Aim The life cycle of many organisms is all but fixed across their distribution range. Most commonly, populations respond to environmental variation by shifting the timing of reproductive events (phenology). More profoundly, populations may (partly) shift their mode of reproduction from sexual to asexual. Life cycle variation can impact reproductive success, gene flow, genetic diversity and, ultimately, the evolutionary trajectory of populations. Understanding the factors that influence life cycle variation is essential for grasping the biology and ecological roles of species. This study investigates the variation in life cycles and its effects on the genetic diversity of a brown seaweed, Dictyota, across its European range.Location North-East Atlantic Ocean and the Mediterranean Sea.Taxon Dictyota dichotoma (Hudson) J.V. Lamouroux (Phaeophyceae, Dictyotales).Methods We monitored phenology, fertility and lifespan in Atlantic and Mediterranean populations at its northern and southern boundaries and used microsatellite markers to assess how these factors influence genetic and genotypic diversity.Results We observed significant differences in phenology, reproductive strategies and genetic diversity among northern and southern European populations. In Mediterranean populations, D. dichotoma exhibited sporophytic dominance with gametophytes being extremely rare, suggesting a shift towards asexual reproduction. In contrast, North-East Atlantic populations displayed more pronounced seasonal reproductive patterns with higher frequencies of gametophytes, indicating predominant sexual reproduction. However, genetic analysis showed lower allelic richness and unique alleles in northern populations, whereas southern populations were genetically more diverse, reflecting historical biogeographic processes. Clonal reproduction was more pronounced in the Mediterranean populations, influencing the spatial genetic substructure and contributing to locally lower genotypic diversity compared to Atlantic populations.Main Conclusions Our findings demonstrate that life cycle variation and phenology in D. dichotoma are closely tied to regional environmental conditions and have significant implications for population structure and genetic diversity. Results highlight how shifts in reproductive strategies contribute to the evolutionary and ecological dynamics of marine macroalgae across biogeographical gradients.

Abstract As one of the earliest-diverging multicellular eukaryotic lineages, the bladed Bangiales (Rhodophyta) possess a deep evolutionary history with a central role in the multi-billion-dollar global seaweed aquaculture industry. Although North Atlantic representatives are emerging candidates for regional mariculture, the scarcity of high-quality genomic resources for these taxa hinders both fundamental research and commercial optimization. To address this, we present the first chromosome-level genome assemblies for two native European species: Porphyra dioica (150.44 Mbp) and Porphyra linearis (95.22 Mbp). By integrating Oxford Nanopore Technologies (ONT) long-read sequencing with Hi-C proximity ligation, we generated highly contiguous nuclear genomes resolved into five chromosomes. Structural gene models were predicted through the BRAKER3 pipeline, identifying 12,548 and 10,382 protein-coding genes for P. dioica and P. linearis , respectively. Subsequent homology-based functional annotation characterized 57.4% and 59.8% of these predicted proteins. Supplemented by circularized organellar genomes, these reference genomes provide a critical framework for future research, enabling comparative studies of Atlantic-Pacific divergence and facilitating the development of selective breeding programs for sustainable European aquaculture.

The genus Dictyota is a widespread group of brown algae mostly found in tropical and subtropical waters. The phenotypic variability of many of its species has caused taxonomic confusion, making molecular techniques necessary for accurate species identification. In this study, we integrate morphological observations with molecular phylogenetic analyses based on psbA and cox1 sequences to describe Dictyota pervagata sp. nov., a previously hidden lineage within Dictyota ceylanica. This species has a broad distribution across tropical basins and exhibits a notable morphological variation despite low genetic diversity.

Since the late 19th century, studies of the genus Porphyra sensu lato (Bangiales, Rhodophyta) have revealed a broad spectrum of life history strategies and reproductive modes. These variations are often interpreted as adaptive responses to the selective pressures imposed by spatially and temporally heterogeneous environments. However, the dynamics and prevalence of sexual versus asexual reproduction in natural populations remain poorly understood and insufficiently documented. In this study, we investigated the spatio-temporal variation in reproductive strategies of Porphyra umbilicalis, an emerging target species for aquaculture in the Northeast Atlantic, across a broad European range. Through microscopic examination and tracking the germination of spores released from fertile individuals in multiple populations, four main patterns were identified: (1) clear geographic structuring of reproductive strategies, with asexual reproduction prevailing in the Southern Bight of the North Sea and English Channel, and sexual populations more common in the South European Atlantic Shelf and Celtic Seas; (2) persistent dominance of asexual reproduction in populations with mixed reproductive modes, with a seasonal increase in the frequency of sexually reproductive individuals during winter; (3) microhabitat partitioning within the high intertidal zone, with asexual individuals occupying uppermost elevations and sexual individuals concentrated below, indicating ecologically driven niche differentiation; and (4) no consistent link between thallus size and reproductive mode, although sexual individuals were significantly larger during winter and spring. Collectively, these findings illustrate how environmental gradients shape reproductive strategies in P. umbilicalis, and suggest that asexuality may confer adaptive advantages in marginal intertidal zones.

The red algal order Halymeniales (Rhodophyta) exhibits remarkable morphological and taxonomic diversity but its higher-level relationships remain poorly resolved. Here, we present a comprehensive phylogenomic analysis based on newly generated plastid (170 protein-coding genes), mitochondrial (23 genes), and complete nuclear ribosomal cistron sequences from 56 taxa, complemented with an expanded rbcL dataset encompassing 334 sequences. Our results provide a robust phylogenomic framework for the Halymeniales, offering a taxonomic backbone for future systematic studies. The analyses consistently recover six early-diverging lineages (Acrodiscus, Isabbottia, Norrissia, Pachymenia, Zymurgia, and Tsengia) and two strongly supported larger clades (Halymenia s.l. and Grateloupia s.l.). While most small and recently described genera are monophyletic, several traditional genera (e.g., Halymenia, Cryptonemia, Grateloupia) are poly- or paraphyletic, requiring considerable taxonomic revision. At the family level, the data indicate that reinstatement of the Grateloupiaceae sensu Kim et al. (2021) would entail a revised circumscription of the Halymeniaceae and the recognition of at least five small families to accommodate the early-diverging lineages. Although such a revised classification would result in monophyletic families, it is not supported by morpho-anatomical characters. Instead, we propose a more stable two-family system, recognizing a broadly circumscribed Halymeniaceae that is sister to the Tsengiaceae. Female reproductive characters, particularly the structure of carpogonial and auxiliary cell ampullae, support this two-family system and further characterize many genus-level clades, although substantial convergence across lineages exists.

One hundred diatom species have been selected for genome and transcriptome sequencing. The 100 Diatom Genomes Project aims to provide a scalable framework for understanding diatom biodiversity, ecology and evolution, and for investigating their use in biotechnology.

The genus Dictyota includes ecologically important brown seaweed species that, apart from contributing to the foundation of the marine ecosystem, are gaining traction for their economic value. Substantial research has focused on taxonomy, chemical composition, ecological roles, and economic potential of Dictyota, including studies on genetics and genomics. Here, we developed twelve novel microsatellite markers for Dictyota dichotoma by using Ion Torrent sequencing. The markers were tested using 50 diploid individuals collected from five natural populations of D. dichotoma. The number of alleles per locus varied between five and thirteen. The total heterozygosity ranged from 0.587 to 0.887 per locus, and from − 0.147 to 0.483 in five populations across its European range. These polymorphic microsatellite markers are valuable for studying population genetic diversity and differentiation in D. dichotoma and may also be beneficial for other genetic research related to the reproductive biology of this model species, which displays considerable variation across the species’ range.

Over the past decades, improvements in water quality-particularly increased oxygen and reduced nitrogen concentrations-have led to changes in phytoplankton biomass and community composition in the Schelde estuary, a macrotidal estuary in Belgium/SW Netherlands. We argue that these changes have affected SPM dynamics by modifying floc stability and size. Seasonal and spatial variability in SPM flocculation dynamics were examined using water samples collected monthly from December 2021 to December 2022 at five stations in the freshwater and brackish tidal reaches of the estuary. In a custom-built flocculation chamber, these samples were first subjected to a high turbulent shear rate (45 s(-1)) to break the flocs, followed by a lower shear rate (20 s(-1)) that promoted aggregation for 120 min. Floc size distribution changes were analyzed to determine key flocculation parameters, in particular, equilibrium floc size (D-e), and flocculation speed (V-f). Using generalized additive models, we assessed the influence of seasonal, spatial, environmental, and biotic factors on D-e and V-f. Unlike in the brackish stations, the freshwater stations displayed clear seasonal patterns in flocculation dynamics, with D-e and V-f increasing in spring and summer. The strong positive correlations between D-e, V-f, and Chl a, as well as between V-f and phytoplankton-derived particulate organic carbon, suggest that phytoplankton plays a key role in the flocculation process. Transparent exopolymer particles (TEP), which because of their sticky properties can promote particle coagulation, were only weakly correlated with enhanced flocculation, suggesting that TEP properties may be affected by factors such as its specific composition, age, and remineralization.

The effect of spatial factors reflecting dispersal potential between sites versus local environmental conditions on freshwater planktonic communities remains poorly understood. We assessed differences in the relative importance of local and seasonal environmental conditions versus spatial factors in explaining differences in community composition (i.e., beta-diversity patterns) in microbial plankton of 39 mid-latitude Chilean lakes spanning representative ecological gradients in altitude, mixing depth and water chemistry. The assemblages were taxonomically profiled by paired-end high throughput sequencing of the V3-V4 region of the 16S and the V4 region of the 18S rRNA genes. Variation partitioning analyses revealed that the explanatory power of environmental and seasonal factors versus spatial variables and their mutual overlap varied considerably among taxa and functional groups. More than 12 % of the variation in community structure was uniquely explained by environmental factors in the phytoplankton groups Dinophyta, Ochrophyta and Cyanobacteria, as well as in oligotrophic ultramicrobacteria, such as small rhodopsin containing Actinobacteria and LD12 Alphaproteobacteria. In phago-heterotrophic and saprotrophic groups, including heterotrophic micro-eukaryotes, and Bacteroidetes, environmental factors explained a smaller or even insignificant portion of the differences in the community structure. Our findings suggest that in Chilean lake microplankton, complex traits related to ecological and trophic strategy appear to affect the relative effect of local environmental properties on their community composition and hence the strength of species sorting along limnological gradients.

Sexual reproduction is a nearly universal characteristic of the eukaryotic life cycle, yet it is rarely observed in natural populations of micro-eukaryotes. Sex is particularly relevant for diatoms, a key group of marine and freshwater phytoplankton, where sexual reproduction counters a progressive cell size reduction due to cellular division. Here, we leveraged controlled sex transcriptome experiments of four diatom species to develop a robust method for in situ monitoring of sexual reproduction events. The resulting panel of conserved marker genes was validated for specificity and sensitivity using metatranscriptomic profiling of a natural estuarine community undergoing massive sexual reproduction of multiple species in response to increased salinity. Analysis of metatranscriptomic data linked with Metagenome-Assembled Genomes from the Tara Oceans expedition revealed widespread and coordinated expression of these markers across nine diatom genera, complemented by observations of sexual stages in automated imaging resources. Our results reveal that diatom sexual reproduction is more widespread in the global ocean than previously thought, encompassing both dominant bloom-forming species and rare taxa. Our panel of markers to detect sexual reproduction in natural environments paves the road to better understand the interplay between endogenous and environmental controls of this pivotal process, essential for the diatoms' evolutionary success.

Species of Dictyota with dentate margins exhibit notable diversity and a broad distribution across the Greater Caribbean. Oceanic islands such as Saint Kitts (Lesser Antilles) and the Archipelago of San Andr & eacute;s (Colombia) play a key role in expanding our understanding of these taxa. In this study, we report Dictyota canariensis as a new record for both countries and confirm the presence of Dictyota ciliolata and Dictyota jamaicensis using molecular and morphological evidence. Phylogenetic analyses based on psbA and cox1 sequences support the identity of these species, and the cox1 haplotype network reveals some geographic structure. Overall, our findings underscore the value of molecular data in addressing taxonomic complexity and highlight the importance of oceanic islands in shaping the regional diversity of dentate Dictyota species in the Caribbean basin.

While DNA-assisted identifications have significantly enhanced our understanding of Ulva diversity, they have also widened the gap between historical taxonomic and floristic studies based solely on morphology and contemporary studies utilizing DNA sequences. To bridge this gap, we compared historical assessments of Ulva sensu lato diversity in the Netherlands and Belgium with molecular-based identifications. By combining DNA barcoding of recent field collections with NGS data from historical herbarium voucher specimens, we confirmed the presence of 17 Ulva species using tufA barcoding, including three unidentified clades. Additionally, we identified Blidingia marginata, B. minima, Monostroma grevillei, Umbraulva dangeardii, and a taxonomic entity that matched reference sequences of both Gayralia oxysperma and Kornmannia leptoderma. Of the 24 species previously reported in the southern North Sea based on published literature, only 13 species were molecularly confirmed, highlighting the substantial discrepancy between traditional and DNA-based species identifications in this group of algae. Integrating historical herbarium vouchers into our biodiversity assessment revealed that this mismatch was largely due to misinterpretation of names and to a lesser extent changing species concepts. Plastid genome and nuclear ribosomal DNA assemblies of Ulva intestinaloides and U. pseudolinza type material showed that their ITS, rbcL, and tufA sequences were identical or highly similar to reference sequences of U. compressa and U. intestinalis, respectively, indicating that they are synonyms of these species. Finally, we report four new species records for the southern North Sea: Ulva capillata and Umbraulva dangeardii that are native to the Northeast Atlantic, and the non-indigenous Ulva californica and U. shanxiensis. The latter is a freshwater species that has not been recorded outside China until now. The discovery of unidentified clades and non-native species in the southern North Sea emphasizes the importance of molecular monitoring in uncovering cryptic diversity and improving our understanding of Ulva biodiversity.

The green seaweed Ulva relies on associated bacteria for morphogenesis and is an important model to study algal-bacterial interactions. Ulva-associated bacteria exhibit high turnover across environmental gradients, leading to the hypothesis that bacteria contribute to the acclimation potential of the host. However, the functional variation of these bacteria in relation to environmental changes remains unclear. We analyzed 91 Ulva samples across a 2000-kilometer Atlantic-Baltic Sea salinity gradient using metagenomic sequencing. Metabolic reconstruction of 639 metagenome-assembled genomes revealed widespread potential for carbon, nitrogen, sulfur, and vitamin metabolism. Although the R2 value for salinity explained 70% of taxonomic variation, it accounted only for 17% of functional variation. The limited variation was attributed to typical high-salinity bacteria exhibiting enrichment in genes for thiamine, pyridoxal, and betaine biosynthesis, which likely contribute to stress mitigation and osmotic homeostasis in response to salinity variations. Our results emphasize the importance of functional profiling to understand the seaweed holobiont and its collective response to environmental change.

The evolution of differences in gamete size and number between sexes is a cornerstone of sexual selection theories. The green macroalga Ulva, with incipient anisogamy and parthenogenetic gametes, provides a unique system to investigate theoretical predictions regarding the evolutionary pressures that drive the transition from isogamy to anisogamy, particularly in relation to gamete size differentiation and sexual selection. Its minimal gamete dimorphism and facultative parthenogenesis enable a rare window into early evolutionary steps toward anisogamy. By analyzing the expression profiles of sex-biased genes (SBGs) during gametogenesis, we found that SBGs evolve faster than unbiased genes, driven by higher rates of non-synonymous substitution (dN), indicating that SBGs are under stronger selective pressures. Mating type minus-biased genes (mt-BGs) exhibit higher dN/dS values than mating type plus-biased genes (mt+BGs), suggesting stronger selective pressures on mt-BGs, although this difference was not statistically significant (P = 0.08). Using branch-site and RELAX models, we found positive selection and relaxed purifying selection acting on a significant proportion of SBGs, particularly those associated with flagella function. This study highlights the selective pressures shaping anisogamy and provides insights into the molecular mechanisms underlying its evolution. The faster evolution of SBGs, particularly mt-BGs, and the positive selection on genes associated with motility, such as those related to flagella function, suggest the importance of enhanced gamete motility in the transition to anisogamy. These findings contribute to our understanding of sexual selection and the evolutionary forces that drive the differentiation of gamete size and number between sexes.

The drivers of spatiotemporal changes in microorganism's functional community structure remain poorly understood. Using DNA-amplicon sequencing we studied the spatiotemporal dynamics of bacterial and eukaryotic microbial communities in the freshwater and brackish tidal reaches of the Schelde estuary (Belgium) from 2018 to 2021. Our analyses revealed pronounced seasonal and longitudinal turnover in autotrophic and heterotrophic microbiota, mainly driven by changes in freshwater discharge, which modulate the salinity and turbidity gradient. Higher discharge in early spring led to a more uniform community composition across the estuary, with higher relative abundances of heterotrophic eukaryotes. As discharge decreased in late spring, the salinity gradient and associated turnover in community composition became more accentuated, with Actinomycetota and diatoms dominating the upstream reaches, and ciliates, fungi and marine bacteria being relatively more important downstream from the maximum turbidity zone (MTZ). This study revealed fine-scale turnover in (semi)cryptic phytoplankton taxa and spatiotemporal changes in parasitism linked to bloom termination. High discharge due to exceptionally heavy rainfall resulted in the disruption of the phytoplankton bloom, more downstream spreading of freshwater species and a decline in brackish and polyhaline species. These results emphasise the intricate link between hydrodynamics and microbial community dynamics and ecological functions in estuarine ecosystems.

The macroalgal family, Ulvaceae, holds promising candidates for cultivation in land-based Integrated Multitrophic Recirculated Aquaculture Systems (IMRAS) due to their fast growth and nutrient uptake capabilities. Selection of appropriate strains, however, is crucial before implementation in IMRAS. In this study, an evaluation of Ulvaceae strains was conducted through an initial screening of in total nine strains, eight sourced from natural habitats and one commercial Ulva producer. The abiotic conditions were characterised by high nutrient concentrations (883 mu M NO3--N) and were kept uniform for all strains during the screening. Following the initial screening, the effect of temperature on growth was investigated (10, 16, 22, and 28 degrees C) in two selected strains ( Ulva compressa and Ulvaria obscura) under high nutrient conditions. This study demonstrated that four investigated Ulvaceae strains achieved high and stable growth rates (15-22% fresh weight d- 1 ) in indoor free-floating cultures. Further, there was consistent and significant nitrogen uptake potential of a single Ulva compressa strain across temperatures between 10 and 22 degrees C (0.03 g N L- 1 Week- 1 corresponding to 74% of added dissolved inorganic nitrogen). Ulva compressa grew across all investigated temperatures with weekly variations in biomass yields (18-40 g dry weight m- 2 day- 1 ) while Ulvaria obscura grew stably at 10, 16, and 22 degrees C (15-16 g dry weight m- 2 day- 1 ). The findings of this study enhance our understanding of the potential uses of Ulvaceae strains in land-based cultivation and serves as a stepping stone for the integration of Ulvaceae cultivation into IMRAS on a commercial scale.

In this study we explore the introduction of the brown alga Dictyota acutiloba in the Mediterranean Sea and provide a substantive update on the geographic distribution of this species, which was long thought to be confined to the Pacific Ocean. A critical assessment of published distribution records and additional identifications based on cox1, psbA and rbcL genetic markers confirm the presence of D. acutiloba at a number of locations in the Indo-Pacific as well as three locations along the Israeli coastline in the south-eastern Mediterranean Sea. The close genetic affinity between introduced specimens and those from a population in Hurghada (Red Sea) strongly suggests an introduction via the Suez Canal. The occurrence of D. acutiloba in these regions is further supported by predictions made by correlative ecological niche models (ENMs), which show high suitability values in the northern Red Sea and the Levantine Basin. In contrast, environmental conditions in the western Mediterranean and parts of the north-eastern Mediterranean are currently less favourable, as evidenced by the lower predicted probability of occurrence. Under future scenarios, the suitability of these regions increases. The further spread of D. acutiloba in the eastern Mediterranean seems imminent, and the species may even extend its range to the western Mediterranean Sea, depending on the climate change scenario considered. While D. acutiloba can be relatively easily distinguished from the majority of Mediterranean Dictyota species, it remains difficult to differentiate this species from narrow growth forms of D. dichotoma. Therefore, we recommend the use of molecular markers such as cox1, psbA and rbcL, to unequivocally identify this species and monitor its further spread.

The green seaweed Ulva depends on its associated bacteria for morphogenesis and is an important model to study algal-bacterial interactions. Ulva-associated bacteria exhibit high turnover across environmental gradients, leading to the hypothesis that bacteria contribute to the acclimation potential of the host. Yet little is known about the variation in the functional profile of Ulva-associated bacteria in relation to environmental changes. To test which microbial functions shift alongside a strong environmental gradient, we analysed microbial communities of 91 Ulva samples across a 2,000 km Atlantic–Baltic Sea salinity gradient using metagenomic sequencing. Metabolic reconstruction of 639 metagenome-assembled genomes revealed widespread potential for carbon, sulphur, nitrogen, and vitamin metabolism, including amino acid and vitamin B biosynthesis. While salinity explained 70% of taxonomic variation, it only accounted for 17% of functional variation, indicating extensive functional stability. The limited variation was attributed to typical high-salinity bacteria exhibiting enrichment in genes for thiamine, pyridoxal, and betaine biosynthesis. These metabolic modules likely contribute to oxidative stress mitigation, cellular osmotic homeostasis, and membrane stabilization in response to salinity variations. Our results emphasise the importance of functional profiling to understand the seaweed holobiont and its collective response to environmental change. ### Competing Interest Statement The authors have declared no competing interest.

Third-generation sequencing platforms, such as Oxford Nanopore Technology (ONT), have made it possible to characterize communities through the sequencing of long amplicons. While this theoretically allows for an increased taxonomic resolution compared to short-read sequencing platforms such as Illumina, the high error rate remains problematic for accurately identifying the community members present within a sample. Here, we present and validate CONCOMPRA, a tool that allows the detection of closely related strains within a community by drafting and mapping to consensus sequences. We show that CONCOMPRA outperforms several other tools for profiling bacterial communities using full-length 16S rRNA gene sequencing. Since CONCOMPRA does not rely on a sequence database for profiling communities, it is applicable to systems and amplicons for which little to no reference data exists. Our validation test shows that the amplification of long PCR products is likely to produce chimeric byproducts that inflate alpha diversity and skew community structure, stressing the importance of chimera detection. CONCOMPRA is available on GitHub (https://github.com/willem-stock/CONCOMPRA).

Using a DNA barcoding approach, we document an extensive number of inter-species cryptic introductions of bladed Bangiales (Pyropia) at an historic oyster aquaculture site in the Southern North Sea. We sampled the intertidal of 20 locations along the Belgian and Dutch coastline, ranging from sheltered to exposed, between February 2022 and April 2023 for bladed Bangiales. 230 individuals of bladed Bangiales were collected, morphological and ecological characteristics described and identified based on chloroplast rbcL gene sequences, revealing the presence of 13 species belonging to the genera Porphyra and Pyropia. While seven species (P. dioica, P. linearis, P. purpurea, P. umbilicalis, Py. collinsii, Py. elongata, Py. leucosticta) are regarded as native to the Northeast Atlantic, four species (Py. katadae, Py. koreana, Py. kinositae and Py. yezoensis) are considered non-indigenous. The records of Py. katadae, Py. kinositae and Py. koreana are the first confirmed observations for the Northeast Atlantic region. In addition, we identified two distinct rbcL clades, for which a definite species identification could not be established due to a lack of matching reference sequences. Species diversity was generally higher during winter and at exposed sites facing the open North Sea. The surprisingly high species diversity of the bladed Bangiales could only be revealed by molecular identification – a crucial tool for reliable species identification in this group of organisms.