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Plant & Agricultural Bioscience Publications

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

Publications from the cluster

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

Genetic Variation of Turnip Yellows Virus in Arable and Vegetable Brassica Crops, Perennial Wild Brassicas, and Aphid Vectors Collected from the Plants

Ricardo J G Pimenta, Kyle Macleod, Robyn Babb, Kaitlyn Coleman, Joni MacDonald, Elvis Asare-Bediako, Max J Newbert, Carol E Jenner, John A Walsh

Turnip yellows virus (TuYV; Polerovirus, Solemoviridae) infects and causes yield losses in a range of economically important crop species, particularly the Brassicaceae. Although the incidence and genetic diversity of TuYV has been extensively investigated in recent years, little is known about how the diversity within host plants relates to that in its vectors. Arable oilseed rape (Brassica napus) and vegetable brassica plants (Brassica oleracea), wild cabbage (B. oleracea), and aphids present on these plants were sampled in the field in three regions of the United Kingdom. High levels of TuYV (82 to 97%) were detected in plants in all three regions following enzyme-linked immunosorbent assaysComparative analyses between TuYV sequences from host plants and B. brassicae collected from respective plants revealed differences between some ORF0 sequences, which possibly indicated that at least two of the aphids might not have been carrying the same TuYV isolates as those present in their host plants. Maximum likelihood phylogenetic analyses revealed three distinct major clades for ORF0 and one for ORF3, with some distinct subclades. Some clustering was related to geographic origin. Explanations for TuYV sequence differences between plants and the aphids present on respective plants and implications for the epidemiology and control of TuYV are discussed.

Plant Disease. March 2024

Manipulating multi-level selection in a fungal entomopathogen reveals social conflicts and a method for improving biocontrol traits

Zoltan Erdos, David J. Studholme, Manmohan D. Sharma, David Chandler, Chris Bass, Ben Raymond

Changes in parasite virulence are commonly expected to lead to trade-offs in other life history traits that can affect fitness. Understanding these trade-offs is particularly important if we want to manipulate the virulence of microbial biological control agents. We hypothesized that manipulating selection intensity at different scales would reveal virulence trade-offs in a fungal pathogen of aphids, Akanthomyces muscarius. Starting with a genetically diverse stock we selected for speed of kill, parasite yield or infectivity by manipulating competition within and between hosts and between-populations of hosts over 7 rounds of infection. We found that early sporulation led to reduced competitive fitness but could increase yield of spores on media, a trade-off characteristic of social conflict. Notably, the selection regime with strongest between-population competition and lowest genetic diversity produced the most consistent shift to early sporulation, as predicted by social evolution theory. Multi-level selection therefore revealed social interactions novel to fungi and showed that these biocontrol agents have the genomic flexibility to improve multiple traits—virulence and spore production—that are often in conflict in other parasites.

PLoS Pathogens. March 2024

Early Detection of Fusarium Basal Rot Infection in Onions and Shallots Based on VOC Profiles Analysis

Malgorzata Wesoly, Emma Daulton, Sascha Jenkins, Sarah van Amsterdam, John Clarkson and James A. Covington

In this work, we employed Gas chromatography ion-mobility spectrometry (GC-IMS) technology for early detection of Fusarium basal rot in brown onion, red onion, and shallot bulbs and for tracking disease progression during storage. The volatile profiles of the infected and healthy control bulbs were characterized using GC-IMS and gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS). GC-IMS data combined with principal component analysis and supervised methods provided discrimination between infected and healthy control bulbs as early as 1 day after incubation with the pathogen, classification regarding the proportion of infected to healthy bulbs in a sample, and prediction of the infection’s duration with an average R2 = 0.92. Furthermore, GC-TOF-MS revealed several compounds, mostly sulfides and disulfides, that could be uniquely related to Fusarium basal rot infection.

Agricultural and Food Chemistry. February 2024

Genome assembly and transcriptomic analysis to elucidate the ability of Nasonovia ribisnigri to break host plant resistance

Dion Garrett, Graham Teakle, Rosemary Collier, James R. Bell, Sergio Cerezo-Medina, Ramiro Morales-Hojas

The currant-lettuce aphid (Nasonovia ribisnigri (Hemiptera: Aphididae) (Mosley)) is a cosmopolitan pest of outdoor lettuce. Until recently, the use of resistant cultivars was an effective method for managing N. ribisnigri. A resistant cultivar containing a single gene (Nr-locus), introduced in the 1980s, conferred complete resistance to feeding. Overreliance of this Nr-locus in lettuce resulted in N. ribisnigri's ability to break resistance mechanism. Our work attempts to understand which candidate gene(s) are associated with this resistance-breaking mechanism. We present two de novo draft assembles for N. ribisnigri genomes, corresponding to both avirulent (Nr-locus susceptible) and virulent (Nr-locus resistant) biotypes.. Out of the 18,872 differentially expressed genes, a single gene/locus was identified in N. ribisnigri that was shared between two resistant-breaking biotypes. This locus was further explored and validated in Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) experiments and has predicted localisations in both the cytoplasm and nucleus. This is the first study to provide evidence that a single gene/locus is likely responsible for the ability of N. ribisnigri to overcome the Nr-locus resistance in the lettuce host.

Insect Molecular Biology. February 2024

Genetic manipulation of Indian mustard genotypes with WRR-gene(s) confers resistance against Albugo candida

Nirwan, Shradha, Chatterjee, Anupriya, Cevik, Volkan, Holub, Eric B., Jones, Jonathan D. G., Tewari, Anand Kumar, Shrivastava, Neeraj, Agnihotri, Abha and Sharma, Pankaj

In an effort to develop resistant plants, Agrobacterium mediated genetic transformation of three B. juncea genotypes viz., susceptible host var. Varuna, along with its doubled haploid mutant lines C66 and C69 (showing moderate tolerance to field isolates of A. candida) was initiated to transfer resistance genes (WRR8Sf-2 and WRR9Hi-0) identified in Arabidopsis thaliana against race Ac2V, that encode for Toll-like/interleukin-1 receptor-nucleotide binding-leucine-rich repeat proteins that recognize effectors of the pathogen races. Our results demonstrate that introduction of resistance genes from a tertiary gene pool by genetic transformation enhances disease resistance in B. juncea genotypes to a highly virulent Ac2V isolate.

Molecular Biology Reports. January 2024

Slow release of a synthetic auxin induces formation of adventitious roots in recalcitrant woody plants

O Roth, S Yechezkel, O Serero, A Eliyahu, I Vints, P Tzeela, A Carignano, DP Janacek, V Peters, A Kessel, V Dwivedi, M Carmeli-Weissberg, F Shaya, i Faigenboim-Doron, KL Ung, B Panyella Pedersen, J Riov, E Klavins, C Dawid, Z Hammes, N Ben-Tal, R Napier, E Sadot, R Weinstain

Clonal propagation of plants by induction of adventitious roots (ARs) from stem cuttings is a requisite step in breeding programs. Due to the central role of auxin in organogenesis, indole-3-butyric acid is often used as part of commercial rooting mixtures, yet many recalcitrant plants do not form ARs in response to this treatment. Here we describe the synthesis and screening of a focused library of synthetic auxin conjugates in Eucalyptus grandis cuttings and identify 4-chlorophenoxyacetic acid-L-tryptophan-OMe as a competent enhancer of adventitious rooting in a number of recalcitrant woody plants, including apple and argan. Comprehensive metabolic and functional analyses reveal that this activity is engendered by prolonged auxin signaling due to initial fast uptake and slow release and clearance of the free auxin 4-chlorophenoxyacetic acid. This work highlights the utility of a slow-release strategy for bioactive compounds for more effective plant growth regulation.

Nature Biotechnology. January 2024

Interactions of long-term grazing and woody encroachment can shift soil biogeochemistry and microbiomes in savanna ecosystems

Ryan M. Mushinski, Yong Zhou, Ayumi Hyodo, Claudio Casola, Thomas W. Boutton

We investigated the interactions between livestock grazing history (none, moderate, heavy) and vegetation cover (grassland, juniper, oak) using a ∼ 70-year grazing experiment in west-central Texas. We explored effects on soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), microbial community composition, and function. The findings highlight how long-term livestock grazing and woody plant encroachment influence soil C, N, P cycles, altering soil microbial community structure and function. This study provides insights for savanna ecosystem management and integrating land cover effects into biogeochemical models for global change scenarios.

Geoderma.  January 2024

Gary Bending publications

Quantifying microplastic dispersion due to density effects

Stride, Ben, Abolfathi, Soroush, Bending, Gary D. and Pearson, Jonathan M

An experimental study was conducted on how polymer density affects the transport and fate of microplastics in aquatic flows. For the first time, polypropylene (PP), polyethylene (PE), polymethyl methacrylate (PMMA), polyetheretherketone (PEEK), and polyvinyl chloride (PVC) were chemically stained and tested using solute transport techniques and velocities found among rivers in the natural environment (0.016 – 0.361 m/s). Except for PP, in most conditions microplastics exhibited similar transport characteristics to solutes regardless of density and established solute transport models were successfully implemented to predict their transport and fate.. This data is the first to provide microplastic suspension and deposition thresholds based on river velocity and polymer density, making a key contribution to research predicting microplastic fate and organismal exposure.

Journal of Hazardous Materials. January 2024

Distinct biogeographic patterns in Glomeromycotinian and Mucoromycotinian arbuscular mycorrhizal fungi across China: A meta-analysis

Zihao Liu, Jie Fang, Yucheng He, Gary D Bending, Bin Song, Yaping Guo, Xiaojie Wang, Zemin Fang, Jonathan M Adams

Fine root endophytes, recently reclassified as Mucoromycotinian arbuscular mycorrhizal fungi (M-AMF), are now recognized as functionally important as Glomeromycotinian AMF (G-AMF). Here, we investigated the biogeographic assemblies and ecological diversity patterns of both G-AMF and M-AMF, using published 18S rDNA amplicon datasets and associated metadata from 575 soil samples in six ecosystems across China. This study provides solid evidence that the two AMF groups have distinct ecological preferences at the continental scale in China, and also highlights the potential impacts of anthropogenic activities on distributions of AMF. These results advance our knowledge of the ecological differences between the two fungal groups in terrestrial ecosystems, suggesting the need for further field-based investigation that may lead to a more sophisticated understanding of ecosystem function and sustainable management.

Science of the Total Environment. December 2023

Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controls shade avoidance syndrome in Arabidopsis

María Florencia Mammarella, Leandro Lucero, Nosheen Hussain, Aitor Muñoz-Lopez, Ying Huang, Lucia Ferrero, Guadalupe L Fernandez-Milmanda, Pablo Manavella, Moussa Benhamed, Martin Crespi, Carlos L Ballare, Jose Gutierrez-Marcos, Pilar Cubas, Federico Ariel

The long noncoding RNA (lncRNA) AUXIN-REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA–DNA hybrids (R-loops) and modulating local three-dimensional chromatin conformation. Here, we show that APOLO regulates shade avoidance syndrome by dynamically modulating expression of key factors. We show that direct application of APOLO RNA to leaves results in a rapid increase in auxin signaling that is associated with changes in the plant response to far-red light. Collectively, our data support the view that lncRNAs coordinate shade avoidance syndrome in A. thaliana, and reveal their potential as exogenous bioactive molecules. Deploying exogenous RNAs that modulate plant–environment interactions may therefore become a new tool for sustainable agriculture.

EMBO Journal. December 2023

George Bassel publications

A quantitative morphospace of multicellular organ design in the plant Arabidopsis

Salva Duran-Nebreda, Matthew D.B. Jackson, George W. Bassel

The investigation of cellular organization can provide insight into organ function following structure-function relationships. Here, we investigate the extent to which properties in cellular organization can arise ‘‘for free’’ as an emergent property of embedding cells in space versus those that are actively generated by patterning processes. A 3D cellular-resolution digital tissue atlas for the model plant species Arabidopsis was generated, and the extent to which the organs in this organism conform to the default configurations was established through statistical comparisons with digital tissue models. This work establishes a quantitative morphospace to understand the principles of organ construction and its diversity within a single organism.

Current Biology. November 2023

Toward uncovering an operating system in plant organs

Gwendolyn V Davis, Tatiana de Souza Moraes, Swanand Khanapurkar, Hannah Dromiack, Zaki Ahmad, Emmanuelle M Bayer, Rishikesh P Bhalerao, Sara I Walker, George W Bassel

Molecular motifs can explain information processing within single cells, while how assemblies of cells collectively achieve this remains less well understood. Plant fitness and survival depend upon robust and accurate decision-making in their decentralised multicellular organ systems. Mobile agents, including hormones, metabolites, and RNAs, have a central role in coordinating multicellular collective decision-making, yet mechanisms describing how cell-cell communication scales to organ-level transitions is poorly understood. Here, we explore how unified outputs may emerge in plant organs by distributed information processing across different scales and using different modalities. Mathematical and computational representations of these events are also explored toward understanding how these events take place and are leveraged to manipulate plant development in response to the environment.

Trends in Plant Science. November 2023

The effect of organic matter amendments on soil surface stability in conventionally cultivated arable fields

Jacqueline L. Stroud, Simon J. Kemp, Craig J. Sturrock

In this study, new and traditional organic wastes (green waste compost, farmyard manure (FYM), anaerobic digestate or straw) were ploughed into an arable field experiment at a range of rates (1–3 t C ha−1) and under spring and winter cropping rotations for 5 years. The stability of the soil surface structure (<5 cm) was assessed in Years 3, 4 and 5 to guide the use of organic wastes in arable field management. In conclusion, to achieve a stable soil surface structure, a 150% improvement in aggregate stability would be needed here and ploughing in organic wastes was not a successful management approach on these arable field experiments.

Soil Use and Management. November 2023

Mechanism of substrate binding and transport in BASS transporters

Patrick Becker, Fiona B. Naughton, Deborah H. Brotherton, Raul Pacheco-Gomez, Oliver Beckstein, Alexander D. Cameron

The bile acid sodium symporter (BASS) family transports a wide array of molecules across membranes, including bile acids in humans, and small metabolites in plants. These transporters, many of which are sodium-coupled, have been shown to use an elevator mechanism of transport, but exactly how substrate binding is coupled to sodium ion binding and transport is not clear. Here, we solve the crystal structure at 2.3 Å of a transporter from Neisseria meningitidis (ASBTNM) in complex with pantoate, a potential substrate of ASBTNM.. Comparison of structures in the presence and absence of pantoate demonstrates that pantoate elicits a conformational change in one of the cross-over helices. This modifies the interface between the two domains that move relative to one another to elicit the elevator mechanism. These results have implications, not only for ASBTNM but for the BASS family as a whole and indeed other transporters that work through the elevator mechanism.

eLife. November 2023