CCM2-Artigos (em revistas ou actas indexadas)
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- Reduced N2 fixation in the tropical Atlantic Ocean during the warm late PliocenePublication . Yehudai, Maayan; Farmer, Jesse R.; Straub, Marietta; Ogretmen, Nazik; Studer, Anja S.; Oesch, Lukas; Creel, Roger C.; Schiebel, Ralf; Auderset, Alexandra; Lawrence, Kira; Haug, Gerald H.; Sigman, Daniel M.; Martínez-García, AlfredoWater column denitrification, a major oceanic nitrogen (N) sink, decreased under past warmer-than-present climates, but the response of N2 fixation, the main oceanic N source, remains unresolved. Here we address this gap using foraminifera-bound N isotope records from the tropical Atlantic spanning the warm late Pliocene, a geological analog for projected 21st century warming. Our records show that tropical North Atlantic N2 fixation was reduced during the late Pliocene and had increased markedly by the late Pleistocene, likely due to an increase in water column denitrification, a process that globally engenders N-poor, phosphorus (P)-bearing surface waters. After ~ 2.8 million years ago, as glaciations intensified, our records show that obliquity-paced variations in the intensity of N2 fixation emerged, likely reflecting sea-level controlled changes in continental shelf area and benthic denitrification in the western tropical Atlantic, again through the generation of N-poor, P-bearing surface waters. These findings show that N2 fixation responds to the ocean’s N loss processes both over millions of years and on orbital timescales, suggesting that the global marine fixed N budget may rebalance under warmer climates by reducing both water column denitrification and N2 fixation.
- Occurrence and anthropogenic threats affecting humpback whales (Megaptera novaeangliae) inthe Southern Iberian Atlantic WatersPublication . Gennari, Ginevra; Marçalo, Ana; Rodrigues, Alfredo; Magalhães, Sara; Abrantes, Gonçalo; Dias, André; Climaco, Rodrigo; Truluck, Steve; Pignata, Eleonora; Lubansky, Tanya; Jones, Lindsey; Wenzel, Frederick; Castilho, Rita; Peres dos Santos, Rui PedroMigration is crucial behavior for many animals, allowing them to adapt their life history requirements to their environments' temporal and spatial variability (Kettemer et al. 2022). Among marine mammals, humpback whales (Megaptera novaeangliae) stand out as a highly migratory species, and their survival is heavily reliant on established migratory routes (Kennedy et al. 2013; Peres dos Santos et al. 2022; Stone et al. 1990). Although this species is one of the most researched marine mammals worldwide, very little is known about its behavior in various parts of the world. For nearly 50 years, photographic identification (photo-ID) techniques have facilitated in-depth studies of their long-distance migration patterns (Chosson et al. 2024; Katona and Whitehead 1981; Reeves et al. 2006; Schevill and Backus 1960). This type of identification is possible because individual humpback whales possess distinctive pigmentation patterns on the ventral surface of their flukes, as well as scars and variations in the serration of the trailing edges (Carlson et al. 1990; Katona and Beard 1990; Reeves et al. 2006; Schevill and Backus 1960). These unique features are often complemented by shape variations and marks in the dorsal fins (Blackmer et al. 2006; Franklin et al. 2020). Notably, the North Atlantic Humpback Whale Catalog (NAHWC), maintained by Allied Whale at the College of the Atlantic, Bar Harbor, Maine, USA (https://www.coa.edu/allied-whale/), has documented over 12,000 individual humpback whales from the North Atlantic Ocean basin (Jones et al. 2025).
- Quaternary Arctic planktonic foraminifera: morphological differentiation and taxonomic reassessment of subpolar spinose taxaPublication . Coxall, Helen K.; Cronin, Thomas M.; Darling, Kate; Husum, Katrine; Handl, Tamara; Huber, Brian T.; Kanvinde, Megh M.; Razmjooei, Mohammad; Vermassen, Flor; Voelker, Antje; Weitkamp, Tirza M.; O'Regan, MattPlanktonic foraminifera in the modern Arctic Ocean are dominated by the non-spinose polar species Neogloboquadrina pachyderma. Acmes of two spinose, presumed subpolar taxa in Quaternary central Arctic sediment cores are therefore anomalous, implying significantly different past conditions. Currently the names Turborotalita quinqueloba (Natland) and Turborotalita egelida (Cifelli and Smith) are applied to the subpolar morphotypes, which have been associated with marine isotope stages (MISs) 5 and 11, respectively, although the latest age models challenge this. Besides age uncertainties, a major obstacle to fully interpreting these plankton events is unclear taxonomy, which complicates species identification, core correlations, and paleoenvironmental reconstructions. We address this by analyzing Arctic and sub-Arctic planktonic foraminifera using light and SEM imaging and conducting morphometric analysis. Our results reveal consistent morphological and stratigraphic differences between the two Arctic spinose morphotypes, providing a basis for their taxonomic differentiation. We confirm that the younger morphotype corresponds to T. quinqueloba, characterized by tight coiling; an elongate final chamber overhanging the umbilicus; and, on average, a smaller proloculus. However, the central Arctic forms exhibit overall smaller tests than Nordic Sea counterparts and display smooth, non-encrusted wall textures. The older spinose morphotype is distinguished by larger size, a globular final chamber, an open umbilicus, evolute coiling, and a wider range and larger mean proloculus size. Compared to T. quinqueloba, it also has a lower chamber count and a distinctive wall texture that is never encrusted and characterized by sparse, robust spine bases and occasional linear ridges formed by aligned pustules. Our taxonomic investigation shows that the species name egelida is not appropriate for the older morphotype. We therefore reinstate the original species name exumbilicata, established by Herman in 1974. We highlight several morphospecies that may be confused with exumbilicata and that have contributed, or may contribute, to misassignments: Globigerina atlantisae Cifelli and Smith is consistent with the non-spinose Tenuitellita iota, whereas smooth-walled morphotypes of N. pachyderma that have been conflated with exumbilicata (egelida) can be seen under SEM to have a non-spinose wall. While it remains possible that the exumbilicata morphotype is an ecophenotype of T. quinqueloba, the absence of primary turborotalitid features and possession of some other features seen in the Globigerina falconensis lineage are instead suggestive of genus Globigerina. We here adopt a conservative taxonomic approach, referring to the older morphotype as “Globigerina” exumbilicata, pending future investigation. Our conclusions are outlined in a focused taxonomic framework covering relevant Arctic and subpolar planktonic foraminifera. The latest available biostratigraphic age constraints imply that “G.” exumbilicata is older than 0.44 Ma and younger than 1.8 Ma. It is possible that the “G.” exumbilicata acme represents a polar occupation by planktonic foraminifera in the central Arctic Ocean before ecological dominance by N. pachyderma. These new insights provide a foundation for advancing our understanding of Arctic planktonic foraminiferal evolution, the development of polar ecosystems, and Quaternary climate dynamics.
- Gene expression-based classification of European Seabass Larval batches according to saddleback syndrome incidence using machine learningPublication . Tsipourlianos, Andreas; Printzi, Alice; Fytsili, Alexia; Tzioga, Lamprini; Santos, Soraia; NAJAFPOUR, BABAK; Power, Deborah Mary; Koumoundouros, George; Moutou, Katerina A.Skeletal deformities remain a major challenge in marine fish hatcheries, affecting larval quality, animal welfare, production efficiency, and market value. In European seabass (Dicentrarchus labrax), saddleback syndrome (SBS) is a relevant skeletal abnormality that develops during larval ontogeny and has been associated with defects of the primordial marginal finfold around the flexion stage. This study investigated whether gene expression markers, combined with machine learning, could provide a stage-specific molecular approach for assessing SBS-associated larval batch quality. Larval populations from commercial hatcheries were classified as GOOD or POOR according to SBS incidence at mid-metamorphosis. Gene expression was analyzed at first feeding, flexion, post-flexion, and mid-metamorphosis, targeting genes involved in osteogenesis, myogenesis, metabolism, oxidative phosphorylation, and stress response. Stage-specific random forest models were used to classify gene expression profiles derived from larval populations with contrasting SBS incidence and to identify candidate informative genes. The models showed cross-validated area under the receiver operating characteristic curve (ROC AUC) values ranging from 0.83 to 0.962, with the highest performance at flexion. Reduced models based on the three most informative genes retained comparable internal cross-validation performance. Key candidate genes were mainly related to mitochondrial energy production, iron metabolism, stress response, muscle development, and extracellular matrix formation. These findings suggest that gene expression profiling combined with machine learning may support stage-aware discrimination of larval populations with contrasting SBS incidence, although validation in larger independent datasets is required before hatchery application.
- Color-modulated spirulina biomass produced under heterotrophic cultivation as a sustainable food ingredientPublication . Brito, Gabriela Moura Kurowiski de; Costa, Jorge Alberto Vieira; Barreira, Luísa; Morais, Michele Greque deThe intense green coloration of Spirulina biomass limits its incorporation into food products despite its high nutritional and bioactive value. This study evaluated the heterotrophic fed-batch cultivation of Spirulina sp. LEB 18 using glucose and sodium acetate, aiming to modulate biomass color and preserve a nutritionally relevant composition for its application as a food ingredient. After 10 days, all heterotrophic cultures exhibited attenuation of the green coloration, with total color differences greater than ΔE >7 relative to the controls. The reduction in chlorophyll a was consistent with the observed color changes, whereas phycocyanin and carotenoid contents did not differ significantly from the autotrophic controls. Cultivation supplemented with sodium acetate fed at 0.2 g L−1 showed a protein composition similar to the control and was the condition that exhibited the greatest color attenuation (ΔE = 10.33) without a pronounced reduction in protein content. Cultures supplemented with glucose resulted in higher lipid and carbohydrate accumulation, reflecting the redirection of carbon toward energy storage compounds. The results demonstrate that heterotrophic cultivation of Spirulina sp. LEB 18 is a promising strategy to modulate biomass color and composition, expanding its applicability, particularly in food matrices where green coloration limits consumer acceptance.
- Drivers and patterns of sediment organic carbon in European regional seasPublication . Lønborg, Christian; Graversen, Anna Elizabeth Løvgren; Addamo, Anna Maria; Assis, Jorge; Burrows, Michael Timothy; Stewart, Eleanor; Lillis, Helen; Costello, Mark John; Krause‐Jensen, DorteMapping organic carbon (OC) stores in marine sediments is a management priority to potentially minimize the anthropogenic release of organic carbon from the seabed. Sediment OC content shows high regional variability, shaped by a complex interplay of physical, chemical, biological and anthropogenic factors. In this study, we present an assessment of the drivers and patterns of sediment OC across European regional seas, with a particular focus on the role of large‐scale habitats, substratum characteristics, and environmental conditions. To investigate these relationships, we integrated data sets encompassing sediment OC, benthic habitats, sediment substrata and 11 environmental variables. Applying machine learning techniques, we identified wave exposure (estimated from wave fetch), light availability, seafloor geomorphic features, and maximum bottom water temperature as the most important environmental predictors of sediment OC content across European regional seas. While the model captured broad spatial patterns in sediment OC, it did not resolve local scale variability, making it better suited for regional assessments than for site‐specific predictions. Overall, the highest OC contents were found in sediments underlying vegetated habitats such as Posidonia oceanica and other seagrass meadows as well as in mud, and mixed sediment substrata. OC hotspots were generally located in inshore areas with low wave fetch and temperature; these include areas of the Baltic Sea, North Sea, Adriatic Sea, Barents Sea, and the Black Sea. Our data‐driven approach provides a robust foundation for identifying OC‐rich sediments, which are critical for conservation planning and assessing anthropogenic impacts on marine OC.
- Collaborative science narrows knowledge gaps in marine biological invasions to advance a national framework.Publication . Ribeiro, Romeu S.; Espírito Santo, Cristina; Celestino, Susana; Mamede, Marta; Castro, João J.; Cruz, Teresa; Silva, Teresa; Jacinto, David; Bartilotti, Cátia; Lobo-Arteaga, Jorge; Tuaty-Guerra, Miriam; Canning-Clode, João; Duarte, Sofia; Lavrador, Ana S.; Costa, Ana Cristina; Parente, Manuela Isabel; Parretti, Paola; Ramalhosa, Patrício; Castro, Nuno; Morais, Pedro; Teodosio, Maria; Encarnação, João; Afonso, Inês; Cabral, Sara; Carvalho, Frederico; Dionísio, Maria Ana; Melo, Ricardo; Amorim, Ana; Sousa, António; Cidade, Tiago; Chainho, PaulaLarge-scale data synthesis is a foundation pillar of modern macroecology, necessary for transitioning fragmented regional data into scalable biosecurity frameworks. This study presents the outcomes of a coordinated nationwide effort to analyze marine Non-Indigenous Species (NIS) records across mainland Portugal, the Azores and Madeira archipelagos using a dual-framework design. Our goals were to update the morphologically confirmed NIS inventory, identify primary introduction pathways, examine temporal and spatial trends, and evaluate genetic database coverage. We delivered an updated checklist comprising 231 morphologically confirmed marine NIS, including five new regional records. Spatial analysis reveals distinct biogeographical divergence: mainland NIS predominantly originate from the temperate North Pacific, probably due to shipping and aquaculture vectors, whereas archipelago NIS originate from the North Atlantic. This pronounced regional variability in pathway dynamics underscores the need for spatially specific management rather than uniform national policies. Also, a systematic genetic gap analysis showed that 71% of these species are cataloged in global repositories, whereas only 12.5% feature locally sourced sequences. To bridge this gap, the second framework introduces a precautionary molecular watchlist of 22 species detected exclusively via DNA-based methods awaiting morphological confirmation. Ultimately, this dual-framework structure demonstrates how integrating taxonomy with provisional molecular data provides a reliable, data-driven baseline, while moving beyond a localized dataset update to offer a scalable reference frame capable of informing regional and global marine biosecurity frameworks.
- Taxonomy, biogeography and evolution of thirty-four taxa in Phytophthora Clade 7a including eleven new species from natural forests and updated descriptions for P. fragariae, P. rubi and the ‘P. ×alni hybrid complex’Publication . Nagy, Z. Á.; Horta Jung, M.; Milenković, I.; Kudláček, T.; Bourret, T.; Kageyama, K.; Hieno, A.; Masuya, H.; Uematsu, S.; Chi, N. M.; Thu, P. Q.; Chang, T-T; Fu, C-H; Corcobado, T.; Janoušek, J.; Májek, T.; Mullett, M.; Tomšovský, M.; Ferreira, M.; Singh, R.; Maia, Cristiana; Stanivuković, Z.; Tomić, Z.; Bakonyi, J.; Webber, J. F.; Brasier, C. M.; Jung, T.Over the past three decades, surveys in natural and managed ecosystems, driven mainly by forest biosecurity issues, have greatly expanded knowledge of the global diversity and biogeography of the plant pathogen genus . In subclade 7a alone, 16 new species were described raising the number of validly described species in this subclade to 18. Recently, in further surveys conducted in natural forests of Japan, Vietnam, Europe and North America, 11 more new Clade 7a species and one other 7a taxon have now been identified. All are considered to be endemic to the surveyed sites. They are formally described here, including their morphological properties, colony and temperature-growth characteristics and their phylogenetic relationships. Informal, updated descriptions without nomenclatural act are also presented for the known species , , , × and ×. With now 34 taxa including hybrids, Clade 7a is currently the largest subclade. It is essentially a Northern Hemisphere subclade, with a disjunct distribution in North America, Europe and Asia which probably reflects an original Laurasian ancestral distribution ~90-80 Mya and subsequent post-Laurasian migrations and radiations. It is comprised of predominantly soilborne and aquatic species with non-papillate non-caducous sporangia, though some may have facultative adaptations to a degree of aerial dispersal. The largest diversity hotspots are in Southeast and East Asia, and both adaptive sympatric and non-adaptive radiations are indicated in the data. All 22 'pure' or non-hybrid species are self-fertile and exhibit relatively low nuclear heterozygosity levels. In contrast, high heterozygosity levels, relatively high numbers of tri- and partly tetra-allelic sites and maternal lines partly shared with other Clade 7a taxa are consistent with ten of the taxa (30 %) originating via interspecific hybridisation. Of these five are self-fertile, but unusually, given their likely self-fertile parents, the other five, including the ' × hybrid complex', have an A1/A2 or outcrossing breeding system. Some of the hybrids, such as the '. × hybrid complex', are known to have emerged as a result of anthropogenic disturbance events. Numerous species, including several in Clade 7a, have become highly damaging pathogens of trees and agricultural crops as a result of historical introductions via global plant trade. However, for the 11 new species described here, no symptoms were observed at the natural sample sites and their natural and potential hosts are unknown. The same applies to well over 150 species in other Clades and subclades, representing a significant plant health evidence gap. It is recommended that the biosecurity risk to forests, natural ecosystems and agriculture posed by these previously scientifically unknown taxa be actively investigated.
- High-throughput assessment of gametophyte survival and growth in the kelp Laminaria ochroleuca through autofluorescence analysisPublication . Félix de Azeredo Pinto e Melo, Francisca; Alves-Lima, Cicero; de Matos Barreto, Luís António; Monico, Carina; Serrao, Ester A.; Pearson, Gareth Anthony; Martins, NeusaThe viability of kelp microscopic gametophytes is currently analyzed using subjective visual methods based on bright-field (BF) microscope images. Fluorescence microscopy (FM) can be employed, but the dyes used can be toxic and blue/UV light intensity may induce gametogenesis. This study aimed to develop a non-invasive and accurate methodology for assessing gametophyte viability over time, using FM observation of chlorophyll autofluorescence emitted by live gametophytes. Six isolated gametophyte strains of Laminaria ochroleuca (Italy), maintained at CCMAR Biobank, were cultured in triplicate (female, male, and both sexes combined) in Petri dishes containing 10 mL of half-strength Provasoli’s enriched seawater medium (PES), under red light for 1 month. Survival and growth were assessed on days 1, 7 and 14 by photographing 20 fields-of-view, both in BF and FM. Then, cultures were transferred to white light to induce gametogenesis and test whether the autofluorescence analysis (AFA) method affected gametophyte reproduction. Image analysis was performed using FIJI software either by manually counting live gametophytes (survival) and measuring their area (growth), or by implementing a machine-learning (ML) model using FIJI’s WEKA segmentation plugin. Results revealed that both methods were correlated, validating our ML model. However, the AFA method was faster and more accurate than BF image analysis, especially for male gametophytes, and did not compromise reproductive capacity. After 9 days under white light, sporophytes were present in mixed cultures. The AFA method provides a reliable technique for assessing gametophyte viability without compromising gametogenesis.
- Comprehensive chemical and biological assessment of Orobanche racemosa extracts using chromatographic, in vitro, in silico, and cell‐based techniquesPublication . Nilofar, Nilofar; Saka, Enver; Cetiz, Mehmet Veysi; Rodrigues, Maria João; Fernandes, Eliana; Custódio, Luísa; Yildiztugay, Evren; Yapıcı, Ismail; Gulcin, Ilhami; Elhawary, Esraa A.; Eldahshan, Omayma A.; Singab, Abdel Nasser B.; Cespedes‐Acuna, Carlos L.; Zengin, GokhanThe growing interest in natural product research as a safer and sustainable alternative to synthetic drugs has triggered this study,which evaluates the chemical profile and biological activity of Orobanche racemosa extracts. In the current study, extraction wasperformed from O. racemosa using the maceration method with several extraction solvents. The extracts were examined for theirantioxidant and enzyme-inhibitory activities and their effects on cell viability. In high-performance liquid chromatography–MS/MS analysis, a total of 31 compounds was detected across all studied extracts. The EtOH and EtOH/water extracts consistentlyexhibited the highest antioxidant capacities in almost all tested assays. Similarly, EtOH and EtOH/water extracts showed vigorousanti-AChE activity, measuring 2.88 and 2.35 mg/GALAE, respectively. In the cell viability assay, both EA and EtOH extracts ofO. racemosa demonstrated potent cytotoxicity, significantly reducing viability in normal (HEK293) and cancer cell lines (HepG2,SH-SY5Y), indicating high toxicity without selectivity. Molecular docking screened 384 theoretical compound–target combina-tions and retained 251 unique complexes with docking scores of −7.0 kcal/mol or lower after duplicated entries were removed. Subsequent single-trajectory molecular dynamics analysis of seven representative high-scoring complexes generated hypotheses regarding structural persistence under the simulated conditions; however, these computational predictions require experimental validation