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Plant & Agricultural Bioscience Publications

See our "Latest Publications" page for a full list of SLS publications

Publications from the cluster

Development of biological soil crusts at the soil surface influences the persistence and movement of crop protection products

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

Population genetics show that aphids (Hemiptera: Aphididae) are limited by summer host-plant distribution at the regional scale

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

Foliimonas ilicis gen. nov., sp. nov., a carbon monoxide-oxidizing bacterium belonging to a novel genus of the family Phyllobacteriaceae isolated from leaves of Ilex aquifolium

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 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 C ω7c, C ω7c 11-methyl and C 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 , showing sequence identities of 97.7%, 97.6% and 97.5%, with its closest relatives , and , respectively. Phylogenomic analyses using whole-genome sequences consistently placed this strain within the family . 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 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 within the family for which the name gen. nov., sp. nov. is proposed. The type of strain is SB112T (=LMG 33802T, =NCAIM B.02691T

Microbiology Society

Mitochondrial ROS trigger interorganellular signaling and prime ER processes to establish enhanced plant immunity

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

Impact of seasonal climate variability on constructed wetland treatment efficiency

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

Rootrainertrons: a novel root phenotyping method used to identify genotypic variation in lettuce rooting

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

Impact of Phage Therapy on Pseudomonas syringae pv. syringae and Plant Microbiome Dynamics Through Coevolution and Field Experiments

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

Historic manioc genomes illuminate traditional maintenance of diversity under long-lived clonal cultivation

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

Quantifying integrated pest management adoption in food horticulture

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

Stephen Parnell Publications

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

John Ellis, Elena Lázaro, Beatriz Duarte, Tomás Magalhães, Amílcar Duarte, Jacinto Benhadi-Marín, José Alberto Pereira, Antonio Vicent, Stephen Parnell, Nik J. Cunniffe

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

Knockout of fatty acid elongase1 homeoalleles in amphidiploid Brassica juncea leads to undetectable erucic acid in seed oil

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

Piperideine-6-carboxylic acid regulates vitamin B6 homeostasis and modulates systemic immunity in plants

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

A comparative study of ionic pesticide sorption and degradation in contrasting Brazilian soils and the development of a novel 3-Phase Assay to assess sorption reversibility

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

Regional scale diversity and distribution of soil inhabiting Tetracladium

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

Metabolic profiling and antibacterial activity of tree wood extracts obtained under variable extraction conditions

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

Characterisation of Itersonilia spp. from Parsnip and Other Hosts

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

Understanding the ecological versatility of Tetracladium species in temperate forest soils

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

Comparative genomics and transcriptomics reveal differences in effector complement and expression between races of Fusarium oxysporum f.sp. lactucae

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

A regulatory module mediating temperature control of cell-cell communication facilitates tree bud dormancy release

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

Genetic-epigenetic interplay in the determination of plant 3D genome organization

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

Establishment of single-cell transcriptional states during seed germination

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

Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability

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

Improved control of Trialeurodes vaporariorum using mixture combinations of entomopathogenic fungi and the chemical insecticide spiromesifen

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

Development of inoculation methods for Pythium violae to evaluate resistance of carrot cultivars and efficacy of crop protection products for cavity spot control

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

An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac distribution

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

Coevolutionary analysis of Pseudomonas syringae–phage interactions to help with rational design of phage treatments

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

Phenotypic and genotypic characterization of fifty strains of Beauveria spp. (Ascomycota, Cordycipitaceae) fungal entomopathogens from diverse geographic origins against the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae)

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

Response patterns of the microbiome during hexavalent chromium remediation by Tagetes erecta L

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

Multiple toxins and a protease contribute to the aphid-killing ability of Pseudomonas fluorescens PpR24

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

Imaging Single-Cell Ca2+ Dynamics of Brainstem Neurons and Glia in Freely Behaving Mice

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

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