Latest Publications
Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus
Joshua Cole, Sébastien Raguideau, Payman Abbaszadeh-Dahaji, Sally Hilton, George Muscatt, Ryan M. Mushinski, R. Henrik Nilsson, Megan H. Ryan, Christopher Quince, Gary D. Bending
Background: Recent evidence shows that arbuscular mycorrhizal (AM) symbiosis, as defined by the presence of arbuscules, is established by two distinct fungal groups, with the distinctive ‘fine root endophyte’ morphotype formed by fungi from the subphylum Mucoromycotina rather than the sub-phylum Glomeromycotina. While FRE forming fungi are globally distributed, there is currently no understanding of the genomic basis for their symbiosis or how this symbiosis compares to that of other mycorrhizal symbionts.
Results: We used culture-independent metagenome sequencing to assemble and characterise the metagenome-assembled genome (MAG) of a putative arbuscule forming fine root endophyte, which we show belonged to the family Planticonsortiaceae within the order Densosporales. The MAG shares key traits with Glomeromycotina fungi, which indicate obligate biotrophy, including the absence of fatty acid and thiamine biosynthesis pathways, limited enzymatic abilities to degrade plant cell walls, and a high abundance of calcium transporters. In contrast to Glomeromycotina fungi, it exhibits a higher capacity for degradation of microbial cell walls, a complete cellulose degradation pathway, low abundances of copper, nitrate and ammonium transporters, and a complete pathway for vitamin B6 biosynthesis.
Conclusion: These differences, particularly those typically associated with saprotrophic functions, highlight the potential for contrasting interactions between Mucoromycotina and Glomeromycotina fungi with their host plant and the environment. In turn, this could support niche differentiation in resource acquisition and complementary ecological functions.
The 2025 report of the Lancet Countdown on health and climate change
Marina Romanello, Maria Walawender, Shih-Che Hsu, Annalyse Moskeland, Yasna Palmeiro-Silva, Daniel Scamman, James W Smallcombe, Sabah Abdullah, Melanie Ades, Abdullah Al-Maruf, Nadia Ameli, Denitsa Angelova, Sonja Ayeb-Karlsson, Joan Ballester, Xavier Basagaña, Hannah Bechara, Paul J Beggs, Wenjia Cai, Diarmid Campbell-Lendrum, Gina E C Charnley, Orin Courtenay, Troy J Cross, Carole Dalin, Niheer Dasandi, Shouro Dasgupta, Michael Davies, Matthew Eckelman, Chris Freyberg, Paulina Garcia Corral, Olga Gasparyan, Joseph Giguere, Georgiana Gordon-Strachan, Sophie Gumy, Samuel H Gunther, Ian Hamilton, Yun Hang, Risto Hänninen, Stella Hartinger, Kehan He, Julian Heidecke, Jeremy J Hess, Slava Jankin, Ollie Jay, Dafni Kalatzi Pantera, Ilan Kelman, Harry Kennard, Gregor Kiesewetter, Patrick Kinney, Dominic Kniveton, Vally Koubi, Rostislav Kouznetsov, Pete Lampard, Jason K W Lee, Bruno Lemke, Bo Li, Andrew Linke, Yang Liu, Zhao Liu, Rachel Lowe , Siqi Ma, Tafadzwanashe Mabhaudhi, Carla Maia, Anil Markandya, Greta Martin, Jaime Martinez-Urtaza, Mark Maslin, Lucy McAllister, Celia McMichael, Zhifu Mi, James Milner, Kelton Minor, Jan Minx, Nahid Mohajeri, Natalie C Momen, Maziar Moradi-Lakeh, Karyn Morrisey, Simon Munzert, Kris A Murray, Nick Obradovich, Papa Orgen, Matthias Otto, Fereidoon Owfi, Olivia L Pearman, Frank Pega, Andrew J Pershing, Ana-Catarina Pinho-Gomes, Jamie Ponmattam, Mahnaz Rabbaniha, Tim Repke, Jorge Roa, Elizabeth Robinson, Joacim Rocklöv, David Rojas-Rueda, Jorge Ruiz-Cabrejos, Matilde Rusticucci, Renee N Salas, Adrià San José Plana, Jan C Semenza, Jodi D Sherman, Joy Shumake-Guillemot, Pratik Singh, Henrik Sjödin, Matthew R Smith, Mikhail Sofiev, Cecilia Sorensen, Marco Springmann, Jennifer D Stowell, Meisam Tabatabaei, Federico Tartarini, Jonathon Taylor, Cathryn Tonne, Marina Treskova, Joaquin A Trinanes, Andreas Uppstu, Nicolas Valdes-Ortega, Fabian Wagner, Nick Watts, Hannah Whitcombe, Richard Wood, Pu Yang, Ying Zhang, Shaohui Zhang, Chi Zhang, Shihui Zhang, Qiao Zhu, Peng Gong, Hugh Montgomery, Anthony Costello
Driven by human-caused greenhouse gas emissions, climate change is increasingly claiming lives and harming people's health worldwide. Mean annual temperatures exceeded 1·5°C above those of pre-industrial times for the first time in 2024. Despite ever more urgent calls to tackle climate change, greenhouse gas emissions rose to record levels that same year. Climate change is increasingly destabilising the planetary systems and environmental conditions on which human life depends.
iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis
Nosheen Hussain, Ryan Merrit, Julia Engelhorn, Javier Antunez-Sanchez, Anjar Wibowo, David Latrasse, Travis Wrightsman, Maximillian Collenberg, Ilja Bezrukov, Hidayah Alotaibi, Elsa Carrasco, Moussa Benhamed, Detlef Weigel, Nicolae Radu Zabet, Jose Gutierrez-Marcos
We present iNOMe-seq, a novel method for in vivo simultaneous profiling of chromatin accessibility, nucleosome occupancy, DNA-binding protein sites, and DNA methylation in living tissues. iNOMe-seq utilizes an m5C methyltransferase to mark accessible cytosines in a GpC context, bypassing nucleosome-restricted regions. Using Arabidopsis thaliana, we demonstrate that iNOMe-seq improves chromatin accessibility quantification compared to existing methods. Furthermore, it allows for the spatial and temporal analysis of chromatin dynamics, transcription factor binding, and DNA methylation, offering insight into the role of epigenetic components in transcriptional regulation across tissues and genetic variations in natural populations.
Structural characterization of the YbbAP-TesA ABC transporter identifies it as a lipid hydrolase complex that extracts hydrophobic compounds from the bacterial inner membrane
McAndrew, Martin B. L., Cook, Jonathan P., Gill, Amy, Sahoo, Kavya, Thomas, Clare, Stansfeld, Phillip J. and Crow, Allister
Type VII ABC transporters are ATP-powered membrane protein complexes that drive key biological processes in the bacterial cell envelope. In Escherichia coli, three of the four Type VII ABC systems have been extensively characterized, including: the FtsEX-EnvC cell division complex, the LolCDE-LolA lipoprotein trafficking machinery, and the MacAB-TolC efflux pump. Here we describe a fourth E. coli Type VII ABC system, YbbAP-TesA, which combines a Type VII ABC transporter with a multifunctional hydrolytic enzyme. Structures of the complete YbbAP-TesA complex, and of YbbAP with and without bound ATP analogues, capture implied long-range transmembrane conformational changes that are the hallmark of this ABC superfamily’s mechanotransmission mechanism. We further show that YbbAP-TesA can hydrolyze a variety of ester and thioester substrates and experimentally confirm a constellation of active site residues in TesA. Our data suggests YbbAP has a role in extracting hydrophobic molecules from the inner membrane and presenting these to TesA for hydrolysis. The work extends collective knowledge of the remarkable diversity of the ABC superfamily and establishes a new function for Type VII ABC transporters in bacterial cells.
Identification of Race-Specific, Clade-Specific and Broad-Spectrum Resistance to Xanthomonas campestris pv. campestris in Brassica Diversity Fixed Foundation Sets
Shannon F. Greer, Jamie Harrison, Daisy Bown, Maria Serrano, Rana Muhammed Fraz Hussain, Srayan Ghosh, Graham R. Teakle, Vardis Ntoukakis, David J. Studholme, Joana G. Vicente, Murray Grant
Black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is the most damaging bacterial disease of vegetable brassicas (Brassica oleracea) worldwide. The prevalence of several genetically diverse Xcc races makes breeding for varietal resistance challenging. In this study, we have screened diversity fixed foundation sets (DFFSs) of B. oleracea and Brassica napus for resistance against isolates belonging to prevalent Xcc races 1, 4, 5 and 6. The DFFSs are designed to capture the genetic diversity available within the respective Brassica species gene-pools in smaller subsets of lines. Our findings revealed that resistances to race 1 and 4 were largely absent in B. oleracea but more prevalent in B. napus. Notably, resistance to race 4 was particularly common in B. napus (63% of lines showed resistance, 13% of lines showed partial resistance). Conversely, resistance to races 5 and 6 was more common in B. oleracea than in B. napus. In B. oleracea, there was no significant association between disease index and morphotype but, among the B. napus morphotypes, swede was the most susceptible to races 1, 5 and 6 but not to race 4. Ten B. oleracea and 67 B. napus lines showed resistance to more than one isolate. Further testing of a subset of these lines demonstrated that resistances were effective against additional diverse Xcc isolates in a race-specific, clade-specific or broad-spectrum manner. The resistant lines identified in this study offer a valuable resource for breeding programmes aimed to achieve durable and sustainable control of Xcc.
Enset Bacterial Wilt (Xanthomonas vasicola pv. musacearum): Farmer Perspectives, Physicochemical Characterization, and Phenotypic Variation Among Strains
Tafesse Kibatu, Sebsebe Demissew, Diriba Muleta, Getahun Haile, Seman Abrar, Denberu Kebede, Murray Grant, Sadik Muzemil, Tileye Feyissa
Enset is a staple food for approximately 25% of Ethiopia’s population. It is threatened by a range of biotic and abiotic stress, of which bacterial wilt is the most significant. This study investigated the enset bacterial wilt (EBW) status on farms in Gedeo, Kembata Tembaro, Gurage, Hadiya zones, and the Basketo special woreda of Southern Ethiopia. In addition, infected enset plant samples were collected from Hadiya, Kembata Tembaro, and Gedeo zones to assess bacterial strain diversity using physicochemical and morphological approaches. Representative Kebeles were selected using purposive sampling based on their agroecological conditions. Data was collected through in-depth interviews, questionnaires, group discussions, and field observation. The morphology of bacterial wilt isolates was characterized by color, texture, form, elevation, margin, and motility. In addition, a combination of oxidase, aesculin hydrolysis, catalase, gram reaction, hydrogen sulfide (H2S), gelatin liquefaction, and fructose, lactose, mannitol, and sorbitol utilization tests were conducted to capture physiochemical differences. Tolerance to salt and high temperatures was also evaluated. The bacterial wilt impact varies significantly across enset growing regions, with highlands experiencing the highest. This research emphasizes the importance of assessing both spatial and temporal variation, as well as integrating local knowledge and robust scientific approaches for effective bacterial wilt management and enset landrace conservation efforts. The research also provides valuable insights into the characteristics of bacterial wilt isolates in Southern Ethiopia. Analyses of morphology, potassium hydroxide solubility, catalase activity, and carbohydrate utilization were consistent, however, variations in bacterial isolates response to tests of easculin, oxidase, gelatin liquid, H2S tests and response to osmotic and temperature exposures. This study reveals a strong association between the bacterial wilt effect and the enset growing regions. EBW exhibits seasonal fluctuations. Bacterial wilt isolates displayed consistent morphological characteristics. All isolates similarly utilized sorbitol, mannitol, lactose, and fructose carbohydrates. All isolates exhibited positive potassium hydroxide solubility and catalase activity. However, the isolates displayed variations in responses to easculin, oxidase, gelatin liquefaction, and H2S production. The isolates also displayed variations in tolerance to salt and high temperatures. These variations can be valuable for understanding disease epidemiology and management.