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Journal of Phycology

○ Wiley

Preprints posted in the last 90 days, ranked by how well they match Journal of Phycology's content profile, based on 14 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

1
High ammonium suppresses nitrate transporter expression and constrains thermal plasticity in the green macroalga Codium cylindricum

Zhong, K.-L.; FERNANDEZ, P. A.; Russell, B.; Gaitan Espitia, J. D.

2026-09-12 ecology 10.64898/2026.09.10.750591 medRxiv
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Nitrogen source and availability can modulate thermal stress responses in marine macroalgae, yet the transcriptional mechanisms underpinning these effects in green seaweeds remain poorly understood. We tested how three N sources (ammonium, nitrate, urea) at low (5 M) and high (100 M) concentrations influence the thermal physiology and gene expression of Codium cylindricum. Thermal performance curves were constructed for growth, photosynthesis, and pigment content across a 5-29 {degrees}C gradient, coupled with transcriptomic analysis at three key temperatures. At high concentrations, ammonium reduced maximum growth rate by 25% and lowered the thermal optimum relative to nitrate and urea, while nitrate supported the broadest thermal performance. Urea constrained thermal breadth regardless of concentration. These responses were linked to differential expression of Nitrogen assimilation genes. Ammonium suppressed nitrate transporter genes (NRT) and nitrite transporter (FNT), and drove pigment accumulation with rising temperature despite reduced growth, suggesting resource reallocation from growth to photoprotection. In contrast, nitrate upregulated photosystem and phosphorylation-related genes. Our findings demonstrate that Nitrogen source and concentration jointly determine the thermal threshold of C. cylindricum, with high ammonium reducing both maximum growth and the temperature at which it is achieved. This highlights how shifting coastal nutrient regimes may alter macroalgal resilience under ocean warming.

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The proposed Baltic Sea endemic green alga Monostroma balticum represents a foliose morphotype of Ulva intestinalis (Ulvales, Ulvophyceae).

Johansson, N. R.; Blomster, J.; Wärri, T.; Laiho, E.; Schrofner-Brunner, E.; Straube, N.; Rauch, C.; Steinhagen, S.

2026-09-18 plant biology 10.64898/2026.09.16.751975 medRxiv
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Green algae in Ulva, Monostroma and similar genera are notoriously difficult to identify morphologically, due to high phenotypic plasticity and the presence of cryptic species - which has historically resulted in a challenging taxonomy, poorly resolved species boundaries, and potentially numerous invalid species descriptions. DNA-based specimen identification, especially combined with analysis of historical herbarium voucher DNA, has huge potential in resolving many unresolved taxonomical problems in these algae. One such example is Monostroma balticum, which has been described as foliose, monostromatic green seaweed known only free-floating, and reported to be endemic to the Baltic Sea. Previous studies have highlighted major uncertainty in the status of this taxon. We conducted an extensive sampling campaign of monostromatic green algae across the Baltic Sea to molecularly, morphologically and ecologically characterise this enigmatic taxon. Additionally, we investigated original exciccate material of M. balticum by using a museomic approach. We show that Monostroma balticum represents a monostromatic, foliose morphotype of the cosmopolitan and ubiquitous species Ulva intestinalis. This foliose growth form is seen in low salinity conditions, and, so far, reported only from the inner basin of the Baltic Sea. Our work shows that using morphology- and DNA-based museomic approaches for contemporary and historical specimens is a powerful combination to resolve long-standing taxonomical uncertainties and to produce new biodiversity information, even in relatively well-studied regions.

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Pigment and isoprostanoid responses to cold atmospheric plasma-induced oxidative conditions in a natural epipelic diatom assemblage

Desparmet, A.; Oger, C.; Vigor, C.; Durand, T.; Reversat, G.; Gros, V.; Dufour, T.; Hubas, C.

2026-09-18 biophysics 10.64898/2026.09.13.751231 medRxiv
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Intertidal mudflats hosting diatom-dominated microphytobenthic communities experience strong variability in environmental conditions, which can lead to cellular oxidative stress. These constraints can, in some cases, affect diatom metabolism and photosynthetic performance in the short term, potentially compromising their survival and even leading to cell death. This study investigates pigment, isoprostanoid, and photophysiological changes in a diatom assemblage originating from a natural microphytobenthic biofilm under different durations of helium-oxygen bubbling cold atmospheric plasma experimental treatments, mimicking complex oxidative conditions of the environment. To this end, 2-min and 5-min treatments were applied to the diatom assemblage, and metabolic parameters were monitored over time up to +180 min after plasma treatment cessation. Despite physicochemical changes and slight perturbations in metabolite profiles induced by plasma treatments, photosynthetic capacities of the diatoms remained largely preserved. The duration-dependent effects of plasma treatments induced selective and mostly reversible changes, primarily characterized by an increase in the relative proportions of pheopigments and a decrease in the relative proportions of {beta}-carotenes following the 5-min treatment. A transient decrease in the relative proportions of the isoprostanoids 10-F4t-neuroP and 5-F2t-IsoP was also observed. By exposing natural diatom assemblage to plasma-generated oxidative conditions, this study provides novel insights into how marine microbiome respond to oxidative perturbations, contributing to our understanding of diatom success in fluctuating intertidal environments.

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Seasonality of protists in the oligotrophic Gulf of Aqaba revealed by imaging flow cytometry

Steinsdottir, H. G. R.; Frada, M. J.; Akkaynak, D.

2026-09-11 ecology 10.64898/2026.09.09.749164 medRxiv
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Oligotrophic subtropical waters are some of the ocean's largest continuous ecosystems, yet their protist diversity and community succession remain poorly understood. We examined the protist community in the surface waters of the Gulf of Aqaba at near-daily resolution from March 2024 to July 2025 using an Imaging FlowCytobot. The record revealed a clear seasonal succession. Total cell density increased nearly threefold during winter mixing, driven mainly by an increase in cells smaller than 5 microns. Cells were generally larger during summer, making total biovolume similar in summer and winter. Biovolume reached its highest sustained values during the spring bloom. Despite its low cell density, the summer community was dynamic, with sudden appearances of euglenophytes, flagellates and dinoflagellates at high densities. Coccolithophores and cryptophytes increased during winter, followed by diatoms and ciliates in spring. We also provide a dataset of 31,700 annotated IFCB images.

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The genome of the coral model sea anemone Exaiptasia diaphana (Aiptasia) strain F003

Doerr, M.; Sharaf, A.; Colin, L.; Schuster, K.; Bell, A.; Voolstra, C. R.

2026-08-28 genomics 10.64898/2026.08.25.747183 medRxiv
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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.

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The distribution of particle-associated Prochlorococcus across the global oceans

Anjur-Dietrich, M. I.; Vo, N. N.; Jones, K. G.; Mullet, J. I.; Parker, S. M.; Castro, K. G.; Stein, A. M.; Silvestri, S. M.; Biller, S. J.; Longnecker, K.; Chisholm, S. W.

2026-08-26 ecology 10.64898/2026.08.24.746807 medRxiv
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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.

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Characterization of starch metabolism pathways in dinoflagellates, chromerids and apicomplexans highlights the presence of a starch accumulating symbiont in their common ancestor

Cenci, U.; Chabi, M.; Fermont, L.; Deschamps, P.; Leleu, M.; Tirtiaux, C.; Archibald, J. M.; Obornik, M.; Colleoni, C.; Ball, S.

2026-10-02 evolutionary biology 10.64898/2026.09.25.754361 medRxiv
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Unlike most other heterotrophic protist lineages which synthesize glycogen, alveolates accumulate -glucan storage polysaccharides in the form of starch. Within Alveolata, ciliates do so by using a simple pathway analogous to that used for glycogen metabolism in eukaryotes. However, Myzozoa have evolved five additional enzymatic steps which are common to Dinoflagellata, Chromerids and Apicomplexa. Moreover, dinoflagellates have acquired seven additional enzymes that distinguish them from the Chromerids-Apicompexa lineages, while chromerids possess only a single enzyme not found in dinoflagellates. Such modifications are not found in other eukaryotic lineages save for those resulting directly from primary or secondary plastid endosymbiosis. The many differences affecting the starch pathway of Myzozoa can be explained by a single secondary or tertiary plastid endosymbiosis of a starch-containing alga followed by distinct compartmentalisation outcomes of starch metabolism in Dinoflagellata relative to chromerids and Apicomplexa.

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Patterns and Drivers of Diatom Diversity and Biogeography in the North Pacific

Barral, A.; Suzuki, K.; Kikuchi, Y.; Nakaoka, S.-i.; Takao, S.; Nakaoka, S.

2026-08-31 ecology 10.64898/2026.08.30.746603 medRxiv
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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.

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COMPARATIVE PHENOMICS IN Limnospira platensis STRAINS REVEALS PHOTOBIOENERGETIC SIMILARITIES AND DIFFERENCES IN AMERICAN AND AFRICAN STRAINS

Zavala, M.; Perez-Loera, J. A.; Peters, C.; Zavafer, A.

2026-09-28 bioengineering 10.64898/2026.09.25.754581 medRxiv
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This study addresses the functional diversity of wild Limnospira platensis strains from two continents. Wild strains retain regulatory and metabolic flexibility often lost during domestication, making them essential for exploring natural adaptation within the species evolutionary history. We investigated the comparative growth performance of five Limnospira strains under controlled temperature and light regimes to identify phenotypic differences attributable to single environmental variables. We then evaluated their biochemical and biophysical responses under naturally fluctuating light conditions, linking energy use strategies to phylogenetic relationships. Our analyses reveal that while certain traits, such as fine-tuning of photosynthetic reactions, are shared among closely related strains, overall growth performance is highly variable even within phylogenetically similar groups. For example, photosensitive strains (e.g., UTEX 3086) differ markedly from high light tolerant strains (e.g., UTEX LB 2342) in their mechanisms of coping with light stress. Together, these comparative analyses highlight how environmental sensitivity and energy-use strategies vary across strains of the same species, reflecting broader patterns of diversification within Limnospira.

10
Revisiting Hydractiniidae (Hydrozoa): Mitogenomic Insights into the Diversity, Systematics and Life-Cycle Evolution of North Atlantic and Arctic Species

Beckmann, L. M.; Hosia, A.; Ronowicz, M.; Martell, L.; Soto-Angel, J. J.

2026-10-12 evolutionary biology 10.64898/2026.10.09.757902 medRxiv
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Hydractiniidae is a diverse family of colonial hydrozoans exhibiting substantial variation in colony organization, reproduction and life-cycle strategies, including species with and without a medusa stage. Several hydractiniids are also established model organisms, yet species boundaries and distributions remain incompletely resolved, limiting comparisons of reproductive and developmental traits across taxa. Here, we combine morphological and molecular data to reassess hydractiniid diversity, species identities, and life-cycle variation in material from the North Atlantic and Arctic Ocean. We integrate detailed observations of colonies and reproductive structures with DNA barcoding and mitochondrial genomes to evaluate species boundaries and provide molecular support for taxonomic identifications. Our results confirm 10 species in the study area, occurring from shallow waters to 2600 m depth and from coastal fjords to deep-sea hydrothermal vents. We further show that some historical species identifications and distribution records require reassessment. We establish a new genus for Arctic hydractiniid species (Bonneviactinia gen. nov.) and reassign two species to Schuchertinia. Mapping reproductive strategies onto the phylogeny reveals a broad pattern of increasing retention of medusa characters, from fixed sporosacs through reduced and fixed medusoids and non-liberated eumedusoids to fully developed, free-swimming feeding medusae, suggesting a progressive evolutionary trajectory in life-cycle complexity across Hydractiniidae. Furthermore, we clarify the identity of Podocoryna carnea and, through rearing experiments from polyp stage to medusae, characterize its morphological variation and developmental stages. By linking morphologically documented specimens and vouchers to genetic data, we establish reference resources that will facilitate future taxonomic, phylogenetic and biodiversity studies, including molecular surveys of marine communities. Together, these results demonstrate the value of integrative taxonomy for resolving hydractiniid diversity and provide a comparative foundation for investigating the evolution of reproductive strategies and life-cycle complexity in Medusozoa.

11
Aquatic bacterial metabolic rates from RNA quantitative stable isotope probing (RNA-qSIP) depend on experimental design

Ahern, O.; Bulseco, A.; Smith, A.; Weissman, J.; Vallino, J. J.; Huber, J. A.

2026-07-29 molecular biology 10.64898/2026.07.28.739216 medRxiv
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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.

12
Defining traits of low-light adapted Prochlorococcus inhabiting surface waters of the Equatorial Pacific Ocean

Berube, P. M.; LeMaster, T.; Cain, K. R.; Raut, Y.; Bartolek, Z.; Graff van Creveld, S.; Arsenieff, L.; Kunde, K.; Sulcius, S.; Coe, A.; Fisher, N. L.; Blaskowski, S.; Jones-Kellett, A. E.; Lindell, D.; Bundy, R. M.; Armbrust, V.; Chisholm, S. W.

2026-09-24 microbiology 10.64898/2026.09.23.753768 medRxiv
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A diverse array of photosynthetic phytoplankton drives primary production in equatorial surface waters. Among these, the cyanobacterium Prochlorococcus is an important contributor to net primary production in these typically iron-limited, high-nutrient and low-chlorophyll (HNLC) regions. Here, we explore the diversity of these organisms, in part, through targeted enrichment of Prochlorococcus cells using field-based high-speed cell sorting techniques. We demonstrate that the genomes of Prochlorococcus belonging to the low-light adapted LLI clade, and isolated from the surface of the Equatorial Pacific Ocean, are depleted in functions related to the assimilation of urea, nitrite, and amino acids. These are the first examples of LLI Prochlorococcus that have lost the ability to use nitrite, a trait considered to be a core feature of this clade. All new equatorial cultures of LLI Prochlorococcus appear to use a distinct isoform of protoporphyrinogen IX oxidase (HemG), for the biosynthesis of a chlorophyll precursor, that does not require the use of iron-containing heme. In contrast, the heme-dependent HemJ isoform is typically used by Prochlorococcus found outside equatorial HNLC waters. Together, these findings suggest that low-light adapted Prochlorococcus in the equatorial ocean possess accessory gene content that reflects adaptation to the generally iron-limited but nitrogen-replete conditions of surface waters.

13
Hydrodynamics structure the physiological trajectory and bloom dynamics of a harmful diatom species across neighboring coastal ecosystems

Le Gac, M.; Prigent, L.; Quere, J.; Caradec, F.; Herve, F.; Rabiller, E.; Amzil, Z.; Plus, M.

2026-10-06 ecology 10.64898/2026.10.05.756714 medRxiv
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Hydrodynamics is a strong regulator of phytoplankton cell densities and population connectivity. However, the extent to which hydrodynamics, specifically dilution and advection, dictates the internal physiological state and overall bloom dynamics remains poorly understood. We conducted an integrated study of the harmful diatom Pseudo-nitzschia australis in two neighboring coastal bays with similar abiotic conditions but contrasting bloom trajectories. Using a combination of field observations, transcriptomics, domoic acid (DA) measurements, and hydrodynamic simulations, we show that a three-fold difference in dilution rates alone explains a 25-day shift in bloom timing and an order-of-magnitude difference in cell densities. Transcriptomic profiling revealed distinct metabolic and stress-associated gene modules that synchronized with hydrodynamically-mediated nutrient depletion rate, linking residence times to cellular mortality. Furthermore, directional connectivity between the bays may explain population-level toxin heterogeneity, as advection of older cells, releasing DA outside the cells, may have decreased the proportion of intracellular DA in the destination bay. Our results illustrate that hydrodynamics do not merely modulate population transport; they structure the full physiological life cycle of a bloom, from initiation to nutrient-driven demise. This highlights the necessity of considering hydrodynamics as a primary explanation for bloom dynamics with cascading effects on bloom onset, cell density, nutrient consumption, cell physiology and mortality.

14
Host and environment shape the giant clam-associated photosymbiont community

Quijano, J. B.; Tayaban, K.; Baquiran, J. I. P.; Maala, G. J.; Requilme, J. N. C.; Sayco, S. L. G.; Dolorosa, R. G.; Cabaitan, P. C.; Conaco, C.

2026-08-07 ecology 10.64898/2026.08.07.743467 medRxiv
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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.

15
Genomics and biogeography of novel Trichodesmium isolates from the Sargasso Sea

Cleveland, C. S.; Bhatnagar, A. M.; Barnes, S. J.; Zhao, Y.; Webb, E. A.

2026-07-31 microbiology 10.64898/2026.07.30.741789 medRxiv
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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.

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Within-colony color variation in a chalice coral is associated with region-specific pigment expression and higher photoconvertible pigment transcripts

Baumgarte, O.; Moore, Z. J.

2026-09-03 genomics 10.64898/2026.08.29.746859 medRxiv
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A single colony of colonial coral often demonstrates conspicuous color variation. However, the molecular basis of this variation within a single, clonal individual is poorly understood. While coral tissues within a single colony have distinct colors, they share the same genetic background, suggesting differences between them are regulatory rather than genetic. This pilot study aims to characterize the transcriptional mechanisms of color regions in a green-and-orange chalice coral colony through an end-to-end transcriptomic analysis. First, we sampled the green body, an orange oral region, and a transition region between them. Then, a holobiont transcriptome was assembled de novo from paired-end RNA-seq of each color region. In the holobiont transcriptome, coral host transcripts were separated from dinoflagellate symbiont transcripts. Green fluorescent protein (GFP)-like pigment genes were classified phylogenetically. Their expression was then quantified using host-only normalization, which corrects for a large regional difference in symbiont read fraction, and compared across color regions. Relative to the green body, the orange oral region showed higher expression of two sets of host pigment genes: distinct orange fluorescent-protein and chromoprotein transcripts, and green-to-red photoconvertible EosFP-family proteins whose unconverted state is green, implicating photoconversion as a contributing mechanism. This study reveals that distinct color regions within a single colony are associated with region-specific up-regulation of different pigment transcripts, including both directly colored proteins and photoconvertible proteins. Further research is needed to confirm spectrally that photoconversion contributes to the coloration and test whether the pattern holds across multiple colonies.

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Fluorescence Lifetime Imaging Microscopy (FLIM) as a method to elucidate trends in marine planktonic symbioses

Coots, N. L.; Blanco Bercial, L. L.; Cutten, I. H.; Beaven, C.; Keeling, P. J.

2026-09-18 ecology 10.64898/2026.09.16.750219 medRxiv
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The Retaria are an abundant planktonic protist lineage that play a substantial role in biogeochemical cycling, primary production, and food web dynamics in open ocean ecosystems. Their impact is, in large part, due to their capacity to host photosynthetic endosymbionts. Despite the importance of these relationships in the global oceans, our knowledge about the diversity of photosymbionts associated with the planktonic Retaria is still limited due to the difficulty of collecting and analyzing these cells. Here we apply a new protocol to assess retarian photosymbiont diversity: Fluorescence Lifetime Imaging Microscopy (FLIM) is an easy-to-use method to distinguish between different sources of fluorescence during confocal microscopy. We applied FISH probes that hybridize with the most commonly reported retarian photosymbiont lineages to environmental plankton samples and used FLIM to confirm the presence or absence of our FISH probes in retarian cells. By analyzing the fluorescence lifetime of 92 photosymbionts, we found that the retarian photosymbiosis is far more complex than originally described, where Retaria commonly host multiple algal lineages per cell, and regularly host algal lineages outside of the two most common lineages. These efforts demonstrate that FLIM is an overlooked tool in the study of host-microbe associations, with significant potential to be used across diverse host lineages and environmental samples.

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A quick and efficient method enabling lncRNA functional studies in the marine diatom Phaeodactylum tricornutum using a multiplexed CRISPR-Cas9 editing approach

Charton, F.; Revillon, N.; Pierre-Elies, P.; Matsui, H.; Bowler, C.; Matsuda, Y.; Cruz de Carvalho, H.

2026-10-09 molecular biology 10.64898/2026.10.08.756992 medRxiv
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Background: Long non protein coding (lnc)RNAs are ubiquitous transcripts known to be major regulators of cellular processes in eukaryotes. In diatoms, specific lncRNA expression is tightly correlated to nutrient fluctuations, which suggests function, but their biological relevance remains to be established. In order to fill this knowledge gap, we sought to design a protocol to generate diatom lncRNA knockout mutants by CRISPR-Cas9 enabling subsequent functional studies to shed light into their mechanistic roles. Since lncRNAs do not contain open reading frames that can be targeted by point mutations for the generation of functional knockouts, we designed a multiplexed CRISPR-Cas9 plasmid harboring two independent gRNA for the specific ablation of lncRNA loci in P. tricornutum. As proof of concept, we used our plasmid-based system to target three phosphate depletion responsive lncRNAs. Results: Using the golden gate based uLoop system, we assembled a single plasmid containing all the necessary components to generate CRISPR-Cas9 large genomic ablations of lncRNAs in P. tricornutum using bacterial conjugation. Three intergenic lncRNAs (Linc91, Linc77 and Linc24) responsive to phosphate fluctuations were selected and independently targeted. Around 32% of the exconjugants presented a monoallelic ablation of the targeted loci and 11% presented a biallelic ablation on the first PCR-screening round. Mutated lines, harboring biallelic lncRNAs ablations for each lncRNA targeted, were successfully generated for each of the targeted lncRNAs. Additionally, a first line of phenotypic analysis revealed significant growth rate differences for one of the mutants ({Delta}Lnc24) under both full and phosphate depleted conditions, suggesting its involvement in cell division regulation under nutrient fluctuations. Conclusions: This work provides a simple and efficient method for the generation of lncRNA knock-out mutants in P. tricornutum. Furthermore, this approach can be easily adapted to other microalgae amenable to transformation, enabling the enhancement of our understanding of these important cellular regulatory transcripts in the marine environment.

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High cryptic diversity of invertebrates in varying nearshore habitats of the Beaufort Sea

Heiser, S.; Salel, L.; Schonberg, S.; Erdner, D. L.; Dunton, K. H.

2026-09-12 ecology 10.64898/2026.09.08.750166 medRxiv
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The Alaskan Beaufort Sea lagoon system supports a diverse invertebrate community shaped by a complex glacial and biogeographic history, yet it remains severely understudied relative to the rapid environmental changes it is experiencing. As Arctic amplification accelerates habitat loss, shifts dispersal pathways, and facilitates the introduction of boreal and invasive species, accurately documenting current biodiversity is increasingly urgent. In this study, we used DNA barcoding of the mitochondrial cox1 gene for various invertebrates, and the nuclear 28S rRNA gene for Porifera, to examine invertebrate genera across coastal sites in the Alaskan Beaufort Sea, including the unique Boulder Patch kelp community in Stefansson Sound. We sequenced specimens belonging to five phyla: Annelida, Arthropoda, Mollusca, Porifera, and Priapulida. Specimens were identified by morphology, and their cox1 or 28S rRNA gene sequences were matched against the GenBank and Barcode of Life Data Systems (BOLD) databases. Molecular identification revealed substantially higher species diversity than morphology alone in three of five phyla: Annelida (12 versus six species), Arthropoda (14 versus 11), and Mollusca (five versus four). In Porifera and Priapulida the number of species were the same for morphological and molecular identification; however, we still found different species identifications between the two methods. Other notable findings include the discovery of multiple cryptic species within Terebellides sp., Pontoporeia femorata, Onisimus litoralis, and Micronephthys minuta, as well as the first published sequences for Acanthostepheia incarinata, Haliclona gracilis, Onisimus affinis, and Saduria sibirica. Our results highlight the extent to which morphology-based surveys underestimate invertebrate diversity in Arctic ecosystems and underscore the need for comprehensive surveys and molecular reference databases to support future molecular-based biodiversity monitoring in this rapidly changing region.

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Can an original be found? Mitochondrial species identity does not predict nuclear genome similarity in the photosymbiotic jellyfish Cassiopea andromeda and C. xamachana

Muffett, K. M.; Sporre, M.; Mammone, M.; Miglietta, M. P.

2026-08-27 ecology 10.64898/2026.08.26.747389 medRxiv
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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.