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Journal of Phycology

Wiley

All preprints, 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. Older preprints may already have been published elsewhere.

1
Growth dynamics and genetic variation in attached and free-living populations of the filamentous brown seaweed, Pilayella littoralis

Miller, S. L.; Wilce, R. T.

2023-06-04 ecology 10.1101/2023.05.31.543056 medRxiv
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We used common garden growth experiments to study genetic variation among geographic isolates (Greenland, Massachusetts, and Connecticut, USA) of the filamentous brown seaweed Pilayella littoralis, including the free-living form unique to Nahant Bay, Massachusetts. Ecotypic variation for temperature growth maximum was demonstrated for a west Greenland isolate (10{degrees} C versus 15{degrees} C for other attached isolates) and between Nahant Bay attached (narrower phenotypic plasticity) and free-living forms (broader phenotypic plasticity) of the species. Morphological and reproductive characteristics of attached and free-living isolates remained distinctive under identical culture conditions after four years. The attached forms were characteristically cabled, twisted, and clumped; unilocular reproductive cells were common and plurilocular reproductive cells were present. The free-living form was characteristically loosely branched and ball-like; only vegetative reproduction occurred, with a few unilocular reproductive cells observed in one experiment. Free-living and attached isolates cultured using no water movement and turbulent conditions to mimic surf and surge conditions did not develop forms that resembled each other after eight months. We additionally used starch gel electrophoresis to study genetic variability in attached and free-living forms of P. littoralis from Nahant Bay. Free-living and attached populations were not different at the isozyme level because a limited number of isozymes were resolved (six out of 39 enzymes tested). One isozyme (PGI) was polymorphic, with two alleles present. The two alleles shared in the attached and free-living populations suggest that the free-living form is not one large identical clone. For attached and free-living P. littoralis, both transplant and growth studies in the laboratory provide convincing evidence of ecotypic differentiation.

2
pH induced motility pattern change in a marine dinoflagellate

Kalliyil, A.; Tikoti, S. G. R.; S, A.; Roy, S.

2025-08-01 ecology 10.1101/2025.07.29.667351 medRxiv
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Flagella-driven motility is a conserved feature across eukaryotic lineages, from unicellular plankton to mammals. In marine dinoflagellates, such as Lingulodinium polyedra, motility underlies diel vertical migration (DVM), a key adaptive strategy that enables access to spatio-temporally segregated resources in the water column. To investigate how pH influences motility, we used L. polyedra and two other dinoflagellates as a model and used a multi-particle tracking algorithm to monitor and quantitatively analyze cellular motility. Under normal pH conditions, L. polyedra displays linear, random motility with variable speeds. Upon CO{superscript 2}-induced acidification, we observed a dose-dependent decrease in motility speed accompanied by a striking behavioral shift: within minutes of pH reduction, over 90% of the cells transitioned to spiral motility. This effect was both reversible and reproducible, including when pH was modified chemically rather than via CO{superscript 2}. The rapid onset of these changes suggests a non-genomic mode of regulation, an area that remains largely unexplored in phytoplankton. We hypothesize that external pH modulates flagellar dynamics in dinoflagellates. Our findings offer new insights into the link between environmental pH and flagellar motility and provide a platform for investigating non-genomic responses to ocean acidification in marine phytoplankton.

3
Cytometric Analysis of Diverse Glaucophyte Species Reveals Distinctive Signals Useful for Fluorescence-Based Detection and Sorting

Calvaruso, R.; Lawrence, J.; Reyes-Prieto, A.

2021-10-22 plant biology 10.1101/2021.10.21.465165 medRxiv
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Glaucophytes, red algae and viridiplants (green algae and land plants) are formally united in the supergroup Archaeplastida. Although diverse molecular and genomic evidence suggest the common origin of the three Archaeplastida lineages, the lack of a robust glaucophyte knowledgebase has limited comprehensive evaluations of competing hypotheses. Glaucophytes are rare and apparently confined to freshwater habitats. However, the distribution and diversity of these algae have not been thoroughly explored owing to challenges with detecting and isolating novel specimens. Here we examined the cytometric signatures of representative species of the genera Cyanophora, Cyanoptyche, Glaucocystis and Gloeochaete for a distinctive signal that would aid identification. Most glaucophytes analyzed presented a relatively high red fluorescence signal due to the presence of the blue phycobiliproteins C-phycocyanin and allophycocyanin. Cell-size differences and the concurrent presence of the red phycobiliprotein phycoerythrin in other algal lineages, such as red algae and cryptophytes, allowed us to distinguish glaucophytes from other photosynthetic cells containing blue phycobiliproteins. Our results indicate that the peculiar autofluorescence signal of glaucophytes will facilitate further identification and isolation on novel specimens of this scarce but important algal group.

4
Variation in survival and growth following prolonged darkness in a polar diatom species

Mrazek, P.; Collins, S.

2026-02-04 ecology 10.64898/2026.02.02.703299 medRxiv
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O_LIPhytoplankton are the major primary producers in the Southern Ocean, participate in the global carbon cycle, nutrient cycles, and are at the base of the food-web. These polar ecosystems are unique in their extended periods of darkness in the winter. C_LIO_LIProlonged darkness has the potential to exert selection that affects the composition of diatom communities if there is differential survival of diatoms in the dark, variation in population growth rates in subsequent light periods, or both. C_LIO_LIWe tested whether prolonged darkness has the potential to exert within-species selection on a model polar diatom species by exposing 5 strains of the polar diatom Porosira glacialis to prolonged darkness at two different temperatures in the laboratory. We measured population survival in the dark, growth rate upon re-illumination, and between strain variability in these traits. C_LIO_LIWe found a pronounced decline in survival and growth rate with time spent in the dark, as well as important intraspecific variation in these. C_LIO_LIHigher temperature exacerbated declines in growth and survival. C_LIO_LIOur results show that the darkness of polar night can exert selection within diatom species, with implications for phytoplankton community composition and subsequent impacts on Southern Ocean biogeochemical cycles. C_LI

5
An ice-bucket challenge: investigating ice algae physiology in laboratory microcosms.

Baker, M. L.; Forss, E.; Kolzenburg, R.; Collins, S.; Kranz, S. A.

2026-07-13 ecology 10.64898/2026.07.10.737583 medRxiv
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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.

6
Consequences of light spectra for pigment composition and gene expression in the cryptophyte Rhodomonas salina

Schomaker, R. A.; Richardson, T. L.; Dudycha, J. L.

2023-09-22 ecology 10.1101/2023.09.20.558689 medRxiv
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SummaryAlgae with a more diverse suite of pigments can, in principle, exploit a broader swath of the light spectrum through chromatic acclimation, the ability to maximize light capture via plasticity of pigment composition. We grew Rhodomonas salina in wide-spectrum, red, green, and blue environments and measured how pigment composition differed. We also measured expression of key light-capture and photosynthesis-related genes and performed a transcriptome- wide expression analysis. We observed the highest concentration of phycoerythrin in green light, consistent with chromatic acclimation. Other pigments showed trends inconsistent with chromatic acclimation, possibly due to feedback loops among pigments or high-energy light acclimation. Expression of some photosynthesis-related genes was sensitive to spectrum, although expression of most was not. The phycoerythrin -subunit was expressed two-orders of magnitude greater than the {beta}-subunit even though the peptides are needed in an equimolar ratio. Expression of genes related to chlorophyll-binding and phycoerythrin concentration were correlated, indicating a potential synthesis relationship. Pigment concentrations and expression of related genes were generally uncorrelated, implying post-transcriptional regulation of pigments. Overall, most differentially expressed genes were not related to photosynthesis; thus, examining associations between light spectrum and other organismal functions, including sexual reproduction and glycolysis, may be important. Originality-Significance StatementMost work on light and algal photophysiology focuses on light intensity rather than light spectrum. Given the large spectral variation of light in aquatic systems, explaining how such algae respond to spectral variation will provide a better foundation for understanding the base of aquatic food webs. Much of the light spectrum is poorly absorbed by chlorophyll, which creates an opportunity for photosynthetic species with other pigments. We quantified physiological and genetic responses to light spectrum in replicate experimental populations of Rhodomonas salina, an alga with a phycoerythrin in addition to chlorophylls. We predicted photophysiology and gene expression would change to maximize R. salinas capacity to capture available light, in accordance with the theory of chromatic acclimation. Our results show that responses to light spectra are more complex than predicted. Some aspects of photophysiology did support the theorys predictions, but gene expression was generally unrelated to variation of light spectrum or photophysiology. This not only suggests that chromatic acclimation is potentially regulated post-transcriptionally, but also that physiological processes - notably glycolysis and the transition to sexual reproduction - that may be regulated by light spectrum. Our work adds to the generally limited work on light spectrum and physiology by investigating a eukaryote from a phylum with a great diversity of photosynthetic pigments.

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Dissolved inorganic carbon driven dynamics of calcite shell formation in 12 strains of the freshwater algae Phacotus lenticularis (Chlorophyta)

Gruenert, U.; Benda, J.; Bossdorf, O.; Raeder, U.

2025-05-09 ecology 10.1101/2025.05.04.652085 medRxiv
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This article explores the close relationship between dissolved inorganic carbonate ion concentration (DIC) and the calcification state of Phacotus lenticularis, a globally abundant freshwater phytoplankton that is responsible for a significant part of modern lake carbonate production during bloom formation. We cultured 12 freshly isolated P. lenticularis strains under an ecologically relevant range of DIC (0.2 to 12 mmol l-1 total scale) for 14 days. From this experiment we gained information on responses in shell formation and growth that highlight strong lower boundaries in morphometric calcite shell variables with regards to DIC. All P. lenticularis strains showed reduced shell thickness by up to 60 % and dissolved calcite crystals structures at declining DIC < 4 mmol l-1. Increasing DIC > 4 mmol l-1 had no significant effect on shell thickness and crystal length in the culture experiments. We found a significant preadaptation of all 12 strains to ambient DIC concentrations measured in their lake of origin, but no dependence of growth rates up to a lethal DIC of > 10 mmol l-1. The simulation experiments illustrate the close relationship between shell function and dissolved inorganic carbonate ion concentration in lakes and highlight the need of continued research of important roles in biogenic carbon transformation and storage in a future world.

8
Rapid sexual reproduction in a mixotrophic dinoflagellate revealed through temporal partitioning of cellular processes

Sung-Clarke, S.; Ayache, N.; Zhang, W.; Tong, M.; Smith, J.; Brosnahan, M.

2025-04-26 ecology 10.1101/2025.04.24.649572 medRxiv
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Dinophysis are specialist mixotrophs that must balance prey capture, cell division, and sexual recombination during blooms, yet relatively little is known about the occurrence and role of sex in their ecology. Here, mating was investigated in D. acuminata through continuous automated microscopy of cells in culture and during natural blooms. Both in culture and in situ, vegetative division and mating were phased on a diel timescale, occurring primarily at night and near dawn, regardless of prey availability. When prey were available, feeding occurred primarily during daylight hours. The sequencing of division and mating phases, the correlation of their daily amplitudes, and the timing of their establishment after a two-day light block suggests linkage of these processes. Mating, though frequent (up to 14% day-1 in culture), was also not associated with zygote accumulation or resting stage formation but rapid cell reproduction via meiosis. Confinement of division and mating to nighttime and early morning may minimize conflict with photosynthesis-related metabolism and/or predator exposure. Sexual reproduction was the dominant mode of proliferation during the observed blooms, accounting for 71% and 64% of new cell production in 2015 and 2021, respectively. Because it is dependent on encounter of a compatible gamete, sexual reproduction is increasingly accessible as blooms intensify. This sexual mode of proliferation may also alleviate populations susceptibility to pathogens, parasites, and other threats via genetic recombination, an example of Red Queen dynamics.

9
Convergent responses to light stress in oligohymenophorean ciliates bearing green algal symbionts

Kelly, J. B.; Futterknecht, N.; Ernst, S.; Becks, L.

2026-05-27 genomics 10.64898/2026.05.24.727488 medRxiv
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Photosymbiosis has evolved multiple times independently in ciliates. However, these associations can be antagonized by shifts in environmental parameters that impose stress on the host, necessitating the evolution of mechanisms to contend with this stress and to control the symbiont population. To investigate whether convergent strategies have evolved among algae-bearing ciliates in the class Oligohymenophorea, we imposed light stress on three host species that represent at least two independent evolutionary origins of photosymbiosis and measured their cellular responses. Under high light, all three species experienced an initial drop in host cell density which recovered to levels commensurate with those under low-light conditions as they decreased their symbiont loads. We then performed a comparative transcriptomic study to investigate whether a core set of genes exists that is involved in this response. Thirty-one gene families possess differentially expressed transcripts across all three species that included the upregulation C1 and S28 class peptidases, genes involved in ROS mitigation, and a gene with potential involvement in mitochondrial remodeling associated with changes in algal symbiont load. We additionally found downregulation in Dicer, which could mitigate the processing of algal transcripts by the hosts RNAi machinery that are freed upon algal digestion, and downregulation of motor proteins that may reflect changes in the hosts swimming behaviors and transport of intracellular vesicles in response to light. The 31 gene families are present and widespread in non-symbiotic oligohymenophoreans, illustrating that a pre-existing genetic toolkit exists in this clade that helps explain how it is predisposed to evolving photosymbioses.

10
Thriving to surviving: light wavelength modulates photoacclimation response in the siphonous green alga Derbesia

Hossen, R.; Bjornson, S.; Pelle, J.; West, J. A.; Bringloe, T.; Tandon, K.; Deore, P.; Verbruggen, H.

2026-06-11 ecology 10.64898/2026.06.07.730690 medRxiv
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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.

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Temperature stress resilience in polar Chlamydomonas is regulated by acclimation to light and salinity: implications for survival in a changing world

Osmers, P.; Szenasi, A.; Kostyniuk, L.; Caputo, S.; Bradette, N.; Cvetkovska, M.

2026-04-07 plant biology 10.64898/2026.04.03.716389 medRxiv
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O_LIAquatic algae are key primary producers in the Arctic and Antarctic, yet how cold-water species respond to environmental change is poorly understood. The Polar Regions are increasingly exposed to frequent heat waves, leading to declining ice cover, increased light availability, and decreasing salinity in polar waters. We compared three phylogenetically related but geographically distant polar Chlamydomonas species to test how habitat history shapes algal responses to light, salinity, and temperature stress. C_LIO_LIWe assessed the growth, morphology, and photochemistry of psychrophilic Chlamydomonas acclimated to native-like (lower light, higher salinity) and climate-shifted conditions (higher light, lower salinity). Next, we exposed acclimated cultures to a lethal heat shock and observed how acclimation affects algal temperature stress resilience. C_LIO_LIAll three species acclimated to climate-shifted conditions grew rapidly but showed the greatest sensitivity to temperature stress, with rapid loss of viability and photosynthetic efficiency. In contrast, slow-growing cultures acclimated to native-like conditions exhibited significantly greater resilience to temperature stress. C_LIO_LIOur work is the first to directly link light and salinity acclimation with temperature resilience in psychrophilic algae, suggesting that fast-growing polar green algae may be particularly vulnerable to increasingly frequent heat waves, with major implications for primary productivity in polar environments. C_LI

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Adaptation to heat and ocean fertilization, two keys for understanding the massive Sargassum growth in the Atlantic

Velzquez-Ochoa, R.; Enriquez, S.

2025-12-10 ecology 10.64898/2025.12.08.692933 medRxiv
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O_LIA floating ecosystem constituted by three genetic variants of holopelagic Sargassum has extended since 2011 throughout the tropical North Atlantic without spatial restrictions. C_LIO_LIWe characterized the differential capacity and efficiency of each variant to collect light and fix this energy in photosynthesis under variable light and temperature regimes, focusing on the description of key physiological and optical traits the differential response to light and temperature. C_LIO_LIOur results revealed metabolic adaptations of two genetic variants to the warmer conditions of the tropical Atlantic and contrasting efficiencies in light absorption and use in photosynthesis, indicative of distinct competitive abilities under growth limitations. C_LIO_LIWe concluded that the increased fertility of a warmer ocean is the most plausible explanation for the massive presence of holopelagic Sargassum in the tropical Atlantic, which also may explain the current ecological success of the opportunistic strategy of a previously rare variant. The optical and physiological descriptors documented can assist in developing quantitative models for predicting Sargassum biomass in the Atlantic. C_LI

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Laboratory evolution can improve algal cell yield and lipid production under mildly cold conditions

Lu, S.-Y.; Zhang, S.-Y.; Zhang, Q.-G.

2025-08-20 ecology 10.1101/2025.08.15.670636 medRxiv
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One challenge to large-scale microalgae cultivation, e.g., for biodiesel production, is the seasonal low-temperature conditions. We argue that seasonally varying selection in natural environments has prevented algae from better adapting to cold temperatures, and that laboratory evolution offers a promising approach for obtaining cold-adapted algal materials. We conducted a population-level artificial selection experiment with the unicellular green microalgae Chlorella sorokiniana at both a benign temperature (25) and a mildly cold temperature (15). Four artificial selection regimes were established: random selection, selection for high biomass (i.e., cell yield), selection for high lipid production, and rotation between high-biomass and high-lipid selection. We did not observe significant differences among the four selection regimes in evolutionary changes of algal cell yield or lipid yield, suggesting that natural selection at the individual level had dominated the evolutionary changes in our experiment. Compared with the ancestral strain, selection lines that had evolved at 15 typically exhibited increased cell yield and reduced lipid content per cell, indicating a trade-off relationship. However, substantial increases in cell yield may compensate for the reduction in lipid content per cell. Notably, three out of 16 selection lines showed > 1-fold increase in cell yield, and one exhibited > 1-fold increase in population-level lipid yield. Selection lines that had evolved at 25 displayed even greater increases in both cell and lipid yields, with a positive relationship between cell yield and lipid content per cell. Our results demonstrated the potential for laboratory evolution to obtain algal materials suitable for biofuel production under seasonal low-temperature conditions. HighlightsO_LIAlgae from natural environments not well-adapted to seasonal cold conditions. C_LIO_LILaboratory evolution under constant conditions with Chlorella sorokiniana. C_LIO_LIBoth cell yield and lipid production at a low temperature increased. C_LI

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Freshwater "microcroissants" shed light on a novel higher-level clade within Trebouxiophyceae and reveal the genus Chlorolobion as a trebouxiophyte

Barcyte, D.; Hodac, L.; Elias, M.

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Trebouxiophyceae is a widespread and species-rich green algal class encompassing mostly coccoid algae with a simple ovoid or ellipsoidal outline. However, some poorly-sampled lineages have evolved more elaborate shapes or even complex thalli, adding to the classs morphological diversity. Led by new and previously established strains, this study additionally uncovered a clade of croissant-like trebouxiophytes. Phylogenetic analyses inferred from nuclear 18S rDNA and chloroplast rbcL sequences confirmed the monophyly of the microcroissant clade, which we propose to be classified as a new family, Ragelichloridaceae. This family includes two novel genera, Ragelichloris and Navichloris, and the previously described Thorsmoerkia. The position of Ragelichloridaceae within Trebouxiophyceae stayed unresolved but chloroplast phylogenomics showed that the family belongs to the broader incertae sedis group, which also includes Xylochloris and Leptosira. In addition, our study showed that the microcroissant-like genus Chlorolobion, previously classified within Chlorophyceae, is a genuine trebouxiophyte, potentially related to Ragelichloridaceae. HighlightsO_LIA new family-level clade uncovered within Trebouxiophyceae. C_LIO_LITwo new genera described. C_LIO_LIThe genus Chlorolobion shown to be a trebouxiophyte. C_LI

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Intraspecific trait variation modulates the temperature effect on elemental quotas and stoichiometry in marine Synechococcus

Davis, A.; Garcia, N.; Martiny, A. C.

2023-09-21 ecology 10.1101/2023.09.20.558568 medRxiv
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Diverse phytoplankton modulate the coupling between the ocean carbon and nutrient cycles through life-history traits such as cell size, elemental quotas, and ratios. Biodiversity is mostly considered at broad functional levels, but major phytoplankton lineages are themselves highly diverse. As an example, Synechococcus is found in nearly all ocean regions and contain extensive intraspecific variation. Here, we grew four closely related Synechococcus isolates in semi-continuous cultures across a range of temperatures (16-25{degrees}C) to quantify for the relative role of intraspecific trait variation vs. environmental change. We report differences in cell size (p<0.01) as a function of strain and clade (p<0.01). The carbon (QC), nitrogen (QN), and phosphorus (QP) cell quotas all increased with cell size. Furthermore, cell size has an inverse relationship to growth rate. Within our experimental design, temperature alone had a weak physiological effect on cell quota and elemental ratios. Instead, we find systemic intraspecific variance of C:N:P, with cell size and N:P having an inverse relationship. Our results suggest a key role for intraspecific life history traits in determining elemental quotas and stoichiometry. Thus, the extensive biodiversity harbored within many lineages may modulate the impact of environmental change on ocean biogeochemical cycles.

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Evaluating acidotropic dyes for detecting mixotrophy in protists: Insights from cultures and field communities

Cook, C. C. Z.; Ewton, E. M.; Marchetti, A.; Menden-Deuer, S.; Millette, N.; Slomka, S.; Speciale, E. V.; Wilken, S.; Cohen, N. R.

2025-10-01 ecology 10.1101/2025.09.29.679303 medRxiv
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Mixotrophic protists combine photoautotrophic primary production with heterotrophic phagotrophy, and distinctly impact nutrient cycling and microbial food web dynamics in aquatic environments. Despite their biogeochemical importance, detecting and quantifying mixotrophic presence and grazing in situ remains challenging, preventing a comprehensive understanding of their ecology and biogeography. Fluorescently labeled particle (FLP) incubations are commonly used to quantify mixotroph abundance and ingestion but may underestimate activity due to prey and size preferences of grazers. Acidotropic dyes that stain acidic vacuoles associated with phagotrophy have emerged as an alternative to FLP incubations for estimating mixotroph abundance, yet have not been thoroughly tested among a diverse suite of marine eukaryotes. Here, we evaluate the effectiveness and specificity of two dyes, LysoTracker Green and LysoSensor Blue, in laboratory cultures and natural marine communities. In laboratory cultures, both dyes correctly did not stain one photoautotrophic species. However, LysoSensor failed to stain several known mixotrophs, indicating false negatives, while both dyes stained photoautotrophic diatoms, indicating false positives. In the field, LysoTracker staining broadly tracked with FLP-derived results in the North East Shelf (NES) and the diatom-rich California Current System (CCS). Both methods indicated lower mixotroph abundance and proportion in the CCS, suggesting acidotropic dyes may more reliably reflect mixotrophy in the field than in monoculture. This study highlights the utility and limitations of acidotropic dyes for detecting mixotrophy and underscores the importance of incorporating community composition and complementary grazing estimates for reliable interpretation.

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High throughput in situ imaging reveals complex ecological behaviour of giant marine mixotrophic protists

Panaïotis, T.; Biard, T.; Caray--Counil, L.; Faillettaz, R.; Luo, J. Y.; Guigand, C. M.; Cowen, R. K.; Irisson, J.-O.

2025-08-15 ecology 10.1101/2025.08.12.669610 medRxiv
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Different trophic modes coexist among planktonic organisms, with a continuum between strict heterotrophy and strict autotrophy. Indeed, mixotrophic organisms have the ability to combine photosynthetic and heterotrophic nutrition. Here, we focus on an iconic group of mixotrophic protists, Rhizaria. They are particularly delicate and are often crushed by standard plankton nets. Rhizaria are a very good model organism to study mixotrophy in plankton because they are easily observed in their environment by in situ imaging, allowing us to monitor their true ecological mixotrophic behaviour. While their substantial contribution to planktonic biomass has recently been revealed, their trophic ecology is poorly described - some taxa are mixotrophic and host photosynthetic symbionts, others are not - and knowledge of their reproductive cycle is even scarcer. Using high-frequency in situ imaging, we study the ecology of these mixotrophic organisms directly in their undisturbed environment. We examined the fine-scale distribution and orientation of [~]230,000 organisms belonging to three groups of Rhizaria, including the mixotrophic taxa Acantharia and Collodaria, and the non-mixotrophic Phaeodaria. Overall, our results suggest that mixotrophic protists have better ability to control their position within the water column (depth, orientation) than non-mixotrophic ones. Our observations also point to several steps in the obscure life cycle of the mixotrophic Collodaria, during which de novo symbiont acquisition appears to involve active fine-scale buoyancy control. Taken together, these unprecedented results demonstrate that complex ecological behaviour can be achieved by "simple" single-celled organisms.

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Unveiling the Intricate Sinking behavior of Large Diatoms: Insights from Time-Frequency Analysis of Palmerina hardmaniana Sinking under Silicate-Depleted Conditions

Ping, Z.; Lu, J.; Li, L.; Zhuang, J.; Lai, J.; Shi, T.; Li, J.

2024-03-05 plant biology 10.1101/2024.03.03.582478 medRxiv
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Nutrient limits impact diatom sinking in time domain, but response in time-frequency domain is unclear. Studying the response of large diatoms to nutrients exclusively in the time domain fails to fully capture the complete impact of nutrient limitations on sinking behavior due to the absence of crucial information, including period and frequency. Wavelet analysis provides valuable insights into the period and frequency of signals and unveils their positions in the time. This study investigated the sinking behavior response of the large diatom Palmerina hardmaniana to silicate-depleted conditions in the time-frequency domain using wavelet analysis. The results showed that P. hardmaniana was capable of regulating its sinking speed, and this regulation occurred intermittently in time. The predominant frequency of intermittent regulation fell within the range of 0.13-0.50 Hz (equivalent to a period of 2-8 s) for both control and silicate-depleted conditions. The similarity in the frequency range of regulation between the two groups suggests the involvement of shared physiological mechanisms. P. hardmaniana responded to silicate depletion by intensifying the regulation of 0.13-0.50 Hz, which was reflected in the time domain as a change in the proportion of different instantaneous sinking speeds and consequently lead to a significant increase or decrease in the mean sinking speed (p<0.05). Additionally, the regulation of P. hardmaniana sinking behavior was also influenced by the physiological state of the cells. Short-term silicate stress (30 min) enhanced the oscillation power of sinking regulation, while prolonged silicate stress ([&ge;] 3 d) led to a decline in oscillation power.

19
Multiple trade-offs between defense and competitiveness traits in a planktonic predator-prey system

Reveillon, T.; Becks, L.

2023-08-16 ecology 10.1101/2022.05.02.490268 medRxiv
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Predator-prey interactions play a central role in community dynamics and depends on the covariation of traits of the interacting organisms. Intraspecific trade-off relationships between defense and competitiveness traits are important for understanding trophic interactions. However, quantifying the relevant traits forming defense-competitiveness trade-offs and how these traits determine prey and predator fitness remain major challenges. Here, we conducted feeding and growth experiments to assess multiple traits related to defense and competitiveness in 6 different strains of the green alga Chlamydomonas reinhardtii exposed to predation by the rotifer Brachionus calyciflorus. We found large differences in defense and competitiveness traits among prey strains and negative relationships between defense and competitiveness traits. Because we compared trait differences among strains whose ancestors previously evolved in controlled environments where selection favored defense or competitiveness, these negative correlations suggest the presence of a trade-off between defense and competitiveness. This trade-off was found for multiple combinations of defense and competitiveness traits. Furthermore, the differences in traits translated into differences in prey and predator fitness, which demonstrated the contribution of intraspecific trade-offs for predicting the outcome of predator-prey interactions.

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Thalassolituus haligoni sp. nov., BB40, a model species for non-cyanobacterial diazotrophs within Oceanospirillales isolated from a Fjord-like Inlet in Kjipuktuk

LaRoche, J.; Rose, S. A.; Bertrand, E. M.; Duffy, S. L. G.; Tolman, J.; Ludovic, P.; Chaillou, G.

2026-02-11 ecology 10.64898/2026.02.10.701148 medRxiv
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Marine non-cyanobacterial diazotrophs (NCDs) are recognized as globally distributed, however, few representatives have been isolated in pure cultures. As a result, understanding the physiology, growth rate, substrate preference and dinitrogen (N2) fixation capabilities proves difficult. Thalassolituus haligoni. sp. nov., BB40 was isolated from a fjord-like inlet within Kjipuktuk (Halifax), Nova Scotia. The fully sequenced genome displayed all necessary genes required for N2 fixation, and various carbon uptake pathways. The gram-negative flagellated rod shape bacterium displayed significantly higher growth rates in medium amended with nitrate (NO3-) or ammonia (NH3), compared to dissolved N2, as the sole nitrogen source. Biological N2 fixation rates were detectable across all conditions, measuring a range from 9.34 x 10-6 to 1.4 x 10-1 fmol N cell-1 day-1. Growth of the isolate was successful between 4 {degrees}C up to 35 {degrees}C, with a Topt of 20 {degrees}C for N2, and between 27 - 30 {degrees}C for fixed nitrogen (NO3- and NH3). The closest relatives to T. haligoni, were found to be the uncultured Arc-gamma-03 (99% average nucleotide identity (ANI)) and Oceanobacter antarcticus (81% ANI). T. haligoni also displays versatile capabilities for growth on various carbon, and nitrogen sources, and antibiotics. Collectively this study provides an in-depth physiological assessment of an Oceanospirillales diazotrophic species which we presently have limited knowledge of.