Latest Publications
PRC1-mediated H2A.Zub promotes gene expression by preventing H3.1K27me1 incorporation in Arabidopsis
Fernando Baile, Javier Antúnez-Sánchez, Jose Gutierrez-Marcos, Myriam Calonje
Background: PcG complexes are pivotal in orchestrating the transition from embryonic to vegetative development in plants. However, the mechanisms underlying the gene expression reprogramming that takes place during this developmental transition are still not fully understood. Several studies suggest that incorporating PcG modifications into distinct histone variants may play a key role in this process. However, while PRC2-mediated H3K27me3 is essential for gene repression, the timing of PRC2 action on canonical H3.1 or variant H3.3 remains unclear. Furthermore, the exact role of PRC1 in transcriptional regulation is still unresolved, partly owing to limited knowledge of the conditions under which this complex monoubiquitinates canonical H2A or H2A.Z variant.
Results: Here, we demonstrate that H2A.Z undergoes monoubiquitination during the seed-to-seedling transition. H2A.Zub facilitates the recruitment of PRC2 to mediate H3.3 trimethylation, repressing seed-specific genes; however, H2A.Zub also promotes the activation of vegetative-specific genes by preventing H3K27me1 incorporation into H3.1. Notably, the histone demethylase REF6 initiates this process by removing two methyl groups from stably repressed H3.1K27me3-marked genes, enabling the subsequent H2A.Zub incorporation. This result suggests that REF6 activity is a critical early step in PRC1-mediated transcriptional activation.
Conclusions: Our findings reveal the long-sought mechanism by which PRC1 participates in transcriptional activation. We demonstrate that PRC1-mediated H2A.Zub, acting as a “switcher”, plays a pivotal role in reprogramming active and repressed genes during the transition from embryonic to vegetative development. Moreover, our results provide new insights into the intricate relationship between histone modifications and histone variants in reprogramming and maintaining gene expression patterns.
Bee-mediated delivery of bacteriophage for biocontrol of the cherry canker pathogen Pseudomonas syringae pv. syringae
Shannon F. Greer, Sneha Chakravorty, Kieran Cooney-Nutley, Dave Chandler*, Gregory Firth, Rajesh Odedra, Mojgan Rabiey
Bacteriophages, phages or viruses that specifically infect bacteria, have shown promise for the biocontrol of bacterial plant diseases. However, one of the main challenges of using phages in agricultural systems is their precision application, being able to deliver an effective dose to the site of bacterial infection. In this study, a series of artificial and real cherry flower experiments was conducted to test whether commercially managed bumblebees (Bombus terrestris audax) could deliver phage effective against the cherry canker pathogen Pseudomonas syringae pv. syringae (Pss). Freeze-dried phage powder was formulated with powdered-skimmed milk and when tested, was found to retain viability for seven days in artificial bee feed after storage at 4 °C, room temperature or under glasshouse conditions. In both artificial and cherry flower experiments, bees successfully transferred the formulated phage from their hive to up to 88 % of flowers, resulting in significant reduction in Pss populations. Bees were also able to transfer phage between cherry flowers. The application of phages disrupted the cycle of Pss transmission by bees. These results highlight the potential of bee-mediated phage delivery as an effective biocontrol strategy against floral pathogens like Pss.
Genomic insights into the ecological versatility of Tetracladium spp.
Anna Lazar, Fabrizio Alberti, George Muscatt, Ryan M. Mushinski, Christopher Quince, Gary D. Bending
Background: Tetracladium spp. represent a group of fungi that inhabit various ecological niches, including soil and aquatic environments, where they are considered to have a saprotrophic lifestyle and within plant roots as endophytes. To date, a lack of sequenced Tetracladium spp. genomes has inhibited our understanding of their metabolic potential and ecological interactions. In this study, we aimed to elucidate the genetic differences between aquatic saprotrophic and endophytic strains of Tetracladium spp. by sequencing and analysing the genomes of T. maxilliforme (isolated from Brassica napus roots) and T. marchalianum (isolated from freshwater), alongside 41 publicly available saprotrophic and endophytic Ascomycetes.
Results: Genomic sequencing revealed that T. maxilliforme possesses a genome size of 35.5 Mbp with 9657 predicted genes, while T. marchalianum has a genome size of 33.2 Mbp with 15,230 predicted genes. Our analyses primarily focused on carbohydrate-active enzymes (CAZymes). Both genomes possessed the full range of enzymatic machinery for cellulose degradation, as well as the complete repertoire of genes necessary to degrade plant cell walls. Notably, the genomes lacked essential enzymes for lignin degradation or modification. Furthermore, we observed a complete repertoire of known fungal chitin-degrading enzymes in both genomes, which might be related to potential interactions with other fungi. Enzyme composition profiles revealed distinct groupings, with T. maxilliforme primarily clustering with endophytic or ecologically versatile species, while T. marchalianum was predominantly associated with saprotrophic species. We also identified secondary metabolite biosynthetic gene clusters in both genomes, including several that showed high homology to those of known bioactive compounds.
Conclusions: In summary, our findings offer valuable insights into the genomic adaptations of Tetracladium spp. to various ecological niches, highlighting their enzymatic capabilities for carbohydrate degradation and potential interactions within fungal communities.
The Use of Ecoacoustics to Monitor Soil Ecology: A Critical Review With Reference to Earthworms
Jacqueline L. Stroud, Michał K. Kalkowski, Kirsty L. Hassall, Miriam Treadway, Jessica Fannon, Aidan Keith, Siul Ruiz, Keith Attenborough
The use of ecoacoustics to monitor soil ecology was identified as a priority in the 2024 horizon scan of global biological conservation issues. Proponents suggest it will have societal impacts by improving soil health assessments, enhance soil biodiversity monitoring and facilitate the conservation, remediation and management of soil ecosystems. Here we review soil ecoacoustics in terms of its definition, theoretical basis, acoustic indices and statistical inferences. To do this we explain mechanical wave behaviour, mechanoreception by fauna, and tactical signal design with reference to earthworms as ecosystem engineers. Ecoacoustics emerged from research on animal long‐distance communication systems, and its direct application to soils has been identified as a problem area. A new field within ecoacoustics has been created for soils, sonoscape investigations, to capture spatio‐temporal complexity of ecological features (rather than soil ecology). There is a good case for reclassifying soil ecoacoustic ‘soundscape’ studies as sonoscapes. We identify that further refinement of ecoacoustics is required for applications to soil habitats. The performance of sonoscape investigations is dependent on acoustic indices and statistical inferences, and we question why stationary signal processing is used as the base transform for soils data, and highlight the issue of unbalanced data sets, particularly pertinent to soils as there is limited understanding of what exactly is being detected. We list the key research needs and highlight that integrating soil science and mechanistic modelling of soil processes and wave propagation as an essential component of developing reliable monitoring solutions. Embracing these interdisciplinary avenues will help develop sensing capabilities for soils in robust scientific principles and mitigate the risks of speculative overreach.
European Journal of Soil Science, November 2025
Maximizing the Biocontrol Potential of Bacteriophages: A Call for Critically-Needed Field Research
George W Sundin, Sara M Villani, Quan Zeng, Michelle Hulin, Mojgan Rabiey, Kerik Cox
Bacteriophages are viruses capable of infecting bacterial cells. Lytic phages, which infect and kill bacterial cells, are of interest in disease management in human, animal, and plant systems. In plant pathology, the biocontrol of bacterial diseases is of heightened interest because of the lack of efficacious options in many pathosystems. Numerous papers have been published in the past few decades on phage that target plant pathogenic bacteria, and a large majority of these have been focused on phage isolation and characteristics that highlight the promise and potential of phage as biocontrol agents. In contrast, relatively few of these papers have reported results from studies conducted in the field. Of the recent papers (2022 to 2025) reporting field studies, disease efficacy results are inconsistent. We argue that field studies should be an essential component of phage biocontrol research to understand how to best utilize and deploy phages to generate consistently effective disease management.
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.