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  • Journal article
    Liu J, Zhang X, Gulakhmadov A, Kumar PR, Kganyago M, Costa V, Ma H, Gu X, Wang L, Xiao W, Subhaprada D, Charan MU, Xiang L, Nam WH, Marengo JA, Chen Net al., 2026,

    Quantifying fragile carbon balance by multiple remote sensing based vegetation optical depth datasets

    , International Journal of Applied Earth Observation and Geoinformation, Vol: 151, ISSN: 1569-8432

    Tropical forests in the Americas play a pivotal role in the global carbon cycle, yet their net contribution to carbon balance remains uncertain due to competing processes of disturbance and recovery. While widespread deforestation, degradation, and fire drive persistent carbon losses, secondary and old-growth forests are often assumed to function as compensatory sinks. Here, we aim to provide a process-explicit and regionally consistent assessment of aboveground carbon (AGC) dynamics by disentangling carbon losses and gains across tropical America. However, the magnitude and persistence of these carbon losses and gains have not been systematically quantified at wide scale. To address this key issue, we integrate satellite-based AGC estimates derived from L-band vegetation optical depth (L-VOD), high-resolution (0.001°) disturbance mapping from AGC dataset and the Tropical Moist Forest (TMF) dataset, along with simulations from 9 dynamic global vegetation model (DGVMs) to provide a comprehensive assessment of AGC dynamics across tropical America during 2011–2020. L-VOD observations revealed that tropical America stored a mean AGC stock of 87.3 ± 18.8 PgC, with a modest but positive net annual increase of 159.2 ± 35.3 TgC yr⁻<sup>1</sup> during 2011–2020. This net gain, however, masks substantial internal carbon fluxes driven by opposing disturbance and recovery processes. Disturbances collectively caused 475.6 TgC yr⁻<sup>1</sup> of AGC loss, 301.7 TgC yr⁻<sup>1</sup> of which originated from forests, indicating that forest ecosystems remain the primary source of carbon emissions in the region. Among disturbance types, fires dominated carbon losses (252.5 ± 24.1 TgC yr⁻<sup>1</sup>), followed by deforestation (115.8 ± 29.4 TgC yr⁻<sup>1</sup>), edge degradation (79.1 ± 30.4 TgC yr⁻<sup>1</sup>), and other forms of degradation (28.2 ± 7.2 T
  • Journal article
    Paracuellos P, Bexter A, Patkowski JB, Kelly SD, Omelchenko O, Macé K, Ilangovan A, Subramoni S, Whitney JC, Filloux A, Costa TRDet al., 2026,

    Molecular basis of type VI secretion system effector loading

    , Nature Microbiology, Vol: 11, Pages: 1992-1994, ISSN: 2058-5276

    Type VI secretion systems (T6SSs) are widespread bacterial nanomachines that deliver effectors into prokaryotic and eukaryotic cells. How an effector cargo is recruited and loaded into the Hcp ring assemblies that form the tube injected by the T6SS remains poorly understood. Pseudomonas aeruginosa has four T6SSs, each associated with a different Hcp protein. Here we use cryo-electron microscopy to resolve the structure of the Tce1 cargo loaded into a Hcp3 ring from the P. aeruginosa H3-T6SS. We show that a single Tce1 monomer interacts asymmetrically with, and is enclosed by, two hexameric Hcp3 rings, engaging key residues lining the inner surface of the Hcp3 disc. Our data indicate a stepwise loading mechanism, where an initial heterodimeric Hcp–cargo complex forms before ring encapsulation around the effector. Structural modelling suggests similar effector–Hcp3 interactions for a second T6SS effector, Tce2, which has antifungal activity. We propose that this mechanism enables coordinated delivery of a broad payload into target cells.
  • Journal article
    Gottweis J, Weng W-H, Daryin A, Tu T, Sirkovic P, Myaskovsky A, Glowaty G, Weissenberger F, Orlandi A, Popovici D, Palepu A, Rong K, Tanno R, Saab K, Zhang F, Blum J, Carroll A, Kulkarni K, Tomašev N, Zverinski D, Rendulic I, Vedadi E, Hasler F, Rimanic L, Boia M, Budiselic I, Feinstein B, Bellaiche M, Sheffer T, Freyberg J, Ratcliff J, Bertolli O, Chou K, Hassidim A, Gokturk B, Vahdat A, Guan Y, Dhillon V, Vaishnav ED, Lee B, Costa TRD, Penadés JR, Peltz G, Matias Y, Manyika J, Hassabis D, Xu Y, Kohli P, Pawlosky A, Karthikesalingam A, Natarajan Vet al., 2026,

    Accelerating scientific discovery with Co-Scientist

    , Nature, ISSN: 0028-0836

    Scientific discovery is driven by scientists generating hypotheses for complex problems that undergo rigorous experimental validation. To augment this process, we introduce Co-Scientist, a multi-agent artificial intelligence (AI) system built on Gemini for structured scientific thinking and hypothesis generation. Co-Scientist aims to help scientists discover new original knowledge. Conditioned on their research objectives and previous scientific evidence, it formulates demonstrably novel research hypotheses for experimental verification. The system’s design involves agents continuously generating, critiquing and refining hypotheses accelerated by scaling test-time compute. Key contributions include (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling, and (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute scaling, improving hypothesis quality over time. Although this is a general-purpose system, we focus the validation in three biomedical applications: drug repurposing; novel-target discovery1; and explaining mechanisms of antimicrobial resistance2. Specifically, Co-Scientist helped to identify new drug-repurposing candidates and synergistic combination therapies for acute myeloid leukaemia that were validated through in vitro experiments. These real-world validations demonstrate the potential of Co-Scientist to accelerate scientific discovery and usher in an era of AI-empowered scientists.
  • Journal article
    Souza FC, Maia VA, Françoso R, de Oliveira MCF, Ligo AB, Pinho BX, Aguirre-Gutiérrez J, Sullivan M, Rocha-Santos L, de Brito Évora L, de Sousa Miranda L, Umaña MN, Stevenson PR, Tavares PA, Esquivel-Muelbert A, da Silveira AB, Teixeira AMC, Manzatto ÂG, Oliveira Á, Levesley A, Marimon BS, Junior BHM, Joly C, Peres CA, Castilho CV, Silva CA, Storck-Tonon D, Cardoso D, de Jesus Rodrigues D, Villela DM, Morton DC, de Oliveira EL, de Oliveira EA, Hase E, Ramos E, Veenendaal E, Berenguer E, Dugachard E, Almeida E, Carvalho FA, de Souza FC, Elias F, França FM, Costa FRC, Santana FD, Barbosa FR, Brown F, Ishida FY, Guilherme FAG, Damasco G, Pickavance G, Fernandes GW, de Lima HC, Rocha HL, Mews HA, do Amaral IL, Broggio I, de Almeida JS, Cunha JEBL, Silva JO, Ferreira J, Barroso JG, Gomes JAMA, Pinto JRR, Schietti J, Melgaço K, BVedovato L, Ferreira LV, da Silva LF, Blanc L, da Silva Rocha LG, da Costa L, de Freitas LJM, Alves LF, de Queiroz LP, Aragão LEOC, de Moura MSB, Benchimol M, de Medeiros MB, Simon MF, Nascimento MT, Vital MJS, Silveira M, Carniello MA, das Dores Magalhães Veloso M, do Espírito Santo MM, Andrade MBT, de Meira Junior MS, Prestes NCCS, Phillips OL, de Souza PCG, Barni PE, Morandi PS, Moonlight P, Fearnside P, Sist P, Rodrigues PMS, Garcia QS, Ramos RF, de Sá Carpanedo Ret al., 2026,

    Climate Predicts Tree Dispersal Strategies Across Brazil's Ecosystems

    , Global Ecology and Biogeography, Vol: 35, ISSN: 1466-822X

    Aim: We investigate the distribution of dispersal modes—endozoochory (via animal ingestion), synzoochory (via animal seed accumulation) and anemochory (via wind)—and seed mass of woody plants across Brazilian ecosystems, testing whether their relative abundance in local plant communities could be predicted by climate, edaphic factors and dispersal agents (e.g., the main vectors moving seeds). We expected climate to be the main predictor of dispersal strategy abundance. Location: Brazilian ecosystems (Amazon, Atlantic Forest, Cerrado and Caatinga). Time Period: 2004–2020. Major Taxa Studied: Woody angiosperms, trees and shrubs. Methods: We assigned seed mass to 1984 species and dispersal mode to 2203 species within 300 old-growth and non-flooded plots. We employed Random Forest regressions to assess the influence of water availability, temperature seasonality, soil fertility, wind and frugivorous primates on the community-weighted means of seed mass and dispersal modes. We mapped predictions and estimated the area of applicability to identify regions where predictions were reliable. Results: Climate was the main factor predicting tree dispersal strategies, followed by dispersal agents or soil properties. Endozoochory was prevalent in wetter regions with high water availability and greater diurnal temperature range. Anemochory was more common in drier regions with low water availability, stronger winds and greater diurnal temperature range, whereas synzoochory was more abundant in areas with low temperature seasonality. Heavier seeds were more prevalent in regions with less seasonal temperatures, smaller diurnal temperature ranges and weaker winds. Main Conclusions: Climate is a key predictor of the distribution and prevalence of plants with contrasting dispersal modes and seed masses. We thus expect functional responses to environmental change associated with shifts in the relative abundance of dispersal strategies, with implications for ecosystem s
  • Journal article
    Costa TRD, Penadés JR, 2026,

    Escaping our own biases: AI, scientific reasoning, and discovery in molecular biology

    , Molecular Cell, ISSN: 1097-2765

    Artificial intelligence may transform molecular biology not by always providing the correct answer, but by exploring mechanistic possibilities unconstrained by the assumptions that shape expert thinking. Its greatest contribution may be exposing the intellectual blind spots of scientists, while experimental validation remains the ultimate arbiter of truth.
  • Journal article
    Pascoe J, Newcombe J, Mendoza J, Birua S, Mendum TA, Anand K, Singh A, Sinha A, Papavinasasundaram K, Bhatt A, Larrouy-Maumus G, Singh A, Goulding CW, Beste DJVet al., 2026,

    Mycobacterium tuberculosis VadK is required for the regulation of the methylcitrate cycle and virulence.

    , EMBO Rep, Vol: 27, Pages: 4100-4123

    The evolution of new enzymatic functions is constrained and guided by the architecture of an organism's metabolic and regulatory networks and environmental constraints. Here, we identify a kinase that has evolved from pyruvate phosphate dikinase. Using biochemical and systems-level analyses, we show that this enzyme, encoded by rv1127c in Mycobacterium tuberculosis (Mtb), has diverged from its ancestral role in central carbon metabolism to function as a histidine kinase in pathogenic mycobacteria and related species. We designate this enzyme Virulence Associated DiKinase (VadK), reflecting its ability to autophosphorylate and its role in virulence. VadK is essential for the utilization of carbon sources critical for survival within the host and to cause tuberculosis (TB) in murine models. Furthermore, VadK interacts with enzymes of the methylcitrate cycle, and 13C-tracer experiments demonstrates that it fine-tunes flux through this pathway, with elevated flux proving growth limiting. Together, these findings identify VadK as a regulatory kinase that integrates metabolic control with virulence in Mtb, revealing a new facet of metabolic regulation in bacterial pathogenesis and a potential target for therapeutic intervention.
  • Journal article
    Ewe CK, Achache H, Schön H, Kontorovich L, Teichman G, Weiss S, Mogilevskaya A, Valenski M, Anava S, Bardapurkar R, Gingold H, Posner R, Antonova O, de Bono M, Tzur YB, Rechavi Oet al., 2026,

    Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress

    , Current Biology, Vol: 36, Pages: 3566-3579.e5, ISSN: 0960-9822
  • Journal article
    Pai H, Sakai T, Posbeyikian A, Frijters R, Sugihara Y, Contreras MP, Kourelis J, Adachi H, Kamoun S, Toghani Aet al., 2026,

    Contrasting evolutionary patterns of helper and sensor NRC NLRs in lettuce reflect functional divergence following subfunctionalization.

    , PLoS Genet, Vol: 22

    Nucleotide-binding domain and leucine-rich repeat immune receptors (NLRs) are known for their rapid evolution, even at the intraspecific level, yet the rates of evolution differ significantly across NLRs. However, the degree to which evolutionary patterns reflect functional divergence remains poorly understood, notably in important crop species. Within the NRC (NLR Required for Cell Death) network in Asterids, sensor NLRs detect pathogen presence but require NRC helpers for signaling and to confer immunity. We conducted a comparative analysis of NLRs across 40 Solanales and 29 Asterales genomes to explore NRC network expansion and diversification within the less-studied Asterales order. Our findings reveal that the NRC network has expanded less in Asterales compared to Solanales. We functionally validated an Asterales NRC network with 2 helpers and 9 sensors in common lettuce (Lactuca sativa). Through selection analysis and structural modeling of NRC gene family in the Lactuca genus, we found distinct evolutionary trajectories between NRC helpers and sensors. Sensors reliant on the phylogenetically conserved helper NRC0 experience limited diversification, whereas sensors dependent on other NRC helpers show higher rates of positive selection and gene duplication. Our results highlight the lineage- and function-specific evolution of the NRC network, offering insights into the evolutionary pressures shaping plant immune receptor networks.
  • Journal article
    Storer F, McClure CD, Gomez AE, Minkley LJ, Wong TL, Markevych N, Southall TDet al., 2026,

    Neuronal protein Sex-lethal modulates tRNA synthesis via the polymerase III subunit Polr3E in male Drosophila neurons.

    , PLoS Biol, Vol: 24

    The RNA-binding protein Sex-lethal (Sxl) is classically known as a master regulator of sex determination and mRNA splicing in Drosophila melanogaster. However, this role is not conserved across species, and functions beyond the canonical pathway remain poorly understood. In this study, we uncover a splicing-independent role for Sxl at the chromatin level in the Drosophila brain. Using Targeted DamID (TaDa) profiling in neurons, we identify widespread binding of Sxl to promoter regions, independent of sex or RNA binding activity. Notably, Sxl chromatin occupancy exhibits near-complete overlap with Polr3E (RPC37), an RNA Polymerase III subunit, with Sxl binding abolished upon Polr3E knockdown. Depletion of Sxl in mature male neurons induces widespread transcriptional changes, particularly in metabolic genes, and improves negative geotaxis during aging, phenotypes that closely mirror Polr3E knockdown. Conversely, overexpression of the brain-specific SxlRAC transcript leads to severe climbing deficits and upregulated gene expression associated with metabolism and translation. Manipulating Sxl levels in the brain significantly impacts select tRNA production and global protein synthesis rates. Together, these findings reveal a previously unrecognized role for Sxl in regulating Pol III activity via Polr3E, modulating tRNA synthesis and supporting neuronal metabolism. Given the emerging tie between Pol III regulation and neuronal aging, our study highlights Sxl as a novel factor in neuronal homeostasis.
  • Journal article
    Sanchez-Garrido J, David S, Rattle J, Bradshaw J, Bagnoli F, Bardelli M, Rodrigues Dos Reis C, Aanensen DM, Frankel G, Wong JLCet al., 2026,

    Type 3 fimbrial regulation underpins anti-MrkA immunotherapeutic efficacy in experimental Klebsiella pneumoniae infection.

    , J Infect Dis

    BACKGROUND: Klebsiella pneumoniae (KP) is a critical-priority organism due to prevalent last-line antibiotic resistance. Alternative treatments, including vaccines and monoclonal antibodies (mAb), depend on antigen (Ag) expression at infection sites for immunotherapeutic activity. However, the relationship between genome-encoded Ag presence and Ag expression is often overlooked. Here, we use the KP type 3 fimbrial (T3F) subunit MrkA as a prototype to build a generalisable framework to assess Ag expression and its correlation with in vivo immunotherapeutic efficacy. METHODS: We perform genomic analysis of 1649 KP genomes for T3F genes, including structural and regulatory components. We generate isogenic mutants with absent, normal or overexpressed MrkA and profile MrkA expression at single-cell level from murine pneumonia and bacteraemia models. We compare anti-MrkA mAb efficacy in vivo against strains with normal and enhanced MrkA expression. RESULTS: T3F structural and regulatory genes are highly conserved, however, regulatory gene disruption (mrkH) is more common than structural gene disruption and, in both cases, MrkA Ag is not expressed. In vivo Ag profiling revealed site-specific differences in MrkA expression, with ∼20% of KP cells expressing MrkA in the lung versus ∼5% in the bloodstream. Anti-MrkA mAb activity was dependent on MrkA abundance, with significantly enhanced efficacy following infection with MrkA-overexpressing KP. CONCLUSIONS: Regulatory genes are as important to characterise as structural gene presence when evaluating antigen candidates in clinical isolates, and Ag expression can vary by anatomical context. For MrkA, Ag abundance determines anti-MrkA mAb activity, suggesting infections with high MrkA expression will respond better to therapy.
  • Journal article
    Ettema TW, Inaba-Inoue S, Thangaratnarajah C, da Silva LA, Senning N, Clarke A, Stepien P, Shah A, Ma Y, Hardman K, David S, El Mkami H, Heddle JG, Nomura N, Ogasawara S, Iwata S, Ghilarov D, Pliotas C, Stockner T, Slotboom DJ, Beis Ket al., 2026,

    Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters

    , Nature Communications, Vol: 17, ISSN: 2041-1723

    SbmA is a membrane transporter from Escherichia coli that imports antimicrobial peptides. SbmA belongs to the SbmA-like peptide transporter (SLiPT) family. Although the protein is a secondary active transporter that is energized by the proton gradient, it is structurally related to the transmembrane domain (TMD) of ATP-binding cassette (ABC) transporters. SbmA therefore bridges the structural divide between primary and 61 secondary transporters. However, it remains unclear, if SbmA also shares the mechanism of alternating access with ABC transporters, because only a single (outward-open) state is resolved. Here, we show by sequence analysis that SbmA is likely evolved from the TMD of an early ancestor of the ABC transporter YddA. We determine the cryogenic electron microscopy structures of SbmA in occluded and inward-facing states. These conformations closely resemble equivalent states found in ABC trans- porters, indicating a shared structural mechanism of transport. In contrast to ABC transporters, where nucleotide binding, hydrolysis and release steer conformational changes necessary for substrate translocation, electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations reveal how pH changes induce conformational transitions in SbmA, consistent with a mechanism of substrate internalization that utilizes the transmembrane proton gradient.
  • Journal article
    Nollet M, Ba W, Anuncibay Soto B, Yin C, Lignos L, Jovic K, Wong S, Vyssotski A, Yustos R, Franks N, Wisden Bet al., 2026,

    Modeling the prodromal phase of Alzheimer’s disease: selective amyloid-driven failure of cholinergic medial septal neurons perturbs REM sleep, cognition, emotion, and broadcasts pathology in aging mice

    , eLife, ISSN: 2050-084X

    In humans, decreases in rapid eye movement sleep (REMS) strongly predict Alzheimer's disease (AD), alongside early degeneration of basal forebrain cholinergic neurons. We examined how β- amyloid pathology gradually erodes mouse cholinergic neurons. The familial AppNL-G-F allele was selectively expressed in medial septal (MS) cholinergic neurons of both sexes and compared with mice with global AppNL-G-F expression and selective genetic lesions of MS cholinergic cells. By 14 months, targeted AppNL-G-F allele expression had caused loss of 25% of MS cholinergic neurons and produced amyloid deposition in their terminal fields, particularly the hippocampus. REMS was reduced, together with cognitive and emotional alterations mirroring phenotypes in global mutants, which also showed selective MS cholinergic cell loss. Genetic lesioning of MS cholinergic cells recapitulated most phenotypes, identifying cholinergic loss, not amyloid deposition, as a probable cause of these phenotypes. Nevertheless, broadcasted amyloid from MS cholinergic neurons likely induced hippocampal astrocyte activation and epileptiform spikes.
  • Journal article
    Groff A, Lu Y, Feeney M, Whitelegge JP, Shao S, Morimoto K, Nixon PJet al., 2026,

    Sustainable production of myoglobin meat protein in plant chloroplasts

    , Frontiers in Plant Science, Vol: 17, Pages: 1-15, ISSN: 1664-462X

    Alternative routes for producing animal proteins are crucial for reducing the reliance on traditional livestock farming, which contributes significantly to greenhouse gas emissions, deforestation, and water consumption. Myoglobin (Mb) is an important oxygen-binding hemoprotein found in vertebrate muscle, that enhances the nutritional and sensorial properties of meat. Due to its unique functionality, Mb has been heterologously expressed in a variety of organisms, although only transient expression in Nicotiana benthamiana has been reported for higher plants. In this study, we used chloroplast transformation technology to express porcine Mb in higher plants (tobacco, a non-edible model plant, and lettuce, an edible host) and bovine Mb in the green alga Chlamydomonas reinhardtii. Mb accumulation was estimated by immunoblotting and found to be much higher in tobacco (2.7% total soluble protein (TSP)) and lettuce (1.5% TSP) than Chlamydomonas reinhardtii (<0.25% TSP). The expression in tobacco chloroplasts is also superior to tobacco nuclear expression (using either the cauliflower mosaic virus 35S promoter or Arabidopsis thaliana ubiquitin promoter). Total heme levels were elevated in myoglobin-producing mutants compared to control plants, although porcine Mb purified from tobacco leaves exhibited approximately 35% heme-binding (compared to 80% heme-binding in E. coli-expressed Mb), despite being correctly folded, suggesting that heme availability might be a bottleneck. Overall, our work describes the first report of stable Mb production in higher plants and its effect on photosynthesis and heme levels. This provides a foundation for future plant-made animal proteins for food applications.
  • Journal article
    Tolstenkov O, Norland S, Chatzigeorgiou M, 2026,

    Embodied postural dynamics underlie behavioral diversity in a benthic sessile chordate.

    , iScience, Vol: 29

    Sessile benthic animals are thought to have limited behavioral repertoires due to immobility and simple nervous systems. Here, we characterize the spontaneous and stimulus-evoked behaviors of adult Ciona intestinalis, a basal chordate with a sessile adult stage. Using time-lapse imaging and markerless pose estimation, we extracted detailed body outlines and kinematic features and showed that Ciona organizes behavior into three postural engagement states distinguished by configuration, kinematics, temporal structure, and transitions. These states are strongly modulated by external cues: mechanical pokes across the body and water flow elicit distinct sensorimotor responses, while chemical cues drive compound-specific motor patterns. Dimensionality reduction revealed that five "eigencionas'' capture most postural variance, and spatiotemporal embedding uncovered 16 stereotyped behavioral modules deployed in a context-dependent manner. Hidden Markov modeling showed that mechanical, hydrodynamic, and chemical stimuli reorganize transitions within a shared state space. Together, these results reveal a rich, modular behavioral repertoire in adult Ciona.
  • Journal article
    Fuhrmann E, Toda S, Leins J, Cetraro P, Deshpande V, Rowell J, Chapman EA, Jacobsen C, Kropp KA, Lamers MM, Loliashvili E, Saleban M, Verstraten R, Vogt C, Wongwiwat W, Ouwendijk WJD, Viejo-Borbolla A, White RE, Wilson AC, Burgess HM, Depledge DPet al., 2026,

    Extended poly(A) tails are a shared feature of herpesvirus mRNAs

    , PLoS Pathogens, Vol: 22, ISSN: 1553-7366

    Poly(A) tails are present on most cellular and viral mRNAs, providing a platform for poly(A)-binding proteins that stimulate translation and regulate the deadenylation and stability of transcripts in the cytoplasm. Here we leverage nanopore direct RNA sequencing to analyse the distribution of poly(A) tail lengths on cellular and viral mRNAs across Herpesviridae and other DNA and RNA virus infections. We find that herpesvirus mRNA poly(A) tails are consistently longer than those on cellular and other viral transcripts, presenting a previously unrecognized yet widespread mechanism to potentially advantage herpesviral gene expression. This contrasts with the templated poly(A) tails on coronavirus RNAs and those on cytoplasmically transcribed poxviral mRNAs, which are more similar in length to those on host mRNAs. Herpesviral noncoding RNAs display differential poly(A) tailing patterns while individual herpesviral mRNAs also show variation in the extent to which their poly(A) tail lengths change during the virus lifecycle, suggestive of additional uncharacterised layers of poly(A) tail length regulation. Importantly, while we detect non-adenosine nucleotides within herpesviral poly(A) tails, which are known to oppose deadenylase activity, this “mixed tailing” is not at sufficient frequency to explain the widespread extended tails of herpesvirus mRNAs.
  • Journal article
    Tarantola L, Tyler EJ, Liu Y, Maniati E, Thornton KA, Martín-Otal C, Hanna D, Kumar R, Gauthier V, Hirani P, Burger Ramos M, Roth NJ, Bragg J, Puttock EH, McDermott J, Rajeeve V, Cutillas P, Maiques O, Soulier A, Correa de Sampaio P, Jones LJ, Davies DM, Maher J, Haslam SM, Läubli H, Pearce OMTet al., 2026,

    Glycosylated extracellular matrix drives immune suppression by modulating macrophage-T cell crosstalk in triple-negative breast cancer

    , Nature Communications, Vol: 17, ISSN: 2041-1723

    The tumor extracellular matrix (ECM) is increasingly recognized as a key driver of immune suppression and therapy resistance in cancer. However, the specific ECM components and mechanisms that create this immunosuppressive environment remain poorly understood, hindering the development of new therapies. Here, we use comprehensive multi omics profiling of triple-negative breast cancer (TNBC), an aggressive and treatment-resistant subtype, to investigate this issue. We report that ECM immunomodulation in TNBC is mediated by post-translational glycan modifications on ECM proteins. Using decellularized human TNBC samples, we show that targeted enzymatic removal of these ECM glycans modifies the tumor immune microenvironment. This modification reprograms tumor-associated myeloid cells toward an immunomodulatory phenotype and improves infiltration of T cells. Notably, ECM desialylation alters selectin and selectin-ligand programs on T cells, consistent with improved trafficking and intratumoral access. In parallel, macrophage–T cell interactions are reshaped, leading to reduced T cell exhaustion. Our findings identify ECM glycan modifications as critical regulators of the innate and adaptive TNBC immune microenvironment. They suggest that targeting ECM glycosylation could offer potential strategies to boost anti-tumor immunity in this aggressive breast cancer subtype.
  • Journal article
    Ribardo DA, Singh NK, Beeby M, Hendrixson DRet al., 2026,

    The Campylobacter jejuni flagellar V-ring discerns viscosity levels to alter swimming velocity, metabolic gene expression, and fitness.

    , Proc Natl Acad Sci U S A, Vol: 123

    Campylobacter jejuni is an intestinal commensal of birds and animals and a leading cause of bacterial diarrheal disease in humans. In hosts, C. jejuni primarily resides in the mucus layer atop the lower intestinal epithelium. Persistence in this niche requires a single flagellar motor at both C. jejuni poles that generates high torque for flagellar rotation to facilitate motility and high swimming velocities. Unlike many bacterial flagellates, C. jejuni swimming velocity increases as external viscosity increases. We identified a complex formed by FlgV, VidA, and VidC (Cjj81176_1732) positioned near the MS-ring-rotor junction in the flagellar motor we annotated as the V-ring. Viscosity-influenced growth, modulation of swimming velocity, and transcription of iron/heme acquisition, respiratory, and energy-generating systems were dependent on the V-ring. C. jejuni ΔflgV and ΔvidC populations lacking a complete V-ring were motile, but could not optimally modulate swimming velocity. Like nonmotile flagellar stator or filament mutants, motile V-ring mutants had in vivo and in vitro growth and viability defects and dysregulated transcription of genes likely impacting physiology. Because the V-ring mutants behaved similarly as nonmotile mutants that experience little to no viscous drag on the filament, we propose C. jejuni V-ring mutants cannot detect viscous drag on their rotating filaments. We propose the V-ring evolved in C. jejuni and potentially other bacteria producing high torque flagellar motors to monitor external viscosity information via viscous drag on the rotating flagellar filament to adjust swimming velocity, transcription, and physiology for optimal fitness in different host lower intestinal niches.
  • Journal article
    Xing Z, Li X, Frappart F, De Lannoy G, Jagdhuber T, Peng J, Fan L, Ma H, Karthikeyan L, Liu X, Wang M, Zhao L, Liu Y, Wigneron JPet al., 2026,

    An operational global L-band soil moisture and vegetation optical depth dataset from optimized 40° SMOS brightness temperatures for 2010–2024

    , Earth System Science Data, Vol: 18, Pages: 4047-4073, ISSN: 1866-3508

    The Soil Moisture and Ocean Salinity (SMOS) mission delivers the first multi-angular L-band observations for retrieving global soil moisture (SM) and vegetation optical depth (VOD), two critical variables for understanding terrestrial water and carbon cycles. However, the combined effects of non-identical fields of view and aliasing in multi-angular SMOS brightness temperature (TB) observations can introduce noise and biases when the TBs are averaged to a nominal incidence angle, as done in the SMOS L3 dataset, thereby degrading land parameter retrievals. To address this issue, an optimized SMOS TB dataset was initially produced at a fixed 40° incidence angle, consistent with the Soil Moisture Active Passive (SMAP) mission. We then developed the first SMOS mono-angular SM and VOD products designed to achieve performance comparable to SMAP and improved relative to conventional multi-angle SMOS retrievals. The 40° TB optimization was performed using the L-band Microwave Emission of the Biosphere (L-MEB) model, and the inversion relied on the SMAP-INRAE-BORDEAUX (SMAP-IB) algorithm, yielding a global 40° SMOS TB record and associated SM and VOD products for 2010–2024 at 25 km spatial resolution, collectively referred to as SMOS-IB. Results showed that the optimized 40° TB reached a performance level comparable to SMAP and improved relative to SMOS-L3, both in its sensitivity to in-situ SM from the International Soil Moisture Network (ISMN) and in the reduction of global pixel-scale noise. When multiple evaluation metrics are considered, the SMOS-IB SM and VOD data, benefiting from the use of the optimized TB as input and a newly optimized soil roughness (Hr) parameterization, showed improved performance compared with those derived from SMOS L3 40° TB or from the multi-angular SMOS products. The SMOS-IB TB, SM and VOD products can be used for L-band algorithm development and SMAP harmonization, global drought monitoring, and studies of vegetati
  • Journal article
    Lombardi P, Ramon-Gil E, Raja RQ, Brunetti L, Manfredi GF, Zhou Z, Merces G, Cappuyns S, Maria Fulgenzi CA, D'Alessio A, Torkpour A, Celsa C, Stefanini B, Yang H, Crowley F, Marron TU, Saeed A, Pinter M, Scheiner B, Huang Y-H, Lee P-C, Nishida N, Po-Ting Lin R, Dalbeni A, Vivaldi C, Masi G, Rohlen N, von Felden J, Kaseb A, Galle PR, Kudo M, Hsu W-F, Rimassa L, Parisi A, Kelley RK, Toyoda H, Pirisi M, Jabar F, Rakaee M, Cabibbo G, Cammà C, Piscaglia F, Hwang S, Shin DJ, Li M, Dekervel J, Guerra N, Meyer T, Reeves HL, Bengsch B, Daniele G, Mann DA, Chon HJ, Leslie J, Pinato DJet al., 2026,

    A myeloid immunosuppressive phenotype defines primary refractoriness to atezolizumab plus bevacizumab in hepatocellular carcinoma.

    , J Hepatol

    BACKGROUND & AIMS: Despite improved outcomes with atezolizumab plus bevacizumab (A+B) in hepatocellular carcinoma, primary refractoriness (PRef), characterised by early progression or short-lived disease stabilisation following treatment, remains a significant challenge. METHODS: We analysed 1,296 patients with hepatocellular carcinoma treated with frontline A+B (AB-real) and validated findings in 645 trial participants recruited to IMbrave150 and GO30140. PRef was defined by SITC (Society for the Immunotherapy of Cancer) criteria. We performed a multi-parametric analysis of pre-treatment tumour tissue, including machine learning-based quantification of tumour-infiltrating lymphocytes, imaging mass cytometry and RNA sequencing (RNA-seq) to evaluate differences in the tumour microenvironment (TME) of patients with PRef vs. responders. Two independent cohorts were further used to refine the TME characterisation through single-cell RNA-seq (n = 20) and imaging mass cytometry (n = 16). We employed conditional inference tree analyses to provide a hierarchical organisation of PRef determinants. RESULTS: Among 677 AB-real patients and 378 trial participants evaluable by SITC criteria, PRef was associated with inferior median overall survival compared to response (AB-real: 7.3 vs. 31.5 months, p <0.001; Trials: 10.8 vs. not reached, p <0.001). Patients with PRef exhibited higher baseline systemic inflammation (neutrophil-to-lymphocyte ratio [NLR] ≥3), a distinctly immunosuppressive TME enriched in CD163+ tumour-associated macrophages and vascular cancer-associated fibroblasts, a higher Treg/Teff cell ratio, and pro-tumour supportive cellular interactions. RNA-seq of tumour tissue confirmed lower intrinsic immunogenicity in PRef samples with elevated myeloid infiltration. Conditional inference tree analysis identified IFN-γ signature downregulation combined with NLR ≥3 as the strongest contributor of PRef. CONCLUSIONS: PRef to A+B identifies a distinct
  • Journal article
    Oliver TJ, Elias E, Consoli G, Leong HF, Cordón-Preciado V, Fantuzzi A, Cardona T, Rutherford AW, Croce Ret al., 2026,

    Far-red chlorophyll d clusters extend photosystem I absorption toward the red limit.

    , Sci Adv, Vol: 12

    Oxygenic photosynthesis is usually limited to visible light, but the marine cyanobacterium Acaryochloris marina pushes this boundary by harvesting far-red photons with chlorophyll d. The best-studied strain, MBIC11017, unexpectedly lacks low-energy chlorophylls ("red forms") in photosystem I, limiting absorption beyond 740 nanometers. Here, we show that another strain, A. marina NIES-2412, has evolved a strategy to absorb far-red photons up to 760 nanometers. Combining time-resolved fluorescence spectroscopy with cryo-electron microscopy at 2.64-angstrom resolution, we identify two distinct classes of chlorophyll d red forms in its photosystem I. One class originates from classical charge-transfer-exciton mixing, while the other arises purely from excitonic interactions. Mapping all 96 chlorophylls d reveals the precise pigments responsible for these far-red states. We also uncover a previously unreported subunit, PsaX2, which stabilizes the photosystem I complex and shapes pigment geometry and energetics to enable the formation of red forms. Last, we show that the protein modifications responsible for binding and tuning these red forms are widespread across the Acaryochloris genus but not within the model MBIC11017 strain. Far-red photons lie close to the energetic limit of oxygenic photosynthesis; their efficient use therefore requires fine-tuning of the photosynthetic machinery. To our knowledge, our findings provide the structural and mechanistic basis of one of the most red-shifted photosystem I complexes identified to date, highlighting a distinct adaptive strategy in far-red light environments and offering design principles for extending photosynthesis in crops into the infrared.
  • Journal article
    Biswas P, Mishra V, Sanchez-Garrido J, Frankel Get al., 2026,

    Context-dependent epithelial and immune programs shape intestinal resilience or vulnerability following prior colitis

    , Cellular and Molecular Gastroenterology and Hepatology (CMGH), ISSN: 2352-345X

    Background & AimsPrior intestinal inflammation can leave durable immune and epithelial alterations, yet how these changes influence responses to subsequent injury remains unclear. Infectious and sterile colitis share core features, including barrier disruption and cytokine secretion. We therefore investigated whether the nature of the initial inflammatory event shapes protection or susceptibility during later intestinal insult.MethodsWe used reciprocal mouse models of Citrobacter rodentium (CR) infection and dextran sodium sulphate (DSS)-induced colitis to define how prior infectious versus sterile colitis shapes secondary disease. Barrier integrity, immune cell populations, cytokine production, and susceptibility to wild-type and CR mutants that cause limited epithelial barrier disruption were assessed.ResultsMice recovered from CR infection were protected against DSS-induced colitis, displaying reduced weight loss, preserved epithelial architecture, and lower inflammatory pathology. This protection required type III secretion system effector-mediated epithelial injury during primary infection and was associated with sustained IL-17A signalling, which contributed to the protective phenotype. In contrast, mice recovered from DSS colitis exhibited persistent epithelial barrier defects, chronic colonic neutrophilia, and heightened susceptibility to CR infection despite elevated IL-17A. Infection with CR mutants that cause minimal epithelial damage still resulted in severe disease in DSS-experienced mice, indicating that unresolved epithelial barrier dysfunction is a major contributor to vulnerability.ConclusionsThe nature of the primary colitis is associated with distinct epithelial and immune programs that persist beyond resolution of inflammation. Infectious colitis is associated with a protective mucosal state where IL-17A is a key contributor in a broader protective response, whereas sterile colitis is associated with persistent epithelial barrier dysfunction
  • Journal article
    Kim S, Matas-Gil A, Endres RG, 2026,

    How nature discovers rare Turing islands: Exploration by common limit cycles.

    , Proc Natl Acad Sci U S A, Vol: 123

    Turing patterns are a cornerstone of biological self-organization, yet their emergence typically requires finely tuned parameters occupying narrow regions of high-dimensional space. This poses a fundamental challenge: how can evolving biological systems reliably find and exploit such rare conditions? In this work, we propose that common biochemical limit cycles, such as those arising from genetic feedback loops, can act as natural explorers of Turing space. By coupling a reaction-diffusion system to an orbit that modulates some of its parameters, we show that the system can dynamically sweep through Turing-permissive regimes and generate transient spatial patterns. We use an entropy-based measure in Fourier space to quantify pattern formation and demonstrate how cycles enhance the detectability and robustness of Turing islands. We further explore how coupling to positional gradients increases reproducibility, suggesting a route from oscillatory dynamics to stable developmental programs. Our results highlight a powerful mechanism by which nature might bootstrap complex spatial structure from simple temporal motifs.
  • Journal article
    Grilli S, Vertsimakha O, Marston L, Gonzalez IA, Burt A, Crisanti A, Bernardini Fet al., 2026,

    Sex distorter male drive for resistance-resilient population control of the human malaria vector Anopheles gambiae

    , Nature Communications, Vol: 17, ISSN: 2041-1723

    Progress in malaria control has plateaued, prompting the exploration of additional tools. Here, we characterise two germline-specific promoters, spo11 and vasa1, in the malaria vector Anopheles gambiae. These promoters display distinct temporal and spatial expression patterns, making them well-suited for potential applications in CRISPR-based gene drives and sex ratio distortion systems. Leveraging these unique promoter features, we developed a Sex Distorter Male Drive (SDMD) technology that generates a highly male-biased progeny while spreading through super-Mendelian inheritance. This approach greatly simplifies previous genetic construct designs, potentially improving genetic stability and resilience against the development of target site resistance, a major challenge for the efficacy of genetic strategies. Our findings position SDMD as a promising and potentially resistance-resilient tool for the population suppression of Anopheles mosquitoes in malaria-endemic regions.
  • Journal article
    Bennison DJ, Chaudhary I, Chaudhuri D, Wong JCN, Punwatkar A, Biswas P, Stephenson M, Zhong Q, Kallemeijn WW, Guenot M, Koigi S, Papp D, Thomas JP, Dixit D, Korcsmaros T, Talman AM, Frickel E-M, Tate EW, Visweswariah SS, Frankel G, Shenoy ARet al., 2026,

    GBP1 recruitment to actin-rich pedestals of extracellular Gram-negative bacteria promotes pyroptosis

    , EMBO Journal, ISSN: 0261-4189

    The IFNγ-induced GTPase guanylate-binding protein 1 (GBP1) binds to lipopolysaccharide (LPS) on cytosolic gram-negative bacteria and promotes pyroptosis via the recruitment and activation of caspase-4 on the bacterial outer membrane. Enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC and EHEC, respectively) are extracellular pathogens that adhere to host cells and stimulate dense actin polymerisation underneath their attachment sites, generating structures described as actin-rich pedestals. Here, we show that GBP1 traffics to actin-rich pedestals in human cells infected with EPEC or EHEC in vitro and mouse colonocytes infected with the EPEC-like murine pathogen Citrobacter rodentium in vivo. GBP1 promotes caspase-4 recruitment to actin-rich pedestals, leading to pyroptosis and IL-18 release. GBP1 mutants defective in LPS coatomer formation also localise to EPEC pedestals. A novel assay that mimics pathogenic effector activity reveals GBP1 recruitment to sterile actin polymerisation sites. We conclude that cytosolic GBP1 is mobilised to sites of pathogen-induced actin remodelling independently of LPS. Our study establishes that GBP1 not only operates as a pattern-recognition receptor but also orchestrates effector-triggered immunity against pathogens that hijack the actin cytoskeleton.
  • Journal article
    Ba W, Harding E, Nollet M, Tossell K, Li-Li L, Wong S, Anuncibary Soto B, Yustos R, Ostaszewska J, Zeilhofer H, Vyssotski A, Coutney M, William W, Franks Net al., 2026,

    Wake-active brainstem GABA neurons signal sleep pressure by upregulating AMPA receptors to drive rebound sleep

    , Current Biology, Vol: 36, Pages: 2823-2839.e4, ISSN: 0960-9822

    How the brain compensates for sleep deprivation (SD) by generating recovery sleep (RS) is not understood. Using Ca²⁺ photometry, we identified a WAKE/rapid eye movement sleep (REMS)-active somatostatin/parvalbumin GABAergic population in the mouse brainstem oral pontine reticular nucleus (PnOVgat). Following SD, PnOVgat cells transiently switched for the first hour to higher activity during non-REMS (NREMS), promoting RS. Chemogenetic activation of PnOVgat neurons prolonged NREMS, whereas ablation blunted electroencephalogram (EEG) delta power rebound and slowed RS accumulation. During RS, the selective switch of PnOVgat cells to having higher Ca2+ levels in NREMS correlated with elevated levels of synaptic proteins PSD95, activated calmodulin-dependent kinase II CaMKII (pCaMKII T286), activated PKA (pPKA T197), and GluA1-containing AMPA receptor subunits with enhanced serine phosphorylation. All increases started during SD and persisted after the first hour of RS. Patch-clamp recordings demonstrated increased postsynaptic AMPA/sleep homeostasis (NMDA) receptor ratios in PnOVgat cells 1 h after RS, indicating increased excitability and greater capacity to drive RS. In contrast, an intermingled population of GABA/glycinergic neurons did not respond to SD, despite having similar baseline WAKE/REMS activities and an ability to promote NREMS. The PnO also contained an intermingled population of excitatory PnOVglut2 WAKE/REMS-active neurons; lesioning them caused hypoactivity, but sleep or WAKE amounts were unaffected. The synaptic homeostasis hypothesis (SHY) proposes that as wakefulness progresses, synaptic AMPA receptor activity is enhanced, and subsequently downregulated during NREMS to rebalance circuit function. We suggest that a variation of SHY implements catching up on lost sleep, with glutamate receptor plasticity in the PnO tracking time awake and adjusting NREMS amounts accordingly.
  • Journal article
    Madhuprakash J, Toghani A, Pai H, Harvey M, Bentham AR, Seager BA, Yuen ELH, De la Concepción JC, Lawson DM, Stevenson CEM, Vergara-Cruces A, Derevnina L, Bozkurt TO, Banfield MJ, Kamoun S, Contreras MPet al., 2026,

    A potato late blight pathogen effector interacts with ENTH-domain protein TOL9a and an activated helper NLR to suppress immunity.

    , Sci Adv, Vol: 12

    Pathogens counteract central nodes of NLR immune receptor networks to suppress immunity. However, the mechanisms by which pathogens hijack helper NLR pathways are poorly understood. We show that an effector from the late blight pathogen Phytophthora infestans interacts with the host protein NbTOL9a and a helper NLR to suppress immunity. We solved the crystal structure of the RXLR-LWY effector AVRcap1b in complex with the ENTH domain of NbTOL9a. The structure revealed that, unlike other RXLR-LWY effectors, AVRcap1b has a previously unidentified L-shaped fold that defines a distinct structural family of effectors in the genus Phytophthora. We defined the AVRcap1b/NbTOL9a binding interface and designed effector mutants that do not bind NbTOL9a, impairing immune suppression. This suggests that ENTH binding is required for full virulence activity. Last, we show that AVRcap1b associates specifically with activated NbNRC2 independently of NbTOL9a binding. We propose a model in which the effector interconnects NbNRC2 with the NbTOL9a pathway. Our results illustrate a previously uncharacterized pathogen mechanism to hijack NLR pathways and suppress immunity.
  • Journal article
    Williams C, Nocka LM, Hedger G, Parashara P, Pardon E, Latorraca NR, Pusapati GV, Sarkar P, Lartey D, Gao L, Milenkovic L, Chalk R, Steyaert J, Marqusee S, Carrique L, Bazan JF, Rouse SL, Kong JH, Siebold C, Rohatgi Ret al., 2026,

    Design principles of a membrane-spanning ubiquitin ligase.

    , Mol Cell, Vol: 86, Pages: 2207-2222.e16

    Receptor-type E3 ubiquitin ligases enable extracellular signals to control ubiquitylation in the cytoplasm, playing widespread roles in development, metabolism, and immunity. Using cryoelectron microscopy, integrated with biophysical and functional studies, we visualized a human E3 complex composed of two transmembrane proteins, MEGF8 and MOSMO, and the intracellular RING-family protein MGRN1. This MEGF8-MOSMO-MGRN1 (MMM) complex attenuates Hedgehog signaling by ubiquitylating Smoothened (SMO), a G-protein-coupled receptor (GPCR) that transduces morphogen signals. A long helix in the MMM complex engages SMO using an intramembrane degron and extends into the cytoplasm to suspend an activated and precisely oriented RING domain below the plasma membrane. This architecture enables ubiquitylation of the cytoplasmic surface of SMO, reducing SMO abundance at primary cilia. Our structure provides insights into MEGF8 mutations, which cause multi-organ birth defects, and defines a paradigm for how transmembrane E3 ligases control the cell surface abundance of GPCRs and other signaling receptors.
  • Journal article
    Cretois B, Rosten CM, Wiel J, Barile C, McEwen B, Bernard C, Boom MP, Bota G, Brotons L, Serrano-Davies E, Glotin H, Kissling WD, Marxer R, Pérez-Granados C, Stowell D, Villero D, van Zweden JS, Sethi Set al., 2026,

    TABMON: Design and deployment of a transnational passive acoustic monitoring network for European birds

    , Methods in Ecology and Evolution, Vol: 17, Pages: 1867-1879

    Ecological surveys are often fragmented, costly and limited in scale, leading to large and long-standing knowledge gaps which threaten our ability to properly safeguard biodiversity. Passive acoustic monitoring (PAM) has promised to deliver automated biodiversity monitoring, but networks are rarely deployed on scales that can offer truly novel insights due to scalability and standardization challenges around collecting, managing, analysing and sharing data. Here we present the Transnational Acoustic Biodiversity Monitoring Network (TABMON), a standardized deployment of 108 autonomous sensors across Norway, the Netherlands, France and Spain along a continental bird migration route. Audio is recorded continuously, uploaded in near real-time and processed through an automated analysis pipeline designed to support expert validation and the generation of datasets for deriving Essential Biodiversity Variables (EBVs). TABMON provides a methodological blueprint for transnational, networked PAM deployments and highlights both the opportunities and current limitations of near real-time acoustic biodiversity monitoring at continental scales.
  • Journal article
    Maretvadakethope S, Perez-Carrasco R, 2026,

    Simple systems, complex dynamics: Lessons from minimal gene regulatory networks

    , Current Opinion in Systems Biology, Vol: 44

    Small gene regulatory networks (GRNs) are well-established biological modules that underpin cellular decisions and dynamical function. Their theoretical understanding has largely been shaped by the motif idea, which links simple network wiring patterns to behaviours. This approach has been extremely influential, providing a clear and widely used language for regulatory logic, facilitating the understanding of behaviours such as bistability, ultra-sensitivity, or oscillations. However, a growing body of theoretical and experimental work now challenges the idea that circuit behaviour is fully determined by topology alone, revealing that even very small GRNs can exhibit much richer dynamics once molecular implementation, stochasticity, and upstream modulation are taken into account. Recent advances show that the timing, precision, and reversibility of cell-fate decisions depend critically on signal history, noise structure, and molecular context, even in minimal circuits. Furthermore, there is growing evidence that small GRNs support a wide range of non-canonical dynamical behaviours including mushroom and isola bifurcations, hybrid oscillatory–switching regimes, and pronounced critical slowing down, substantially expanding their functional repertoire without increasing topological complexity. Crucially, these behaviours are highly sensitive to how regulation is implemented at the molecular level: distinct promoter architectures, regulatory logics, and stochastic mechanisms—often hidden by standard Hill-function descriptions—can qualitatively reshape circuit dynamics, requiring an explicit link between abstract network structure and specific biophysical processes. Together, these results expose fundamental limits to inferring function from topology alone or to reconstructing mechanisms from expression data. Rather than simplified motifs, Small GRNs still provide a uniquely powerful setting in which to explore these open questions in order to progress
  • Journal article
    Silvar-Viladomiu P, Cavan EL, Martin AH, Bentley JW, Hill SL, Reid DGet al., 2026,

    Estimating the contribution of the Irish Sea fish community to carbon sink potential

    , ICES Journal of Marine Science, Vol: 83, ISSN: 1054-3139

    The marine biological carbon cycle plays a crucial role in the sinking and sequestration of atmospheric carbon and in regulating the global climate. Most existing research on biological carbon sequestration has focused on the role of oceanic (off-shelf) species and processes. We know little about how species living on continental shelves contribute to and influence carbon sinks due to the complex dynamics of biological and physical transport processes. However, continental shelves often have high levels of carbon productivity and a high potential for disturbance from human activities such as fishing, which strongly impact fish communities. Fish are important components of ecosystems that interact with the biological carbon cycle. Here, we used an Ecopath with Ecosim food web model of the Irish Sea coupled with biogeochemical equations to provide a novel quantitative assessment of the contribution of the fish community to the annual carbon reaching the continental-shelf seafloor over a four-decade simulation (1973–2016). Similar to the open ocean, faecal pellets dominated estimates of fish-mediated carbon flux in the Irish Sea. Our simulations imply that pelagic fish contribute more than half of the fish-mediated carbon, equivalent to approximately 2% of the plankton-mediated carbon deposited on the seafloor. Our results provide the first quantitative assessment and early insights into the relationship between fish species and the biological carbon sink in a shelf ecosystem.

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