Biology subjects

Thorpe, A. C.

Publications and source records attributed to Thorpe, A. C..

7 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

Resolving eukaryotic river biofilm communities using long-read sequencing for biomonitoring

Freshwater biofilms host diverse microbial eukaryotic communities that are central to ecosystem functioning and serve as key indicators of water quality. Molecular biomonitoring approaches based on environmental DNA (eDNA) sequencing are increasingly used to characterise these communities, offering scalable alternatives to traditional microscopy-based assessments. Understanding how DNA sequencing methods influence the observed community composition and diversity is essential for ensuring accurate ecological interpretation. Here, we compared short-read Illumina and long-read Pacific Biosciences sequencing of the 18S rRNA gene, alongside a trimmed long-read dataset (restricted to the Illumina-primed region), to evaluate how read length and sequencing platform affect community profiling in river biofilms from seven English rivers sampled across three timepoints. Distinct community patterns were observed between the sequencing approaches, with PERMANOVA revealing significant differences in beta diversity (p = 0.001) and modest effect sizes (R2 = 3.8-8.3%). While the long and trimmed datasets produced nearly identical community structures, both diverged strongly from the short-read data, suggesting that short-read sequencing captures a systematically different subset of taxa than long-read sequencing. Long-read sequencing significantly improved taxonomic resolution of the 18S rRNA gene, particularly at the genus and species levels, enabling detection of lineages that were unresolvable in short-read data. However, comparisons of paired long- and trimmed-read ASVs indicated that trimming can increase taxonomic mismatches at finer ranks, likely due to reduced sequence length rather than sequencing platform bias. Collectively, our results demonstrate that sequencing strategy significantly influences inferred community composition and taxonomic precision. Long-read sequencing provides a more robust representation of community diversity, whereas trimmed analyses reveal how shorter amplicons may contribute to misidentification. These findings emphasise the importance of considering read length when interpreting eDNA-based assessments using the 18S rRNA gene and support the adoption of long-read sequencing for high-resolution biomonitoring applications.

molecular biology↗

bioRxiv2026

Evolutionary radiation of Polaromonas from mountain glaciers downstream

Habitat transitions are central to microbial ecology and evolution and have been extensively studied across vastly different environments, such as between saline and non-saline environments. However, microbial habitat transitions along other large-scale environmental gradients remain poorly studied. This is particularly true for transitions involving the cryosphere, despite building evidence suggesting the Cryogenian as important for evolutionary radiation. Here, we investigated ecosystem transitions and related genomic adaptations of the cosmopolitan cryospheric Polaromonas bacterium. We constructed a pangenome from 282 high-quality genomes, sourced from glaciers, glacier-fed streams, lakes, wetlands, groundwater, rivers, and soils. Phylogenetic reconciliation revealed that the ancestral Polaromonas genome radiated from glacier ecosystems into various downstream environments through multiple independent transitions. These transitions were marked by extensive horizontal gene transfer and gene loss, with mobile genetic elements, such as plasmids and prophages playing key roles in genomic diversification. Predicted ancestral genomes encoded versatile metabolic and stress-response capacities, supporting adaptation to fluctuating and extreme conditions in the various cryospheric habitats. Compared to the ancestral Polaromonas genome, distinct genomic signatures were associated with specific habitats: glacier-fed stream lineages possess expanded stress tolerance repertoires, glacier lineages gained chemolithotrophic and anaerobic pathways, lake and wetland genomes acquired phototrophic functions, and soil lineages expanded substrate transport and stress tolerance. Together, our findings highlight the role of genomic plasticity in the ecological success of Polaromonas, and also underscore the cryosphere as a potential evolutionary cradle from which lineages dispersed and adapted to downstream aquatic and terrestrial environments.

microbiology↗

bioRxiv2026

Environmental filtering shapes divergent bacterial strategies and genomic traits across soil niches

Soil pH is a predominant factor in structuring microbial communities; however, its role in shaping microbial life-history traits across large spatial scales remains underexplored. Here, we hypothesised that bacterial ubiquity, or niche breadth, across a diverse collection of soils is linked to genomic traits. We leveraged a national-scale survey of UK soils (the Countryside Survey) and 16S rRNA gene sequencing data with trait annotations (estimated genome size, coding density, and rRNA operon copy number) to examine trait-environment-niche breadth relationships. Our analyses revealed that soil pH was the dominant environmental driver of niche classification and bacterial community traits along the niche range. Low pH soils (pH <5.5) hosted ubiquitous taxa with larger genome sizes, lower coding densities and lower rRNA copy numbers, implying slower growing taxa with higher genetic facilities. Mildly acidic soils (pH 5.5 to 7) favour higher rRNA copy numbers, intermediate genome sizes and moderate coding densities. Alkaline soils (pH >7) feature communities with the smallest niche range, smallest genomes and highest coding densities. Here, specialisation occurs through streamlining with simpler, smaller genomes favoured. We found that generalist taxa were widespread across the pH range, becoming dominant under acidic conditions, while taxa adapted to higher pH were comparatively scarce in their distribution. These findings identify soil pH as a key physiological filter that aligns microbial genomic traits and ecological strategies across landscapes. By extending prior site-specific results to a broad-scale context, our study highlights how trait-based metrics can predict microbial responses to soil conditions, with implications for understanding ecosystem carbon cycling and informing land management practices aimed at sustaining soil health in the future.

microbiology↗

bioRxiv2025

River biofilm bacteria as sentinels of national-scale freshwater ecosystems

Freshwaters face increasing pressures from chemical, hydrological, and climatic changes, yet tools for assessing their condition remain limited. River biofilms, composed of diverse microbial communities, integrate environmental signals over space and time, making them sensitive indicators of river health. Using 16S rRNA gene sequencing of more than 1,600 biofilms collected across a national river network, we quantified bacterial diversity and community composition and applied network analysis to identify ecologically cohesive sub- communities with keystone taxa underpinning community stability. Alkalinity, dissolved oxygen, nitrate-nitrogen, and temperature were among the principal gradients shaping community composition. Threshold indicator analyses identified taxa with breakpoints along these gradients, revealing interpretable ecological thresholds. Our results demonstrate the potential for microbiome-based monitoring frameworks that complement existing biotic indices, enabling early detection of ecological changes and supporting the integration of genomic indicators into routine ecosystem assessment. This scalable approach offers a powerful strategy for managing freshwaters under accelerating anthropogenic pressures.

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

National-scale biogeography and function of river and stream bacterial biofilm communities

Biofilm-dwelling microorganisms coat the surfaces of stones in river and stream ecosystems, forming diverse communities that are fundamental to biogeochemical processes and ecosystem functioning1,2. Flowing water (lotic) ecosystems are under pressure from a wide range of interacting stressors including changes in land use, chemical pollution, and climate3. Despite their ecological importance, the taxonomic and functional diversity of river biofilms and their responses to environmental change are limited by a lack of understanding of their taxonomic composition and physicochemical drivers across large spatial scales. We conducted a national-scale assessment of bacterial diversity and function using metagenomic sequencing from rivers and streams across England, analogous to other large-scale efforts to understand microbial biogeography across diverse environments4,5,6,7. We recovered 1,014 metagenome-assembled genomes (MAGs) from 450 biofilms collected across Englands extensive river network, revealing substantial taxonomic novelty, with [~]20% of the MAGs representing novel genera. We demonstrated that biofilm communities, dominated by generalist bacteria, exhibit remarkable functional diversity and metabolic versatility, and play a significant role in nutrient cycling with the potential for contaminant transformation. Environmental drivers, most notably geology, land cover, and nutrients, explained up to 90% of the variation in community composition. These findings highlight the importance of river biofilms and establish a foundation for future research on the roles of biofilms in ecosystem health and resilience to environmental change.

ecology↗