Biology subjects

Hilton, S.

Publications and source records attributed to Hilton, S..

9 recordsLinked to original sources

bioRxiv2025

Rapid Assembly and Functional Differentiation of the Soil Surface Microbiome in Temperate Agricultural soil

The surface of dryland soils is typically covered by biological soil crusts (BSC) dominated by cyanobacteria, lichens or moss which contribute key ecosystem functions. However, while photosynthetic biota have been observed on the surface of temperate agricultural soils, understanding of the development, biodiversity and functional significance of these communities is extremely limited. We investigated the temporal development of the soil surface community following tillage and during subsequent growth of a wheat crop. Amplicon analysis showed that establishment of the soil surface microbiome was rapid over the winter period, with distinct communities of phototrophs, bacteria and protists detected 60 days after tillage. There was rapid succession with yellow-green algae (Xanthophyceae) dominating early stages of development, followed by Cyanobacteria and Charophytes and finally moss. Temporal dynamics of fungal and protist communities was influenced by eDNA deposition from plant pathogens inhabiting the crop canopy and wild animal parasites. For all groups, assembly processes in the surface soil became increasingly dominated by dispersal limitation over time while assembly of bulk soil communities became predominantly influenced by drift. Metagenome analysis showed that the soil surface had developed a distinct functional profile relative to bulk soil after 9 months, enriched in photosynthetic processes which were largely from eukaryotic algae rather than cyanobacteria. Additionally the 3-Hydroxypropionate bicycle and reductive TCA carbon fixation pathways were enriched in surface soil. The abundance of genes involved in heterotrophic carbon, nitrogen, phosphorus and sulphur cycling processes were also enriched in surface soil. This included reads of carbohydrate active enzymes, nitrification, denitrification and sulphate reduction genes, largely attributed to the enrichment of Actinobacteria, Bacteroidetes and Proteobacteria in the soil surface. Overall, we show overlap in dominant phototrophic taxa between temperate agricultural and BSC in arid soils, but with notable differences, including abundance of Xanthphycae and Charophytes. Furthermore, the functional signatures of the soil surface communities indicate that they may play an important role in the delivery of ecosystem functions in temperate agricultural systems.

microbiology↗

bioRxiv2024

Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus

BackgroundRecent evidence shows that arbuscular mycorrhizal (AM) symbiosis is established by two distinct fungal groups, with the distinctive fine root endophyte morphotype formed by fungi from the sub-phylum Mucoromycotina rather than the sub-phylum Glomeromycotina. While Mucoromycotina AM fungi are globally distributed, there is currently no understanding of the genomic basis for their symbiosis or how this symbiosis compares to that of other mycorrhizal symbionts. ResultsWe used culture-independent metagenome sequencing to assemble and characterise the metagenome-assembled genome (MAG) of a putative fine root endophyte, which we show belonged to the family Planticonsortiaceae within the order Densosporales. The MAG shares key traits with Glomeromycotina fungi, which indicate obligate biotrophy, including the absence of fatty acid and thiamine biosynthesis pathways, limited enzymatic abilities to degrade plant cell walls, and a high abundance of calcium transporters. In contrast to Glomeromycotina fungi, it exhibits a higher capacity for degradation of microbial cell walls, a complete cellulose degradation pathway, low abundances of copper, nitrate and ammonium transporters, and a complete pathway for vitamin B6 biosynthesis. ConclusionThese differences highlight the potential for contrasting interactions between Mucoromycotina and Glomeromycotina AM fungi with their host plant and the environment which could support niche differentiation and complementary ecological functions.

microbiology↗

bioRxiv2023

Ultraconformable cuff implants for long-term bidirectional interfacing of peripheral nerves at sub-nerve resolutions

Implantable devices interfacing with peripheral nerves exhibit limited longevity and resolution. Poor nerve-electrode interface quality, invasive surgical placement and development of foreign body reaction combine to limit research and clinical application of these devices. Here, we develop cuff implants with an ultraconformable design that achieve high-quality and stable interfacing with nerves in chronic implantation scenarios. When implanted in sensorimotor nerves of the arm in awake rats for 21 days, the devices recorded nerve action potentials with fascicle-specific resolution and extracted from these the conduction velocity and direction of propagation. The ultraconformable cuffs exhibited high biocompatibility, producing lower levels of fibrotic scarring than clinically equivalent PDMS silicone cuffs. In addition to recording nerve activity, the devices were able to modulate nerve activity at sub-nerve resolution to produce a wide range of paw movements. The developed implantable devices represent a platform enabling new forms of fine nerve signal sensing and modulation, with applications in physiology research and closed-loop therapeutics.

neuroscience↗

bioRxiv2022

3D Bioelectronics with a Remodellable Matrix for Long-term Tissue Integration and Recording

Bioelectronics hold the key for understanding and treating disease. However, achieving stable, long-term interfaces between electronics and the body remains a challenge. Implantation of a bioelectronic device typically initiates a foreign body response, which can limit long-term recording and stimulation efficacy. Techniques from regenerative medicine have shown a high propensity for promoting integration of implants with surrounding tissue, but these implants lack the capabilities for the sophisticated recording and actuation afforded by electronics. Combining these two fields can achieve the best of both worlds. Here, we show the construction of a hybrid implant system for creating long-term interfaces with tissue. We create implants by combining a microelectrode array with a bioresorbable and remodellable gel. These implants are shown to produce a minimal foreign body response when placed into musculature, allowing us to record long-term electromyographic signals with high spatial resolution. This device platform drives the possibility for a new generation of implantable electronics for long-term interfacing.

bioengineering↗

bioRxiv2022

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere

BackgroundThe rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions. ResultsHere, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1,059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming", which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation. ConclusionsOverall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability.

ecology↗

bioRxiv2021

Tree phyllospheres are a habitat for diverse populations of CO-oxidising bacteria

BackgroundCarbon monoxide (CO) is a naturally occurring and ubiquitous trace gas in the atmosphere. As a product of combustion processes, it can reach concentrations in the mg/m3 range in urban areas, contributing to air pollution. Aerobic CO-degrading microorganisms have been identified previously and are thought to remove ~370 Tg of CO in soils and oceans per year. Based on the presence of genes encoding subunits of the enzyme carbon monoxide dehydrogenase in metagenomes, a large fraction of soil bacteria may have the potential for CO degradation. The activity and diversity of CO-degrading microorganisms in above ground habitats such as the phyllosphere has not been addressed, however, and their potential role in global CO cycling remains unknown. ResultsMonitoring of CO-degradation in leaf washes of two common British trees, Ilex aquifolium and Crataegus monogyna, demonstrated CO uptake in all samples investigated. Leaf washes of I. aquifolium had significantly higher CO oxidation rates than those of C. monogyna. A diverse range of bacterial taxa were identified as candidate CO-oxidising taxa based on high-throughput sequencing and multivariate statistical analysis of 16S rRNA amplicon data, as well as functional diversity analysis based on coxL, the gene encoding the large subunit of CO-dehydrogenase. Candidate CO-oxidising taxa included a range of Rhizobiales and Burkholderiales, of which the Burkholderiales OTUs were abundant colonisers of the phyllosphere at the time of sampling, as indicated by 16S rRNA gene sequencing. In addition, an estimated 12.4% of leaf OTUs in samples of this study contained coxL homologues, based on their predicted genomes. We also mined data of publicly available phyllosphere metagenomes for genes encoding subunits of CO-dehydrogenase which indicated that, on average, 25% of phyllosphere bacteria contained CO-dehydrogenase gene homologues. A CO-oxidising Phyllobacteriaceae strain was isolated from phyllosphere samples which contains genes encoding both CODH as well as a RuBisCO. ConclusionsThe phyllosphere, a vast microbial habitat, supports diverse and potentially abundant CO-oxidising bacteria. These findings identify tree phyllosphere bacteria as a potential sink for atmospheric CO and highlight the need for a more detailed assessment of phyllosphere microbial communities in the global cycle of CO.

microbiology↗

bioRxiv2020

Restoring the pattern of perineuronal net sulphation corrects age-related memory loss

Memory loss is a usual consequence of ageing and aged mice show progressive deficits in memory tasks. In aged brains, perineuronal nets (PNNs), which are implicated in plasticity and memory, become inhibitory due to decreased 6-sulphation of their glycan chains (C6S). Removal of PNNs or digestion of their glycosaminoglycans rescued age-related memory loss. Premature reduction of permissive C6S by transgenic deletion of chondroitin 6-sulfotransferase led to very early memory loss. However, restoring C6S levels in aged animals by AAV delivery or transgenic expression of 6-sulfotransferase restored memory. Low C6S levels caused loss of cortical long-term potentiation, which was restored by AAV-mediated 6-sulfotransferase delivery. The study shows that loss of C6S in the aged brain leads to declining memory and cognition. Age-related memory impairment was restored by C6S replacement or other interventions targeting perineuronal nets

neuroscience↗

bioRxiv2019

Two Receptor-Like Kinases Required For Arabidopsis Endodermal Root Organisation Shape The Rhizosphere Microbiome

The Casparian Strip (CS) constitutes a physical diffusion barrier to water and nutrients in plant roots, and is formed by the polar deposition of lignin polymer in the endodermis. This precise pattern of lignin deposition is thought to be mediated by the scaffolding activity of membrane-bound Casparian Strip domain proteins (CASPs). However, we show that endodermis-specific receptor-like kinase 1 (ERK1) and ROP Binding Kinase1 (RBK1) are also involved in this intricate process, with the former playing an essential role both in the localization of CASP1 and in lignin deposition. We further characterised ERK1 and determined its subcellular localisation in the cytoplasm and nucleus of the endodermis, as well as provide evidence for its involvement in a signalling pathway together with the circadian clock regulator, Time for Coffee (TIC). We also show that disruption to CS organisation and increased suberisation in the endodermis due to loss of function of either ERK1 or TIC collectively leads to an altered root microbiome composition. Thus, our work reveals additional players in the complex cascade of signalling events operating in the root endodermis to establish both the CS diffusion barrier and the microbial composition of the rhizosphere.

plant biology↗

bioRxiv2018

Incomplete reprogramming of cell-specific epigenetic marks during asexual reproduction leads to heritable phenotypic variation in plants

Plants differ from animals in their capability to easily regenerate fertile adult individuals from terminally differentiated cells [1]. This unique developmental plasticity is commonly observed in nature where many species can reproduce asexually through the ectopic initiation of organogenic or embryogenic developmental programs [2, 3]. However, it is not currently known if this developmental reprogramming is coupled to a global epigenomic resetting, or what impact it has on the phenotype of the clonal progeny. Here we show that plants asexually propagated via induction of a zygotic developmental program do not fully reset cell-specific epigenetic imprints. These imprints are instead inherited even over multiple rounds of sexual reproduction, becoming fixed in hybrids and resulting in heritable molecular and physiological phenotypes that depend on the founder cell used. Our results demonstrate how novel phenotypic variation in plants can be unlocked through the incomplete reprogramming of cell-specific epigenetic marks during asexual propagation.

plant biology↗