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Journal articleWayman JP, Sadler JP, Martin TE, et al., 2024,
Unravelling the complexities of biotic homogenization and heterogenization in the British avifauna
, JOURNAL OF ANIMAL ECOLOGY, Vol: 93, Pages: 1288-1302, ISSN: 0021-8790 -
Journal articleLingche H, Miguel-Romero L, Patkowski JB, et al., 2024,
Tail assembly interference is a common strategy in bacterial antiviral defenses
, Nature Communications, Vol: 15, ISSN: 2041-1723Many bacterial immune systems recognize phage structural components to activate antiviral responses, without inhibiting the function of the phage component. These systems can be encoded in specific chromosomal loci, known as defense islands, and in mobile genetic elements such as prophages and phage-inducible chromosomal islands (PICIs). Here, we identify a family of bacterial immune systems, named Tai (for ‘tail assembly inhibition’), that is prevalent in PICIs, prophages and P4-like phage satellites. Tai systems protect their bacterial host population from other phages by blocking the tail assembly step, leading to the release of tailless phages incapable of infecting new hosts. To prevent autoimmunity, some Tai-positive phages have an associated counter-defense mechanism that is expressed during the phage lytic cycle and allows for tail formation. Interestingly, the Tai defense and counter-defense genes are organized in a non-contiguous operon, enabling their coordinated expression.
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Journal articleMoratto E, Tang Z, Bozkurt T, et al., 2024,
Reduction of Phytophthora palmivora plant root infection in weak electric fields
, Scientific Reports, Vol: 14, ISSN: 2045-2322The global food security crisis is partly caused by significant crop losses due to pests and pathogens, leading to economic burdens. Phytophthora palmivora, an oomycete pathogen, affects many plantation crops and costs over USD 1 billion each year. Unfortunately, there is currently no prevention plan in place, highlighting the urgent need for an effective solution. P. palmivora produces motile zoospores that respond to weak electric fields. Here, we show that external electric fields can be used to reduce root infection in two plant species. We developed two original essays to study the effects of weak electric fields on the interaction between P. palmivora’s zoospores and roots of Arabidopsis thaliana and Medicago truncatula. In the first configuration, a global artificial electric field is set up to induce ionic currents engulfing the plant roots while, in the second configuration, ionic currents are induced only locally and at a distance from the roots. In both cases, we found that weak ionic currents (250–550 μA) are sufficient to reduce zoospore attachment to Arabidopsis and Medicago roots, without affecting plant health. Moreover, we show that the same configurations decrease P. palmivora mycelial growth in Medicago roots after 24 h. We conclude that ionic currents can reduce more than one stage of P. palmivora root infection in hydroponics. Overall, our findings suggest that weak external electric fields can be used as a sustainable strategy for preventing P. palmivora infection, providing innovative prospects for agricultural crop protection.
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Journal articleGeffen AJ, Nash RDM, Fox CJ, 2024,
How well do connectivity tools agree over the full life cycle? A case study of Irish Sea plaice <i>Pleuronectes platessa</i> Linnaeus, 1758
, JOURNAL OF FISH BIOLOGY, ISSN: 0022-1112 -
Journal articleBoyle MJW, Sharp AC, Barclay MV, et al., 2024,
Tropical beetles more sensitive to impacts are less likely to be known to science
, Current Biology, Vol: 34, Pages: R770-R771, ISSN: 0960-9822Insects are posited to be declining globally. This is particularly pertinent in tropical forests, which exhibit both the highest levels of biodiversity and the highest rates of biodiversity loss. However, for the hyper-diverse tropical insects there are scant data available to evidence declines. Understanding tropical insect diversity and its response to environmental change has therefore become a challenge, but it is estimated that 80% of tropical insect species remain undescribed1. Insect biodiversity predictions are based mostly on well-studied taxa and extrapolated to other groups, but no one knows whether resilience to environmental change varies between undescribed and described species. Here, we collected staphylinid beetles from unlogged and logged tropical forests in Borneo and investigated their responses to environmental change. Out of 252 morphospecies collected, 76% were undescribed. Undescribed species showed higher community turnover, reduced abundance and decreased probability of occurrence in logged forests. Thus the unknown components of tropical insect biodiversity are likely more impacted by human-induced environmental change. If these patterns are widespread, how accurate will assessments of insect declines in the tropics be?
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Journal articleMorales-Castilla I, Davies TJ, Legault G, et al., 2024,
Phylogenetic estimates of species-level phenology improve ecological forecasting
, NATURE CLIMATE CHANGE, ISSN: 1758-678X -
Journal articleBenucci B, Spinello Z, Calvaresi V, et al., 2024,
Neisserial adhesin A (NadA) binds human Siglec-5 and Siglec-14 with high affinity and promotes bacterial adhesion/invasion
, MBIO, Vol: 15, ISSN: 2150-7511 -
Journal articlePatin EC, Nenclares P, Hak CCW, et al., 2024,
Sculpting the tumour microenvironment by combining radiotherapy and ATR inhibition for curative-intent adjuvant immunotherapy
, NATURE COMMUNICATIONS, Vol: 15 -
Journal articleSethi S, Bick IA, Chen M-Y, et al., 2024,
Large-scale avian vocalization detection delivers reliable global biodiversity insights
, Proceedings of the National Academy of Sciences of USA, Vol: 121, ISSN: 0027-8424Tracking biodiversity and its dynamics at scale is essential if we are to solve global environmental challenges. Detecting animal vocalizations in passively recorded audio data offers an automatable, inexpensive, and taxonomically broad way to monitor biodiversity. However, the labor and expertise required to label new data and fine-tune algorithms for each deployment is a major barrier. In this study, we applied a pretrained bird vocalization detection model, BirdNET, to 152,376 h of audio comprising datasets from Norway, Taiwan, Costa Rica, and Brazil. We manually listened to a subset of detections for each species in each dataset, calibrated classification thresholds, and found precisions of over 90% for 109 of 136 species. While some species were reliably detected across multiple datasets, the performance of others was dataset specific. By filtering out unreliable detections, we could extract species and community-level insight into diel (Brazil) and seasonal (Taiwan) temporal scales, as well as landscape (Costa Rica) and national (Norway) spatial scales. Our findings demonstrate that, with relatively fast but essential local calibration, a single vocalization detection model can deliver multifaceted community and species-level insight across highly diverse datasets; unlocking the scale at which acoustic monitoring can deliver immediate applied impact.
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Journal articleGarcia YR, Marrazzo J, Martinon-Torres F, et al., 2024,
Urgent Need to Understand and Prevent Gonococcal Infection: From the Laboratory to Real-World Context
, JOURNAL OF INFECTIOUS DISEASES, Vol: 230, Pages: e758-e767, ISSN: 0022-1899 -
Journal articleHossain MB, Uchiyama Y, Rajib SA, et al., 2024,
A micro-disc-based multiplex method for monitoring emerging SARS-CoV-2 variants using the molecular diagnostic tool Intelli-OVI
, COMMUNICATIONS MEDICINE, Vol: 4, ISSN: 2730-664X -
Journal articleIliopoulou M, Bajur AT, McArthur HCW, et al., 2024,
Extracellular matrix rigidity modulates physical properties of subcapsular sinus macrophage-B cell immune synapses
, Biophysical Journal, Vol: 123, Pages: 2282-2300, ISSN: 0006-3495Subcapsular sinus macrophages (SSMs) play a key role in immune defense by forming immunological barriers that control the transport of antigens from lymph into lymph node follicles. SSMs participate in antibody responses by presenting antigens directly to naive B cells and by supplying antigens to follicular dendritic cells to propagate germinal center reactions. Despite the prominent roles that SSMs play during immune responses, little is known about their cell biology because they are technically challenging to isolate and study in vitro. Here, we used multicolor fluorescence microscopy to identify lymph node-derived SSMs in culture. We focused on the role of SSMs as antigen-presenting cells, and found that their actin cytoskeleton regulates the spatial organization and mobility of multivalent antigens (immune complexes [ICs]) displayed on the cell surface. Moreover, we determined that SSMs are mechanosensitive cells that respond to changes in extracellular matrix rigidity by altering the architecture of the actin cytoskeleton, leading to changes in cell morphology, membrane topography, and IC mobility. Changes to extracellular matrix rigidity also modulate actin remodeling by both SSMs and B cells when they form an immune synapse. This alters synapse duration but not IC internalization nor NF-κB activation in the B cell. Taken together, our data reveal that the mechanical microenvironment may influence B cell responses by modulating physical characteristics of antigen presentation by SSMs.
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Journal articleRogers J, Bajur AT, Salaita K, et al., 2024,
Mechanical control of antigen detection and discrimination by T and B cell receptors
, BIOPHYSICAL JOURNAL, Vol: 123, Pages: 2234-2255, ISSN: 0006-3495 -
Journal articleConnolly JB, Burt A, Christophides G, et al., 2024,
Publisher Correction: Considerations for first field trials of low-threshold gene drive for malaria vector control
, Malaria Journal, Vol: 23, ISSN: 1475-2875 -
Journal articleBa W, Nollet M, Yin C, et al., 2024,
A REM-active basal ganglia circuit that regulates anxiety
, Current Biology, Vol: 34, Pages: 3301-2214.E4, ISSN: 0960-9822REM sleep has been hypothesized to promote emotional resilience, but any neuronal circuits mediating this have not been identified. We find that in mice, somatostatin (Som)neurons in the entopeduncular nucleus (EP Som )/internal globus pallidus are predominantly active during REM sleep. This unique REM activity is necessary and sufficient formaintaining normal REM sleep. Inhibiting or exciting EPSom neurons reduced or increased REM sleep duration, respectively. Activation of the sole downstream target of EPSom neurons, Vglut2 cells in the lateral habenula (LHb), increased sleep via the ventral tegmental area (VTA). A simple chemogenetic scheme to periodically inhibit the LHb over 4 days selectively removed a significant amount of cumulative REM sleep. Chronic, but not acute, REM reduction correlated with mice becoming anxious and more sensitive to aversive stimuli. Therefore, we suggest that cumulative REM sleep, in part generated by the EP→LHb→VTA circuit identified here, could contribute to stabilizing reactions to habitual aversive stimuli.
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Journal articleWorboys JD, Davis DM, 2024,
Do inhibitory receptors need to be proximal to stimulatory receptors to function?
, Genes and Immunity, Vol: 25, Pages: 343-345, ISSN: 1466-4879 -
Journal articleRebuffet L, Melsen JE, Escaliere B, et al., 2024,
High-dimensional single-cell analysis of human natural killer cell heterogeneity
, Nature Immunology, Vol: 25, Pages: 1474-1488, ISSN: 1529-2908Natural killer (NK) cells are innate lymphoid cells (ILCs) contributing to immune responses to microbes and tumors. Historically, their classification hinged on a limited array of surface protein markers. Here, we used single-cell RNA sequencing (scRNA-seq) and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to dissect the heterogeneity of NK cells. We identified three prominent NK cell subsets in healthy human blood: NK1, NK2 and NK3, further differentiated into six distinct subgroups. Our findings delineate the molecular characteristics, key transcription factors, biological functions, metabolic traits and cytokine responses of each subgroup. These data also suggest two separate ontogenetic origins for NK cells, leading to divergent transcriptional trajectories. Furthermore, we analyzed the distribution of NK cell subsets in the lung, tonsils and intraepithelial lymphocytes isolated from healthy individuals and in 22 tumor types. This standardized terminology aims at fostering clarity and consistency in future research, thereby improving cross-study comparisons.
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Journal articleChik HYJ, Mannarelli M-E, Dos Remedios N, et al., 2024,
Adult telomere length is positively correlated with survival and lifetime reproductive success in a wild passerine
, Mol Ecol, Vol: 33, ISSN: 0962-1083Explaining variation in individual fitness is a key goal in evolutionary biology. Recently, telomeres, repeating DNA sequences capping chromosome ends, have gained attention as a biomarker for body state, physiological costs, and senescence. Existing research has provided mixed evidence for whether telomere length correlates with fitness, including survival and reproductive output. Moreover, few studies have examined how the rate of change in telomere length correlates with fitness in wild populations. Here, we intensively monitored an insular population of house sparrows, and collected longitudinal telomere and life history data (16 years, 1225 individuals). We tested whether telomere length and its rate of change predict fitness measures, namely survival, lifespan and annual and lifetime reproductive effort and success. Telomere length positively predicted short-term survival, independent of age, but did not predict lifespan, suggesting either a diminishing telomere length-survival correlation with age or other extrinsic factors of mortality. The positive association of telomere length with survival translated into reproductive benefits, as birds with longer telomeres produced more genetic recruits, hatchlings and reared more fledglings over their lifetime. In contrast, there was no association between telomere dynamics and annual reproductive output, suggesting telomere dynamics might not reflect the costs of reproduction in this population, potentially masked by variation in individual quality. The rate of change of telomere length did not correlate with neither lifespan nor lifetime reproductive success. Our results provide further evidence that telomere length correlates with fitness, and contribute to our understanding of the selection on, and evolution of, telomere dynamics.
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Journal articleRosenkranz M, Nkumama IN, Ogwang R, et al., 2024,
Full-length MSP1 is a major target of protective immunity after controlled human malaria infection
, Life Science Alliance, Vol: 7, ISSN: 2575-1077The merozoite surface protein 1 (MSP1) is the most abundant protein on the surface of the invasive merozoite stages of Plasmodium falciparum and has long been considered a key target of protective immunity. We used samples from a single controlled human malaria challenge study to test whether the full-length version of MSP1 (MSP1FL) induced antibodies that mediated Fc-IgG functional activity in five independent assays. We found that anti-MSP1FL antibodies induced complement fixation via C1q, monocyte-mediated phagocytosis, neutrophil respiratory burst, and natural killer cell degranulation as well as IFNγ production. Activity in each of these assays was strongly associated with protection. The breadth of MSP1-specific Fc-mediated effector functions was more strongly associated with protection than the individual measures and closely mirrored what we have previously reported using the same assays against merozoites. Our findings suggest that MSP1FL is an important target of functional antibodies that contribute to a protective immune response against malaria.
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Journal articleSasidharan S, Davis DM, Dunlop IE, 2024,
Bioinspired Materials for Immunoengineering of T Cells and Natural Killer Cells
, ADVANCED FUNCTIONAL MATERIALS, Vol: 34, ISSN: 1616-301X -
Journal articleJaillais Y, Bayer E, Bergmann DC, et al., 2024,
Guidelines for naming and studying plasma membrane domains in plants
, NATURE PLANTS, Vol: 10, Pages: 1172-1183, ISSN: 2055-026X -
Journal articleKabasakal BV, McFarlane CR, Cotton CAR, et al., 2024,
The crystal structure of Shethna protein II (FeSII) from <i>Azotobacter vinelandii</i> suggests a domain swap
, ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, Vol: 80, Pages: 599-604, ISSN: 2059-7983 -
Journal articleDarby AM, Okoro DO, Aredas S, et al., 2024,
High sugar diets can increase susceptibility to bacterial infection in Drosophila melanogaster
, PLoS Pathogens, Vol: 20, ISSN: 1553-7366Overnutrition with dietary sugar can worsen infection outcomes in diverse organisms including insects and humans, through generally unknown mechanisms. In the present study, we show that adult Drosophila melanogaster fed high-sugar diets became more susceptible to infection by the Gram-negative bacteria Providencia rettgeri and Serratia marcescens. We found that P. rettgeri and S. marcescens proliferate more rapidly in D. melanogaster fed a high-sugar diet, resulting in increased probability of host death. D. melanogaster become hyperglycemic on the high-sugar diet, and we find evidence that the extra carbon availability may promote S. marcescens growth within the host. However, we found no evidence that increased carbon availability directly supports greater P. rettgeri growth. D. melanogaster on both diets fully induce transcription of antimicrobial peptide (AMP) genes in response to infection, but D. melanogaster provided with high-sugar diets show reduced production of AMP protein. Thus, overnutrition with dietary sugar may impair host immunity at the level of AMP translation. Our results demonstrate that dietary sugar can shape infection dynamics by impacting both host and pathogen, depending on the nutritional requirements of the pathogen and by altering the physiological capacity of the host to sustain an immune response.
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Journal articleMansfield M, Roviello G, Thacker M, et al., 2024,
The association between conditioned pain modulation and psychological factors in people with chronic spinal pain: A systematic review
, British Journal of Pain, Vol: 18, Pages: 314-324, ISSN: 2049-4637<jats:p> Chronic spinal pain has negative effects on physical and mental well-being. Psychological factors can influence pain tolerance. However, whether these factors influence descending modulatory control mechanisms measured by conditioned pain modulation (CPM) in people with chronic spinal pain is unclear. This systematic review investigated the association between CPM response and psychological factors in people with chronic spinal pain. Published and unpublished literature databases were searched from inception to 23rd October 2023 included MEDLINE, EMBASE, CINAHL, and PubMed. Studies assessing the association between CPM response and psychological factors in people with chronic spinal pain were eligible. Data were pooled through meta-analysis. Methodological quality was assessed using the AXIS tool and the certainty of evidence measured through GRADE. From 2172 records, seven studies ( n = 598) were eligible. Quality of included studies was moderate. There was very low certainty of evidence that depression ( r = 0.01 [95% CI −0.10 to 0.12], I<jats:sup>2</jats:sup> = 0%), and anxiety ( r = −0.20 [95% CI −0.56 to 0.16], I<jats:sup>2</jats:sup> = 84%), fear avoidance ( r = −0.10 [95% CI −0.30 to 0.10], I<jats:sup>2</jats:sup> = 70%) had no statistical associations with CPM responder status. Higher pain catastrophising was associated with CPM non-responder status (r = −0.19; 95% CI: −0.37 to −0.02; n = 545; I2: 76%) based on a very low certainty of evidence measured by GRADE. There is currently limited available evidence demonstrating an association between CPM response and psychological factors for people with chronic pain. Managing an individual’s chronic pain symptoms irrespective of comorbid psychological distress, should continue until evidence offer insights that more targeted interventions are needed. </jats:p>
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Journal articleHuisman D, Fernhout F, Moxham F, et al., 2024,
Managing patients’ reports of abdominal pain and irritable bowel syndrome-like symptoms during quiescent inflammatory bowel disease: a role for shared sensemaking
, British Journal of Pain, Vol: 18, Pages: 325-336, ISSN: 2049-4637<jats:sec><jats:title>Background</jats:title><jats:p> Patients with inflammatory bowel disease (IBD) are often faced with distressing and confusing abdominal pain during remission. Some people respond adversely to healthcare professionals’ (HCPs) suggestions that this pain and related symptoms are due to secondary irritable bowel syndrome (IBS). Exploring how HCPs view, manage, and explain pain during quiescent disease may provide insights into how communication can be improved to increase understanding and mitigate negative responses. </jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p> In-depth semi-structured interviews were conducted with 12 IBD-nurses ( n = 4) and gastroenterologists ( n = 8) working in the United Kingdom or the Netherlands. Reflexive thematic analysis was used to analyse interviews. </jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p> Findings suggest that HCPs pay relatively little attention to pain when there is no underlying pathology and prefer to concentrate on objectifiable causes of symptoms and treating disease activity ( Theme 1: Focus on disease activity, not pain and associated symptoms). Explanations of abdominal pain and IBS-like symptoms during remission were not standardised ( Theme 2: Idiosyncratic and uncertain explanations for pain during remission). Processes of shared decision-making were outlined and shared sensemaking was reported as a strategy to enhance acceptance of IBS explanations ( Theme 3: Shared decision making versus shared sensemaking). </jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p> Future work should focus on establishing how pain during remission may be best defined, when to diagnose IBS in the context of IBD, and how to explain both to patients. The formulation of standardised explanations is recommended as they
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Journal articleSchlenker P, Salis A, Leroux M, et al., 2024,
Minimal Compositionality versus Bird Implicatures: two theories of ABC-D sequences in Japanese tits.
, Biol Rev Camb Philos Soc, Vol: 99, Pages: 1278-1297It was argued in a series of experimental studies that Japanese tits (Parus minor) have an ABC call that has an alert function, a D call that has a recruitment function, and an ABC-D call that is compositionally derived from ABC and D, and has a mobbing function. A key conclusion was that ABC-D differs from the combination of separate utterances of ABC and of D (e.g. as played by distinct but close loudspeakers). While the logic of the argument is arguably sound, no explicit rule has been proposed to derive the meaning of ABC-D from that of its parts. We compare two analyses. One posits a limited instance of semantic compositionality ('Minimal Compositionality'); the other does without compositionality, but uses instead a more sophisticated pragmatics ('Bird Implicatures'). Minimal Compositionality takes the composition of ABC and D to deviate only minimally from what would be found with two independent utterances: ABC means that 'there is something that licenses an alert', D means that 'there is something that licenses recruitment', and ABC-D means that 'there is something that licenses both an alert and recruitment'. By contrast, ABC and D as independent utterances yield something weaker, namely: 'there is something that licenses an alert, and there is something that licenses recruitment', without any 'binding' across the two utterances. The second theory, Bird Implicatures, only requires that ABC-D should be more informative than ABC, and/or than D. It builds on the idea, proposed for several monkey species, that a less-informative call competes with a more informative one (the 'Informativity Principle'): when produced alone, ABC and D trigger an inference that ABC-D is false. We explain how both Minimal Compositionality and Bird Implicatures could have evolved, and we compare the predictions of the two theories. Finally, we extend the discussion to some chimpanzee and meerkat sequences that might raise related theoretical problems.
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Book chapterGrob A, Enrico Bena C, Redwood-Sawyerr C, et al., 2024,
Simultaneous plate-reader characterization of promoter activity and cell growth in engineered mammalian cells
, Synthetic Promoters Methods and Protocols, Editors: Marchisio, Publisher: Humana, Pages: 85-96, ISBN: 9781071640623Automated high-throughput methods that support tracking of mammalian cell growth are currently needed to advance cell line characterization and identification of desired genetic components required for cell engineering. Here, we describe a high-throughput noninvasive assay based on plate reader measurements. The assay relies on the change in absorbance of the pH indicator phenol red. We show that its basic and acidic absorbance profiles can be converted into a cell growth index consistent with cell count profiles, and that, by adopting a computational pipeline and calibration measurements, it is possible to identify a conversion that enables prediction of cell numbers from plate measurements alone. The assay is suitable for growth characterization of both suspension and adherent cell lines when these are grown under different environmental conditions and treated with chemotherapeutic drugs. The method also supports characterization of stably engineered cell lines and identification of desired promoters based on fluorescence output.
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Journal articleRutter JW, Dekker L, Clare C, et al., 2024,
A bacteriocin expression platform for targeting pathogenic bacterial species
, NATURE COMMUNICATIONS, Vol: 15 -
Journal articleArmstrong E, Chiu MKL, Foo S, et al., 2024,
Combination of oncolytic Maraba virus with immune checkpoint blockade overcomes therapy resistance in an immunologically cold model of advanced melanoma with dysfunctional T-cell receptor signalling
, JOURNAL FOR IMMUNOTHERAPY OF CANCER, Vol: 12, Pages: 1-16 -
Journal articleGauci V, Pangala SR, Shenkin A, et al., 2024,
Global atmospheric methane uptake by upland tree woody surfaces
, Nature, Vol: 631, Pages: 796-800, ISSN: 0028-0836<jats:title>Abstract</jats:title><jats:p>Methane is an important greenhouse gas<jats:sup>1</jats:sup>, but the role of trees in the methane budget remains uncertain<jats:sup>2</jats:sup>. Although it has been shown that wetland and some upland trees can emit soil-derived methane at the stem base<jats:sup>3,4</jats:sup>, it has also been suggested that upland trees can serve as a net sink for atmospheric methane<jats:sup>5,6</jats:sup>. Here we examine in situ woody surface methane exchange of upland tropical, temperate and boreal forest trees. We find that methane uptake on woody surfaces, in particular at and above about 2 m above the forest floor, can dominate the net ecosystem contribution of trees, resulting in a net tree methane sink. Stable carbon isotope measurement of methane in woody surface chamber air and process-level investigations on extracted wood cores are consistent with methanotrophy, suggesting a microbially mediated drawdown of methane on and in tree woody surfaces and tissues. By applying terrestrial laser scanning-derived allometry to quantify global forest tree woody surface area, a preliminary first estimate suggests that trees may contribute 24.6–49.9 Tg of atmospheric methane uptake globally. Our findings indicate that the climate benefits of tropical and temperate forest protection and reforestation may be greater than previously assumed.</jats:p>
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