Life Sciences » Latest Publications (tag [Environment & Ecology])

Rapid assembly and functional differentiation of the soil surface microbiome in temperate agricultural soil

Wed, 25 Mar 2026 08:49:32 GMT

Christopher James O’Grady, Sally Hilton, Emma Picot, Sebastien Raguideau 2, Christopher Quince, Christopher J. van der Gast, Hendrik Schaefer, Gary D. Bending

Biological soil crusts (BSCs) are formed by phototrophic organisms at the soil surface and play a key role in structuring microbial communities and biogeochemical processes in dryland ecosystems. Similar surface associated communities occur in temperate agricultural soils, but their development, assembly dynamics and functional significance remain poorly understood. We investigated the temporal development of the soil surface microbiome following tillage and during subsequent growth of a winter wheat crop, integrating multi-kingdom amplicon sequencing with metagenomic analysis to track phototrophic, bacterial, fungal and protist communities, together with co-amplified macroscopic phototrophs. Distinct surface communities of phototrophs, bacteria and protists established rapidly, within 4 weeks of tillage, and underwent marked succession from early dominance by yellow-green algae (Xanthophyceae) to cyanobacteria, charophytes and ultimately mosses. Across all taxonomic groups, community assembly at the soil surface increasingly shifted towards dispersal limitation over time, whereas bulk soil communities were predominantly shaped by ecological drift. By the end of the growing season, the soil surface had developed a functional profile distinct from bulk soil, characterised by a greater representation of photosynthetic processes, largely due to eukaryotic algal carbon fixation, alongside increased genetic potential for heterotrophic carbon, nitrogen, phosphorus and sulphur cycling. These functional shifts were associated with enrichment of Actinobacteria, Bacteroidetes and Proteobacteria. Our results demonstrate that the soil surface of temperate agricultural systems represents a dynamic and functionally differentiated microbial habitat, which shares key biological features with dryland BSCs while exhibiting distinct functional and successional trajectories, revealing an overlooked component of managed temperate ecosystems.

Soil Biology and Biochemistry, June 2026

Genomic Surveillance of Epiphytic Pseudomonas syringae Highlights Shared Reservoirs and Cross-Habitat Threats to Cherry Orchards and Nearby Woodland Plants

Thu, 19 Mar 2026 08:29:41 GMT

Ziyue Zeng, John W. Mansfield, Andrea Vadillo-Dieguez, John Connell, James Irvine, Michelle T. Hulin, Fernando Duarte Frutos, Mojgan Rabiey, Nastasiya F. Grinberg, Richard J. Harrison, Xiangming Xu, Robert W. Jackson

Plant surfaces host diverse microbial communities acting as reservoirs for pathogenic lineages, yet the ecological dynamics and evolutionary consequences of such reservoirs remain underexplored. We conducted landscape-scale genomic surveillance of Pseudomonas syringae on symptomless leaves of cultivated cherry in orchards and wild plant species in adjacent woodlands across the UK, aiming to understand how phyllosphere populations contribute to the emergence of bacterial canker. Whole genome sequencing of 540 isolates collected over two years and across four regions revealed 10 diverse P. syringae phylogroups (PGs) on symptomless leaves. Both orchard and woodland environments harboured a similar range of PGs, but recovery frequency was very different. PG2d strains dominated cherry orchards, whereas PGs 2b and 13a were prevalent in woodlands. Certain PG2d subclades, recovered from both environments, caused disease on cultivated and wild cherry leaves. Additional strains were found to be pathogenic to Phaseolus bean pods. The pathogens of cherry were characterised by the presence of genes encoding the synthesis of the pathotoxin syringolin A and a subset of effector proteins including HopAW1, AvrRpm1 and HopAR1. Resolution of subclades within PG2d provided insights into the emergence of virulent epiphytic strains that have not yet reached the mostly northerly sampling sites but are threats to both cultivated and environmental Prunus spp. Fine-scale analysis of subclade PG2d-3 revealed potential divergence between orchard and woodland populations, with 49 genes exclusive to a woodland lineage. Thirty-eight of these genes were found within prophages, indicating the potential role of bacteriophage-mediated horizontal gene transfer in adaptation to non-agricultural reservoirs.

Molecular Plant Pathology, February 2026

Status and future of seed conservation of threatened plants in the post-2020 era

Wed, 18 Mar 2026 09:25:09 GMT

Andreas Ensslin, Adelaide Clemente, Udayangani Liu, Elke Zippel, Carla Pinto-Cruz, Carolina Sanchez Romero, Simone Schneider, Agustí Agut Escrig, Charlotte Allender, Külli Annamaa, Marina Antic, Bertille Asset, Gianluigi Bacchetta, Oz Baranzani, Anamaria Barata, Philippe Bardin, Joze Bavcon, Anabela D. F. Belo, Marina Belovarska, Karim Benkhelifa, Christian Berg, Karl-Georg Bernhardt, Marcin Beza, Kristina Bjureke, Sina Bohm, Peter Borgmann, Josep Borrell, Stéphane Buord, Jocelyne Cambecedes, Francesca Carruggio, Angelino Carta, Pedro Casimiro, Ted Chapman, Iveta Cicova, Regis Crisnaire, Antonia Cristaudo, Lucia De la Rosa, Maîte Delmas, Gergana Desheva, Valter Di Cecco, Luciano Di Martino, Katia Diadema, Lara Dixon, Denise Dostatny, Marie Duval, Roland K. Eberwein, Mikel Etxeberria-Okariz, Caroline Favier, Nick Fenby, Mariana P. Fernandes, Inmaculada Ferrando-Pardo, Pablo Ferrer, Noémie Fort, Luigi Forte, Catia F. Freitas, Agnese Gailite, Katarzyna Galej-Ciwis, Rosa Maria Garcia, Ana Irene García-del Bao, Catherine Gautier, Bronislovas Gelvonauskis, Gian Petro Giusso del Galdo, Miguel Angel González Pérez, Johan Gourvil, Luisa Gouveia, Thierry Helminger, Brais Hermosilla Lorenzo, Laetitia Hugot, Marko Hyvärinen, Ignac Janžekovič, Andreas König, Nikos Krigas, Emilio Laguna, Ludivine Lapébie, Denis Larpin, Maja Lazarević, Dikla Lifshitz, Vincent Lipa, Carlos Lobo, Ulrike Lohwasser, Sandrine Loriot, Sara Magrini, Francesca Mantino, Mauro Mariotti, Evi Matiatou, Lubomir Mendel, Marine Millet, Mari Miranto, Andrea Mondoni, Santiago Moreno Vázquez, Valeria Negri, Peter Nick, Maciej Niemczyk, Humberto Nobrega, Pawel Olejniczak, Małgorzata Pałucka, Katerina Papanastasi, Ioanna Papanikolaou, Miguel A. A. Pinheiro de Carvalho, Marco Porceddu, Sotirios Porevis, Peter Poschlod, Lorenzo Raggi, Sarmite Rancane, Leonid Rasran, Blanka Ravnjak, Stéphane Rivière, Axelle Roumier, Anna Rucińska, Felix Schlatti, Marco Schmidt, Guy-Xavier Seznec, Manuela Sim-Sim, Ana Luisa Soares, Nora Stoeckl, Silvia Strajeru, Gitana Stukeniene, Andrej Šušek, Andreas Titze, Sarah Trinder, Zlatina Tsvetanova, Theo Van Hintum, Nils Van Rooijen, Magdalena Vicens Fornés, Mariacristina Villani, Silvia Villegas, Fiona J. White, Sabine Zachago, Elena Zappa, Vince Zsigmond, Sandrine Godefroid

Ambitious targets have been set to backup seeds of threatened plants by the global strategy for plant conservation (GSPC), but it is unclear in how far these targets have been met and how seed collection should be organized to meet future challenges. Here, we provide an overview of the status of 44 countries in achieving seed conservation targets. We show that progress varies strongly across countries, but in general, targets of the 2011–2020 GSCP have not been reached. By a regional example, we illustrate how seed collection could be organized to safeguard our threatened flora.

Plants People Planet, March 2026

Gapless pangenome analyses reveal fast Brassica rapa subspeciation

Fri, 13 Mar 2026 08:57:36 GMT

Wei Ma, Yuanming Liu, Xiaochun Wei, Xiaomeng Zhang, Xiaonan Li, Zhaokun Liu, Lingyun Yuan, Guangguang Li, Shu Zhang, Qihang Yang, Xiaocong Chang, Zizhuo Han, Hao Liang, Zhaoshui Luan, Qianyun Wang, Yujie Gu, Xinlong Wang, Xianlei Zhao, Qing Liu, Xiaoxue Sun, Mengyang Liu, Daling Feng, Yin Lu, Shuangxia Luo, Lei Yang, Mengyuan Li, Robin Allaby, Kai Wang, Tianzhen Zhang, Shuxing Shen, Yves Van de Peer, Yiguo Hong, Yuxiang Yuan, Jianjun Zhao

Brassica rapa (Br) encompasses many morphotypes and subspecies, so it is a good model with which to investigate plant diversification and subspeciation. Here, we resequenced the genomes of 1720 Br accessions and de novo assembled 11 representative telomere-to-telomere gapless genomes for seven elite subspecies that underwent intensive morphotypification and developed distinct agronomic traits valued to agriculture. We identified 6992 unknown genes, 110 complete (peri)centromeres, and five new satellites associated with Br morphotypes and subspecies and Brassica species evolution. The pangenome, built on 11 gapless and 20 published genomes, reveals structural variations and gene diversities among Br subspecies. Pangenome-wide association studies uncovered that the gene BrLH1 controls leaf-head formation. We show that structural changes have occurred in satellites, (peri)centromeres, and genes, contributing to fast subspeciation and morphotypification during the short history of Br cultivation, providing invaluable resources for Brassica breeding.

Science, February 2026

Genome sequences of distinct genotypes of bacterial pathogen Xanthomonas euvesicatoria pv. euvesicatoria from pepper (Capsicum annuum L.) in Serbia

Thu, 12 Mar 2026 09:22:03 GMT

Tatjana Popović Milovanović, Shannon F. Greer, Renata Iličić, Aleksandra Jelušić, Daisy Bown, Murray Grant, Joana G. Vicente, David J. Studholme

This Technical Resource presents genome sequence data for three strains of the bacterial pathogen Xanthomonas euvesicatoria pv. euvesicatoria (Xeu) collected in Serbia. We isolated these strains from pepper crops showing bacterial spot symptoms in 2016 at the municipality of Irig, in the Srem district. The presented data comprise raw sequencing reads and annotated, contig-level genome assemblies. We checked for the presence of sequences of known type-3 secretion system (T3SS) effector genes and plasmid-like sequences. Phylogenomic reconstruction revealed that the three strains fell in the same clade within Xeu. Strain X13 is most closely related to strain 66b, collected in Bulgaria in 2012. Strains X22 and X31 are most closely related to Tu-10 collected in the Southeastern Anatolia region of Türkiye in 2020. In common with other members of the clade, all three strains share a 75 kb plasmid that carries T3SS effector genes avrBs3, xopBA, xopAQ and xopE. Additionally, strain X13 shares extensive sequence similarity to the pXCV183 plasmid, including T3SS effector gene xopAX, and shares extensive sequence similarity with plasmid pXap41, including T3SS effector gene xopE3. This difference in plasmid content might contribute to the observed difference in virulence among the Serbian Xeu strains. The three Serbian strains lack a 31 kb plasmid, pLMG730.4, that is seen in several Vietnamese and Canadian strains within this clade of Xeu. The data presented will be a useful resource for future molecular epidemiology and genomic surveillance of this pathogen in the Balkan region, augmenting the previously available draft genome sequences of Xeu strains 66b (Bulgaria) and 83M (North Macedonia).

Access Microbiology, February 2026

Nanocomposite Reduces Volatile and Aqueous Reactive Nitrogen Losses From Soil Compared to Conventional and Alternative Fertilisers

Tue, 10 Mar 2026 10:32:08 GMT

Jessica Chadwick, Jingyi Shi, Megan L. Purchase, Peng Zhang, Iseult Lynch, Sami Ullah, Deying Wang, Ryan M. Mushinski

Reactive nitrogen losses from agriculture contribute substantially to greenhouse gas emissions, water pollution and ecosystem degradation. Controlled-release fertiliser technologies offer potential solutions, yet few comprehensively evaluate performance across multiple nitrogen loss pathways and soil types. This study evaluated the environmental performance and agronomic efficacy of urea-doped amorphous calcium phosphate (U-ACP) nanoparticles compared to conventional urea across three contrasting soil types (sandy, sandy loam, clay loam) using lettuce (Lactuca sativa) as a model crop. U-ACP nanoparticles (20–100 nm) were synthesised and characterised for dissolution kinetics in simulated soil environments. Controlled glasshouse experiments (8 weeks, 100 kg N ha ⁻ ¹ application rate) quantified gaseous emissions (ammonia, nitrous oxide, nitric oxide), aqueous leaching losses, soil biochemical properties, plant nitrogen uptake and functional gene abundances for nitrogen cycling processes. U-ACP demonstrated significantly reduced reactive nitrogen losses across all pathways and soil types. Cumulative ammonia volatilisation decreased by 53%–57% in sandy and sandy loam soils compared to conventional urea (p < 0.001), whilst nitrous oxide emissions declined by 19%–27% across all soil types (p < 0.001). Total nitrogen leaching concentrations were 44% lower in sandy soils where losses are typically highest (p < 0.001), with ammonium leaching reduced by 71%–85% across soil types. Cumulative gaseous nitrogen losses decreased by 20%–48% depending on soil type. Despite these substantial reductions in nitrogen losses, U-ACP maintained comparable plant biomass whilst achieving 52%–89% higher nitrogen uptake index across soil types (p < 0.001). U-ACP also supported enhanced soil microbial functionality, with significantly elevated complete ammonia oxidiser (comammox) and alkaline phosphatase (phoD) gene abundances (p < 0.05). Calcium phosphate-based nanocomposite fertilisers offer a viable pathway towards sustainable intensification of agriculture by simultaneously reducing environmental nitrogen pollution whilst maintaining or improving crop productivity across diverse soil conditions.

Journal of Sustainable Agriculture and Environment, March 2026

The perception to practice pathway of integrated pest management in horticulture: an extended Technology Acceptance Model

Wed, 04 Mar 2026 09:04:11 GMT

Jennifer Byrne, Lael Walsh, Robert Lillywhite, Henry Creissen, Antonia dos Santos, Fiona Thorne

An extended Technology Acceptance Model (TAM) was used to explore the pathway between the perception of Integrated Pest Management (IPM) by growers and its practical uptake. IPM is an established framework for the management of crop health based on a range of strategic and tactical horticultural techniques. In this research, IPM adoption is quantified through the application of a novel IPM metric. Policy makers need to understand the perception to practice pathway for IPM in order to increase adoption in line with regulatory frameworks. The TAM examines perceived usefulness (PU) and perceived ease of use (PEOU) on the attitude and subsequent acceptance of a technology; extended TAM frameworks incorporate additional antecedent variables. In this study, we include the additional latent variables of business features and innovativeness to examine their capacity to predict the adoption of IPM at the farm business level for growers of horticultural crops (n = 100) in the Republic of Ireland, surveyed in 2023. Findings verify the correlation between PU, PEOU and attitude and the effect of PEOU on PU. PU has a stronger association with attitude than PEOU. Neither business features nor innovativeness were significantly related to PU or PEOU, respectively. The hypothetical correlation between attitude and IPM adoption was rejected, demonstrating a divide in the perception to practice trajectory and adding to the literature on the attitude to adoption gap. The findings demonstrate the value of empirical assessment of behavioural data. An implication for IPM policy direction is that grower perception does not always infer future grower adoption. Therefore, a cautionary reliance on perception data during the ex-ante stages of IPM incentivisation development is recommended.

Crop Protection, February 2026

Biofilm growth is insufficient to retain large buoyant microplastics in constructed wetlands

Mon, 02 Mar 2026 09:39:00 GMT

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.

Journal of Hazardous Materials, February 2026

Cicada necrobiome mediates greenhouse and trace gas pulses following periodic mass emergence

Thu, 26 Feb 2026 09:38:42 GMT

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.

Applied Soil Ecology, March 2026

Beyond the clipboard: data collection with GridScore NEXT

Wed, 25 Feb 2026 09:34:00 GMT

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.

BMC Bioinformatics, January 2026