Journal of Phycology

Amino acid catabolism is a vital metabolic process in bacteria, providing energy, carbon and potentially nitrogen as resources, and affecting global cycles of these elements. The ability of a bacterium to catabolize an amino acid is often inferred from the presence of the relevant catabolic pathways in its genome, yet the "gene=function" inference is not straightforward. Here, we use growth assays in 96 well plates on individual amino acids and their combinations to directly measure the ability of a model marine bacterium, Alteromonas macleodii ATCC 27126, to utilize these resources for growth. With the exception of aspartate and glutamate, which did not support growth in any of our experiments, ATCC 27126 grew on all other amino acids. However, the probability of growth, together with growth yield and rate, differed depending on the entry point of the catabolic pathway to central carbon metabolism, with robust growth occurring only on amino acids catabolized into pyruvate or acetyl CoA. Growth on combinations of two amino acids revealed reproducible patterns, the clearest being inhibition of growth on other amino acids by asparagine, aspartate and their degradation product, oxaloacetate. Finally, growth was different in test tubes compared with 96 well plates. Our results reveal hidden complexity in amino acid utilization and suggest a "TCA-centric" viewpoint for amino acid utilization, perhaps reflecting the high metabolic flexibility of pyruvate and specific regulatory aspects of the TCA cycle in Alteromonas.

Tropical coral reef ecosystems worldwide are being impacted by combined pressures of climate change and human activities that introduce large quantities of nutrients and sediments into coastal areas. In this context, phytoplankton represent a critical link between dissolved inorganic nutrients and coral reef food webs, yet their role in these ecosystems remains understudied. We investigated ecological responses of the summer phytoplankton community of Shiraho Reef (Ishigaki Island, Okinawa, Japan) to nutrient enrichment using field-based microcosm experiments under natural light and temperature conditions in September 2022 and 2023. Treatments included single and combined additions of nitrogen, phosphorus, and silicon. Chlorophyll a (Chl a) concentrations increased after three days under combined nutrient conditions, whereas single-nutrient additions produced limited responses, indicating a strong co-limitation by nitrogen and phosphorus in the reef. Analysis of size-fractionated Chl a revealed shifts from picophytoplankton that typically dominate tropical oligotrophic ecosystems toward larger groups supported by enhanced nutrient availability. Our results show short-term impacts of nutrient enrichment events on phytoplankton size structure and biogeochemical cycling in coral reefs, and highlight the importance of pelagic processes in coral reef carbon dynamics under nutrient-enrichment.

Labyrinthulomycetes are a class of fungus-like heterotrophic protists from the Stramenopiles lineage, recognized for their ecological role as decomposers and contributors to nutrient cycling. They colonize various substrates, from seaweed to terrestrial environments, utilizing ectoplasmic networks for nutrient absorption. This study characterized a novel Labyrinthula strain associated with the marine diatom Biddulphia. Phylogenetic analysis of the full-length 18S rRNA gene positioned this strain as a new species, Labyrinthula merlionensis sp. nov. Scanning electron and light microscopy observations revealed bi-flagellated zoospores and spindle-shaped vegetative cells with ectoplasmic networks. Time-series observations of the interactions between L. merlionensis and Biddulphia were categorised into different phases: establishment, infection, and aggregation. Scanning electron and confocal microscopy observations during the infection phase established the use of ectoplasmic nets to target the marginal ridge regions between diatoms, and the detection of labyrinthulid cells within diatom frustules. These findings enhance the understanding of the diversity, morphology, and ecological roles of Labyrinthulomycetes, particularly their intra- and extra-cellular interactions with diatom hosts.

Ocean warming is currently leading to distributional shifts of species and an alternation of coastal communities. Vulnerable species that are most sensitive to ocean warming are able to use several acclimation mechanisms, with one of the fastest being a shift in and shuffling of their partnerships with symbiotic microorganisms. Assessing symbiosis-focused mechanisms of acclimation and adaptation in response to ocean warming is a technical challenge due to the difficulty of accurately simulating the de novo formation of coastal communities. Here, we use the Kiel Outdoor Benthocosm facility to assess which sponges species are experimentally recruited and whether they exhibit symbiosis-focused mechanisms of acclimation following selection to ocean warming. We observed one sponge species (Haliclona sp.) and found that this sponge exhibited significant shifts in the membership and composition of its associated microbiome in response to ocean warming, with much of this being attributed to the rare microbiota. Moreover, Haliclona sp. maintained the diversity and dominance of its microbiome members. Four bacteria taxa were differentially abundant at elevated temperatures, with two being a Francisella sp. that is a suspected pathogen and an uncultured Francisellaceae that is most closely related to sulfur-oxidizing endosymbionts. Changes to the Haliclona sp. microbiome are largely consistent with a limited acclimation response, which could indicate that this sponge may use microbial symbionts as part of a mechanism to acclimate and adapt to a warmer future ocean.

BackgroundRed macroalgae (Rhodophyta) are ecologically and economically important marine primary producers, yet genomic resources for most species remain scarce. Delisea pulchra, a temperate red alga known for its halogenated furanone-based chemical defenses, serves as a model for studying algal-microbe interactions, antifouling mechanisms, and disease dynamics. ResultsHere we present a high-quality genome assembly of this species. The nuclear genome comprises 134 Mbp across 271 contigs with an N50 of 1.47 Mbp and encodes 13,387 predicted protein-coding genes. Comparative genomics with other red algae revealed expansions in gene families involved in DNA methylation, and oxidative stress responses, including glutathione S-transferases and superoxide dismutases. Analysis of glycosyltransferases, sulfatases, and sulfurylases implicated in galactan biosynthesis suggests D. pulchra possesses a complex and potentially novel extracellular matrix. We also identified several vanadium haloperoxidases (vHPOs), heme-dependent haloperoxidases (hHPOs), and two type III polyketide synthase (PKS) genes unique to the D. pulchra, which together represent promising candidate genes for bromofuranone production. ConclusionThe D. pulchra genome provides a foundation for molecular investigations into defense, signaling, and host-microbe interactions. It has been deposited at the European Nucleotide Archive under accession number PRJEB101077. All datasets, annotations, and interactive tools for exploring the genome are also available through the Rhodoexplorer portal at https://rhodoexplorer.sb-roscoff.fr.

Biodiversity is expected to enhance the stability of ecological communities under environmental stress, but the relative roles of functional, interspecific, and intraspecific diversity remain poorly resolved, particularly under multiple concurrent stressors. We tested how these diversity dimensions shaped the growth and recovery of marine Synechococcus communities in a microcosm experiment manipulating strain composition across four strain-richness levels and two interspecific diversity levels under control, atrazine, warming, and combined atrazine-plus-warming treatments. Functional diversity was quantified from flow-cytometric trait data and analyzed as initial functional diversity during the stress phase and assembled functional diversity during recovery. Contrary to our expectations, higher initial functional diversity was associated with lower community growth during stress, while higher assembled functional diversity was generally associated with weaker recovery. However, these relationships depended on stressor identity and interspecific diversity: in two-species communities, the negative effects of functional diversity were reduced, and under combined stress, higher assembled functional diversity was associated with improved recovery. In contrast, intraspecific diversity consistently enhanced community growth and recovery, while interspecific diversity primarily promoted functional recovery. Together, our results show that functional, interspecific, and intraspecific diversity can influence stress responses through distinct pathways.

In the next years, several space missions will search for evidence of life on exoplanets, focusing on robust biosignatures associated with oxygenic photosynthesis, including atmospheric oxygen accumulation and the Vegetation Red-Edge in surface reflectance spectra. Many potentially habitable rocky exoplanets orbit M-dwarf stars, whose spectral energy distribution may challenge oxygenic photosynthesis. Differently from the Sun, M-dwarf stars emit predominantly far-red (700- 750 nm) and infrared (750-1000 nm) light, and relatively little visible (400-700 nm) radiation, which constitutes photosynthetically active radiation. Some organisms have been found to photosynthesize under such spectrum but less efficiently than under solar light, as their photosynthetic apparatus evolved to harvest visible light emitted by the Sun. Around M-dwarfs, such different irradiation might have selected adaptations optimized for harvesting far-red / infra-red light. On Earth, similar selection can be found in Acaryochloris marina strains, constitutively presenting high chlorophyll d content in photosystem II & I, with in vivo absorption peaks beyond 700 nm. Here we tested the Moss Beach strain under a simulated M-dwarf spectrum and a simulated primeval atmosphere - anoxic and enriched in carbon dioxide. Results underline how this permanently red-shifted photosynthetic apparatus does not require acclimation to the stellar spectrum and enables for a strong growth and oxygen production, higher than under simulated solar light. Moreover, cells reflectance spectrum highlights a shift of the canonical red-edge toward longer wavelengths, resulting in a Chl d-near-infrared edge, suggesting a similar metabolism on exoplanets orbiting M-dwarfs could successfully produce both a gaseous biosignature and a characteristic surface biosignature. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/719884v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@7f91bdorg.highwire.dtl.DTLVardef@1391bdborg.highwire.dtl.DTLVardef@53f7b4org.highwire.dtl.DTLVardef@ab59fa_HPS_FORMAT_FIGEXP M_FIG C_FIG Created in BioRender. Liistro, E. (2026) https://BioRender.com/j2de4ay

Populations of the same species inhabiting distinct geographical regions must meet the requirements of local thermal regimes to survive. While individuals integrate both deeply conserved and genotype-specific transcriptional responses to temperature shifts, unique local requirements may diversify the balance between these two mechanisms in distinct populations. The sea anemone Nematostella vectensis inhabits highly variable estuarine environments across a broad geographic range, providing an excellent system to investigate how local adaptations shape responses to temperature stress. While studies have explored the genotypic and phenotypic diversity among N. vectensis populations, the diversity in transcriptional responses to heat and cold remain poorly understood. We used RNA sequencing to characterize transcriptional programs in N. vectensis from Nova Scotia (NS), Maryland (MD), and Florida (FL) under acute temperature treatments at 10{degrees}C and 38{degrees}C. Individuals exhibited a stronger response at 38{degrees}C than at 10{degrees}C, with NS and MD responses being similar and FL exhibiting a unique response. A core set of genes was differentially expressed across all populations under heat stress, while responses to cold were highly population specific. To evaluate the role of a key transcription factor, heat shock factor (HSF), we analyzed the presence of HSF binding sites (HSEs) in promoters of differentially expressed genes (DEGs). Upregulated genes containing three or more promoter HSEs were strongly induced at 38{degrees}C in MD and FL, but not in NS. To identify the involvement of other transcription factors, we searched for overrepresented motifs in the promoters of the top 100 DEGs at 38{degrees}C, revealing a differential enrichment of motifs across the three populations. Together, these findings suggest that N. vectensis populations utilize diverse transcriptional programs in response to common hot and cold temperatures.

Nutrient availability, ecosystem productivity, and consumer assemblages are intricately linked through complex interactions and feedbacks. Nutrients influence the diversity and functional roles of consumers via shifts in resource quality and quantity, and consumers can alter ecosystem production and nutrient availability. However, our understanding of how characteristics of consumers respond to and influence concomitant shifts in nutrient availability and production is limited. We quantified the response of well-studied consumer assemblages (benthic invertebrates and zooplankton) to realistic nutrient loads that altered gross primary production (GPP) and ecosystem respiration (ER). We fertilized 14 outdoor experimental ponds for 2 months and monitored total water column carbon (TC), nitrogen (TN), and phosphorus (TP), GPP, ER, and net ecosystem production (NEP) weekly. Then, we evaluated how fertilization and the variation in nutrients and metabolism caused by fertilization were related to shifts in consumer assemblages. Fertilization increased water column TN and TP and reduced TC:TP ratios, TN:TP ratios, and rates of GPP and ER. However, consumer assemblages were more tightly linked to variation in nutrient availability and production across ponds than to fertilization. Greater declines in benthic diversity occurred in ponds with higher average TN:TP ratios during the experiment. Consistent with predicted effects of cladocerans on nutrient availability, shifts in cladoceran abundances were positively associated with average water column TN:TP ratios during the experiment. Finally, elevated GPP and ER were associated with greater increases in the abundance of benthic invertebrate predators, suggesting the possibility of top-down control. Our study highlights the critical role of consumer-mediated processes in the interaction between nutrient availability and production. Manuscript HighlightsO_LIFertilization reduced pond gross primary production and ecosystem respiration rates. C_LIO_LIInvertebrate predator abundance was inversely related to gross primary production. C_LIO_LIShifts in consumer assemblages were tightly linked to nutrients and production. C_LI

Benthic remineralization of organic matter is key to carbon and nutrient cycling, influencing both long-term carbon storage in the sediments and the release of nutrients that support primary production in the water column. With its multiple forms and ages of sea ice, Nares Strait in the Canadian Arctic offers a unique opportunity to address the knowledge gap of variability of benthic remineralization rates along a natural sea ice gradient. Here, we incubated sediment cores in different locations in Nares Strait characterised by different sea ice conditions ranging from first-year ice to multi-year ice, to measure oxygen and nutrient fluxes. To identify potential drivers, we measured environmental variables, identified macrofauna and calculated a suite of taxonomic and functional diversity indices. Our analyses showed that benthic fluxes varied significantly between the northern and southern regions of Nares Strait. The presence of deposit feeders and sea ice cover (number of days since ice-free) were the main drivers in benthic fluxes, explaining 22.6% and 13.9% of the benthic flux variation, respectively. Overall, functional diversity was a better predictor of benthic fluxes than taxonomic diversity, indicating its primary importance in controlling benthic ecosystems functioning. Our results reveal that, from a benthic biogeochemical point of view, Nares Strait seems to be dissected into two main sub-regions: (i) a permanently and highly sea ice-covered area north of Kennedy Channel, resembling deeper regions of the Arctic Ocean and (ii) a seasonally ice-covered area between the North Water Polynya and Kane Basin, where benthic fluxes values are equivalent to those reported in similar continental Arctic shelves. Consequently, the rapid functional shifts resulting from the ongoing decline in sea ice could enhance benthic remineralisation rates if deposit feeder were to become dominant in certain areas, reducing the role of the region and by extension, the Arctic, as a carbon sink.

Understanding how warming alters estuarine plankton communities is essential for predicting future changes in biodiversity and ecosystem functioning. We conducted a four-week indoor mesocosm experiment using natural summer plankton from the Elbe River to examine the effects of warming (+2 {degrees}C and +4 {degrees}C) on abiotic conditions and responses of the plankton community. In this study, oxygen concentrations, primary producer biomass (chlorophyll a, microphytoplankton) and microzooplankton abundances declined sharply during the first 10 days across all treatments while mesozooplankton abundances increased. This suggests a strong top-down control by mesozooplankton on lower trophic levels across all temperature treatments. Primary producers biomass and oxygen concentrations recovered after an initial decline, however to lower levels compared to the onset of the experiment while micro- and mesozooplankton remained low during the second half of the experiment. Nutrient dynamics indicated progressive remineralization, with increasing ammonium, NOx, and silicate concentrations, while phosphate concentrations remained low throughout the experiment. Complementary DNA and RNA metabarcoding revealed similar community turnover over time in all treatments and temperature effects became only pronounced at the end of the experiment. Overall, warming effects were subtle relative to the strong internal trophic dynamics likely caused by the artificial mesocosm setup. Our findings of changes in plankton community dynamics indicate that biotic interactions, changes in trophic diversity and other environmental factors, i.e. oxygen concentrations are likely the drivers of this estuarine system rather than warming alone.

Using linear inverse ecosystem modeling as a data assimilation tool, we compare spawning grounds of Atlantic and Southern Bluefin Tuna (ABT and SBT, respectively) based on results from field campaigns in the Gulf of Mexico (GoM) and eastern Indian Ocean off northwest Australia (Argo Basin). Both regions are warm, stratified, low-nutrient waters dominated by cyanobacteria (Prochlorococcus). Despite these similarities, the Argo Basin is more productive, with [~]1.5X higher net primary production and nearly 2X higher production of top trophic levels in the model (tuna larvae, planktivorous fish, and predatory gelatinous zooplankton). Higher primary production in the Argo Basin is mainly driven by higher N2 fixation and storm mixing of new nutrients in the upper and lower euphotic zone, respectively. Increased ecosystem efficiency (secondary production of top trophic levels / primary production) results from differences in plankton food web organization. In the GoM, protistan zooplankton are the direct consumers of nearly all phytoplankton production. In contrast, higher rates of herbivory by crustaceans feeding on nanophytoplankton combines with a higher impact of appendicularians on cyanobacteria to convert plankton production into larval tuna prey more efficiently in the Argo Basin. Despite similarities in the proportions of phytoplankton production mediated by cyanobacteria and other picoplankton in both systems, food web pathways to larval tuna and other planktivorous fish are substantially shorter in the Argo Basin. Our results highlight the impact of distinct zooplankton ecological niches on ecosystem efficiency and suggest a need for better inclusion of plankton food-web structure in models simulating climate impacts on fisheries production. HIGHLIGHTSO_LIDeveloped food web models of tuna spawning habitat (Indian Ocean & Gulf of Mexico) C_LIO_LISpawning habitats in the Argo Basin and Gulf of Mexico (GoM) are both oligotrophic C_LIO_LIArgo Basin had higher net primary production in part as a result of nitrogen fixation C_LIO_LIArgo Basin had higher rates of direct herbivory by metazoan zooplankton C_LIO_LIThis resulted in greater ecosystem efficiency in the Argo Basin. C_LI

The Mediterranean Sea harbors a rich diversity of macroalgae with pharmacological potential. In this study, metabolite composition, antioxidant and antifungal activities of methanol and ethyl acetate extracts from Rugulopteryx okamurae, Dictyota fasciola, Batophora sp., Codium fragile, and Palisada tenerrima from the southeastern coast of Spain were evaluated. R. okamurae, Batophora sp. and C. fragile are non-native. All extracts exhibited antioxidant activity, particularly those obtained with methanol. R. okamurae and Batophora sp. showed the highest activity, inhibiting the DPPH{middle dot}radical by more than 40% at 1 mg/ml. All extracts contained phenolics and flavonoids, which may contribute to the observed antioxidant activity. Moreover, the methanolic extracts of R. okamurae and P. tenerrima exhibited in vitro fungistatic activity against the wilt pathogen Fusarium oxysporum f. sp. cubense tropical race 4. R. okamurae extracts showed the strongest antifungal activity against F. oxysporum f. sp. cubense TR4, with inhibition values of 23.3% and 30.5% at doses of 10 and 20 mg/well, respectively. The methanolic P. tenerrima also showed notable activity (19.8% and 20.7% inhibition), whereas other extracts displayed lower effect. LC-MS/MS analysis of R. okamurae extract revealed a diverse metabolite profile including oxylipin-type metabolites, terpenoid-like compounds and carotenoids. Our findings highlight coastal macroalgae from SE Spain as sources of bioactive compounds and support the valorization of biomass from invaders such as R. okamurae.

Tigriopus copepods are found in splash pools on all seven continents from the equator to Arctic and Antarctic regions. Given their geographic distribution, frequent exposure to extreme environmental conditions in the high intertidal zone, and strong signatures of local adaptation, these copepods have become models for exploring patterns of adaptation to stressful environments. However, most studies focus on a relatively small subset of Tigriopus species, and there are few genome resources representing the diversity of Tigriopus species and populations. Here, we combine long-read, Pacific Biosciences HiFi data with short-read, Illumina HiC and RNA-seq data to assemble and annotate a genome sequence representing a Tigriopus population from the coast of central Chile. Based on the level of divergence that we observed in mitochondrial genes, we also performed a comparison of morphological characteristics between individuals of this population and members of the T. angulatus complex. The haplotypes that we assembled (qhTigAngs1.1.hap1 & qhTigAngs1.1.hap2) are placed into 12 major scaffolds (N50 18-19 Mbp, L50 6-7), equivalent to the number of chromosomes in other Tigriopus species. BUSCO and k-mer analyses of each haplotype and BUSCO analyses of gene models are relatively complete (95-99%) with respect to gene and k-mer content. Analyses of mitochondrial data also suggest that the Chilean population of Tigriopus we sampled may represent a novel species that we call Tigriopus aff. angulatus. These genomic resources will help us understand the diversity and structure of Tigriopus species and populations as well as facilitate future comparisons of adaptation across parallel environmental gradients.

Chlamydomonas reinhardtii is a model green alga extensively used to study photosynthesis and cilia using molecular biology and genetics. Electroporation is a very common technique to transform DNA into the nuclear genome, which is essential to generate mutant collections and express transgenes. Here, we describe a simple, fast, and efficient protocol to transform strains with an intact cell wall. It achieves a good transformation efficiency without cell wall digestion or use of commercial kits and is compatible with the widely available Gene Pulser electroporation system. Key featuresO_LIHigh transformation efficiency of Chlamydomonas reinhardtii strains with an intact cell wall. C_LIO_LIFaster than currently available electroporation protocols. C_LI

Near-shore coral reefs in southern Guam (Mariana Islands) experience severe sedimentation, in particular during the wet season when rainfall and erosion are high. We sampled fragments of the reef-forming coral Porites lobata from opposite ends of a sedimentation gradient in Fouha Bay, southern Guam, during dry and wet seasons. Using DNA metabarcoding, we characterized the diversity and composition of P. lobata-associated Symbiodiniaceae and bacterial microbiome communities. As in many species of Porites, Symbiodiniaceae communities of P. lobata were dominated by variants of Cladocopium C15 with sites showing differences in Symbiodiniaceae communities attributable to variation in these Cladocopium C15 variants. Bacterial microbiomes of P. lobata were dominated by Endozoicomonadaceae, a family of putative coral bacterial endosymbionts involved in nutrient cycling. Site and seasonal differences in bacterial diversity and community composition were apparent. In close proximity to the mouth of the river draining into Fouha Bay, bacterial diversity was highest during the wet season when sedimentation is generally severe. Microbiome reorganization in response to sedimentation may explain this result, but we also found overrepresentation of bacteria associated with terrestrial origin close to the river mouth and/or during the wet season. Together these patterns highlight that coral Symbiodiniaceae and bacterial communities are both spatially and temporally structured in this disturbed system. IMPORTANCEThis study provides a time series dataset of coral-associated microorganisms, including dinoflagellate algae and bacteria, from a tropical bay impacted by sedimentation that results from upstream erosion of disturbed soils. Characterizing temporal patterns of coral-associated microbes provides insights into the dynamic nature of these communities. While microbiome variability across sites and seasons may be a result of acclimatization to different environmental conditions, we identified bacterial groups of putative terrestrial origin in sampled coral microbiomes that may have been exported from eroded soils to the near-shore reef. Considering that disturbed soils act as hotspots for the proliferation of potentially harmful substances, such as antimicrobial resistance genes, understanding microbial community connections at the marine-freshwater-terrestrial interface is an important step toward evaluating environmental impacts across connected ecosystems from ridge to reef.

Phosphorus is a vital nutrient required for the functioning of living organisms. In aquatic environments, dissolved inorganic phosphate is considered its most bioavailable form. However, phosphate can be scarce, which has the potential to limit microbial metabolism and ecosystem functioning. To overcome phosphate scarcity, microbes produce alkaline phosphatase (AP) to access dissolved organic phosphorus (DOP). Here, we conducted a year-long study of alkaline phosphatase activity (APA) at the Ellen Browning Scripps Memorial Pier, a nutrient-rich coastal site. APA was observed throughout the year despite phosphate-replete conditions, suggesting that the role of APs in microbial nutrition is not completely understood. We tested the hypothesis that APA may promote acquisition of organic carbon liberated from DOP hydrolysis by growing the heterotrophic marine bacterium Ruegeria pomeroyi on three DOP compounds as sole carbon sources and assessing APA. Controlling for carbon concentration, all DOP sources supported growth, but at lower levels than glucose, with the highest growth observed on glucose-6-phosphate (G6P), followed by adenosine monophosphate (AMP) and adenosine triphosphate (ATP). Moreover, cell-specific APA was significantly enhanced in carbon-deplete conditions and during growth on G6P, relative to cultures grown on replete glucose or nucleotides. These findings suggest alkaline phosphatases (APs) are part of a generic carbon stress response and likely play a role in acquiring certain forms of organic carbon by R. pomeroyi, with implications for other taxa. Overall, this study helps advance the current state of knowledge regarding microbial phosphorus cycling and carbon utilization in aquatic environments.

Reef restoration practitioners aim to preserve coral genetic diversity by protecting reefs and cultivating diverse genotypes in coral nurseries. However, cryptic genetic lineages in most corals complicate restoration strategies, as the role of between-lineage genetic divergence remains unclear regarding adaptation. In Montastraea cavernosa, researchers have identified cryptic lineages, some strongly segregated by depth. We conducted a ten-week reciprocal transplantation experiment using two cryptic lineages restricted to shallow water (<10m depth), with one lineage more common on nearshore reefs and the other on offshore reefs. We aimed to quantify lineage-specific responses to the environment that explain the genetic and ecological divergence between the two lineages. Surprisingly, the strongest response was not lineage-specific. Instead, both lineages exhibited strong and similar changes in growth and metabolomic profiles, depending on the transplantation habitat. These results suggest that cryptic lineages employ similar mechanisms of adaptation and acclimatization to environmental challenges, despite their genetic distinction.

Pocillopora is a widespread, dominant reef-building coral genus in the Indo-Pacific that exhibits high morphological similarity and plasticity. Given this, genetic tools are needed to robustly identify Pocillopora individuals to the species level. Quick and accurate identification approaches for Pocillopora species are critical to estimating biodiversity patterns under current and future environmental challenges. In recent years, the mitochondrial open reading frame (mtORF) and a histone region (PocHistone) have been validated using genome-wide data to become the most widely used species-level markers for Pocillopora. However, Sanger sequencing of a large number of samples can be prohibitively expensive and sequencing facilities are not always readily available. Therefore, we present restriction fragment length polymorphism (RFLP) digests here that identify the six species of Pocillopora (P. acuta, P. cf. effusa, P. grandis, P. meandrina, P. tuahiniensis, and P. verrucosa) found in French Polynesia, without sequencing. In uninformed validation tests (in silico and in vitro), our protocol identified each Pocillopora species with 100% accuracy. Given their cost-effective, rapid nature, the tailoring of additional RFLP digest protocols to identify cryptic coral species in reef regions around the world will support foundational reef science, conservation and restoration initiatives.

O_LIGlobal temperature anomalies increasingly disrupt the cnidarian-algal symbiosis through a phenomenon coined bleaching. In contrast to heat stress, the mechanisms underlying symbiotic breakdown under cold stress remain largely unknown. C_LIO_LICombining physiological and metabolomic measurements, we investigated the response of the photosymbiotic sea anemone holobiont Aiptasia couchii to an experiment mimicking a cold spell in the Mediterranean Sea. C_LIO_LIWithin four weeks, we observed the onset of symbiotic breakdown reflected in reduced algal endosymbiont density and chlorophyll a content. While photosynthetic efficiency remained largely unaffected, no gross photosynthesis was detectable in cold-stressed anemones and decreases in glycosyldiacylglycerols and fatty acyl glycosides indicated chloroplast lipid remobilization. This breakdown of symbiotic carbon cycling was reflected in increased dipeptide and ceramide levels suggesting anemones catabolized protein reserves and induced pre-apoptotic pathways. C_LIO_LITaken together, these responses suggest a decoupling of light and dark reactions of photosynthesis in cold-stressed endosymbionts, resembling chilling injury in higher plants and free-living microalgae. This chilling-induced collapse of symbiotic nutrient cycling eventually leads to host starvation in cold-stressed Cnidaria. Hence, while cold and heat stress may invoke contrasting physiological effects on endosymbionts, our results suggest that both stressors destabilize the symbiosis through similar mechanisms rooted in host starvation. C_LI Plain language summaryOcean warming is the main cause of coral bleaching, but little is known about how cold affects the Cnidarian-algal symbiosis. Exposing the sea anemone Aiptasia couchii to cold stress, we observed reduced symbiont populations and disrupted carbon cycling, leading to lipid mobilization and protein breakdown. This suggests that, like heat stress, cold destabilizes the symbiosis through host starvation.