Biology subjects

Goodall, T. I.

Publications and source records attributed to Goodall, T. I..

4 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

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

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↗

bioRxiv2024

Soil properties in agricultural systems affect microbial genomic traits

Understanding the relationships between bacterial taxa, their ecological and genomic traits, and their environment, is important for elucidating the mechanisms that drive microbial community dynamics and their roles in ecosystem functioning. This is especially true for soils, where dramatic shifts in resource input or physicochemical properties occur through land use and agricultural practices. Here, we examined the relationships between soil properties and bacterial traits within highly managed agricultural soil systems subjected to arable crop rotations or management as permanent pasture. We assessed the bacterial communities within these soils using amplicon sequencing and assigned each amplicon trait scores for rRNA copy number, genome size, and GC content, which are classically associated with potential growth rates and specialisation. We also calculated the niche breadth trait of each amplicon as a measure of social ubiquity within the examined samples. Within this soil system, we demonstrated that pH was the primary driver of bacterial traits. The weighted mean trait scores of the samples revealed that bacterial communities associated with soils at lower pH (<7) tended to have larger genomes (possess more potential plasticity), have more rRNA (higher growth rate potential), and are more ubiquitous (have less niche specialisation) than the bacterial communities from higher pH soils. Our findings highlight not only the association between pH and bacterial community composition but also the importance of pH in driving community functionality by directly influencing genomic and niche traits.

microbiology↗