Journal of Phycology

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 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.

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.

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.

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.

High-quality reference genomes provide an essential foundation for elucidating the molecular basis of organismal ecophysiology. Here, we sequenced and assembled chromosome-scale genomes of two Heterosigma akashiwo strains isolated from coastal waters of Japan and France. The assembly sizes were 1.18 Gb and 1.43 Gb for the Japanese and French strains, respectively. The scaffold N50 of the Japanese strain assembly was 66 Mb, whereas the one of the unscaffolded French strain assembly was 33 Mb. To our knowledge, these assemblies represent among the largest and most contiguous genome resources currently available for members of the Stramenopiles (Ochrophyta). Evidence-based gene prediction in the Japanese strain recovered approximately 90% of conserved stramenopile core genes, indicating a highly complete gene repertoire, and was complemented by extensive functional annotation. In the French strain, homology-based gene prediction recovered approximately 80% of conserved core genes. Comparative genome analysis revealed extensive synteny conservation between the two strains, although several putative duplication and translocation events were detected. These genomic resources provide a robust framework for investigating the molecular, cellular, and ecological mechanisms underlying the physiology, adaptation, and bloom-forming capacity of H. akashiwo.

Intertidal mudflats are low hydrodynamic energy environments hosting microphytobenthic communities that experience strong spatiotemporal variability in light regimes, including changes in spectral quality and light intensity that can lead to cellular photooxidative stress. To cope with these fluctuations, autotrophs exhibit diverse and highly plastic adaptations that are often species-dependent and shaped by their ecological niches. This study investigates photophysiological responses and metabolic remodeling in a diatom assemblage originating from a natural winter microphytobenthic biofilm under contrasting red and blue light intensities. To this end, photosynthetic parameters were monitored alongside changes in lipophilic metabolites, including untargeted lipids and lipophilic pigments. While few metabolites showed temporal remodeling, rapid and contrasting changes were observed within 30 minutes in response to both spectral quality and light intensity. Red light treatments induced broader remodeling of lipophilic metabolites than blue light, whereas blue light appeared to have a greater impact on photosynthetic parameters. Moreover, red light induced xanthophyll-cycle responses comparable to those observed under blue light at equivalent incident intensity. We discuss these metabolic responses in relation to diatom photoadaptive strategies, placing these findings within the intertidal environmental framework. This work further underlines the importance of understanding rapid metabolic plasticity in coping with light fluctuations, providing new insights into the photoregulatory strategies of natural microphytobenthic communities.

Arcellidae is a family of testate amoebae within Arcellinida (Amoebozoa), comprising three recognized genera: Arcella, Galeripora, and Antarcella. Although species in the family have been studied for nearly two centuries, many historically described taxa and major morphological groups remain unsampled at the molecular level. Here, we provide a comprehensive review of Arcellidae and generate new cytochrome c oxidase subunit I (COI) sequences for arcellid species from Canadian peatlands, focusing on tall-shelled Arcella historically classified in section Altae sensu Deflandre. COI phylogenetic analyses recover a strongly supported monophyletic clade corresponding to North American representatives of Altae, providing the first molecular corroboration of this morphologically defined group. Within this clade, we redescribe Arcella leidyana based on modern material from Eeyou Istchee (Quebec). We further describe Galeripora purdoni sp. nov. from a calcareous fen in eastern Ontario, representing a novel terrestrial lineage within the genus, and redescribe Galeripora artocrea, which we transfer to Arcella based on congruent molecular and morphological evidence. Phylogenomic analyses of Arcellidae isolates from the Protist 10,000 Genomes Project reveal an additional deep lineage basal to Arcella and Galeripora. Together, these results highlight hidden diversity and demonstrate the importance of integrative approaches for resolving arcellid systematics and refining its classification.

Blue Economy models position aquaculture as a key pathway to securing global food security. Species selected for aquaculture typically show rapid growth, high stress tolerance and fast biomass accumulation, but these same traits may increase their potential to become invasive when introduced beyond their native range. We investigated the invasion history and current status of the commercially important red seaweed Kappaphycus alvarezii in the Palk Bay-Gulf of Mannar region of India. This is one of the worlds largest cultivation hubs, a climatically vulnerable marine biodiversity hotspot, and one of the three regions to report invasion. We combined in-water surveys, interviews with wild seaweed collectors, and a review of published literature to reconstruct the history of invasion and assess current status. Invasion has declined substantially, with interviews indicating that the disappearance of invasive populations began around 2014. We discuss several non-mutually exclusive explanations for this decline, including climate change, loss of coral substrate, herbivory, and reduced vitality of the seaweed. Although the decline in invasion is encouraging for coral reefs, our findings raise questions about the ecological and socioeconomic consequences of introducing non-native aquaculture species under Blue Economy initiatives, particularly in ecologically sensitive regions vulnerable to climate change.

Symbioses are widespread and highly successful but vulnerable to the stress sensitivity of either symbiont. In some symbioses, turnover of symbionts has been shown to confer resilience to stressors. While similar mechanisms have been proposed for lichen symbioses, direct evidence for rapid adaptive symbiont turnover has not been shown. We tested the photobiont community composition and physiological responses of the foliose lichen symbiosis Flavoparmelia caperata-Trebouxia to urbanization-induced stress in a transplant experiment. We found evidence for significant compositional change in the photobiont community along an urbanization gradient (measured as vegetation cover), reflecting a turnover in dominance of Trebouxia OTUs from A46 to I05 in more urbanized transplant sites. This change in symbiont composition is associated with a greater physiological tolerance for urbanization, consistent with the hypothesized adaptive role of photobiont turnover. These findings support rapid photobiont turnover as a potential adaptive response to environmental change in lichen symbioses.

The marine biodiversity inhabiting rocky shores in the Colombian Pacific remains largely undocumented, primarily due to geographic isolation, logistical challenges, and socio-political constraints. To address the existing knowledge gap, we conducted an expedition to enhance baseline biodiversity knowledge in rocky shores by integrating multiple complementary approaches, including visual censuses, specimen collection with morphological identification, environmental DNA (eDNA) metabarcoding and DNA barcodes. eDNA samples were collected at four coastal sites adjacent to rocky substrates, along with biological specimens obtained from fourteen locations through SCUBA diving at depths ranging from 1 to 25 meters. Tissue samples were subjected to genomic DNA isolation, followed by the generation and validation of cytochrome c oxidase subunit I (COI) barcode sequences, which were subsequently corroborated through taxonomic assessment to ensure accurate species identification. eDNA metabarcoding analyses yielded over 7 million high-quality sequence reads. Although taxonomic resolution at the species level was constrained by the limited completeness of reference sequence databases, a total of 106 species and 83 families were successfully identified, predominantly within the classes Actinopteri, Chondrichthyes, and marine mammals. From the 769 specimens obtained we generated 871 sequences, including 414 validated COI barcodes representing 76 species across 64 families. The integration of DNA barcoding and eDNA approaches resulted in over 1,400 taxonomic detections spanning five phyla, with only six species shared between methodologies. Richness and diversity varied among sites, and revealed significant differences along the coastline between Jurado and Cupica Gulf. All sequences were deposited in BOLDsystems database under the CCBIO project and were visualized through OBIS and GBIF databases. These findings provide the first molecular-based baseline for rocky shore biodiversity in the Colombian Pacific, highlighting the value of integrative approaches for monitoring and conservation.

Temperature plays a central role in marine phytoplankton biogeographical dynamics, physiology and gene expression. Nonetheless, the transcriptional regulatory mechanisms controlling temperature acclimation in marine phytoplankton are yet to be characterized. Ostreococcus tauri was chosen as a model species for green marine phytoplankton due to its cellular and genomic simplicity, as well as its evolutionary position within the green lineage. In this study, epigenomic and transcriptomic data were integrated to characterize changes induced by temperature in the trimethylation of histone 3 at lysines 27 and 4 (H3K27me3 and H3K4me3) epigenetic marks established by the Polycomb (PcG) and Trithorax group (TrxG) complexes, respectively. H3K27me3 was found to be a repressive mark responding to temperature, showing predominantly significant increased levels at high temperatures. While H3K4me3 was associated with active transcription, presenting less evident variations in cultures acclimated to different temperatures. H3K27me3 was found only marginally associated with transposable elements, being mostly involved in the repression of specific biological processes, such as gene expression control by transcription factors, meiosis, motors proteins and cytoskeletal structures. No significant conservation was found between the H3K27me3 gene targets in the model plant Arabidopsis thaliana and Ostreococcus tauri. Nonetheless, transcriptions factors belonging to the MADS-box, WRKY and AP2 families were consistently repressed by H3K27me3 in both species, unveiling that, although the specific downstream targets of this epigenetic mark have diversified during evolution, its role in modulating higher order regulatory nodes remains evolutionary conserved.

Rising ocean temperatures disrupt previously stable coral-microbe interactions, leading to widespread coral mortality and threatening reef ecosystems worldwide. Growing evidence demonstrates the coral microbiome, including protists, plays a critical role in the host response to thermal stress. Specifically, corallicolids (Phylum: Apicomplexa) are positively correlated with thermal stress mortality in soft corals. This study investigates changes in the eukaryotic microbiome of the stony coral, Pocillopora damicornis, across an experimental thermal stress event. Using anti-metazoan 18S rRNA gene metabarcoding, protist communities were assessed at four time-points during experimental thermal stress. Outside of the Symbiodiniaceae, a prominent shift in microbiome composition during thermal stress was observed, most notably a significant increase and dominance in Corallicolida abundance in heat-stressed corals, while other protists declined substantially. Increased corallicolid abundance concurrent with bleaching suggests an overlooked compounding stressor beyond the loss of algal symbionts during heat stress. These results contrast with previous research on Pocillopora microbiomes showing prokaryotic community stability throughout stress, and support the hypothesis that thermal stress may alter the coral-corallicolid relationship, potentially shifting corallicolids from a commensal to a parasitic role, and synergistically contributing to coral mortality during and after heat stress. This work provides critical insight into the role of protists in marine holobionts, supports their inclusion in future microbiome studies, and informs strategies to improve coral resilience under climate change.

The Deep Chlorophyll Maximum (DCM) is likely the most important feature organizing the marine epipelagic environment. Within this layer, opposing gradients of light and nutrients create a stratified habitat that supports high phytoplankton biomass and a substantial fraction of oceanic primary production. Despite its ecological importance, most studies treat the DCM as a single depth, overlooking its fine-scale heterogeneity. Here we investigated prokaryotic community organization across the DCM in the northwestern Mediterranean Sea through high-resolution sampling of four profiles collected over two days. Free-living (0.2-3 {micro}m) and particle-associated (3-20 {micro}m) communities were characterized using 16S rRNA gene amplicon sequencing. Prokaryotic communities changed progressively along the vertical gradient, revealing the DCM as a microbial coenocline with continuous community turnover. Fuzzy clustering identified distinct assemblages associated with environmental transitions from warm surface waters to the chlorophyll maximum, the nitrite peak below the DCM, and deeper nitrate-rich layers. In both the free-living and particle-associated fractions, most ASVs remained consistently associated with the same depth-defined clusters across all samplings, indicating stable niche partitioning over short timescales. However, these temporally stable ASVs accounted for a substantially smaller fraction of community sequences in particle-associated communities, suggesting higher dynamism, likely driven by particle-mediated transport. Nevertheless, phylogenetic analyses revealed that closely related ASVs tended to occupy similar depth niches, indicating that habitat preferences are phylogenetically conserved in both size fractions. Our results demonstrate prokaryotic niche partitioning over scales of only a few meters within the DCM, highlighting the importance of fine-scale sampling for understanding microbial community structure and responses to ocean change.

The morphology of cyanobacterial colonies plays a key role in harmful cyanobacterial blooms, with implications for their vertical migration, resistance against grazing, and light availability. In this study, we introduce the use of Optical Coherence Tomography (OCT) to investigate the three-dimensional morphology of cyanobacterial colonies. The technique enables non-invasive 3D imaging of colonies up to several millimeters in size, providing access to detailed mesoscale morphological features. Gas vesicles inside cells were shown to strongly improve image quality. We describe the sample preparation and image acquisition protocol, as well as an image processing pipeline that extracts mesoscale morphological features and provides a volumetric visualization of colonies. The method was tested for representative colonies of different cyanobacterial species while a dataset of volumetric images and measured mesoscale features was acquired for natural colonies of Microcystis. We demonstrate the utility of 3D imaging by quantifying the effects of irregular colony morphologies on their flotation velocity and the light availability within colonies. We anticipate OCT to become a key imaging technique to monitor populations of cyanobacterial colonies and investigate colony formation, with potential extensions to other colonial and aggregated organisms in freshwater and marine environments.

While the suppression of toxic cyanobacteria by aquatic plants has long been recognized, few studies have clearly differentiated between the allelopathic effects of the plant itself and the inhibitory influence of its associated microbiome. This study aimed to clarify the primary inhibitory agent by pre-culturing Myriophyllum spicatum (Eurasian watermilfoil) under three conditions: (1) BG11 medium, (2) live Microcystis aeruginosa KW culture, and (3) a Microcystis-symbiotic microbiome (excluding Microcystis cells). After a 7-day pre-culture, Myriophyllum shoots were transferred to fresh Microcystis culture. The Myriophyllum pre-cultured in Microcystis culture exhibited rapid inhibition against Microcystis (84% within day 1), whereas the Myriophyllum pre-cultured in BG11 medium showed delayed responses (89% by day 7). In contrast, inhibition remained below 50% in the Myriophyllum pre-cultured with the Microcystis-symbiotic microbiome. Notably, plant-derived soluble compounds exhibited weak inhibitory effects, whereas the microbiome showed stronger inhibitory activity, indicating that the plant-associated microbiome plays a more dominant role than the plant itself. Exposure to Microcystis triggered significant shifts in plant-symbiotic microbial community composition, leading to rapid enhancement of inhibitory activity in the Myriophyllum microbiome. Microbial community analysis identified 28 bacterial taxa closely associated with the inhibitory response, including strains involved in organic matter degradation, adhesion, biofilm formation, and predatory behavior. Meta-transcriptomic analysis further confirmed increased expression of genes related to bacterial adhesion, biofilm formation, and carbohydrate metabolism following Microcystis exposure, highlighting functional adaptations linked to cyanobacterial suppression. These findings underline the role of microbiome-mediated cyanobactericidal mechanisms, providing new insights into a nature-based solution for mitigating Microcystis-dominated harmful algal blooms.

Non-photochemical quenching (NPQ) dissipates excess absorbed light energy and protects photosynthetic organisms from photodamage, but its role in regulating the balance between growth, stress tolerance and astaxanthin accumulation in Haematococcus lacustris remains unclear. Here, we investigated how enhanced NPQ affects photosynthetic performance, stress-induced differentiation, and productivity in this astaxanthin-producing microalga. We isolated and characterized an NPQ-enhanced mutant line, A116, using cultivation assays under different stress conditions, analysis of photosynthetic parameters, pigment profiling, and whole-genome resequencing. A116 displayed stronger and faster NPQ induction, driven by increased LHCSR accumulation, resulting in decreased photosynthetic electron transport and lower photochemical efficiency under moderate-to-high light. Enhanced NPQ delayed the transition to astaxanthin-rich cysts under high light, allowing greater biomass accumulation under CO2-limiting conditions. However, under high CO2 availability, where carbon fixation relieved excitation pressure supporting efficient photosynthesis, the enhanced NPQ phenotype reduced growth and astaxanthin productivity compared with the wild type. These results show that NPQ modulates a context-dependent trade-off between photoprotection and productivity in Haematococcus lacustris. Increased energy dissipation can improve high-light tolerance under carbon limitation, but becomes detrimental when absorbed light can be efficiently used for carbon assimilation. Thus, optimal algal productivity requires tuning photoprotective capacity to environmental conditions rather than maximizing NPQ.

Photoendosymbiosis between the ciliate Paramecium tritobursaria and the green alga Chlorella variabilis provides a model for understanding stable photoendosymbiosis. A defining feature of this association is the perialgal vacuole (PV) membrane, a host-derived membrane that encloses each alga and prevents its digestion. However, the timing of PV membrane maturation remains poorly understood because of the lack of molecular markers to distinguish between immature and mature PV membranes. Previous studies have shown that the establishment of symbiosis proceeds through multiple regulated steps following algal uptake; however, the molecular maturation of the PV membrane has not been directly examined. Here, we report a monoclonal antibody that specifically recognizes the PV membrane in symbiotic P. tritobursaria. Time-course immunofluorescence analysis showed that the PV membrane antigen was absent in the early stages after algal uptake, appeared at 48 h, and was detected in all PV membranes by 72 h. The antigen persisted before and after synchronous PV swelling, an experimentally inducible state associated with the loss of normal PV membrane function, but was absent from the membranes surrounding the digested algae. Our findings provide the first molecular evidence that PV membrane maturation is a temporally regulated checkpoint during the establishment of photoendosymbiosis.

The impact of invasive species on marine ecosystems is rapidly increasing, where they often outcompete native species in the absence of natural enemies. The parasite release hypothesis states that the success of invasive species relates partly to the loss of natural parasites during introduction and lower susceptibility to native parasites. Barnacles are highly successful invaders due to broad environmental tolerance and dispersal via shipping, but whether parasite release also participates in this success remains unknown. In this study, we analyse parasite infection patterns in native and invasive barnacles in the Wadden Sea by surveying communities across tidal zones. Additionally, year-round molecular monitoring of larval stages and a literature review were used to track the distribution of the invasive Pacific barnacle Balanus glandula in Europe and document its appearance in the Wadden Sea. The long-established invasive Austrominius modestus dominated the high and middle intertidal zone, whereas native species (Balanus crenatus and Amphibalanus improvisus) prevailed in lower zones. Native and invasive barnacles differed in parasite infection frequency (mostly cestodes and trematodes). The native Semibalanus balanoides had the highest prevalence (27%), followed by the invasive A. modestus (11%), and no infections were found in B. glandula. Lower parasite prevalence in invasive barnacles is consistent with the hypothesis that parasite release supports invasion success. In the absence of competent parasites, B. glandula could impact native barnacles through competition. Continued monitoring of B. glandula is recommended to track its distribution, interactions with native species, and parasite acquisition, providing further insight into the parasite release hypothesis.

Experimentally evolved, heat-tolerant algal symbionts (heat-evolved; HE) offer a promising means of enhancing coral holobiont thermotolerance under rapidly warming oceans. However, translating their benefits into restoration practices requires scalable delivery methods. Coral tissue fusion may provide one such pathway by facilitating HE symbiont transfer to wild corals; however, its feasibility remains largely untested. As an initial test, we paired adult isografts of Galaxea fascicularis and Psammocora columna hosting HE Cladocopium proliferum (SS8) with chemically bleached, SS8-naive recipients. Fusion was first observed after three days in G. fascicularis and nine days in P. columna. In both species, fusion was followed by increased pigmentation and photochemical efficiency at the recipients fusion interface relative to distal tissue and unfused controls. After [~]50 days, SS8 was detected at low levels (<3.5%) in 15/19 fused G. fascicularis recipients, although detection was also common among unfused horizontal-transmission controls maintained in the same water column (13/18). These findings provide the first empirical evidence that conspecific coral tissue fusion is associated with localised physiological recovery and can coincide with HE symbiont acquisition, while highlighting the need to distinguish tissue-mediated transfer from background horizontal transmission. Fusion may therefore represent a complementary pathway for beneficial symbiont delivery in assisted-evolution frameworks.