Environment & Ecology Publications

Matt Bawn, Nigel Francis, Liz Alvey, Christopher Hassall, Andre Pires-daSilva, Pedro Barra, Denise Hough, Hannah Campbell, Matt Hardy, Juanvi Canet-Perez

The advent of Generative Artificial Intelligence (GenAI) is already impacting pedagogic strategies and assessment methodologies in higher education, particularly in the biological sciences which have traditionally relied heavily on written assessments. GenAI's rapid and plausible text generation capabilities challenge traditional written assessments and prompt a shift towards more authentic assessment types. This paper explores innovative applications of GenAI in biology education through case studies presented at a recent workshop. These case studies illustrate how GenAI has the potential to enhance academic activities, from developing learning resources to fostering student engagement through active learning strategies. The discussion highlights a shift from product-oriented assessments to process-oriented approaches that prioritize continuous interaction, iteration, and reflection among learners. Despite GenAI's reliance on pre-existing data raising concerns about originality and contextual accuracy, and its limitations in tasks requiring high creativity and deep understanding, it has the potential to enhance educational practices when applied with awareness of its constraints. The paper concludes with a balanced analysis of the transformative impact and inherent challenges of integrating GenAI into biology education, advocating for thoughtful implementation to ensure it augments rather than replaces traditional teaching methods.

Advances in Physiology Education- 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

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.

Biological Control, December 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

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

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

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.

The Lancet, 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

Naomi S. Prosser, Eamonn Ferguson, Jasmeet Kaler, Edward M. Hill, Michael J. Tildesley, Matt J. Keeling, Martin J. Green

BACKGROUND: Psychosocial factors are important for the uptake of livestock disease control measures by farmers and can differ by region, which would have implications for disease control nationally.

METHODS: We investigated altruism, trust, psychological proximity and the COM-B behaviour change framework in a survey of 475 British cattle farmers in 2020. Using regression models, we studied associations between the country farmers lived in and psychosocial and behaviour change factors. RESULTS: There were many between-country differences in farmers' psychosocial and COM-B profiles. Accounting for multiple tests, Scottish cattle farmers reported higher trust in governmental judgements for disease control and greater social opportunity to control disease than English cattle farmers.

LIMITATIONS: There were relatively low numbers of respondents from Scotland and Wales. As such, the results should be interpreted with caution. Northern Irish farmers could not be included in the analyses as there were too few responses.

CONCLUSION: Cattle farmers differed in their psychosocial profiles by country. Our sample of Scottish farmers reported higher trust in, and felt better supported by, government in the context of disease control than the English farmers, which could be due to different disease control approaches between devolved governments. Understanding between-country differences in farmer psychosocial attributes has implications for animal health governance and approaches to disease control.

Veterinary Record, October 2025

Christophe Corre, Gideon A. Idowu, Lijiang Song, Melanie E. Whitehead, Lona M. Alkhalaf, Gregory L. Challis

The methylenomycins are highly functionalized cyclopentanone antibiotics produced by Streptomyces coelicolor A3(2). A biosynthetic pathway to the methylenomycins has been proposed based on sequence analysis of the proteins encoded by the methylenomycin biosynthetic gene cluster and the incorporation of labeled precursors. However, the roles played by putative biosynthetic enzymes remain experimentally uninvestigated. Here, the biosynthetic functions of enzymes encoded by mmyD, mmyO, mmyF, and mmyE were investigated by creating in-frame deletions in each gene and investigating the effect on methylenomycin production. No methylenomycin-related metabolites were produced by the mmyD mutant, consistent with the proposed role of MmyD in an early biosynthetic step. The production of methylenomycin A, but not methylenomycin C, was abolished in the mmyF and mmyO mutants, consistent with the corresponding enzymes catalyzing the epoxidation of methylenomycin C, as previously proposed. Expression of mmyF and mmyO in a S. coelicolor M145 derivative engineered to express mmr, which confers methylenomycin resistance, enabled the resulting strain to convert methylenomycin C to methylenomycin A, confirming this hypothesis. A novel metabolite (premethylenomycin C), which readily cyclizes to form the corresponding butanolide (premethylenomycin C lactone), accumulated in the mmyE mutant, indicating the corresponding enzyme is involved in introducing the exomethylene group into methylenomycin C. Remarkably, both premethylenomycin C and its lactone precursor were one to two orders of magnitude more active against various Gram-positive bacteria, including antibiotic-resistant Staphylococcus aureus and Enterococcus faecium isolates, than methylenomycins A and C, providing a promising starting point for the development of novel antibiotics to combat antimicrobial resistance.

Journal of the American Chemical Society, October 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

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

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

Niba Rawlings, Ngwa, Bailey, Mark and Courtenay, Orin

This systematic review and meta-analysis of data specific to military populations aims to identify knowledge gaps to mitigate sand fly exposure and Leishmania transmission during deployments. Regular use of long-lasting insecticidal nets to mitigate sand fly exposure demonstrated high potential effectiveness than other reported personal protective measures (PPMs) which yielded mixed or inconclusive results. In summary, the systematic review revealed the substantial variability between study designs and statistical integrity. There is need for more consistent and robustly designed studies including well-define controls and replication. Future studies would be advised to explore the long-term effectiveness and practicality of PPMs, both individually and in combination, across diverse deployment settings.

PLoS Neglected Tropical Diseases. 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

Glen Guyver-Fletcher, Erin E. Gorsich, Chris Jewell, Michael J. Tildesley

In this article we present a spatially-explicit stochastic metapopulation model to simulate the spread and control of foot-and-mouth disease (FMD) in an endemic setting. We parameterise and validate the model using detailed outbreak data from the Republic of Turkey, 2001–2012. Subsequently, we assess the efficacy of ring vaccination, mass vaccination, and livestock movement restrictions with regards to incidence-reduction and likelihood of eradication. Our results suggest countries wishing to control the disease within their borders should focus on comprehensive surveillance and vaccination campaigns as their main policy goals. In summary, vaccination-based policies are more effective than movement restrictions in the endemic context.

Infectious Disease Modelling.; 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

Zdouc, Mitja M. et al inc. Alberti, F

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard.

Nucleic Acids Research. January 2025

Kelsey Cremin, Gabriel N. Meloni, Orkun S. Soyer, Patrick R. Unwin

This work presents an experimental platform combining scanning ion conductance microscopy (SICM) with confocal laser scanning microscopy (CLSM), using intra- and extracellular pH indicator dyes to study the impact of acid delivery on individual HeLa cells within a population.. We find a strong dependency between the intracellular pH and the extracellular pH gradient imposed by local acid delivery. Postdelivery intracellular pH recovery depends on the extent of the acid challenge, with cells exposed to lower pH not returning to basal intracellular pH values after the extracellular pH recovers. This is a unique method for concentration-gradient challenge studies of cell populations that will have broad applications in cell biology. SICM can be used to deliver different chemicals and enables a wide range of local conditions to be applied across a cell population, for which the effects can be investigated at the single-cell level.

ACS Measurement Science. January 2025

Jean B. Contina, Rachel L. Seibel, Bhim Chaulagain, Karasi B. Mills, Michael J. Tildesley, Christopher C. Mundt

We applied a previously published livestock foot-and-mouth disease (FMD) model to estimate host connectivity using a transmission kernel based on contact tracing and measured subsequent to an animal movement ban in the 2001 United Kingdom epidemic. Connectivity within county-level farm landscapes were evaluated by considering the transmission kernel, host species composition, farm-level susceptibility, farm-level transmissibility, and distances between farms.  Connectivity of the initially infected farm and mean connectivity among all farms in a county were strongly associated with effects of cull size, with disease control more effective at lower levels of farm connectivity. Host connectivity provides early information on the host-pathogen landscape and could be used as an assessment tool for predicting epidemic risks, as well as enabling preemptive control strategies to limit the size of disease outbreaks.

Ecosphere. December 2024

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

Adams, Sally, Tandonnet, Sophie and Pires-da Silva, André Francisco

Trioecy, a rare reproductive system where hermaphrodites, females, and males coexist, is found in certain algae, plants, and animals. Though it has evolved independently multiple times, its rarity suggests it may be an unstable or transitory evolutionary strategy. In the well-studied Caenorhabditis elegans, attempts to engineer a trioecious strain have reverted to the hermaphrodite/male system, reinforcing this view. However, these studies did not consider the sex-determination systems of naturally stable trioecious species. The discovery of free-living nematodes of the Auanema genus, which have naturally stable trioecy, provides an opportunity to study these systems. In Auanema, females produce only oocytes, while hermaphrodites produce both oocytes and sperm for self-fertilization. Crosses between males and females primarily produce daughters (XX hermaphrodites and females), while male-hermaphrodite crosses result in sons only. These skewed sex ratios are due to X-chromosome drive during spermatogenesis, where males produce only X-bearing sperm through asymmetric cell division. The stability of trioecy in Auanema is influenced by maternal control over sex determination and environmental cues. These factors offer insights into the genetic and environmental dynamics that maintain trioecy, potentially explaining its evolutionary stability in certain species.

Genetics 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

Richard Olumakaiye, Christophe Corre, Fabrizio Alberti

Fungi are talented producers of secondary metabolites with applications in the pharmaceutical and agrochemical sectors. Aspergillus wentii CBS 141173 has gathered research interest due to its ability to produce high-value norditerpenoid compounds, including anticancer molecules. In this study, we aimed to expand the genomic information available for A. wentii to facilitate the identification of terpenoid biosynthetic genes that may be involved in the production of bioactive molecules.

The results provide a scaffold for the future exploration of terpenoid biosynthetic pathways for bioactive molecules in A. wentii. The terpenoid clusters identified in this study are candidates for heterologous gene expression and/or gene disruption experiments. The description and availability of the long-read genome assembly of A. wentii CBS 141173 further provides the basis for downstream genome analysis and biotechnological exploitation of this species.

BMC Genomics. November 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

Rawlings, Ngwa Niba, Bailey, Mark, Craig, Peter, Courtenay, Orin

British soldiers undergoing jungle training in Belize typically experience a relatively low risk of developing cutaneous leishmaniasis. However, an uncharacteristically large outbreak of cutaneous leishmaniasis occurred in 2022. This study aimed to determine the cumulative incidence of the disease and highlight potential shortcomings in personal protective measures to mitigate exposure to sand fly vector bites. A retrospective analysis was conducted on medical records of cutaneous leishmaniasis cases between 2005 and 2022, as well as on questionnaire responses regarding personal protective measures administered to cutaneous leishmaniasis cases in 2022. The reasons behind the unusually high numbers of cutaneous leishmaniasis cases and cumulative incidence in 2022 remain unclear, emphasising the need to improve personal protective measures provision and implement a comprehensive health education programme for troops undergoing jungle training in Belize.

Parasite Epidemiology and Control. November 2024

Jack A. Weaver, Duha Alkhder, Panward Prasongpholchai, Michaël D. Tadesse, Emmanuel L. de los Santos, Lijiang Song, Christophe Corre, Fabrizio Alberti

Pleurotin is a meroterpenoid specialized metabolite made by the fungus Hohenbuehelia grisea, and it is a lead anticancer molecule due to its irreversible inhibition of the thioredoxin-thioredoxin reductase system. Total synthesis of pleurotin has been achieved, including through a stereoselective route; however, its biosynthesis has not been characterized. In this study, we used isotope-labeled precursor feeding to show that the nonterpenoid quinone ring of pleurotin and its congeners is derived from phenylalanine. This work sets the foundation to fully elucidate the biosynthesis of pleurotin and its congeners, with long-term potential to optimize their production for therapeutic use and engineer the pathway toward the biosynthesis of valuable analogues.

ACS Chemical Biology. October 2024

Luke Richards, Kelsey Cremin, Mary Coates, Finley Vigor, Patrick Schäfer, and Orkun S Soyer

Soil microbial communities host a large number of microbial species that support important ecological functions such as biogeochemical cycling and plant nutrition. The extent and stability of these functions are affected by inter-species interactions among soil microorganisms, yet the different mechanisms underpinning microbial interactions in the soil are not fully understood. Here, we study the extent of nutrient-based interactions among two model, plant-supporting soil microorganisms, the fungi Serendipita indica, and the bacteria Bacillus subtilis. Our findings highlight that ammonia based N-sharing can be a previously under-appreciated mechanism underpinning interaction among soil microorganisms and could be influenced by microbial or abiotic alteration of pH in microenvironments.

ISME Journal. September 2024

Mirjam Seeliger, Sally Hilton, George Muscatt, Christopher Walker, David Bass, Felipe Albornoz, Rachel J Standish, Neil D Gray, Louis Mercy, Leonidas Rempelos, Carolin Schneider, Megan H Ryan, Paul E Bilsborrow, Gary D Bending

Arbuscular mycorrhizas (AM) are the most widespread terrestrial symbiosis and are both a key determinant of plant health and a major contributor to ecosystem processes through their role in biogeochemical cycling. Until recently, it was assumed that the fungi which form AM comprise the subphylum Glomeromycotina (G-AMF), and our understanding of the diversity and ecosystem roles of AM is based almost exclusively on this group. However recent evidence shows that fungi which form the distinctive 'fine root endophyte’ (FRE) AM morphotype are members of the subphylum Mucoromycotina (M-AMF), so that AM symbioses are actually formed by two distinct groups of fungi. We investigated the influence of nitrogen (N) addition and wheat variety on the assembly of AM communities under field conditions. The results demonstrate the need to consider both G-AMF and M-AMF when investigating AM communities, and highlight the importance of primer choice when investigating AMF community dynamics.

Environmental Microbiome. September 2024

Overview of the MOSAiC expedition: Ecosystem

Allison A. Fong, Clara J. M. Hoppe et al. (incl. H Schafer)

The international and interdisciplinary sea-ice drift expedition “The Multidisciplinary drifting Observatory for the Study of Arctic Climate” (MOSAiC) was conducted from October 2019 to September 2020. The aim of MOSAiC was to study the interconnected physical, chemical, and biological characteristics and processes from the atmosphere to the deep sea of the central Arctic system. The ecosystem team addressed current knowledge gaps and explored unknown biological properties over a complete seasonal cycle focusing on three major research areas: biodiversity, biogeochemical cycles, and linkages to the environment. This article provides a detailed overview of the sampling approaches used to address the three main science objectives. It highlights the core sampling program and provides examples of habitat- or process-specific sampling. The initial results presented include high biological activities in wintertime and the discovery of biological hotspots in underexplored habitats. The unique interconnectivity of the coordinated sampling efforts also revealed insights into cross-disciplinary interactions like the impact of biota on Arctic cloud formation. This overview further presents both lessons learned from conducting such a demanding field campaign and an outlook on spin-off projects to be conducted over the next years.

Elementa: Science of the Anthropocene. August 2024  

Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn's disease development

H2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota. The study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD. Microbiome. August 2024

Prioritising older individuals for COVID-19 booster vaccination leads to optimal public health outcomes in a range of socio-economic settings

Bouros, Ioana, Hill, Edward M., Keeling, Matt J., Moore, Sam and Thompson, Robin N.

The rapid development of vaccines against SARS-CoV-2 altered the course of the COVID-19 pandemic. In most countries, vaccinations were initially targeted at high-risk populations, including older individuals and healthcare workers. Policy makers must now determine how to deploy booster vaccinations, particularly when constraints in vaccine supply, delivery and cost mean that booster vaccines cannot be administered to everyone. A key question is whether older individuals should again be prioritised for vaccination, or whether alternative strategies (e.g. offering booster vaccines to the individuals who have most contacts with others and therefore drive infection) can instead offer indirect protection to older individuals. Here, we use mathematical modelling to address this question, considering SARS-CoV-2 transmission in a range of countries with different socio-economic backgrounds. We show that the population structures of different countries can have a pronounced effect on the impact of booster vaccination, even when identical booster vaccination targeting strategies are adopted. However, under the assumed transmission model, prioritising older individuals for booster vaccination consistently leads to the most favourable public health outcomes in every setting considered. PLoS Computational Biology. August 2024

Modelling timelines to elimination of sleeping sickness in the Democratic Republic of Congo, accounting for possible cryptic human and animal transmission

Sleeping sickness (gambiense human African trypanosomiasis, gHAT) is a vector-borne disease targeted for global elimination of transmission (EoT) by 2030. There are, however, unknowns that have the potential to hinder the achievement and measurement of this goal. These include asymptomatic gHAT infections (inclusive of the potential to self-cure or harbour skin-only infections) and whether gHAT infection in animals can contribute to the transmission cycle in humans. Using modelling, we explore how cryptic (undetected) transmission impacts the monitoring of progress towards and the achievement of the EoT goal. This study is the first to simulate an (as-yet-to-be available) screen-and-treat strategy and found that removing a parasitological confirmation step was predicted to have a more noticeable benefit to transmission reduction under the asymptomatic model compared with the others. Our simulations suggest vector control could greatly impact all transmission routes in all models, although this resource-intensive intervention should be carefully prioritised. Parasites & Vectors. August 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

Michael Hymas, Sopida Wongwas, Simin Roshan, Abigail L. Whittock, Christophe Corre, Reza Omidyan and Vasilios G. Stavros

Mycosporine glycine (MyG) was produced by the fermentation of a purposely engineered bacterial strain and isolated from this sustainable source. The ultrafast spectroscopy of MyG was then investigated in its native, zwitterionic form (MyGzwitter), via femtosecond transient electronic absorption spectroscopy. Complementary nonadiabatic (NAD) simulations suggest that, upon photoexcitation to the lowest excited singlet state (S1), MyGzwitter undergoes efficient nonradiative decay to repopulate the electronic ground state (S0). We propose an initial ultrafast ring-twisting mechanism toward an S1/S0 conical intersection, followed by internal conversion to S0 and subsequent vibrational cooling. This study illuminates the workings of the archetype mycosporine, providing photoprotection, in the UV–B range, to organisms such as corals, macroalgae, and cyanobacteria. This study also contributes to our growing understanding of the photoprotection mechanisms of life.

Journal of Physical Chemistry Letters. July 2024

Joshua C. Macdonald, Hayriye Gulbudak, Brianna Beechler, Erin E. Gorsich, Simon Gubbins, Eva Pérez-Martin and Anna E. Jolles

We investigated within-host dynamics and among-host transmission of three strains (SAT-1, -2, -3) of foot-and-mouth disease viruses (FMDVs) in their wildlife host, African buffalo. Our data reveals contrasting within-host dynamics among viral strains, with SAT-2 eliciting more rapid and effective immune responses than SAT-1 and SAT-3. Within-host viral fitness was overwhelmingly determined by variation among hosts in immune response activation rates but not by variation among individual hosts in viral growth rate. Our analyses investigating across-scale linkages indicate that viral replication rate in the host correlates with transmission rates among buffalo and that adaptive immune activation rate determines the infectious period. These parameters define the virus’s relative basic reproductive number (ℛ0), suggesting that viral invasion potential may be predictable from within-host dynamics.

American Naturalist. 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

Carvalho, Bruno M., Maia, Carla, Courtenay, Orin, Llabrés-Brustenga, Alba, Lotto Batista, Martín, Moirano, Giovenale, van Daalen, Kim R., Semenza, Jan C. and Lowe, Rachel

Leishmaniases are neglected diseases transmitted by sand flies. The aim of this modelling study was to develop an indicator that tracks climatic suitability for Leishmania infantum transmission in Europe at the subnational level. Historical records of sand fly vectors, human leishmaniasis, bioclimatic indicators, and environmental variables were integrated in a machine learning framework (XGBoost) to predict suitability in two past periods (2001–2010 and 2011–2020. This study demonstrates how key epidemiological data can be combined with open-source climatic and environmental information to develop an indicator that effectively tracks spatiotemporal changes in climatic suitability and disease risk. The positive association between the model predictions and human disease incidence demonstrates that this indicator could help target leishmaniasis surveillance to transmission hotspots.

The Lancet Regional Health - Europe. June 2024

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

Claire L. Jeffries, Luciano M Tantely, Perparim Kadriaj, Marcus S C Blagrove, Ioanna Lytra, James Orsborne, Hasan Mohammad Al-Amin, Abdul Rahim Mohammed, Mohammad Shafiul Alam, Romain Girod, Yaw A Afrane, Silvia Bino, Vincent Robert, Sebastien Boyer, Matthew Baylis, Enkelejda Velo, Grant L Hughes, Thomas Walker

In this study, we used laboratory vector competence experiments to determine if Cx. tritaeniorhynchus from a Southern European population were competent JEV vectors. We obtained samples from multiple geographically dispersed Cx. tritaeniorhynchus populations from countries within Europe, Africa, Eurasia and Asia to perform phylogenetic analysis to measure the level of mitochondrial divergence using the cytochrome oxidase subunit 1 (CO1) gene. We also undertook bacterial 16S rRNA gene amplicon sequencing to determine microbial diversity and used multi-locus sequence typing (MLST) to determine any evidence for the presence of strains of the naturally occurring endosymbiotic bacterium Wolbachia. Cx. tritaeniorhynchus from a Greek population were shown be be competent vectors of JEV with high levels of virus present in saliva. We found a signficant level of mitochondrial genetic diversity using the mosquito CO1 gene between geographically dispersed populations. Furthermore, we report diverse microbiomes identified by 16S rRNA gene amplicon sequencing within and between geographical populations. Evidence for the detection of the endosymbiotic bacteria Wolbachia was confirmed using Wolbachia-specific PCR and MLST.

Wellcome Open Research. May 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

Klomchit, A, Calabon, MS, Worabandit, S, Weaver, JA, Karima, EM, Alberti, F, Greco, C and Mahanil, S

This study aims to investigate the taxonomy, biosynthetic potential, and application of three newly isolated Neocosmospora species from mangrove habitats in the southern part of Thailand using phylogeny, bioactivity screening, genome sequencing, and bioinformatics analysis.

Two fungal isolates of Neocosmospora and a new species of N. mangrovei were reported in this study. These fungal strains showed activity against pathogenic fungi causing anthracnose in chili. In addition, full genome sequencing and bioinformatics analysis of N. mangrovei MFLUCC 17–0253 were obtained.

Journal of Applied Microbiology. May 2024

Alberto Torcello-Requena, Andrew Murphy, Ian D. E. A. Lidbury, Frances D. Pitt, Richard Stark, Andrew D. Millard, Richard J. Puxty, Yin Chen, David J. Scanlan

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus, the two most abundant phototrophs on Earth, thrive in oligotrophic oceanic regions. While it is well known that specific lineages are exquisitely adapted to prevailing in situ light and temperature regimes, much less is known of the molecular machinery required to facilitate occupancy of these low-nutrient environments. Here, we describe a hitherto unknown alkaline phosphatase, Psip1, that has a substantially higher affinity for phosphomonoesters than other well-known phosphatases like PhoA, PhoX, or PhoD and is restricted to clade III Synechococcus and a subset of high light I-adapted Prochlorococcus strains, suggesting niche specificity.

PNAS. May 2024