Biology subjects

Gweon, H. S.

Publications and source records attributed to Gweon, H. S..

9 recordsLinked to original sources

bioRxiv2026

Antimicrobial resistance as a signature of soil restoration across a 143-year chronosequence

Restoring agriculturally degraded habitats to species-rich grasslands is a vital conservation objective. During restoration, how the soil resistome matures alongside microbial community composition and function remains unclear. Here, we tested two competing hypotheses: whether the soil resistome matures through a microbial warfare model, in which restoration fosters higher-order biotic interactions, or whether antimicrobial resistance (AMR) is instead driven by the competitive pressures of the high taxonomic richness found in disturbed, eutrophic arable land. Using a unique land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly following the cessation of agricultural activity. Our results demonstrate that AMR abundance increases significantly with restoration age, reaching a maximum in >143-year-old soils. Aligned with this rise in AMR abundance were significant increases in microbial biomass, dominance and cross-kingdom interaction as the ecosystem matured. This suggests that resistome expansion is not associated with generalised bacterial competition, but by a structural maturation of the microbiome. We observed an order of magnitude increase in biosynthetic potential, dominated by the emergence of streptomycin clusters. This maturation was characterised by a loss of bacterial diversity and a systematic shift towards high eukaryote-to-prokaryote ratios. This reorientation mirrors the expansion of a core resistome comprised of ancient, intrinsic mechanisms, such as MFS efflux pumps and RbpA target protection, in older soils. We demonstrate that endogenous AMR is a hallmark of healthy, restored soil ecosystems rather than a marker of anthropogenic degradation, positioning the resistome as bio-indicator of edaphic restoration success within calcareous soils.

microbiology↗

bioRxiv2026

Taxonomic filtering accompanies functional expansion during long-term soil restoration

The restoration of species-rich calcareous grasslands is a critical conservation objective, yet the recovery of the invisible below-ground microbiome remains poorly quantified compared to above-ground vegetation. Using a unique 143-year land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly across arable, regenerating (23 and 67 years), and ancient grasslands. By integrating vegetation surveys with soil physiochemistry, microbial profiling, and shotgun metagenomics, we identified a profound functional decoupling between floral and edaphic recovery. While vegetation diversity recovered relatively rapidly, approaching saturation within 23-67 years, soil properties exhibited persistent legacy effects and slow convergence. Bacterial richness decreased with restoration age, reflecting a transition from disturbance-adapted copiotrophs in arable soils to a specialised, oligotrophic community in ancient sites. This taxonomic contraction was conversely matched by an expansion in functional potential, driven by the emergence of specific taxa (e.g., Microthrixaceae, Aquihabitans sp.) and metabolic pathways associated with complex carbon cycling and stress tolerance. Crucially, the soil ecosystem did not reach equilibrium even after 67 years, characterised by persistent legacy phosphorus and a slow accumulation of soil organic matter. These findings suggest that passive regeneration alone may be insufficient for full soil functional recovery, and that strategies targeting microbial assembly and long-term carbon dynamics warrant further evaluation.

ecology↗

bioRxiv2025

Unlocking River Biofilm Microbial Diversity: A Comparative Analysis of Sequencing Technologies

Freshwater ecosystems are under increasing pressure from pollution, habitat degradation, and climate change, highlighting the need for reliable biomonitoring approaches to assess ecosystem health and identify the causes of biodiversity and ecosystem service loss. Characterisation of freshwater microbiomes has the potential to be an important tool for understanding freshwater ecology, ecosystem health and ecosystem function. High-throughput sequencing technologies, such as Illumina short-read and Pacific Biosciences long-read sequencing, are widely used for microbial community analysis. However, the relative performance of these approaches for monitoring freshwater microbiomes has not been well explored. In this study, we compared the performance of long- and short-read sequencing approaches to assess archaeal and bacterial diversity in 42 river biofilm samples across seven distinct river sites in England by targeting the 16S ribosomal RNA gene. Our findings demonstrated that longer reads generated by PacBio sequencing provide a higher taxonomic resolution, enabling the classification of taxa that remained unassigned in the short-read Illumina datasets. This enhanced resolution is particularly beneficial for biodiversity assessments because it improves species-level identification, which is crucial for ecological monitoring. Despite this, both sequencing methods produced comparable bacterial community structures regarding taxon relative abundance, suggesting that the sequencing approach does not profoundly affect the comparative assessment of community composition. However, while Illumina offers higher throughput and cost efficiency, PacBios ability to resolve complex microbial communities highlights its potential for studies requiring precise taxonomic identification.

molecular biology↗

bioRxiv2025

Deciphering landscape-scale plant cover and biodiversity from soil eDNA

Biodiversity surveys are critical for detecting environmental change; however, undertaking them at scale and capturing all available diversity through observation is challenging and costly. This study evaluated the potential of soil-extracted eDNA to describe plant communities and compared these findings to traditional, observation-based, field surveys. We analysed 789 soil samples using high-throughput amplicon sequencing and compared DNA-based diversity metrics, indicator taxa, predicted vegetation class, and plant cover in a comparison with co-located field survey data. The results indicated that taxonomically aggregated (genus) eDNA-derived data, while showing slightly reduced Shannons diversity scores, yielded remarkably similar overall richness and composition estimates. However, the DNA indicator taxa and predictive power for vegetation community classification were also lower overall than those recorded by the field survey. However, in many cases plant cover could be inferred from amplicon abundance data with some accuracy despite widely differing scales of sampling - 0.25 g crumb of soil versus a 1 m2 quadrat. Overall, results from eDNA demonstrated lower sensitivity but were broadly in accordance with traditional surveys, with our findings revealing comparable taxonomic resolution at the genus level. We demonstrate the potential and limitations of a simple molecular method to inform landscape-scale plant biodiversity surveys, a vital tool in the monitoring of land use and environmental change.

molecular biology↗

bioRxiv2020

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm

The prevalence and proliferation of antimicrobial resistant bacteria is considered one of the critical issues of our time. Wastewater is a habitat for complex microbial communities where bacteria share genes of antimicrobial resistance through horizontal gene transfer. Hospital wastewater drainage systems are an ideal reservoir for environmental and pathogenic bacteria to interface and exchange genes of antimicrobial resistance1. Highly resistant Enterobacterales are of the greatest concern because they not only cause human infections but can also thrive in the environment2,3 and have shown to transmit from sink drains to patients4. Replacement of contaminated plumbing may be the most intuitive and widely deployed response once highly resistant potentially pathogenic bacteria are identified in a sink drain. Here we show using shotgun metagenomic sequencing of sink drain biofilms (in 6 intensive care patient rooms, 36 subsamples) paired with microbial culture analysis, an evident shift of biofilm community structure towards increased abundance of Enterobacteriaceae in the newly replaced sink plumbing. Significant increase in resistome load and abundance of clinically relevant resistance and typically mobile genes in the newly replaced plumbing was also observed. Findings from this study demonstrate that exchanging contaminated plumbing for new plumbing may actually have the unexpected consequence of increased abundance of Enterobacterales and genes of antimicrobial resistance in the sink drains. Disruption of preexisting complex environmental biofilms may result in an unintended increase in the amount of antimicrobial resistant Enterobacterales which are targeted for elimination. Temporal variability is an important attribute of ecosystems affecting colonization dynamics and biotic interactions (composition of introduced and resident communities) are key to functional outcomes. Absence of competition within an ecosystem favors invasion.

microbiology↗

bioRxiv2020

Genomic network analysis of an environmental and livestock IncF plasmid population

IncF plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum {beta}-lactamases, particularly in Enterobacteriaceae. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of IncF plasmids from environmental (influent, effluent, and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable IncF plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The recent association of IncF plasmids with AMR likely reflects their suitability for rapid niche adaptation.

bioinformatics↗

bioRxiv2020

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

Escherichia coli and other Enterobacteriaceae are highly diverse species with open pangenomes1,2, where genes move intra- and inter-species via horizontal gene transfer3. These species can cause clinical infections4,5 as well as persist environmentally6,7. Environmental populations have been suggested as important reservoirs of antimicrobial resistance (AMR) genes. However, as most analyses focus on clinical isolates8,9, the pangenome dynamics of natural populations remain understudied, particularly the role of plasmids. Here, we reconstructed near-complete genomes for 828 Enterobacteriaceae, including 553 Escherichia spp. and 275 non-Escherichia species with 2,293 circularised plasmids in total, collected from nineteen locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30km radius at three timepoints over the course of a year. We find different dynamics for the chromosomal and plasmid-borne components of the pangenome, showing that plasmids have a higher burden of both AMR genes and insertion sequences, and AMR plasmids show evidence of being under stronger selective pressure. Focusing on E. coli, we observe that plasmid dynamics are more strongly dominated by niche and local geography, rather than phylogeny or season. Our results highlight the diversity of the AMR reservoir in these species and niches, and the importance of local strategies for controlling the emergence and spread of AMR.

microbiology↗

bioRxiv2020

Metrics for Public Health Perspective Surveillance of Bacterial Antibiotic Resistance in Low- and Middle-Income Countries

Antimicrobial resistance (AMR) is a global health threat, especially in low-/middle-income countries (LMICs), where there is limited surveillance to inform empiric antibiotic treatment guidelines. Enterobacterales are amongst the most important causes of drug-resistant bacterial infections. We developed a novel AMR surveillance approach for Enterobacterales by profiling pooled human faecal metagenomes from three sites (n=563 individuals; Cambodia, Kenya, UK) to derive a taxonomy-adjusted AMR metric ("resistance potential") which could be used to predict the aggregate percentage of resistant invasive Enterobacterales infections within each setting. Samples were sequenced (Illumina); taxonomic and resistance gene profiling was performed using ResPipe. Data on organisms causing bacteraemia and meningitis and antibiotic susceptibility test results from 2010-2017 were collated for each site. Bayesian generalised linear models with a binomial likelihood were fitted to determine the capacity of the resistance potential to predict AMR in Enterobacterales infections in each setting. The most informative model accurately predicted the numbers of resistant infections in the target populations for 14/14 of antibiotics in the UK, 12/12 in Kenya, and 9/12 in Cambodia. Intermittent metagenomics of pooled human samples could represent a powerful pragmatic and economical approach for determining and monitoring AMR in clinical infections, especially in resource-limited settings.

genomics↗

bioRxiv2019

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

BackgroundShotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth ([~]200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open-source software pipeline, ResPipe.\n\nResultsTaxonomic profiling was much more stable to sequencing depth than AMR gene content. 1 million reads per sample was sufficient to achieve <1% dissimilarity to the full taxonomic composition. However, at least 80 million reads per sample were required to recover the full richness of different AMR gene families present in the sample, and additional allelic diversity of AMR genes was still being discovered in effluent at 200 million reads per sample. Normalising the number of reads mapping to AMR genes using gene length and an exogenous spike of Thermus thermophilus DNA substantially changed the estimated gene abundance distributions. While the majority of genomic content from cultured isolates from effluent was recoverable using shotgun metagenomics, this was not the case for pig caeca or river sediment.\n\nConclusionsSequencing depth and profiling method can critically affect the profiling of polymicrobial animal and environmental samples with shotgun metagenomics. Both sequencing of cultured isolates and shotgun metagenomics can recover substantial diversity that is not identified using the other methods. Particular consideration is required when inferring AMR gene content or presence by mapping metagenomic reads to a database. ResPipe, the open-source software pipeline we have developed, is freely available (https://gitlab.com/hsgweon/ResPipe).

microbiology↗