. The multigene phylogenetic tree based on the newly sequenced transcriptome demonstrated its basal position among nucleariids, forming a clade of environmental OTUs. This finding together with unique ultrastructural features, parasitic style of life, and presence of flagellum allowed us to describe a new species, genus, and family in the order Nuclearidida. We emended the diagnoses of the order, class, and phylum Nuclearida. Based on the ribosomal phylogenetic tree where the Insolitus nuclearius has a basal position among the nucleariids we discussed the evolution of this group from the uniflagellated ancestor and provided new insights into the early evolution of Holomycota in a whole, revising hypotheses regarding the opisthokont ancestor.