Genome BiologyPub Date : 2025-06-04DOI: 10.1186/s13059-025-03627-1
Colm Doyle, Krzysztof Herka, Sean M. Flynn, Larry Melidis, Somdutta Dhir, Stefan Schoenfelder, David Tannahill, Shankar Balasubramanian
{"title":"DNA G-quadruplex structures act as functional elements in α- and β-globin enhancers","authors":"Colm Doyle, Krzysztof Herka, Sean M. Flynn, Larry Melidis, Somdutta Dhir, Stefan Schoenfelder, David Tannahill, Shankar Balasubramanian","doi":"10.1186/s13059-025-03627-1","DOIUrl":"https://doi.org/10.1186/s13059-025-03627-1","url":null,"abstract":"Enhancer elements interact with target genes at a distance to modulate their expression, but the molecular details of enhancer–promoter interaction are incompletely understood. G-quadruplex DNA secondary structures (G4s) have recently been shown to co-occur with 3D chromatin interactions; however, the functional importance of G4s within enhancers remains unclear. In this study, we identify novel G4 structures within two locus control regions at the human α- and β-globin loci. We find that mutating G4 motifs by genome editing prevents their folding into G4 structures in cells and disrupts 3D enhancer–promoter interactions and target gene expression in a manner comparable to whole enhancer deletion. Furthermore, restoration of G4 structure formation using a dissimilar G4-forming primary sequence recovers specific enhancer-gene interactions and gene expression. Through proteomic, biophysical, and genomic profiling, we find that enhancer G4s are tightly linked to the maintenance of an active chromatin state and RNA polymerase II recruitment to regulate target gene expression. Our study shows that folded G4 structures can act as functional elements that mediate 3D enhancer–promoter interactions to support enhancer-driven globin gene regulation.\u0000","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"16 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144211028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-06-04DOI: 10.1186/s13059-025-03619-1
Runjia Li, Jason Ernst
{"title":"Identifying associations of de novo noncoding variants with autism through integration of gene expression, sequence, and sex information","authors":"Runjia Li, Jason Ernst","doi":"10.1186/s13059-025-03619-1","DOIUrl":"https://doi.org/10.1186/s13059-025-03619-1","url":null,"abstract":"Whole-genome sequencing (WGS) data has facilitated genome-wide identification of rare noncoding variants. However, elucidating these variants’ associations with complex diseases remains challenging. A previous study utilized a deep-learning-based framework and reported a significant brain-related association signal of autism spectrum disorder (ASD) detected from de novo noncoding variants in the Simons Simplex Collection (SSC) WGS cohort. We revisit the reported significant brain-related ASD association signal attributed to deep-learning and show that local GC content can capture similar association signals. We further show that the association signal appears driven by variants from male proband-female sibling pairs that are upstream of assigned genes. We then develop Expression Neighborhood Sequence Association Study (ENSAS), which utilizes gene expression correlations and sequence information, to more systematically identify phenotype-associated variant sets. Applying ENSAS to the same set of de novo variants, we identify gene expression-based neighborhoods showing significant ASD association signal, enriched for synapse-related gene ontology terms. For these top neighborhoods, we also identify chromatin state annotations of variants that are predictive of the proband-sibling local GC content differences. Overall, our work simplifies a previously reported ASD signal and provides new insights into associations of noncoding de novo mutations in ASD. We also present a new analytical framework for understanding disease impact of de novo mutations, applicable to other phenotypes.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"53 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144211027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-06-03DOI: 10.1186/s13059-025-03623-5
Natalia Martin-Martin, Saioa Garcia-Longarte, Jon Corres-Mendizabal, Uxue Lazcano, Ianire Astobiza, Laura Bozal-Basterra, Nicolas Herranz, Hielke van Splunder, Onintza Carlevaris, Mikel Pujana-Vaquerizo, María Teresa Blasco, Ana M. Aransay, Antonio Rosino, Julian Tudela, Daniel Jimenez, Alberto Martinez, Andrei Salca, Aida Santos-Martín, Sofía Rey, Aitziber Ugalde-Olano, David Gonzalo, Mariona Graupera, Roger R. Gomis, Joaquin Mateo, Miguel Unda, Enrique Gonzalez-Billalabeitia, Ana Loizaga-Iriarte, Isabel Mendizabal, Arkaitz Carracedo
{"title":"Transcriptional analysis of metastatic hormone-naïve prostate cancer primary tumor biopsies reveals a relevant role for SOX11 in prostate cancer cell dissemination","authors":"Natalia Martin-Martin, Saioa Garcia-Longarte, Jon Corres-Mendizabal, Uxue Lazcano, Ianire Astobiza, Laura Bozal-Basterra, Nicolas Herranz, Hielke van Splunder, Onintza Carlevaris, Mikel Pujana-Vaquerizo, María Teresa Blasco, Ana M. Aransay, Antonio Rosino, Julian Tudela, Daniel Jimenez, Alberto Martinez, Andrei Salca, Aida Santos-Martín, Sofía Rey, Aitziber Ugalde-Olano, David Gonzalo, Mariona Graupera, Roger R. Gomis, Joaquin Mateo, Miguel Unda, Enrique Gonzalez-Billalabeitia, Ana Loizaga-Iriarte, Isabel Mendizabal, Arkaitz Carracedo","doi":"10.1186/s13059-025-03623-5","DOIUrl":"https://doi.org/10.1186/s13059-025-03623-5","url":null,"abstract":"Metastatic hormone-naïve prostate cancer (mHNPC) is an infrequent form of this tumor type that is characterized by metastasis at the time of diagnosis and accounts for up to 50% of prostate cancer-related deaths. Despite the extensive characterization of localized and metastatic castration-resistant prostate cancer, the molecular characteristics of mHNPC remain largely unexplored. Here, we provide the first extensive transcriptomics characterization of primary tumor specimens from patients with mHNPC. We generate discovery and validation bulk and single-cell RNA-seq datasets and perform integrative computational analysis in combination with experimental studies. Our results provide unprecedented evidence of the distinctive transcriptional profile of mHNPC and identify stroma remodeling as a predominant feature of these tumors. Importantly, we discover a central role for the SRY-box transcription factor 11 (SOX11) in triggering a heterotypic communication that is associated with the acquisition of metastatic properties. Our study will constitute an invaluable resource for a profound understanding of mHNPC that can influence patient management.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"12 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144201901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-06-03DOI: 10.1186/s13059-025-03631-5
Shuli Sun, Jixin Liu, Guojun Li, Bingqiang Liu
{"title":"DeepGFT: identifying spatial domains in spatial transcriptomics of complex and 3D tissue using deep learning and graph Fourier transform","authors":"Shuli Sun, Jixin Liu, Guojun Li, Bingqiang Liu","doi":"10.1186/s13059-025-03631-5","DOIUrl":"https://doi.org/10.1186/s13059-025-03631-5","url":null,"abstract":"The rapid advancements in spatially resolved transcriptomics (SRT) enable the characterization of gene expressions while preserving spatial information. However, high dropout rates and noise hinder accurate spatial domain identification for understanding tissue architecture. We present DeepGFT, a method that simultaneously models spot-wise and gene-wise relationships by integrating deep learning with graph Fourier transform for spatial domain identification. Benchmarking results demonstrate the superiority of DeepGFT over existing methods. DeepGFT detects tumor substructures with immune-related differences in human breast cancer, identifies the complex germinal centers accurately in human lymph node, and accurately reveals the developmental changes in 3D Drosophila data.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"43 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144201902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-06-03DOI: 10.1186/s13059-025-03616-4
Mengnan Shi, Loren Méar, Max Karlsson, María Bueno Álvez, Andreas Digre, Rutger Schutten, Borbala Katona, Jimmy Vuu, Emil Lindström, Feria Hikmet, Han Jin, Meng Yuan, Xiangyu Li, Hong Yang, Xiya Song, Evelina Sjöstedt, Fredrik Edfors, Per Oksvold, Kalle von Feilitzen, Martin Zwahlen, Mattias Forsberg, Fredric Johansson, Jan Mulder, Tomas Hökfelt, Yonglun Luo, Lynn Butler, Wen Zhong, Adil Mardinoglu, Åsa Sivertsson, Fredrik Ponten, Linn Fagerberg, Cecilia Lindskog, Mathias Uhlén, Cheng Zhang
{"title":"A resource for whole-body gene expression map of human tissues based on integration of single cell and bulk transcriptomics","authors":"Mengnan Shi, Loren Méar, Max Karlsson, María Bueno Álvez, Andreas Digre, Rutger Schutten, Borbala Katona, Jimmy Vuu, Emil Lindström, Feria Hikmet, Han Jin, Meng Yuan, Xiangyu Li, Hong Yang, Xiya Song, Evelina Sjöstedt, Fredrik Edfors, Per Oksvold, Kalle von Feilitzen, Martin Zwahlen, Mattias Forsberg, Fredric Johansson, Jan Mulder, Tomas Hökfelt, Yonglun Luo, Lynn Butler, Wen Zhong, Adil Mardinoglu, Åsa Sivertsson, Fredrik Ponten, Linn Fagerberg, Cecilia Lindskog, Mathias Uhlén, Cheng Zhang","doi":"10.1186/s13059-025-03616-4","DOIUrl":"https://doi.org/10.1186/s13059-025-03616-4","url":null,"abstract":"New technologies enable single-cell transcriptome analysis, mapping genome-wide expression across the human body. Here, we present an extended analysis of protein-coding genes in all major human tissues and organs, combining single-cell and bulk transcriptomics. To enhance transcriptome depth, 31 tissues were analyzed using a pooling method, identifying 557 unique cell clusters, manually annotated by marker gene expression. Genes were classified by body-wide expression and validated through antibody-based profiling. All results are available in the updated open-access Single Cell Type section of the Human Protein Atlas for genome-wide exploration of genes, proteins, and their spatial distribution in cells.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"26 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144201903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-06-03DOI: 10.1186/s13059-025-03632-4
Shangqian Xie, Darren Hagen, Gabrielle M. Becker, Kimberly M. Davenport, Katie A. Shira, Morgan R. Stegemiller, Jacob W. Thorne, Sarem Khilji, Denise Konetchy, Patricia Villamediana, Brenda M. Murdoch, Stephanie D. McKay
{"title":"Publisher Correction: Analyzing the relationship of RNA and DNA methylation with gene expression","authors":"Shangqian Xie, Darren Hagen, Gabrielle M. Becker, Kimberly M. Davenport, Katie A. Shira, Morgan R. Stegemiller, Jacob W. Thorne, Sarem Khilji, Denise Konetchy, Patricia Villamediana, Brenda M. Murdoch, Stephanie D. McKay","doi":"10.1186/s13059-025-03632-4","DOIUrl":"https://doi.org/10.1186/s13059-025-03632-4","url":null,"abstract":"<p><b>Publisher Correction</b><b>: </b><b>Genome Biol 26, 140 (2025)</b></p><p><b>https://doi.org/10.1186/s13059-025-03617-3</b></p><br/><p>Following publication of the original article [1], the authors identified typesetting error, whereby the Jaccard index has a subset 1 in the numerator, however the absolute value bars were missing in the denominator.</p><p>Incorrect index:</p><p>Jaccard index = <span>(frac{left|{G}_{1}bigcap {G}_{j}right|}{{G}_{i}bigcup {G}_{j}})</span></p><p>Correct index:</p><p>Jaccard index = <span>(frac{left|{G}_{i}bigcap {G}_{j}right|}{left|{G}_{i}bigcup {G}_{j}right|})</span></p><p>The original article [1] has been corrected.</p><ol data-track-component=\"outbound reference\" data-track-context=\"references section\"><li data-counter=\"1.\"><p>Xie S, Hagen D, Becker GM, et al. Analyzing the relationship of RNA and DNA methylation with gene expression. Genome Biol. 2025;26:140. https://doi.org/10.1186/s13059-025-03617-3.</p><p>Article CAS PubMed PubMed Central Google Scholar </p></li></ol><p>Download references<svg aria-hidden=\"true\" focusable=\"false\" height=\"16\" role=\"img\" width=\"16\"><use xlink:href=\"#icon-eds-i-download-medium\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"></use></svg></p><h3>Authors and Affiliations</h3><ol><li><p>Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, 83844, USA</p><p>Shangqian Xie, Gabrielle M. Becker, Katie A. Shira, Morgan R. Stegemiller, Jacob W. Thorne, Sarem Khilji, Denise Konetchy, Patricia Villamediana & Brenda M. Murdoch</p></li><li><p>Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, 74078, USA</p><p>Darren Hagen</p></li><li><p>Department of Animal Sciences, Washington State University, Pullman, WA, 99164, USA</p><p>Kimberly M. Davenport</p></li><li><p>Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA</p><p>Stephanie D. McKay</p></li></ol><span>Authors</span><ol><li><span>Shangqian Xie</span>View author publications<p><span>You can also search for this author in</span><span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Darren Hagen</span>View author publications<p><span>You can also search for this author in</span><span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Gabrielle M. Becker</span>View author publications<p><span>You can also search for this author in</span><span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Kimberly M. Davenport</span>View author publications<p><span>You can also search for this author in</span><span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Katie A. Shira</span>View author publications<p><span>You can also search for this author in</span><span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Morgan R. Stegemiller</span>View author publications<p><span>You can also search for this author in</span><span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Jacob W. Thorne</span>View autho","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"53 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144201904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-06-02DOI: 10.1186/s13059-025-03618-2
Pu Wang, Hong Zhang, Yongli Yin, Yue Ge, Binrui Chen, Jing Hu, Yu Wang, Dejiang Ni, Fei Guo
{"title":"Differential epigenetic regulation by blue and UV-A light reveals the key role of CsSDG36-mediated H3K4 methylation in leaf development and secondary metabolism in Camellia sinensis","authors":"Pu Wang, Hong Zhang, Yongli Yin, Yue Ge, Binrui Chen, Jing Hu, Yu Wang, Dejiang Ni, Fei Guo","doi":"10.1186/s13059-025-03618-2","DOIUrl":"https://doi.org/10.1186/s13059-025-03618-2","url":null,"abstract":"There is a Chinese proverb that good tea comes from high mountains with clouds and mists, suggesting the important impact of environmental factors on the development and secondary metabolism in tea plants. However, the epigenetic mechanism involved is still unclear. High altitude results in light enhancement with a higher retention of short-wavelength light in cloudy conditions, suggesting the key role of short-wavelength light in the quality formation of tea plants. Thus, we focus on the representative short-wavelength light, blue and UV-A, and characterize plant responses in epigenome, transcriptome, leaf development, and metabolome. We profile six histone modifications under different light wavelengths and link these to leaf development and secondary metabolism, including changes in gene expression during flavonoid, theanine, caffeine, and β-carotene biosynthesis. There is higher stomatal density and thicker mesophyll tissues under blue light, with higher levels of chlorophyll components under UV-A light. The epigenome results in differential changes of stomatal density and quality components in different light conditions. We further identify crucial histone modifications in leaf development and secondary metabolism. Functional analyses suggest diverse regulations mediated by cryptochrome and phototropin in light adaptation, and we confirm the important role of CsSDG36-mediated histone H3K4 methylation. Our results not only reveal the landscape of histone modifications, transcripts, leaf development, and metabolites from different lights in tea plants, but also provide insight into the roles of photoreceptors and epigenetic mechanisms involved in leaf development and secondary metabolism.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"29 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144193323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-06-02DOI: 10.1186/s13059-025-03601-x
Yi Wang, Kyla Woyshner, Chaichontat Sriworarat, Genevieve Stein-O’Brien, Loyal A. Goff, Kasper D. Hansen
{"title":"mNSF: multi-sample non-negative spatial factorization","authors":"Yi Wang, Kyla Woyshner, Chaichontat Sriworarat, Genevieve Stein-O’Brien, Loyal A. Goff, Kasper D. Hansen","doi":"10.1186/s13059-025-03601-x","DOIUrl":"https://doi.org/10.1186/s13059-025-03601-x","url":null,"abstract":"Analyzing multi-sample spatial transcriptomics data requires accounting for biological variation. We present multi-sample non-negative spatial factorization (mNSF), an alignment-free framework extending single-sample spatial factorization to multi-sample datasets. mNSF incorporates sample-specific spatial correlation modeling and extracts low-dimensional data representations. Through simulations and real data analysis, we demonstrate mNSF’s efficacy in identifying true factors, shared anatomical regions, and region-specific biological functions. mNSF’s performance is comparable to alignment-based methods when alignment is feasible, while enabling analysis in scenarios where spatial alignment is unfeasible. mNSF shows promise as a robust method for analyzing spatially resolved transcriptomics data across multiple samples.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"9 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144193324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-06-01DOI: 10.1186/s13059-025-03621-7
Davide Francioli, Ioannis D. Kampouris, Theresa Kuhl-Nagel, Doreen Babin, Loreen Sommermann, Jan H. Behr, Soumitra Paul Chowdhury, Rita Zrenner, Narges Moradtalab, Michael Schloter, Joerg Geistlinger, Uwe Ludewig, Günter Neumann, Kornelia Smalla, Rita Grosch
{"title":"Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale","authors":"Davide Francioli, Ioannis D. Kampouris, Theresa Kuhl-Nagel, Doreen Babin, Loreen Sommermann, Jan H. Behr, Soumitra Paul Chowdhury, Rita Zrenner, Narges Moradtalab, Michael Schloter, Joerg Geistlinger, Uwe Ludewig, Günter Neumann, Kornelia Smalla, Rita Grosch","doi":"10.1186/s13059-025-03621-7","DOIUrl":"https://doi.org/10.1186/s13059-025-03621-7","url":null,"abstract":"Field inoculation of crops with beneficial microbes is a promising sustainable strategy to enhance plant fitness and nutrient acquisition. However, effectiveness can vary due to environmental factors, microbial competition, and methodological challenges, while their precise modes of action remain uncertain. This underscores the need for further research to optimize inoculation strategies for consistent agricultural benefits. Using a comprehensive, multidisciplinary approach, we investigate the effects of a consortium of beneficial microbes (BMc) (Pseudomonas sp. RU47, Bacillus atrophaeus ABi03, Trichoderma harzianum OMG16) on maize (Zea mays cv. Benedictio) through an inoculation experiment conducted within a long-term field trial across intensive and extensive farming practices. Additionally, an unexpected early drought stress emerged as a climatic variable, offering further insight into the effectiveness of the microbial consortium. Our findings demonstrate that BMc root inoculation primarily enhanced plant growth and fitness, particularly by increasing iron uptake, which is crucial for drought adaptation. Inoculated maize plants show improved shoot growth and fitness compared to non-inoculated plants, regardless of farming practices. Specifically, BMc modulate plant hormonal balance, enhance the detoxification of reactive oxygen species, and increase root exudation of iron-chelating metabolites. Amplicon sequencing reveals shifts in rhizosphere bacterial and fungal communities mediated by the consortium. Metagenomic shotgun sequencing indicates enrichment of genes related to antimicrobial lipopeptides and siderophores. Our findings highlight the multifaceted benefits of BMc inoculation on plant fitness, significantly influencing metabolism, stress responses, and the rhizosphere microbiome. These improvements are crucial for advancing sustainable agricultural practices by enhancing plant resilience and productivity.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"5 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144193325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genome BiologyPub Date : 2025-05-28DOI: 10.1186/s13059-025-03597-4
Udita Chandola, Marinna Gaudin, Camille Trottier, Louis-Josselin Lavier-Aydat, Eric Manirakiza, Samuel Menicot, Erik Jörg Fischer, Isabelle Louvet, Thomas Lacour, Timothée Chaumier, Atsuko Tanaka, Georg Pohnert, Samuel Chaffron, Leïla Tirichine
{"title":"Non-cyanobacterial diazotrophs support the survival of marine microalgae in nitrogen-depleted environment","authors":"Udita Chandola, Marinna Gaudin, Camille Trottier, Louis-Josselin Lavier-Aydat, Eric Manirakiza, Samuel Menicot, Erik Jörg Fischer, Isabelle Louvet, Thomas Lacour, Timothée Chaumier, Atsuko Tanaka, Georg Pohnert, Samuel Chaffron, Leïla Tirichine","doi":"10.1186/s13059-025-03597-4","DOIUrl":"https://doi.org/10.1186/s13059-025-03597-4","url":null,"abstract":"Non-cyanobacteria diazotrophs (NCDs) are shown to dominate in surface waters shifting the long-held paradigm of cyanobacteria dominance. This raises fundamental questions on how these putative heterotrophic bacteria thrive in sunlit oceans. The absence of laboratory cultures of these bacteria significantly limits our ability to understand their behavior in natural environments and, consequently, their contribution to the marine nitrogen cycle. Here, via a multidisciplinary approach, we identify the presence of NCDs within the phycosphere of the model diatom Phaeodactylum tricornutum (Pt), which sustain the survival of Pt in nitrogen-depleted conditions. Through bacterial metacommunity sequencing and genome assembly, we identify multiple NCDs belonging to the Rhizobiales order, including Bradyrhizobium, Mesorhizobium, Georhizobium, and Methylobacterium. We demonstrate the nitrogen-fixing ability of PtNCDs through in silico identification of nitrogen fixation genes and by other experimental assays. We show the wide occurrence of this type of interactions with the isolation of NCDs from other microalgae, their identification in the environment, and their predicted associations with photosynthetic microalgae. Our study underscores the importance of microalgae interactions with NCDs to support nitrogen fixation. This work provides a unique model Pt-NCDs to study the ecology of this interaction, advancing our understanding of the key drivers of global marine nitrogen fixation.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"25 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144153634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}