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Abstract Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.
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Imaging genomics is a rapidly evolving field that combines state-of-the-art bioimaging with genomic information to resolve phenotypic heterogeneity associated with genomic variation, improve risk prediction, discover prevention approaches, and enable precision diagnosis and treatment. Contemporary bioimaging methods provide exceptional resolution generating discrete and quantitative high-dimensional phenotypes for genomics investigation. Despite substantial progress in combining high-dimensional bioimaging and genomic data, methods for imaging genomics are evolving. Recognizing the potential impact of imaging genomics on the study of heart and lung disease, the National Heart, Lung, and Blood Institute convened a workshop to review cutting-edge approaches and methodologies in imaging genomics studies, and to establish research priorities for future investigation. This report summarizes the presentations and discussions at the workshop. In particular, we highlight the need for increased availability of imaging genomics data in diverse populations, dedicated focus on less common conditions, and centralization of efforts around specific disease areas.more » « less
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null (Ed.)Disturbances fundamentally alter ecosystem functions, yet predicting their impacts remains a key scientific challenge. While the study of disturbances is ubiquitous across many ecological disciplines, there is no agreed-upon, cross-disciplinary foundation for discussing or quantifying the complexity of disturbances, and no consistent terminology or methodologies exist. This inconsistency presents an increasingly urgent challenge due to accelerating global change and the threat of interacting disturbances that can destabilize ecosystem responses. By harvesting the expertise of an interdisciplinary cohort of contributors spanning 42 institutions across 15 countries, we identified an essential limitation in disturbance ecology: the word ‘disturbance’ is used interchangeably to refer to both the events that cause, and the consequences of, ecological change, despite fundamental distinctions between the two meanings. In response, we developed a generalizable framework of ecosystem disturbances, providing a well-defined lexicon for understanding disturbances across perspectives and scales. The framework results from ideas that resonate across multiple scientific disciplines and provides a baseline standard to compare disturbances across fields. This framework can be supplemented by discipline-specific variables to provide maximum benefit to both inter- and intra-disciplinary research. To support future syntheses and meta-analyses of disturbance research, we also encourage researchers to be explicit in how they define disturbance drivers and impacts, and we recommend minimum reporting standards that are applicable regardless of scale. Finally, we discuss the primary factors we considered when developing a baseline framework and propose four future directions to advance our interdisciplinary understanding of disturbances and their social-ecological impacts: integrating across ecological scales, understanding disturbance interactions, establishing baselines and trajectories, and developing process-based models and ecological forecasting initiatives. Our experience through this process motivates us to encourage the wider scientific community to continue to explore new approaches for leveraging Open Science principles in generating creative and multidisciplinary ideas.more » « less
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Abstract Clouds can modify terrestrial productivity by reducing total surface radiation and increasing diffuse radiation, which may be more evenly distributed through plant canopies and increase ecosystem carbon uptake (the “diffuse fertilization effect”). Previous work at ecosystem-level observational towers demonstrated that diffuse photosynthetically active radiation (PAR; 400–700 nm) increases with cloud optical thickness (COT) until a COT of approximately 10, defined here as the “low-COT regime.” To identify whether the low-COT regime also influences carbon uptake on broader spatial and longer temporal time scales, we use global, monthly data to investigate the influence of COT on carbon uptake in three land-cover types: shrublands, forests, and croplands. While there are limitations in global gross primary production (GPP) products, global COT data derived from Moderate Resolution Imaging Spectroradiometer (MODIS) reveal that during the growing season tropical and subtropical regions more frequently experience a monthly low-COT regime (>20% of the time) than other regions of the globe. Contrary to ecosystem-level studies, comparisons of monthly COT with monthly satellite-derived solar-induced chlorophyll fluorescence and modeled GPP indicate that, although carbon uptake generally increases with COT under the low-COT regime, the correlations between COT and carbon uptake are insignificant (p > 0.05) in shrublands, forests, and croplands at regional scales. When scaled globally, vegetated regions under the low-COT regime account for only 4.9% of global mean annual GPP, suggesting that clouds and their diffuse fertilization effect become less significant drivers of terrestrial carbon uptake at broader spatial and temporal scales.