Plant & Agricultural Bioscience Publications

Shashank K. Pandey, Tatiana S. Moraes, Aswin Nair, Bibek Aryal, Abdul Azeez, Pal Miskolczi, Guillaume Maucort, Fabrice P. Cordelières, Lysiane Brocard, Gwendolyn V. Davis, Hannah Dromiack, Swanand Khanapurkar, Sara I. Walker, George W. Bassel, Emmanuelle M. Bayer, Rishikesh P. Bhalerao

Dormancy is a key mechanism in perennial plants in boreal and temperate regions, protecting buds from winter damage by repressing precocious bud break before spring onset. How plants robustly time dormancy release under fluctuating environments remains unknown. Here, we show that, rather than simply sensing cold duration, buds leverage warm spikes to sense winter progression and time dormancy release. This timing mechanism is mediated by previously unrecognized regulation of plasmodesmata by warm spikes acting through tree ortholog of FLOWERING LOCUS T (FT1) and the gibberellic acid pathway. Our results reveal FT1 as a previously unrecognized, suppressor of callose levels and show that warm spikes repress cold induction of FT1 and GA pathway to suppress PD opening and dormancy release. Importantly, buds exhibit heterogeneity in bud break. This heterogeneity in bud break crucial for bet hedging is amplified under temperature fluctuations and is associated with the thermal responsiveness of plasmodesmata. Altogether, our work reveals dynamic plasmodesmata regulation as a crucial tissue-level mediator of variable temperature processing by buds, enabling robust adaptation of trees to seasonal changes.

Nature Communications, January 2026

Trupti Gaikwad, Susan Breen, Emily Breeze, Erin Stroud, Rana Hussain, Satish Kulasekaran, Nestoras Kargios, Fay Bennett, Marta de Torres-Zabala, David Horsell, Lorenzo Frigerio, Pradeep Kachroo, Murray Grant

Successful recognition of pathogen effectors by plant disease resistance proteins, or effector-triggered immunity (ETI), contains the invading pathogen through localized hypersensitive cell death. ETI also activates long-range signalling to establish broad-spectrum systemic acquired resistance (SAR). Here we describe a sensitive luciferase (LUC) reporter that captures the spatial–temporal dynamics of SAR signal generation, propagation and establishment in systemic responding leaves following ETI. JASMONATE-INDUCED SYSTEMIC SIGNAL 1 (JISS1) encodes an endoplasmic-reticulum-localized protein of unknown function. JISS1::LUC captured very early ETI-elicited SAR signalling, which surprisingly was not affected by classical SAR mutants but was dependent on calcium and was also wound responsive. Both jasmonate biosynthesis and perception mutants abolished JISS1::LUC signalling and SAR to Pseudomonas syringae. Furthermore, we discovered that ETI initiated jasmonate-dependent systemic surface electrical potentials. These surface potentials were dependent on both glutamate receptors and JISS1, despite neither JISS1 loss-of-function nor glutamate receptor mutants altering SAR to Pseudomonas syringae. We thus demonstrate that jasmonate signalling, usually associated with antagonism of defence against biotrophs, is crucial to the rapid initiation and establishment of SAR systemic defence responses (including the activation of systemic surface potentials) and that JISS1::LUC serves as a reporter to further dissect these pathways.

Nature Plants, January 2026

Nikhil Bhalla, Mojgan Rabiey, Prachi Bendale, Katie Lawther, Janice Spencer, Alberto Longo, Lucky Lucky, Vishal Chaudhary, Paul McCormack, Saikat Jana, Patrick S. M. Dunlop, Linda Oyama

Antimicrobial resistance (AMR) is a silent pandemic that presents a global challenge, urging researchers to develop innovative and transdisciplinary solutions. Our initiative aims to promote collaboration across science, engineering, economics, social sciences, and the arts to address the complex dimensions of AMR. We highlight the unique role of early-career researchers (ECRs) in advancing such cross-cutting approaches and conclude that empowering ECRs through equitable support and recognition is essential to sustaining innovation and mobilising communities against AMR.

Nature Communications, January 2026

Irnia Nurika, Eka Nur Shabrina, Nurul Azizah, Sri Suhartini, Guy C. Barker, Timothy D.H. Bugg

This study assesses the facultative anaerobe Comamonas testosteroni as a mild, chemical-free pre-treatment for valorising oil palm empty fruit bunches (OPEFB) into biomethane and lignin-derived aromatics. Incubation with 2 % (v/v) C. testosteroni for 7 days at 30 °C, reduced lignin to 15.67 % (33.42 % removal), while retaining high cellulose (53.48–56.19 %) and hemicellulose (up to 16.21 %). Pre-treated OPEFB showed 20 % weight loss (vs 8 % in controls) and a 51 % rise in total soluble phenols, evidencing active lignin depolymerisation. GC–MS of liquor and solids qualitatively confirmed lignin breakdown and identified representative low-molecular-weight products (e.g., phenol, betulin, acetic acid and benzoxazole), supporting co-product potential. In biochemical methane potential tests, the pre-treated residue achieved a specific methane potential of 0.173 m³ CH4 kg⁻¹ VS, an 85 % increase over the abiotic residue and higher than non-treated OPEFB. Kinetic fitting with Transference, Modified Gompertz and Logistic models yielded good agreement (R2 up to 0.92), with Modified Gompertz best capturing cumulative methane production and the shortest lag phases. A simple energy check indicates a favourable margin: the incremental methane (ΔSMP ≈ 0.08 m³ CH₄ kg⁻¹ VS) equates ∼0.8 kWh kg⁻¹ VS, whereas estimated mixing for pre-treatment is ∼0.017–0.034 kWh kg⁻¹ VS. Overall C. testosteroni pre-treatment enables dual valorisation (biomethane plus aromatics) under mesophilic conditions, offering a practical route for integrated OPEFB biorefineries.

Biochemical Enigneering Journal, March 2026

Shuya Wang, Tong Li, Matthew Naish, Russell Chuang, Evan K. Lin, Christian Fonkalsrud, Yan He, Suhua Feng, Ian R. Henderson, Steven E. Jacobsen

DNA methylation is a conserved epigenetic modification essential for maintaining genome stability. However, how methyltransferases maintain CG methylation within compact chromatin, including centromeres, remains unclear. In humans, CDCA7 is necessary for the inheritance of DNA methylation at juxta-centromeres. Mutations that impair its ability to bind chromatin result in Immunodeficiency, Centromeric Instability, and Facial Anomalies (ICF) syndrome, characterized by centromeric instability. To investigate whether CDCA7 function is conserved, we identified two Arabidopsis thaliana orthologs, CDCA7α and CDCA7β. The loss of both copies results in CG hypomethylation at pericentromeric regions and centromeric satellite repeat arrays. Machine learning analysis suggested that heterochromatic nucleosomes, with enrichment of H1, H2A.W, and H3K9me2, depend heavily on CDCA7 proteins for CG methylation maintenance of the associated DNA. Loss of H1 restores heterochromatic DNA methylation in cdca7α cdca7β mutants, indicating that CDCA7α and CDCA7β mainly remodel H1-containing nucleosomes for methyltransferases to access DNA. Notably, in h1.1 h1.2 mutants, CG methylation shows a significant increase in centromeres, which reveals a new inhibitory role of H1 in DNA methylation maintenance within satellite repeat arrays. Centromeric DNA hypermethylation is lost in h1.1 h1.2 cdca7α cdca7β quadruple mutants, demonstrating that CDCA7α and CDCA7β can act independently of H1 to enhance MET1 activity at nucleosomes. Overall, these findings establish CDCA7α and CDCA7β as conserved regulators of DNA methylation within heterochromatin and centromeric satellite repeat arrays.

PNAS, December 2025

Kathryn A. Lord, Greger Larson, Robin G. Allaby, Elinor K. Karlsson

We recently provided a new definition for domestication as “the process in which nonhuman populations adapt to an environment created through human activity” (1). It brings domestication fully into an evolutionary framework, obviates the need for assumptions about how domestication occurred, and can be applied equally to plants, animals, and microbes.

In response, Kohl (2) argues that our definition does not recognize domestication as a “special case of evolution.” However, as we describe in our article, extensive literature demonstrates that under modern evolutionary theory, domestication is not a special case of evolution, contrary to views held by many scientists in the 19th and early 20th centuries. Our observation that a population can change its relationship to the anthropogenic niche as a result of environmental shifts is fully consistent with this framework. As R. A. Fisher noted in The Genetical Theory of Natural Selection (3), “fitness may be increased or decreased by changes in the environment.” Because evolution by natural selection proceeds through changes in fitness, alterations in the environment, like genetic change, are integral components of the evolutionary process.

Kohl states that the terms “self-sustaining” and “human-created” are arbitrary. Self-sustaining is a key concept in population biology (4) that is also fundamental to the definition of obligate synanthropes. If a population is not self-sustaining, then it is a sink population that requires immigration to persist and by definition maladapted (5). Populations that are adapted to a human-created niche therefore must be self-sustaining, which makes the concept a critical component for the identification of such populations. Similarly, our definition specifies "an environment created through human activity" as distinct from the human body itself, since organisms adapted to live on or in the human body are not necessarily domestic and the evolutionary processes required to thrive in anthropogenic environments differ from those required to survive on the human body.

PNAS, December 2025

Annabelle R de Vries , Lochlan Chadwick , Mark Carine , Robin G Allaby

Adhesives have been integral to the production of herbaria for paper making, securing plant material to paper, and, in the case of bound volumes, for bookbinding. The adhesives used may be of plant, animal, or synthetic origin. Here we investigated herbarium specimens from the Natural History Museum London (NHM), collected between 1698 and 1970, to determine whether information on the adhesives used in the preparation of herbarium specimens can be established using ancient DNA analysis of the mounted plant material. Ancient DNA was obtained from leaf tissue of 14 herbarium specimens of Trochetiopsis and sequenced using Illumina MiSeq. Non-Trochetiopsis DNA was identified using metagenome analysis software (MEGAN). Reads identified as animal were further analysed using the metagenomics pipeline Phylogenetic Intersection Analysis (PIA). Two specimens showed distinct animal reads. One specimen from 1698, which had glue residue observable on the leaf material, showed evidence for Pecora and Bovidae, specifically Bos, and with lower read counts also for both Leporidae and Ovis. The bones of cattle, rabbits, and sheep are all likely to have been used in the preparation of glue in this period, and consequently the animal DNA retrieved is probably from the glue used for mounting. The second sample was from 1970 and showed reads of Pecora, Bovidae, and Bos. Latex adhesives were used at the NHM during the 1970s with synthetic adhesives used thereafter. We infer that the animal DNA retrieved is probably from gelatine used for paper sizing. The results of this study demonstrate that the genetic analysis of plant material can also provide insights into the process of making herbaria.

Botanical Journal of the Linnean Society, December 2025

Nicola Gorringe , Stephanie Topp , Robin Burns , Sota Yamaguchi , Fernando ARabanal , Joiselle B Fernandes , Detlef Weigel , Tetsuji Kakutani , Matthew Naish , Ian R Henderson

Eukaryotic centromeres mediate chromosome segregation during cell division. Plant centromeres are loaded with CENH3-variant nucleosomes, which direct kinetochore formation and spindle-microtubule interaction. Centromeres are frequently composed of megabase-scale satellite repeat arrays, or retrotransposon nests. In monocentric genomes, such as the model plant Arabidopsis thaliana, pericentromeric heterochromatin surrounds the CENH3-occupied satellite arrays. A zone of suppressed meiotic crossover recombination contains the centromere and extends into the pericentromeres. Here, we explore how natural variation in Arabidopsis influences centromere-proximal crossover frequency and segregation distortion when centromeres are heterozygous. We used fluorescent crossover reporters to quantify the effect of genetic variation on centromere-proximal recombination in 12 F1 hybrids between the reference strain Col-0 and nonreference accessions that captured Eurasian and relict diversity, and in total, we measured 3,037,802 meioses. The majority of the F1 hybrids (49 of 60) had significantly higher or lower centromere-proximal crossover frequency than inbreds. We relate hybrid crossover frequencies to patterns of nucleotide diversity and centromeric structural variation, and in a subset of 7 accessions, to epigenetic patterns of CENH3 enrichment and DNA methylation. Using linear modeling, we observed that chromosome and accession, and their interaction, together explained 85% of variation in crossover frequency, consistent with cis- and trans-acting modifying effects. The fluorescent reporters also allow segregation distortion through meiosis to be quantified between hybrids and inbreds. We observed a minority of hybrids (18 of 60) with distorted segregation through meiosis compared to inbreds, which occurred with or without a simultaneous change to centromere-proximal crossover frequency. Linear modeling revealed that 56% of variation in segregation distortion is explained by chromosome and accession, but with a stronger effect of accession compared to crossover frequency. We discuss how Arabidopsis centromeric structural heterozygosity may modify recombination and cause segregation distortion through meiosis.

Genetics, December 2025

European Food Safety Authority (EFSA), Elena Lázaro, Stephen Parnell, Antonio Vicent Civera, Martijn Schenk, Jose Cortiñas Abrahantes, Juan Navas-Cortes, Hans-Hermann Thulke, Francesco Pecori, Joshua Koh, Jan Schans, Marc Aerts, Gabriele Zancanaro, Sybren Vos, Tomasz Kaluski

At the request of the European Commission, EFSA prepared the general guidelines for surveys of plant pests, describing the legal, international and scientific context in which the surveys are designed, the basic principles implemented for surveillance of quarantine pests and introducing the concepts needed for the design of statistically sound and risk-based surveys. Three types of specific surveys are addressed: detection surveys for substantiation of pest freedom, delimiting surveys to determine the boundaries of a potential infested zone, and monitoring surveys for prevalence estimation when measuring the effectiveness of eradication measures or for the confirmation of a low pest prevalence area. For each type of survey, the survey parameters are introduced and their interactions analysed showing the importance of the assumptions that are taken for each one of them:

1) The aims of the survey are defined as achieving a certain level of confidence of detecting a given pest prevalence (design prevalence), this reflects the trade-off between the acceptable level of the risk and availability of resources that determine the strength of the evidence to support the conclusion of the survey;

2) The target population is described by its structure and size, including the risk factors; and

3) The method sensitivity is defined as the combination of the sampling effectiveness and the diagnostic sensitivity for each inspection unit. EFSA's RiPEST and RiBESS+ tools1 are introduced for calculating the sample size using the survey parameters as input values for a statistically sound and risk-based survey design. The mathematical principles behind the tools are in line with the International Standards for Phytosanitary Measures. The survey design is flexible and can be tailored to each pest and specific situation in the Member States. Once the survey is implemented following this approach, the conclusions allow surveys to be compared across time and space, contributing to the harmonisation of surveillance activities across the EU Member States.

EFSA Supporting Publications, December 2025

Amadeus Plewnia, Brandon D. Hoenig, Stefan Lötters, Christopher Heine, Jesse Erens, Philipp Böning, Gary D. Bending, Henrik Krehenwinkel, Molly Ann Williams

CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats—CRISPR-associated nucleases) systems allow researchers to detect, capture, and even alter parts of an organism's genome. However, while the use of CRISPR-Cas has revolutionised many fields in the life sciences, its full potential remains underutilised in ecology and biodiversity research. Here we outline the emerging applications of CRISPR-Cas in ecological contexts, focusing on three main areas: nucleic acid detection, CRISPR-enhanced sequencing, and genome editing. CRISPR-based nucleic acid detection of environmental DNA samples is already reshaping species monitoring, providing highly sensitive and non-invasive tools for both scientists and the public alike, with reduced costs and minimal experience required. Further, CRISPR-enhanced sequencing, including Cas-mediated target enrichment, enables efficient recovery of ecologically relevant loci and supports diverse applications such as amplification-free metagenomics. Finally, while genome editing on wild species remains largely theoretical in ecology, these tools are already being used in controlled settings to study adaptation and resilience in the face of ongoing global stressors. Together, the applications of CRISPR-Cas are paving the way for more affordable, accessible, and impactful applications for species conservation, and promise to improve our ability to tackle the ongoing global biodiversity crisis.

Molecular Ecology Resources, December 2025

Clara Bergis-Ser, Qingyi Wang, Xiaoning He, Maherun Nisa, Vickie Kaise, Christelle Mazubert, Jeannine Drouin-Wahbi, Rim Brik-Chaouche, Layla Chmaiss, Jelle Van Leene, Geert De Jaeger, Jose Gutierrez-Marcos, Catherine Bergounioux, Clara Bourbousse, David Latrasse, Moussa Benhamed, Cécile Raynaud

Genomic integrity is constantly challenged by transcription/replication conflicts, a major source of replication stress and instability across all life forms. While extensive studies have elucidated mechanisms for resolving transcription/replication conflicts in animals, yeast, and prokaryotes, their counterparts in plants remain largely unexplored. Through a forward genetic screen, we identified LUMINIDEPENDENS (LD), previously known for its role in regulating the flowering repressor FLC, as a key factor in mitigating replication stress in plants. Notably, transcriptomic analyses reveal that LD loss results in the upregulation of over half of the Arabidopsis genes, placing LD as a global transcriptional repressor. Consistent with this role, LD directly binds a substantial portion of the Arabidopsis genome and interacts with the MED18 subunit of the Mediator complex to modulate RNA polymerase II phosphorylation. These findings uncover a fundamental function of LD in fine-tuning transcription at a genome-wide scale, with potentially an additional role in suppressing transcription–replication conflicts by locally dampening transcription and promoting replication fork progression. Our work highlights an intriguing genome-protective strategy in plants, that could shed light on mechanisms involved in transcription–replication conflict management in eukaryotic systems.

PNAS, December 2025

Carmen Sánchez-Cañizares , Raphael Ledermann , Joseph McKenna, Thomas J Underwood , Marcela Mendoza-Suárez , Rob Green , Karunakaran Ramakrishnan , Alison K East , Isabel Webb , Charlotte Kirchhelle , Beatriz Jorrín , Gerhard Saalbach , Euan K James , Flavia Moreira-Leite , Jason Terpolilli , Philip S Poole

Within legume root nodules, rhizobia differentiate into bacteroids, which reduce N2 into NH3 for secretion to the plant. Bacteroids may be swollen and terminally differentiated or non-swollen and can regenerate outside nodules. It is unclear why these different endosymbiotic lifestyles exist and whether they differ in symbiotic efficiency. Here, we compared N2 fixing bacteroids of the near isogenic strains Rhizobium leguminosarum bv. phaseoli 4292 (Rlp4292) and R. leguminosarum bv. viciae A34 (RlvA34), nodulating Phaseolus vulgaris (common bean) and Pisum sativum (pea), respectively. The larger bean plants fixed more N2, but peas fixed 1.6-3-fold more per unit nodule mass. Values per unit volume were similar between bean and pea because bean nodules are 2.7-fold denser (i.e., mass per unit volume). Bean nodules have higher numbers of smaller (∼1/5 the volume) bacteroids than peas. Bean bacteroids are denser (i.e., 2.5-fold protein per unit volume) although less closely packed than pea bacteroids (i.e. more space between bean bacteroids). Critically, pea bacteroids, fix N2 at higher rates versus bean per unit bacteroid protein, as protein expression is skewed towards N2 fixation and TCA-cycle enzymes. Pea bacteroids infect 1.6 times the percentage of nodule volume of beans (i.e., 14.2% versus 9.1%). Overall, the increased packing density of pea bacteroids, as well as the bias of their proteome to nitrogenase, associated N2 fixation processes, and dicarboxylate metabolism, contributes to their greater symbiotic efficiency, which is likely driven by plant antimicrobial peptides.

Plant Physiology, December 2025

Matt Combes, Nathan Brown, Robin N. Thompson, Alexander Mastin, Peter Crow, Stephen Parnell

Invasive plant pests and pathogens cause substantial environmental and economic damage. Visual inspection remains a central tenet of plant health surveys, but its sensitivity (probability of correctly identifying the presence of a pest) and specificity (probability of correctly identifying the absence of a pest) are not routinely quantified. As knowing sensitivity and specificity of visual inspection is critical for effective contingency planning and outbreak management, we address this deficiency using empirical data and statistical analyses. Twenty-three citizen scientist surveyors assessed up to 175 labelled oak trees for three symptoms of acute oak decline. The same trees were also assessed by an expert who has monitored these individual trees annually for over a decade. The sensitivity and specificity of surveyors was calculated using the expert data as the ‘gold-standard’ (i.e., assuming perfect sensitivity and specificity). The utility of an approach using Bayesian modelling to estimate the sensitivity and specificity of visual inspection in the absence of a rarely available ‘gold-standard’ dataset was then examined with simulated plant health survey datasets. There was large variation in sensitivity and specificity between surveyors and between different symptoms, although the sensitivity of detecting a symptom was positively related to the frequency of the symptom on a tree. By leveraging surveyor observations of two symptoms from a minimum of 80 trees on two sites, with reliable prior knowledge of sites with a higher (~0.6) and lower (~0.3) true disease prevalence we show that sensitivity and specificity can be estimated without ‘gold-standard’ data using Bayesian modelling. We highlight that sensitivity and specificity will depend on the symptoms of a pest or disease, the individual surveyor, and the survey protocol. This has consequences for how surveys are designed to detect and monitor outbreaks, as well as the interpretation of survey data that is used to inform outbreak management.

PLOS - Computational Biology, November 2025

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.

Genome Biology, November 2025

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.

BMC Genomics, November 2025

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.

Plant Disease, November 2025.

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.

BMC Genormics, October 2025

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.

Genome Biology, October 2025

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.

Plant Pathology, October 2025

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.

Advances in Agriculture, January 2025

Laurence Hand, Mark C.J. Day, Carol Nichols, Hendrik Schäfer, Samantha Marshall, Gary D. Bending

Laboratory soil biodegradation studies required for approval of crop protection products (CPPs) are performed under continuous darkness, nullifying any potential contributions of algal and moss dominated biological soil crusts (BSC). There is growing evidence for metabolism of CPPs by phototrophic microorganisms under laboratory conditions, but limited data is available under field conditions. In this study we investigated the impact of the BSC on the fate of two 14C-fungicides under semi-field conditions using different light filters to alter formation of the BSC by exclusion/transmission of UV and photosynthetically active (PAR) wavelengths. Attenuation of PAR light significantly reduced formation of a BSC, which resulted in a significant slowing of the dissipation of benzovindiflupyr, which is known to be susceptible to phototrophic metabolism in aquatic systems, with 12–14 % more parent compound remaining at the end of the study when BSC development was impeded. For paclobutrazol, however, no significant difference in dissipation rate was observed. For both compounds there was significantly less non-extractable residue (NER) formation when BSC development was impeded (4–9 % reduction). Additionally, for both fungicides, the presence of a viable BSC resulted in 10–20 % more movement through the surface 5 mm of the soil, although this effect was limited to the period immediately after application and was likely due to increased porosity of the surface layer. This study confirms that the presence of phototrophs can significantly impact the environmental fate of CPPs on the surface of agricultural fields, either directly through metabolism or indirectly by altering the properties of the surface layer.

Science of The Total Environment November 2025

Dion Garrett, Graham Teakle, Rosemary Collier, James R Bell, Ramiro Morales-Hojas

Nasonovia ribisnigri (Mosley) is a severe aphid pest of outdoor lettuce, and the combination of sporadic and unpredictable colonization on outdoor lettuce, along with the breakdown of cultivar resistance, has left few effective control methods. The population structure (spatially and temporally) of N. ribisnigri is currently unknown in England, and therefore microsatellite markers were designed to estimate the impacts of host plant selection pressure (including host plant resistance) and environmental change. Biological samples collected between 2003 and 2020 from 10 sites across England were typed with microsatellite markers. The analysis of 8 microsatellites indicated a clear east-west divide between N. ribisnigri populations, which corresponds with current outdoor lettuce cultivation distribution in England, one of the aphid's summer hosts. Analysis of gene flow indicated that aphids did not leave the eastern region; instead, there was strong evidence for aphids migrating from the West into the secondary host eastern region, possibly from the winter host (Ribes spp.) in Spring. This result suggests that although N. ribisnigri has the potential for long-distance migration, strong ties to the summer host (lettuce) determine migratory behavior at the population level. N. ribisnigri are mostly holocyclic and show a high level of inbreeding. Long-term trends revealed relatively stable populations, despite a recent breakdown of host plant resistance and other environmental changes, including favorable temperatures. The geographic and temporal structure of the N. ribisnigri population is discussed in relation to future pest management strategies.

Journal of Insect Science October 2025

Sinchan Banerjee, Andras Tancsics, Zegin Wu, Tudor Stafioiu, Jiacheng Gao, Erika Toth, Erzsebet Baka, Garry Bending, Hendrik Schaefer

A novel carbon monoxide (CO)-oxidizing bacterial strain designated as SB112T was enriched and isolated from Ilex aquifolium leaves from Tocil Wood Nature Reserve in Coventry, UK. The strain was Gram reaction-negative, aerobic, rod-shaped, motile with a polar flagellum and non-spore-forming. Growth of strain SB112T was observed at 10–45 °C, pH 6.0–12.0 and NaCl concentrations of 1–3%. The genomic DNA G+C content was 58.3 mol%, and the major fatty acids (>10%) of strain SB112T were C18 : 1 ω7c, C18 : 1 ω7c 11-methyl and C19 : 0 cyclo ω7c. Major polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol and a phospholipid. Strain SB112ᵀ contains ubiquinone-10 as the major respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SB112T formed a separate lineage within the family Phyllobacteriaceae, showing sequence identities of 97.7%, 97.6% and 97.5%, with its closest relatives Aminobacter niigataensis, Aminobacter aminovorans and Mesorhizobium plurifarium, respectively. Phylogenomic analyses using whole-genome sequences consistently placed this strain within the family Phyllobacteriaceae. However, its phylogenetic position did not correspond to any known genus within this family. The genome of strain SB112T was found to possess the form II coxL gene, which encodes the large subunit of the CO dehydrogenase and potentially enables CO oxidation. The average nucleotide identity and digital DNA–DNA hybridization with members of closely related genera yielded values below the thresholds for prokaryotic species delineation (95–96 and 70%, respectively). Based on the phenotypic, chemotaxonomic, phylogenetic, genomic and physiological properties, strain SB112T is considered to represent a novel species of a new genus Foliimonas within the family Phyllobacteriaceae for which the name Foliimonas ilicis gen. nov., sp. nov. is proposed. The type of strain is SB112T (=LMG 33802T, =NCAIM B.02691T

Microbiology Society

Yang Yang, Yan Zhao, Wei Zhao, Yingqi Zhang, Hongmei Wang, Murray Grant, Patrick Schäfer, Yuling Meng, Weixing Shan

Reactive oxygen species (ROS) are key signaling molecules in plant development and immunity, but current understanding is primarily focused on apoplastic and chloroplastic ROS. Mitochondria are also a key source of intracellular ROS, yet their contribution to plant immunity is poorly characterized. Here, we studied mitochondrial ROS (mROS) function in plant-pathogen interactions, deploying genetically encoded sensors, assorted fluorescent markers, and genetic approaches to track mROS, specifically H2O2, dynamics and identify interorganelle contact sites. We unexpectedly found a mitochondria–endoplasmic reticulum (ER) ROS signal cascade functioning independently of apoplastic and chloroplastic ROS in plant immunity. mROS initiate immune responses induced by the oomycete pathogen Phytophthora parasitica and promote mitochondria-ER association. These enhanced mitochondria-ER membrane associations are required for transfer of mROS signals and initiation of extensive unfolded protein responses. We conclude that mROS transfer via mitochondria-ER membranes to the ER lumen is an underappreciated yet essential component in plant defense.

Science Advances 2025

Dykes, Charlotte, Pearson, Jonathan M., Bending, Gary D. and Abolfathi, Soroush

Free-water surface constructed wetlands (CWs) are sustainable, low emission, nature-based solutions for water and wastewater treatment. However, the discharge of nutrient-rich effluents from CWs treating wastewater can adversely impact freshwater ecosystems and exacerbate eutrophication. Despite their ecological benefits, limited research exists on the treatment efficiency and pollutant dynamics of CWs under varying seasonal and environmental pressures. This study investigates the treatment efficiency of an integrated CW (ICW) serving as a nature-based solution for treating partially treated wastewater before release into the environment. Our findings highlight the dynamic and sensitive mechanisms influencing nutrient removal in CWs, driven by seasonal hydraulic conditions, vegetation phenology, and climatic factors. The study provides critical insights for optimizing CW design and management under fluctuating environmental conditions to enhance their resilience, ensure regulatory compliance, and maintain long-term treatment efficiency. This understanding is essential for guiding future regulatory policies and ensuring that CWs meet water quality standards in response to climate pressures.

Journal of Water Process Engineering. March 2025

Cara Wharton, Andrew Beacham, Miriam L. Gifford and James Monaghan

There is much interest in how roots can be manipulated to improve crop performance in a changing climate, yet root research is made difficult by the challenges of visualising the root system accurately, particularly when grown in natural environments such as soil. This study reports a novel, low cost, Rootrainer-based system for root phenotyping. This novel Rootrainertron method has many advantages over existing methods of phenotyping seedling roots. Rootrainers are cheap, and readily available from garden centres, unlike rhizotrons which are expensive and only available from specialist suppliers. Rootrainers allow the roots to grow in substrate medium, providing a significant advantage over agar and paper assays.This approach offers an affordable and relevant root phenotyping option and makes root phenotyping more accessible and applicable for researchers.

Plant Methods. March 2025

Matevz Papp-Rupar, Emily R. Grace, Naina Korotania, Maria-Laura Ciusa, Robert W. Jackson, Mojgan Rabiey

Isolation of phages targeting the cherry pathogen Pseudomonas syringae pv. syringae (Pss) led to five distinct phage genotypes. Building on previous in vitro coevolution experiments, the coevolution of the five phages (individually and as a cocktail) with Pss on cherry leaves was conducted in glasshouse and field experiments. Phages effectively reduced Pss numbers on detached leaves, with no evidence of phage resistance emerging in the bacterial population. Field application of phages in a cherry orchard in Southeast England evaluated phage survival, viability and impact on bacterial populations and the microbial community. The bacterial population and phages persisted in the leaf and shoot environment as long as the bacterial host was present. In contrast to in vitro studies, the plant environment constrained the emergence of phage resistant Pss populations.

Environmental Microbiology. March 2025

Logan Kistler, Fabio de Oliveira Freitas, Rafal M. Gutaker, S. Yoshi Maezumi, Jazmín Ramos-Madrigal, Marcelo F. Simon, J. Moises Mendoza Flores, Sergei V. Drovetski, ¬Hope Loiselle, Eder Jorge de Oliveira, Eduardo Alano Vieira, Luiz Joaquim Castelo Branco Carvalho, Marina Ellis Perez, Audrey T. Lin, Hsiao-Lei Liu, Rachel Miller, Natalia A. S. Przelomska, Aakrosh Ratan, Nathan Wales, Kevin Wann, Shuya Zhang, Magdalena García, Daniela Valenzuela, Francisco Rothhammer, Calogero M. Santoro, Alejandra I. Domic, José M. Capriles, Robin Allaby

Manioc—also called cassava and yuca—is among the world’s most important crops, originating in South America in the early Holocene. Domestication for its starchy roots involved a near-total shift from sexual to clonal propagation, and almost all manioc worldwide is now grown from stem cuttings. In this work, we analyze 573 new and published genomes, focusing on traditional varieties from the Americas and wild relatives from herbaria, to reveal the effects of this shift to clonality. We observe kinship over large distances, maintenance of high genetic diversity, intergenerational heterozygosity enrichment, and genomic mosaics of identity-by-descent haploblocks that connect all manioc worldwide. Interviews with Indigenous traditional farmers in the Brazilian Cerrado illuminate how traditional management strategies for sustaining, diversifying, and sharing the gene pool have shaped manioc diversity.

Science. March 2025

Press release

Jennifer Byrne, Robert Lillywhite, Henry Creissen, Fiona Thorne, Lael Walsh

Integrated Pest Management (IPM) is a crop health paradigm offering a framework for sustainable pest management. To optimise adoption it is necessary to understand how growers use IPM, to identify measures lagging in uptake or suitability for uptake and to explore limitations to both. This study has quantified IPM adoption using Irish food horticulture as a case study, through the development and application of an IPM metric based on field, protected and top fruit production systems. While our results demonstrated that IPM has been adopted, it also suggested that there is room for improvement. This presentation of an IPM measurement instrument for temperate horticulture systems provides the means to benchmark IPM performance and chart cumulative progress. This is useful to policy makers and IPM stakeholders to compare performance on a national and cross-national basis with a view to refining best practice, while defining specific components of IPM for improvement.

Crop Protection. February 2025

Assessing delimiting strategies to identify the infested zones of quarantine plant pests and diseases

Koh, Joshua, Cunnifee, Nik and Parnell, Stephen

Following the discovery of a quarantine plant pest or disease, delimitation is urgently conducted to define the boundaries of the infested area, typically through surveys that detect the presence or absence of the pest. Swift and accurate delimitation is crucial after a pest or pathogen enters a new region for containment or eradication. In this study, we used an individual-based model to simulate the spread of Huanglongbing (citrus greening), a priority EU pest, and evaluated three delimiting strategies across various host distribution landscapes. We found that an adaptive strategy was most effective, especially when tailored to the polycyclic nature of the pest. This underscored the need for specific delimiting approaches based on the epidemiological characteristics of the target pest.

Scientific Reports. February 2025

Developing epidemiological preparedness for a plant disease invasion: Modelling citrus huánglóngbìng in the European Union

Huánglóngbìng (HLB) is a bacterial disease of citrus that has significantly impacted Brazil and the United States, although citrus production in the Mediterranean Basin remains unaffected. By developing a mathematical model of spread in Spain, we tested surveillance and control strategies before any future HLB entry in the EU. We found while some citrus production might be maintained by roguing, this requires extensive surveillance and significant chemical control, perhaps also including testing of psyllids (which spread the pathogen) for bacterial DNA. Our work highlights the key importance of early detection (including asymptomatic infection) and vector control for HLB management.

Plants, People, Planet. February 2025

Nelesh Patra , Guy C. Barker , Mrinal K. Maiti

Indian mustard (Brassica juncea L.) seed oil offers valuable dietary benefits due to a balanced ratio of human essential fatty acids, the traditional high oil-yielding varieties contain an elevated level of erucic acid (EA, C22:1) associated with adverse health effects. Therefore, developing low erucic acid (LEA) mustard cultivars is crucial for broader utilization and consumer safety. In this study, CRISPR/Cas9 genome editing tool was employed to disrupt the fatty acid elongase1 (FAE1) gene that encodes a key enzyme in EA biosynthesis in two high erucic acid (HEA) B. juncea cultivars, PCR7 (∼39% EA) and JD6 (∼45% EA). Our findings underscore the effectiveness of CRISPR/Cas9 technology for editing B. juncea genome, developing plant lines producing LEA seed oil with improved nutritional quality and broadening the utility of this important oilseed crop for food and non-food applications.

Plant Physiology & Biochemistry. February 2025

Huazhen Liu, Lakshminarayan M. Iyer, Paul Norris, Ruiying Liu, Keshun Yu, Murray Grant, L. Aravind, Aardra Kachroo & Pradeep Kachroo

Dietary consumption of lysine in humans leads to the biosynthesis of Δ1-piperideine-6-carboxylic acid (P6C), with elevated levels linked to the neurological disorder epilepsy. Here we demonstrate that P6C biosynthesis is also a critical component of lysine catabolism in Arabidopsis thaliana. P6C regulates vitamin B6 homeostasis, and increased P6C levels deplete B6 vitamers, resulting in compromised plant immunity. We further establish a key role for pyridoxal and pyridoxal-5-phosphate biosynthesis in plant immunity. Our analysis indicates that P6C metabolism probably evolved through combining select lysine and proline metabolic enzymes horizontally acquired from diverse bacterial sources at different points during evolution. More generally, certain enzymes from the lysine and proline metabolic pathways were probably recruited in evolution as potential guardians of B6 vitamers and for semialdehyde detoxification.

Nature Plants. February 2025

Baudin, Nastasia, Garrod, Mark, Bramke, Irene, Mckillican, Carol, Schafer, Hendrik, Hand, Laurence, Cione, Ana, Bending, Gary D, Marshall, Samantha

Brazilian soils have distinctive characteristics to European and North American soils which are typically used to investigate pesticide fate. This study aimed to compare soil–water partition coefficient (Kd), reversibility of adsorption and degradation half-life (DT50) of 5 pesticides covering a wide range of physico-chemical properties in contrasting Brazilian soils and a temperate (UK) alfisol soil, and to study their relationship with soil OM, clay and expandable clay content, CEC and pH. The results showed that pesticide behaviour in Brazilian soils was not systematically different from those in European and North American soils. The 3PA was shown to be a reliable and simple method for assessing pesticide desorption in soil and could be adapted to assess pesticide bioavailability. The use of the 3PA allowed a more thorough explanation of the observed differences in degradation behaviour between the compounds.

Environmental Monitoring and Assessment. January 2025

Anna Lazar, Robert I. Griffiths, Tim Goodall, Lisa R. Norton, Ryan M. Mushinski & Gary D. Bending

The genus Tetracladium has historically been regarded as an aquatic hyphomycete. However, sequencing of terrestrial ecosystems has shown that Tetracladium species might also be terrestrial soil and plant-inhabiting fungi. The diversity of Tetracladium species, their distribution across ecosystems, and the factors that shape community composition remain largely unknown. Using internal transcribed spacer (ITS) amplicon sequencing, we investigated the spatial distribution of Tetracladium in 970 soil samples representing the major ecosystems found across the British landscape. Overall, this study provides insights into the community composition patterns of Tetracladium in terrestrial ecosystems and highlights the importance of vegetation characteristics in shaping Tetracladium communities.

Environmental Microbiome. December 2024

Diana Vinchira-Villarraga, Sabrine Dhaouadi, Vanja Milenkovic, Jiaqi Wei, Emily R. Grace, Katherine G. Hinton, Amy J. Webster, Andrea Vadillo-Dieguez, Sophie E. Powell, Naina Korotania, Leonardo Castellanos, Freddy A. Ramos, Richard J. Harrison, Mojgan Rabiey & Robert W. Jackson

This study aimed to develop a methodological approach to obtain extracts from different tree species with the highest reproducibility and chemical diversity possible, to ensure proper coverage of the trees’ metabolome. Each tree species has a unique metabolic profile, which means that no single protocol is universally effective. Extraction at 50 °C for three cycles using 80% methanol or chloroform/methanol/water showed the best results and is suggested for studying wood metabolome. These observations highlight the need to tailor extraction protocols to each tree species to ensure comprehensive metabolome coverage for metabolic profiling.

Metabolomics. December 2024

Lauren HK Chappell, Guy C Barker, John P Clarkson

Parsnips (Pastinaca sativa) are a speciality UK crop with an economic value of at least 31M GBP annually. Currently, the major constraints to production are losses associated with root canker disease due to a range of fungal pathogens, among which Itersonilia pastinacae is of most concern to growers. With limited research conducted on this species, this work aimed to provide a much-needed characterisation of isolates from across the UK, continental Europe, and New Zealand. Following whole genome sequencing, specific primers were designed for the molecular characterisation of the isolates using six housekeeping genes and three highly variable functional genes. Phylogenetic analysis separated isolates into two and six clades, respectively, but the grouping was not associated with hosts or locations. Based on the results of this research, there was no evidence to support more than a single species of Itersonilia among the isolates studied.

Journal of Fungi. December 2024

Anna Lazar, Richard P Phillips, Stephanie Kivlin, Gary D Bending, Ryan M Mushinski

Although Tetracladium species have traditionally been studied as aquatic saprotrophs, the growing number of metagenomic and metabarcoding reports detecting them in soil environments raises important questions about their ecological adaptability and versatility. We investigated the factors associated with the relative abundance, diversity and ecological dynamics of Tetracladium in temperate forest soils. Collectively, our findings highlight the ecological significance of Tetracladium in temperate forest soils and emphasize the importance of site-specific factors and microbial interactions in shaping their distribution patterns and ecological dynamics.

Environmental Microbiology. November 2024

Helen J. Bates, Jamie Pike, R. Jordan Price, Sascha Jenkins, John Connell, Andrew Legg, Andrew Armitage, Richard J. Harrison and John P. Clarkson

This study presents the first genome and transcriptome analyses for Fusarium oxysporum f. sp. lactucae (Fola) which causes Fusarium wilt disease of lettuce. Long-read genome sequencing of three race 1 (Fola1) and three race 4 (Fola4) isolates revealed key differences in putative effector complement between races and with other F. oxysporum ff. spp. following mimp-based bioinformatic analyses.

Frontiers in Plant Science. October 2024

Shashank K Pandey, Jay Prakash Maurya, Bibek Aryal, Kamil Drynda, Aswin Nair, Pal Miskolczi, Rajesh Kumar Singh, Xiaobin Wang, Yujiao Ma, Tatiana de Souza Moraes, Emmanuelle M Bayer, Etienne Farcot, George W Bassel, Leah R Band, Rishikesh P Bhalerao

The control of cell–cell communication via plasmodesmata (PD) plays a key role in plant development. In tree buds, low-temperature conditions (LT) induce a switch in plasmodesmata from a closed to an open state, which restores cell-to-cell communication in the shoot apex and releases dormancy. Using genetic and cell-biological approaches, we have identified a previously uncharacterized transcription factor, Low-temperature-Induced MADS-box 1 (LIM1), as an LT-induced, direct upstream activator of the gibberellic acid (GA) pathway. Mathematical modeling and experimental validation suggest that negative feedback regulation of LIM1 by gibberellin could play a crucial role in maintaining the robust temporal regulation of bud responses to low temperature. These results reveal genetic factors linking temperature control of cell–cell communication with regulation of seasonally-aligned growth crucial for adaptation of trees.

EMBO Journal. October 2024

Xiaoning He, Chloé Dias Lopes, Leonardo I Pereyra-Bistrain, Ying Huang, Jing An, Rim Brik Chaouche, Hugo Zalzalé, Qingyi Wang, Xing Ma, Javier Antunez-Sanchez, Catherine Bergounioux, Sophie Piquerez, Sotirios Fragkostefanakis, Yijing Zhang, Shaojian Zheng, Martin Cresp, Magdy M Mahfouz, Olivier Mathieu, Federico Ariel, Jose Gutierrez-Marcos, Xingwang Li, Nicolas Bouché, Cécile Raynaud, David Latrasse, Moussa Benhamed

The 3D chromatin organization plays a major role in the control of gene expression. In this study, employing a combination of genetics and advanced 3D genomics approaches, we demonstrated that a redistribution of facultative heterochromatin marks in regions usually occupied by constitutive heterochromatin marks disrupts the 3D genome compartmentalisation. This disturbance, in turn, triggers novel chromatin interactions between genic and transposable element (TE) regions. Interestingly, our results imply that epigenetic features, constrained by genetic factors, intricately mold the landscape of 3D genome organisation. This study sheds light on the profound genetic-epigenetic interplay that underlies the regulation of gene expression within the intricate framework of the 3D genome. Our findings highlight the complexity of the relationships between genetic determinants and epigenetic features in shaping the dynamic configuration of the 3D genome.

Nucleic Acids Research. September 2024

Lim Chee Liew, Yue You, Lucas Auroux, Marina Oliva, Marta Peirats-Llobet, Sophia Ng, Muluneh Tamiru-Oli, Oliver Berkowitz, Uyen Vu Thuy Hong, Asha Haslem, Tim Stuart, Matthew E. Ritchie, George W. Bassel, Ryan Lister, James Whelan, Quentin Gouil & Mathew G. Lewsey

Here we describe a temporal analysis of the germinating Arabidopsis thaliana embryo at single-cell resolution. We define the highly dynamic cell type-specific patterns of gene expression and how these relate to changing cellular function as germination progresses. Underlying these are unique gene regulatory networks and transcription factor activity. We unexpectedly discover that most embryo cells transition through the same initial transcriptional state early in germination, even though cell identity has already been established during embryogenesis. Cells later transition to cell type-specific gene expression patterns. Furthermore, our analyses support previous findings that the earliest events leading to the induction of seed germination take place in the vasculature. Overall, our study constitutes a general framework with which to characterize Arabidopsis cell transcriptional states through seed germination, allowing investigation of different genotypes and other plant species whose seed strategies may differ. Nature Plants. September 2024

Habib Bashour, Eva Smorodina, Matteo Pariset, Jahn Zhong, Rahmad Akbar, Maria Chernigovskaya, Khang Lê Quý, Igor Snapkow, Puneet Rawat, Konrad Krawczyk, Geir Kjetil Sandve, Jose Gutierrez-Marcos, Daniel Nakhaee-Zadeh Gutierrez, Jan Terje Andersen & Victor Greiff

Designing effective monoclonal antibody (mAb) therapeutics faces a multi-parameter optimization challenge known as “developability”, which reflects an antibody’s ability to progress through development stages based on its physicochemical properties. To chart natural and engineered DP landscapes, we computed 40 sequence- and 46 structure-based DPs of over two million native and human-engineered single-chain antibody sequences. We show that sequence DPs are more predictable than structure-based ones across different machine-learning tasks and embeddings, indicating a constrained sequence-based design space. Human-engineered antibodies localize within the developability and sequence landscapes of natural antibodies, suggesting that human-engineered antibodies explore mere subspaces of the natural one. Our work quantifies the plasticity of antibody developability, providing a fundamental resource for multi-parameter therapeutic mAb design.

Communications Biology July 2024

Eleanor L. Dearlove, David Chandler, Steve Edgington, Shaun D. Berry, Gareth Martin, Claus Svendsen & Helen Hesketh

Management of T. vaporariorum is problematic because of widespread pesticide resistance, and many greenhouse growers rely on biological control agents to regulate T. vaporariorum populations. However, these are often slow and vary in efficacy, leading to subsequent application of chemical insecticides when pest populations exceed threshold levels. In this study, we evaluated co-applications of the entomopathogenic fungi (EPF) Beauveria bassiana and Cordyceps farinosa and the chemical insecticide spiromesifen in laboratory bioassays. Results indicate the potential for combined applications of EPF and spiromesifen as an effective integrated pest management strategy and demonstrate the applicability of the MixTox model to describe complex mixture interactions.

Scientific Reports. July 2024

Nicole Pereira, Kathryn R. Hales, Andrew Mead, Lauren H. K. Chappell, Guy C. Barker, John P. Clarkson

In Europe, cavity spot disease continues to have a major impact on marketable yield. The lack of reliable inoculation methods for these Pythium pathogens has, for many years, hampered the identification of new effective crop protection products or carrot varieties that are resistant to the disease. In this research, inoculation methods were developed for P. violae using mycelium or oospores, each of which successfully induced typical cavity spot symptoms in both pot- and field-grown carrots as well as consistent root stunting in the former. These methods were also used to successfully identify carrot cultivars with resistance to cavity spot and confirmed the efficacy of the fungicide metalaxylM against the disease. Results therefore demonstrated that the inoculation methods should be reliable for identifying the efficacy of crop protection products, assessing cavity spot resistance and for further studies investigating the biology and epidemiology of the pathogen.

Plant Pathology. July 2024

Jing An, Rim Brik Chaouche, Leonardo I Pereyra-Bistraín, Hugo Zalzalé, Qingyi Wang, Ying Huang, Xiaoning He, Chloé Dias Lopes, Javier Antunez-Sanchez, Catherine Bergounioux, Claire Boulogne, Cynthia Dupas, Cynthia Gillet, José Manuel Pérez-Pérez, Olivier Mathieu, Nicolas Bouché, Sotirios Fragkostefanakis, Yijing Zhang, Shaojian Zheng, Martin Crespi, Magdy M Mahfouz, Federico Ariel, Jose Gutierrez-Marcos, Cécile Raynaud, David Latrasse, Moussa Benhamed

In recent years, the exploration of genome three-dimensional (3D) conformation has yielded profound insights into the regulation of gene expression and cellular functions in both animals and plants. Employing advanced high-throughput sequencing and microscopy techniques, we investigated the landscape of 26 histone modifications and RNA polymerase II distribution in tomato (Solanum lycopersicum). Our study unveiled a rich and nuanced epigenetic landscape, shedding light on distinct chromatin states associated with heterochromatin formation and gene silencing. Moreover, we elucidated the intricate interplay between these chromatin states and the overall topology of the genome. Employing a genetic approach, we delved into the role of the histone modification H3K9ac in genome topology. Notably, our investigation revealed that the ectopic deposition of this chromatin mark triggered a reorganization of the 3D chromatin structure, defining different TAD-like borders. Our work emphasizes the critical role of H3K9ac in shaping the topology of the tomato genome, providing valuable insights into the epigenetic landscape of this agriculturally significant crop species.

PNAS. July 2024

Mojgan Rabiey, Emily R. Grace, Paulina Pawlos, Muscab Bihi, Haleem Ahmed, Georgina E. Hampson, Amna Al Riyami, Leena Alharbi, Rosa Sanchez-Lucas, Naina Korotania, Maria Laura Ciusa, Olivia Mosley, Michelle T. Hulin, Laura Baxter, Sabrine Dhaouadi, Diana Vinchira-Villarraga, Robert W. Jacks

Pseudomonas syringae pathovar syringae (Pss) is a major pathogen of cherry (Prunus avium) causing bacterial canker of the stem, leaf and fruit, impacting productivity and leading to a loss of trees. In an attempt to find a treatment for this disease, naturally occurring bacteriophage (phage) that specifically target Pss is being investigated as a biocontrol strategy. However, before using them as a biocontrol treatment, it is important to both understand their efficacy in reducing the bacterial population and determine if the bacterial pathogens can evolve resistance to evade phage infection. To investigate this, killing curve assays of five MR phages targeting Pss showed that phage resistance rapidly emerges in vitro, even when using a cocktail of the five phages together. This study shows that understanding the genetic mechanisms of bacterial pathogen resistance to phages is important for helping to design a more effective approach to kill the bacteria while minimizing the opportunity for phage resistance to manifest.

Microbial Biotechnology. June 20204

Laura Reyes-Haro, Gillian Prince, Rommel Santiago Granja-Travez, David Chandler

The diamondback moth (DBM) (Plutella xylostella) causes large losses to global crop production. Conventional insecticides are losing effectiveness due to resistance. Consequently, there is a growing interest in sustainable control methods like entomopathogenic fungi (EPF) in Integrated Pest Management. However, the field efficacy of fungi varies due to environmental influences. In this study, a group of 50 Beauveria strains sourced from different locations were characterized by genotype and phenotype with respect to their conidial production, temperature and UV-B radiation tolerance, and virulence against DBM. Survival under environmental conditions is crucial for EPF-based commercial products against DBM. Results suggest strain tolerance to environmental stressors is more tied to specific micro-climatic factors than geographical origin. Each strain exhibited unique characteristics; for example, the most virulent strain (#29) was highly UV-sensitive. Therefore, characterizing diverse strains provides essential genotypic and phenotypic insights, which are fundamental for understanding their role as biocontrol agents while facilitating efficient biopesticide product development and uptake

Pest Management Science. June 2024

Juanjuan Xiao, Deying Wang, Banerjee Sinchan, Ryan Mushinski, Decai Jin, Ye Deng

Chromium pollution, particularly hexavalent chromium [Cr(VI)], may threaten the environment and human health. This study investigated the potential of Tagetes erecta L. (Aztec marigold) for phytoremediation of soil contaminated with Cr(VI), and focused on the effects of varying concentrations of Cr(VI) on both the physicochemical properties of soil and microbiome of Tagetes erecta L.  We observed that Tagetes erecta L. showed tolerance to Cr(VI) stress and maintained normal growth under these conditions, as indicated by bioconcentration factors of 0.33–0.53 in shoots and 0.39–0.70 in roots. Meanwhile, the structure and diversity of bacterial communities were significantly affected by Cr(VI) pollution. This study explored the interactions between heavy metals, microorganisms, and plants, providing valuable insights for developing in situ bioremediation of Cr(VI)-contaminated soils.

Science of the Total Environment. May 2024

Deepa Paliwal, Mojgan Rabiey, Tim H. Mauchline

Aphids are globally important pests causing damage to a broad range of crops. Due to insecticide resistance, there is an urgent need to develop alternative control strategies. In our previous work, we found Pseudomonas fluorescens PpR24 can orally infect and kill the insecticide-resistant green-peach aphid (Myzus persicae). However, the genetic basis of the insecticidal capability of PpR24 remains unclear. This comprehensive host–pathogen transcriptomic analysis provides novel insight into the molecular basis of bacteria-mediated aphid mortality and the potential of PpR24 as an effective biocontrol agent.

Environmental Biology. April 2024

Amol M. Bhandare, Nicholas Dale, Robert T. R. Huckstepp

In vivo brain imaging, using a combination of genetically encoded Ca2+ indicators and gradient refractive index (GRIN) lens, is a transformative technology that has become an increasingly potent research tool over the last decade. We have refined the intravital imaging technique to image deep brain nuclei in the ventral medulla oblongata, one of the most difficult brain structures to image due to the movement of brainstem structures outside the cranial cavity during free behaviour (head and neck movement), whose targeting requires GRIN lens insertion through the cerebellum—a key structure for balance and movement. Our protocol refines the implantation method of GRIN lenses, giving the best possible approach to image deep extracranial brainstem structures in awake rodents with improved cell rejection/acceptance criteria during analysis. This revised method paves the way to image challenging brainstem structures to investigate their role in complex behaviours such as breathing, circulation, sleep, digestion, and swallowing, and could be extended to image and study the role of cerebellum in balance, movement, motor learning, and beyond.

Bio-protocol. April 2024