Latest Publications
Microbial Primer: Ancientbiotics – making modern antimicrobials from historical infection remedies
Freya Harrison, Oluwatosin Q. Orababa
The modern antibiotic era began in the early twentieth century, but humans have long used materials from the natural world to attempt to treat the symptoms of infection. In this primer, we will discuss the rationale for attempting to reconstruct historical infection remedies in order to assess their antimicrobial activity and how this approach could aid the discovery of molecular cocktails with potential for development into novel treatments for infection.
Biofilm growth is insufficient to retain large buoyant microplastics in constructed wetlands
Charlotte Dykes, Jonathan Pearson, Gary Bending, Soroush Abolfathi
Microplastics (MPs) are emerging contaminants, with wastewater treatment plants (WWTPs) as principal hotspots for their release into downstream systems, including constructed wetlands (CWs), a nature-based solution for water treatment. While non-buoyant MPs readily settle, buoyant MPs risk bypassing CWs and entering aquatic environments. Biofilm formation could influence MP transport by altering buoyancy, promoting sinking, and enhancing MP retention, yet its role in CWs remains unknown. This study, for the first time, quantifies the effects of MP polymer type, particle characteristics, exposure time, and seasonality on biofilm colonisation and its impact on terminal rising velocities of initially buoyant MPs in a UK-based CW receiving partially treated wastewater. Polypropylene (PP), expanded polystyrene (PS), and low-density polyethylene (LDPE) particles (3–5 mm) in spherical, beaded, and film shapes were incubated in situ over 12 months. Sampling followed two approaches: (1) a rolling bi-monthly schedule to capture seasonal variation, and (2) a long-term deployment with subsets retrieved every two months. Biofilm biomass was quantified by crystal violet staining, surface characteristics were captured by scanning electron microscopy (SEM), and terminal rising velocity experiments measured buoyancy changes. Biofilm growth showed strong seasonality, with peak biomass in late spring showing up to a 1972 % increase compared to winter. Despite widespread colonisation, changes in terminal rising velocity were minimal and largely non-significant (p < 0.05), indicating that biofilm formation alone is insufficient to retain initially buoyant MPs in CWs. These findings are crucial for deriving MP transport models and challenge assumptions that biofilm-induced density changes drive MP retention in CWs.
Cicada necrobiome mediates greenhouse and trace gas pulses following periodic mass emergence
Megan L. Purchase, Richard P. Phillips, Jonathan D. Raff, Amy I. Phelps, Elizabeth Huenupi, Ryan M. Mushinski
The emergence of periodical cicadas from soil every 13 or 17 years is a unique ecological phenomenon with the potential to affect soil biogeochemistry in forests, with increased emissions of climate-relevant gases as a consequence. While it's well-known that cicada carcasses create resource pulses of carbon and nitrogen (N) in soil when they die in mass, the processes underlying these effects, as well as the consequences of these effects for N losses, are poorly known. We investigated how the emergence of Brood X cicadas (Magicicada spp.) in 2021 affected soil microbial communities – particularly N cycling taxa - in forests of the United States. We found that decaying carcasses led to emissions of nitrous oxide (N2O) and ammonia (NH3) gas at around 0.53 mg-N m−2 h−1, estimated to be a ∼ 35-fold increase over ∼21 days from the annual average emissions from US forest soils (0.015 mg-N m−2 h−1), with the greatest effects occurring at the interface between carcasses and soil surface. Using amplicon sequencing and qPCR, we determined the potential microbial mechanisms behind N2O and NH3 production, including correlations between taxa capable of carrying out less well studied processes DNRA and nitrifier denitrification, and increased emissions of N2O and NH3. Although distinguishing the relative contributions of DNRA, denitrification, and nitrifier denitrification requires direct rate measurements, our results suggest these processes working together contribute to previously unrecognised greenhouse gas emissions following insect emergence events. Collectively, our results indicate that cicadas significantly affect nutrient cycling in forests with the potential to alter soil microbial communities in ways that may enhance ecosystem N emissions.
Beyond the clipboard: data collection with GridScore NEXT
Sebastian Raubach, Miriam Schreiber, Ruth Hamilton, Gaynor McKenzie, Susan McCallum, Benjamin Kilian, Alan Humphries, Loi Huu Nguyen, Tin Huynh Quang, Akanksha Singh, Shivali Sharma, Sarah Trinder, Manuel Feser, Paul D. Shaw
Accurate acquisition of phenotypic data is critical for cataloguing and utilising genetic variation in cultivated crops, landraces, and their wild relatives. The collection of phenotypic data using handwritten notes often introduces errors which can and should be avoided. Electronic data collection is crucial for ensuring error prevention and data standardisation and thus ensuring high-quality, reliable data.
This paper describes the development of GridScore NEXT, a new plant phenotyping application that significantly advances the state of the art for collecting field trial data in plant genetics, pre-breeding and crop improvement research. Building on its predecessor, GridScore, the development of GridScore NEXT was driven by real life, in the field interactions with expert user groups across a number of crops. This iterative design methodology allowed the development and testing of new features. Collaborators from the 'Biodiversity for Opportunities, Livelihoods and Development' (BOLD) project, focusing on crops including rice, grasspea, and alfalfa, along with barley, potato, vegetable and blueberry teams, provided invaluable insights through training sessions and interviews and in the field use of the application.
Key improvements to GridScore NEXT include enhanced data collection tools, supporting individual plant phenotyping within plots and enabling new data types such as GPS coordinates and image traits. GridScore NEXT provides customisable user defined validation rules to help prevent errors and incorporates barcode scanning for accurate, efficient data capture. The application offers an increased toolbox of data visualizations over its predecessor including heatmaps and statistical box plots, which aid in identifying potential data issues and understanding trial performance in the field. GridScore NEXT is cross-platform and can operate without an internet connection, making it ideal for field use in remote areas. Its adoption has led to standardisation of methods, significant error reduction, and the timely sharing of data, enabling quicker decision-making in pre-breeding and characterisation experiments. GridScore NEXT is available under an open-source (Apache 2.0) licence and freely available to all with no restrictions. It offers self-hosting options for enhanced data security and privacy. GridScore NEXT shows broad applicability across a diverse range of not only plant phenotyping experiments, but any experiment that requires the collection of accurate data.
RePol: A high-throughput screen for optimizing membrane protein solubilization and purification using polymers
Adam Evans, Bethan Kelly, Pooja Sridhar, Alice J. Rothnie, Naomi L. Pollock, Philip M. Ireland, David I. Roper, Tim R. Dafforn
Extraction and purification of membrane proteins has for a long time represented a significant challenge. Polymer-based extraction methods, like those using styrene maleic acid co-polymers have provided a fertile approach to generate samples that include the local lipid environment surrounding the protein. However, the wide variety of different polymers now available provides a challenge to identify the optimal solution. In this study we develop and demonstrate a novel high-throughput screening approach for rapid optimization of polymer solubilization agents and chromatography resins for membrane protein purification. Using this approach, we explore whether there are standard conditions that perform well for a range of membrane protein morphologies, sources and functions. These data show that no such standard conditions exist for either polymer solubilization agent or chromatography resin and that some combinations are rarely suitable for membrane protein purifications under these conditions, such as the use of TALON resin at a pH of 7.5 or SMALP300 in the Synthetic Nanodisc Screening Kit MINI kit. Instead, the use of the screening approach developed in this work is the best route to an optimal membrane protein preparation protocol.
Genetically engineered bacteriophages — their roles in combating intracellular bacterial infections and unraveling phage–eukaryote interactions
Joshua Williams, Ioannis P Nezis, Antonia P Sagona
The rising incidence of antimicrobial resistance (AMR) in bacterial infections has strongly necessitated the development and deployment of alternative therapeutics. Bacteriophages (phages) are one such alternative, discovered in the early twentieth century. While a key tool in landmark molecular biology studies throughout the twentieth century, their popularity as an antimicrobial in clinical contexts was largely overshadowed by the development and use of antibiotics. The global threat of AMR has since reignited interest in utilizing phages as therapeutics. A key advantage of phages is their genetic tractability, allowing for the generation of a cornucopia of derivatives armed with numerous exogenous functions depending on the end use. A nascent yet growing interest in this field is the arming of phages for direct and selective human tissue entry to eradicate intracellular bacterial infections, where many bacterial species exert their pathogenesis. Engineering phages in such a way also opens opportunities to study the complex, multilayered cellular mechanisms behind phage–eukaryote interactions. In this review, we discuss the progress of phage genetic engineering with an emphasis on phage–eukaryote interactions and how knowledge of the underlying molecular mechanisms may serve further development of this prospective enhancement of engineered phages.