Fucoidan, a sulfated polysaccharide found primarily in brown algae, represents a significant reservoir of organic carbon in marine ecosystems. Its degradation by bacteria is a vital process that returns carbon to the ocean’s microbial loop, supporting nutrient recycling and energy flow. However, this new research demonstrates that when phosphate—a key nutrient for bacterial growth and enzymatic function—is scarce, bacteria’s enzymatic machinery responsible for fucoidan degradation is substantially impaired. This finding unravels a previously underexplored link between nutrient availability and complex carbohydrate breakdown.

Phosphate is a fundamental element for cellular processes, playing an indispensable role in energy transfer, nucleic acid synthesis, and cellular signaling. Its availability often limits microbial growth in marine environments, resulting in a race among microbial communities for this precious resource. By examining marine bacterial populations subjected to phosphate deprivation, the scientists observed a pronounced decline in the expression and activity of glycoside hydrolases and sulfatases—enzymes crucial for cleaving the complex sugar chains and sulfate groups characteristic of fucoidan.

The study employed state-of-the-art metagenomics and transcriptomics to dissect the bacterial response under variable phosphate concentrations. These high-throughput approaches revealed a coordinated regulatory mechanism wherein phosphate limitation triggers a metabolic shift that deprioritizes the energy-intensive process of fucoidan breakdown. Instead, bacteria appear to conserve resources and shift toward strategies optimized for surviving nutrient stress rather than consuming complex polysaccharides.

This adaptive strategy has important ecological repercussions. Fucoidan is one of the major carbon sources supporting heterotrophic bacterial communities, and its incomplete degradation under phosphate stress means that large pools of organic carbon from brown algae remain locked in molecular forms inaccessible to many marine organisms. Consequently, phosphate scarcity could slow carbon turnover rates, influencing the ocean’s capacity to sequester carbon and modulating nutrient cycling on a global scale.

Moreover, the researchers found that different taxa within marine microbial communities respond variably to phosphate deprivation. Certain bacterial groups showed more pronounced reductions in fucoidan-degrading capacity, suggesting that nutrient availability may shape the microbial composition and function in marine ecosystems. This microbial niche partitioning driven by phosphate limitation adds a layer of complexity to understanding how biogeochemical cycles are modulated in the ocean.

The molecular mechanisms underlying this phenomenon involve phosphate sensing and signaling pathways that regulate gene expression of carbohydrate-active enzymes. The authors identified key regulatory nodes where phosphate-responsive transcription factors likely repress the production of fucoidan-degrading enzymes, highlighting potential targets for future biochemical studies aiming to manipulate or harness these pathways.

Interestingly, the study also explored the role of environmental variables such as temperature and light, concluding that while these factors influence microbial activity, phosphate availability exerts a dominant control over fucoidan degradation. This points to a model where nutrient status is a primary governor of marine polysaccharide cycling, overriding other environmental drivers under certain conditions.

These findings carry implications for our understanding of the ocean’s biological pump—the process whereby carbon is transported from the surface to the deep ocean. As fucoidan degradation is curtailed under phosphate limitation, the sequestration efficiency of organic carbon may be enhanced in regions where phosphate is chronically scarce, such as oligotrophic gyres. Such regions cover vast oceanic areas, underscoring the global significance of this biogeochemical control.

Furthermore, the restriction of fucoidan degradation may affect the dynamics of marine biofilms and particle-associated microbial communities, which rely heavily on polysaccharide breakdown for nutrient access. Any disruption in these processes could have cascading effects on microbial food webs, influencing higher trophic levels and overall ecosystem productivity.

Beyond environmental impacts, the study opens avenues for biotechnological exploitation. Understanding how phosphate modulates polysaccharide degradation pathways may inform the design of microbial consortia or enzymes for industrial applications such as biomass conversion or the production of bioactive compounds from marine polysaccharides.

Nevertheless, the authors caution that the interplay between nutrient availability and microbial degradation is complex and context-dependent. They advocate for continuing investigations combining in situ experiments with advanced omics and biochemical assays to unravel the multifaceted regulatory networks dictating microbial responses to nutrient fluxes in the ocean.

In summary, this pioneering research paints a sophisticated picture of how marine bacteria navigate nutrient scarcity, prioritizing their metabolic investments in a way that modulates the fate of an important class of marine carbohydrates. Phosphate limitation emerges as a critical environmental factor shaping not only microbial metabolism but also broader ecological and biogeochemical processes in the ocean, highlighting the intricate connections between nutrient cycling and microbial carbon turnover.

As marine ecosystems face increasing pressures from climate change and anthropogenic nutrient inputs, appreciating these molecular-level controls over polysaccharide degradation becomes crucial. Such knowledge aids in predicting ecosystem responses and resilience, offering vital insight into the ocean’s role in the Earth system under changing global conditions.

By elucidating a key constraint on fucoidan breakdown, this study advances our grasp of marine microbial ecology and underscores the delicate balance underpinning ocean carbon cycling. It invites a reevaluation of nutrient feedback loops in marine environments and encourages incorporating phosphate availability into models of carbon fluxes within the ocean’s microbial communities.

This comprehensive analysis, bridging molecular biology, microbial ecology, and biogeochemistry, exemplifies how integrative research efforts can uncover hidden drivers of ecosystem function. It sets the stage for future explorations into nutrient-driven regulation of organic matter transformation, a frontier essential for understanding and safeguarding the health of our blue planet.

Subject of Research: Marine microbial degradation of fucoidan under phosphate limitation

Article Title: Phosphate deprivation restricts bacterial degradation of the marine polysaccharide fucoidan

Article References:
Xu, Y., Gu, B., Yao, H. et al. Phosphate deprivation restricts bacterial degradation of the marine polysaccharide fucoidan. Nat Microbiol (2026). https://doi.org/10.1038/s41564-025-02240-z

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DOI: https://doi.org/10.1038/s41564-025-02240-z

The SAR11 clade, long recognized as the most abundant bacterial lineage in the world’s oceans, plays an outsized role in global carbon cycling and nutrient dynamics. Despite their ecological prominence, the vast genetic diversity and microdiverse ecotypes within SAR11 have historically been enigmatic due to challenges in culturing these fastidious organisms and disentangling their complex population structure from metagenomic data. The latest research surmounts these barriers by integrating isolate genomes with a vast corpus of metagenomic sequences sampled across different oceanic biomes and depths, enabling unprecedented granularity in delineating functional and ecological units.

Previous efforts to parse SAR11 diversity often relied on marker gene surveys, which, while instrumental, fell short in resolving fine-scale genomic variation critical to understanding adaptive strategies in fluctuating marine environments. By sequencing a new set of SAR11 isolate genomes, the researchers directly linked genotype to phenotype, capturing high-fidelity genomic architectures absent from fragmented metagenomic assemblies. This integrated dataset allowed them to calibrate metagenomic reads precisely, revealing population structures aligned with ecological niches defined by nutrient availability, temperature gradients, and depth stratification.

The study delineates multiple subclades within the SAR11 lineage that exhibit distinct genomic signatures reflecting ecological adaptation. For example, certain subclades possess expanded repertoires of genes related to nutrient transporters and metabolic flexibility, enabling survival in oligotrophic, nutrient-poor surface waters. Conversely, other subclades appear specialized for mesopelagic zones, harboring genes optimized for oxygen-limited or variable redox conditions. These revelations underscore the evolutionary plasticity within Pelagibacterales and highlight their role in mediating biogeochemical gradients across vertical ocean profiles.

Significantly, the researchers identified ecological units that are consistent not merely with genetic divergence but with discrete functional potential and environmental distribution. This ecological congruence supports a paradigm shift from taxonomic classifications based solely on sequence similarity toward ecologically meaningful units—population clusters that correspond to unique niches and metabolic strategies. This approach fosters predictive models linking microbial community composition to ocean biogeochemistry, with potential to enhance the accuracy of climate models through better representation of microbial contributions to carbon flux.

The integration of single-cell genomics, isolate genome sequencing, and metagenomics datasets stands as a methodological innovation resulting from this study. Single-cell approaches provided high-resolution genomes from individual cells, mitigating the assembly biases endemic to metagenomic binning. Combined with newly cultured isolates characterized with high-quality assembly and annotation, this surrogate database empowered robust comparative genomics and population genomic analyses. The scale of global metagenomic sampling, encompassing contrasting marine provinces, further strengthened the ecological validity of the inferred SAR11 subpopulations.

Aside from refining taxonomic frameworks, the research elucidates the metabolic capacities underpinning the ecological success of SAR11. Genomic data revealed widespread presence of pathways for one-carbon metabolism, sulfur compound oxidation, and efficient carbon scavenging—metabolic traits enabling SAR11 to exploit trace compounds and persist in nutrient-depleted ecosystems. Notably, certain subclades harbor unique gene clusters for the transport and assimilation of amino acids and fatty acids, hinting at niche partitioning driven by substrate specificity and environmental availability.

Importantly, these metabolic insights carry implications far beyond academic taxonomy. SAR11’s influence on oceanic carbon flow is pivotal to global climate regulation, as these organisms accelerate the turnover of dissolved organic carbon and modulate the ocean’s capacity to sequester atmospheric CO2. Enhanced understanding of SAR11 biogeography and functional diversity provides a more mechanistic basis for modeling their role in carbon cycling, particularly under shifting climate regimes and ocean acidification scenarios. The delineation of ecologically coherent units also enables monitoring of microbial responses to environmental perturbations on a granular level.

Moreover, the large-scale metagenomic framework offers avenues for detecting novel bioactive compounds or genes of biotechnological interest embedded within SAR11 diversity. Uncovering previously cryptic metabolic pathways opens possibilities for harnessing marine microbial biosynthetic potential. The ecological stratification observed might inspire biomimetic approaches to improve microbial engineering strategies, particularly those targeting carbon capture or bioenergy production, reflecting the untapped reservoir of natural innovations residing in ocean microbes.

The study also confronts longstanding challenges regarding the ‘rare biosphere’ and microbial dispersal. While SAR11 is globally ubiquitous, individual ecotypes display biogeographical restriction patterns correlating tightly with oceanographic features such as nutrient upwelling zones, temperature gradients, and salinity profiles. This spatial structuring undermines the classical notion of unrestricted microbial dispersal, suggesting intricate dispersal-ecological filtering mechanisms that maintain distinct SAR11 subpopulations across ocean basins.

From a technical perspective, the methodology advances how metagenomic datasets are interrogated to extract meaningful ecological signals from complex microbial mixtures. The combined use of isolate genomes as scaffolds for metagenome read recruitment minimizes confounding by horizontal gene transfer and gene fragmentation, improving taxonomic assignments and resolving strain-level diversity. This integrative framework serves as a blueprint for re-examining other hyperabundant marine bacterial clades and their ecological delineations, potentially revolutionizing marine microbial ecology.

The multidisciplinary team’s approach, merging microbiology, genomics, oceanography, and computational biology, exemplifies the power of integrative science in decoding the ocean’s “microbial dark matter.” Their findings will not only influence the taxonomy of Pelagibacterales but also pave the way for future research exploring the interface between microbial ecology and planetary-scale biogeochemical processes. Importantly, this work lays the foundation for observational systems aimed at tracking microbial community shifts on global scales in near real-time.

Looking forward, this study equips the scientific community with refined genomic tools and ecological context to investigate how SAR11 and other dominant marine microbes respond to ongoing ocean changes, including warming, deoxygenation, and nutrient flux alterations. The ability to delineate ecotypic units with clear environmental relevance moves the field towards predictive ecology, enabling more responsive models that integrate microbial dynamics into ocean health assessments and climate mitigation strategies.

In synthesis, the research by Freel and colleagues represents a quantum leap in marine microbiology. By leveraging new SAR11 isolate genomes and extensive global marine metagenomes, the study disentangles the intricate eco-evolutionary fabric of the most prolific bacterial lineage on Earth. The detailed mapping of ecologically relevant units within Pelagibacterales redefines our understanding of marine microbial biodiversity, ecological function, and their indispensible role in global biogeochemical cycles, offering fresh perspectives for science, climate research, and biotechnology.

Subject of Research: Genomic diversity and ecological differentiation within marine Pelagibacterales (SAR11) elucidated through new isolate genomes and global metagenomic analysis.

Article Title: New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales.

Article References:
Freel, K.C., Tucker, S.J., Freel, E.B. et al. New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales. Nat Commun (2025). https://doi.org/10.1038/s41467-025-67043-6

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Marine bacteria of the genus Cellulophaga baltica, a member of the Flavobacteriia class, are key players in the cycling of organic matter in ocean environments. They engage in continuous interactions with a diverse array of bacteriophages, viruses that infect and replicate within bacterial cells. Traditionally, phage resistance mechanisms have been understood predominantly through the lens of surface receptor mutations, which prevent viral adsorption and entry. However, the research team led by Urvoy et al. has delved deeper, isolating and characterizing thirteen distinct phage-resistant mutants of C. baltica that reveal a wider repertoire of resistance strategies.

The meticulous isolation and full genomic sequencing of these mutants have uncovered two fundamentally different categories of resistance. The first involves mutations in bacterial surface proteins, which confer broad and complete extracellular resistance against multiple phages by reducing viral adsorption efficiency. This prevents the phages from attaching to and infecting the bacterial cells, effectively halting the infection at the very doorstep.

More surprisingly, another subset of mutants revealed intracellular resistance mechanisms. These mutations, occurring in genes related to the metabolism of amino acids such as serine, glycine, and threonine, were philologically more selective, providing resistance against specific phages but allowing viral DNA replication to proceed within the host cell. This nuanced resistance pathway hinted at a complex intracellular defense system, potentially mediated by alterations in cellular lipid composition, as confirmed in one of the mutants.

The implications of these findings extend well beyond the realm of microbial ecology and virology. The researchers demonstrated that the different resistance mechanisms also translate into significant changes in the host metabolisms and physiology, which are tightly linked to marine biogeochemical processes. Notably, all mutants exhibited altered carbon utilization patterns, with surface mutants showing the most drastic changes. This shift indicates that phage resistance traits can influence how marine bacteria metabolize organic carbon, potentially affecting carbon cycling in oceanic ecosystems.

Intracellular resistance mutations also led to increased secretion of metabolites, including acetate, which was experimentally validated in one of the representative mutants. Such enhanced secretion alters the pool of dissolved organic matter available in the marine environment—a key component in the microbial loop and nutrient cycling.

Moreover, an intriguing phenotypic consequence was observed: all mutants demonstrated increased ‘stickiness,’ an enhanced cell surface property that affects bacterial aggregation and sedimentation rates. Surface mutants, in particular, sedimented faster, a trait that could affect microbial distribution in water columns and influence particulate organic carbon export to the deep ocean.

The study illuminates how the evolutionary tug-of-war between phages and their bacterial hosts may reverberate throughout marine ecosystems, influencing the rates and pathways of biogeochemical transformations. It suggests that the microcosmic battle strategies adopted by bacteria can modulate ecosystem functions such as organic carbon flux, nutrient turnover, and ultimately, global carbon cycling. These insights provide a fresh perspective on marine microbial ecology and challenge existing paradigms that mostly consider receptor-mediated phage resistance.

Beyond the ecological insights, the research employed a comprehensive interdisciplinary approach combining classical microbiological experiments, whole-genome sequencing, lipidomics, metabolomics, and ecological modeling. This multifaceted strategy offered unprecedented resolution into the molecular underpinnings of resistance and its cascading effects on cellular metabolism and community ecology.

Critically, the discovered intracellular resistance mechanisms prompt further questions about the co-evolution of phages and marine bacteria. How widespread are such metabolic and lipid-mediated resistance pathways in diverse marine microbial taxa? Do phages have counter-adaptations to these defense systems? The answers could unveil new facets of virus-host dynamics in the oceans, shedding light on their evolutionary arms race.

The ecological ramifications also beckon a deeper investigation into how phage-induced phenotypic shifts affect microbial community interactions, food web structures, and nutrient cycling at a broader scale. Given the central role of marine microbes in global biogeochemical cycles, even subtle changes in bacterial physiology triggered by viral pressures could have amplified effects on atmosphere-ocean exchanges of greenhouse gases like carbon dioxide.

This study, appearing in Nature Microbiology, underscores the importance of integrating evolutionary biology with marine ecology to understand and predict ecosystem functions under viral predation pressures. It exemplifies how micro-scale genetic changes have macro-scale ecological consequences, reminding us that the unseen microbial world is a powerful engine driving planetary health.

In the era of rapid environmental change, where marine ecosystems face unprecedented stressors, understanding the complex interactions between microbial hosts and their viral predators is paramount. These findings spotlight the sophisticated arms race that arms bacteria not just with surface defenses, but with intricate intracellular adaptations that reshape both microbial fitness and elemental cycling.

The research sets the stage for future exploration of microbial ‘stickiness’ and sedimentation dynamics as factors in biogeochemical modeling. Moreover, the discovery that lipid metabolism mediates resistance in some mutants opens new avenues in marine lipidomics, with potential implications for understanding cellular membrane biology in response to viral infection.

In summary, Urvoy and colleagues have fundamentally expanded our comprehension of phage resistance strategies beyond conventional receptor modification. Their work reveals a nuanced metabolic battleground that shapes cellular processes critical for carbon cycling and ecosystem functioning in marine environments. The evolutionary skirmishes between phages and their bacterial hosts thus ripple through marine food webs and biogeochemical cycles, highlighting the interconnectedness of life at microscopic and planetary scales.

This research not only redefines microbial resistance mechanisms but also emphasizes the need for a holistic approach to marine microbial ecology that incorporates viral dynamics, metabolic diversity, and ecosystem feedbacks. As scientists continue to decode these microscopic interactions, our understanding of the ocean’s role in Earth’s climate system and nutrient fluxes will deepen, informing both conservation efforts and biotechnological innovations harnessing marine microbial functions.

Subject of Research: Phage resistance mutations in the marine bacterium Cellulophaga baltica and their impacts on cellular metabolism and marine biogeochemical processes.

Article Title: Phage resistance mutations in a marine bacterium impact biogeochemically relevant cellular processes.

Article References:
Urvoy, M., Howard-Varona, C., Owusu-Ansah, C. et al. Phage resistance mutations in a marine bacterium impact biogeochemically relevant cellular processes. Nat Microbiol (2025). https://doi.org/10.1038/s41564-025-02202-5

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DOI: https://doi.org/10.1038/s41564-025-02202-5

Giant viruses, often dwarfing typical viral particles in size and genetic content, have emerged in recent decades as intriguing subjects that blur the lines between viruses and cellular life. Unlike the minimalist genomes of many viruses, these oceanic leviathans encode thousands of genes, some of which resemble those found in cellular organisms, suggesting complex evolutionary histories involving horizontal gene transfer and co-evolution with hosts. Minch and Moniruzzaman’s study significantly extends the known diversity of such giant viruses by analyzing expansive oceanic metagenomic datasets, sourced from numerous global expeditions encompassing a wide array of marine environments, from surface waters to the deep sea.

This research leverages state-of-the-art sequencing technology, which allows for the assembly of large viral genomes from fragmented environmental samples. Through meticulous genome reconstruction, the team identified an unprecedented number of new viral lineages, many displaying unique gene clusters previously unseen in viral genomes. These newly discovered genetic elements include those responsible for metabolic processes traditionally attributed only to cellular life, implying that these giant viruses could modulate host metabolic pathways during infection, a feature that has profound implications for understanding marine food webs and nutrient cycling.

One of the study’s most captivating revelations pertains to the functional repertoire encoded within these giant virus genomes. Beyond genes for structural proteins and replication machinery, many genomes encode an array of auxiliary metabolic genes (AMGs). These AMGs, involved in photosynthesis, nitrogen and sulfur metabolism, and host cellular signaling pathways, hint at a sophisticated viral strategy to manipulate host cellular environments, effectively reprogramming host metabolism to optimize viral replication. The presence of such genes underscores a subtle yet powerful ecological role of giant viruses as modulators of marine microbial communities and contributors to ecosystem dynamics.

Moreover, the distribution patterns of these giant viruses were found to be highly heterogeneous across global ocean basins. Variations in viral community composition appear to be influenced by factors such as temperature, salinity, nutrient availability, and host population dynamics. The study’s expansive geographic scope revealed viral assemblages adapted to distinct ecological niches, suggesting that these marine viruses have evolved specialized roles in diverse marine habitats ranging from nutrient-rich coastal waters to oligotrophic open ocean gyres.

Intriguingly, some viral genomes contained genes related to nucleotide and amino acid biosynthesis pathways, a remarkable finding that hints at viral autonomy and complexity. These genomes blur the distinction between viral and cellular metabolic capabilities, challenging the traditional view of viruses as strictly dependent on host metabolic machinery for replication. The functional consequences of such metabolic genes remain a tantalizing subject for future research, potentially reshaping our understanding of viral-host interactions in marine biogeochemistry.

In terms of evolutionary biology, the study sheds new light on the origins and diversification of giant viruses. Phylogenomic analyses suggest multiple independent evolutionary trajectories leading to the emergence of diverse giant virus lineages. This diversification likely reflects a mosaic pattern of gene acquisition from various microbial hosts, enabling these viruses to adapt to a wide range of environmental conditions and host species. Such evolutionary dynamics contribute to the ecological success and resilience of giant viruses in the competitive marine milieu.

The researchers also emphasize the potential implications of this expanded genomic and functional diversity for global ocean health and climate regulation. Giant viruses, through their influence on microbial host population dynamics and metabolic processes, may modulate carbon sequestration and nutrient turnover in ways that are only beginning to be appreciated. By forcing host cells to divert energy and resources towards viral production, these viruses can trigger significant shifts in microbial community structure, with cascading effects on ecosystem productivity and carbon cycling.

Furthermore, the discovery of novel viral genes and metabolic capabilities opens exciting avenues for biotechnological applications. Enzymes encoded by giant viruses may possess unique catalytic properties suitable for industrial and pharmaceutical purposes. Additionally, understanding viral manipulation of host metabolism offers new perspectives on harnessing viral components for synthetic biology and environmental biotechnology.

Technological advancements were critical to this research breakthrough. Minch and Moniruzzaman utilized deep metagenomic sequencing coupled with innovative genome assembly algorithms to reconstruct complex viral genomes from mixed environmental DNA. This approach overcame longstanding challenges in marine virology, where the lack of cultured representatives and limited genome references have hindered comprehensive studies. The integration of machine learning models for gene prediction and functional annotation further enhanced the identification of novel viral genes and their potential biological roles.

The study also addresses the implications for marine ecosystem monitoring and the prediction of biological responses to environmental change. Given the sensitivity of viral community composition to oceanographic variables, giant viruses could serve as bioindicators of marine ecosystem states and environmental disturbances. Assessing shifts in viral diversity and function may provide early warning signs of ecosystem stress or resilience in the face of climate change and anthropogenic impacts.

Importantly, this work underscores the interconnectedness of viruses and their microbial hosts as fundamental components of oceanic life. It challenges the classical view of marine microbes as independent entities by highlighting the intricate viral-host symbioses that drive ecological and evolutionary processes. Viruses emerge not merely as pathogens but as pivotal agents facilitating genetic exchange, metabolic innovation, and ecosystem regulation.

The authors advocate for expanded sampling efforts integrating different oceanic zones, seasons, and environmental conditions to further map the diversity and functional landscape of marine giant viruses. They also call for multidisciplinary collaborations that combine genomics, chemistry, microscopy, and ecological modeling to decode the complex interactions between viruses, hosts, and their environment.

In the context of future research, the elucidation of viral infection mechanisms and host-range specificity represents a critical frontier. Understanding how these giant viruses attach, invade, and alter host cells at molecular levels will illuminate the regulatory networks underlying marine microbial community structure. Such insights may also have implications for managing viral impacts on fisheries, aquaculture, and marine biodiversity conservation.

As a concluding reflection, the expansion of known genomic and functional diversity of global ocean giant viruses as documented by Minch and Moniruzzaman heralds a paradigm shift in marine virology. It opens a dynamic window into the hidden viral majority that shapes ocean life on scales from molecular to global. This study not only enriches our comprehension of marine virus ecology but also inspires a deeper appreciation of the ocean’s microbial tapestry and its integral role in sustaining Earth’s biosphere.

Subject of Research: Expansion of genomic and functional diversity of giant viruses in global ocean environments.

Article Title: Expansion of the genomic and functional diversity of global ocean giant viruses.

Article References:
Minch, B., Moniruzzaman, M. Expansion of the genomic and functional diversity of global ocean giant viruses. npj Viruses 3, 32 (2025). https://doi.org/10.1038/s44298-025-00122-z

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