Biology subjects

Busi, S. B.

Publications and source records attributed to Busi, S. B..

At least 19 recordsLinked to original sources

bioRxiv2026

Ecological and metabolic signatures of biofilm viromes across a national river surveillance network

Benthic biofilms are biogeochemical hotspots in rivers, yet their endogenous viral communities remain poorly resolved at national scales. We analysed 447 biofilm metagenomes from 146 sites within England's River Surveillance Network (RSN), sampled in spring and autumn from 2021 to 2023, integrating viral operational taxonomic units (vOTUs), water-quality gradients, predicted host associations and auxiliary metabolic genes (AMGs). We recovered 38,534 vOTUs, revealing extensive viral novelty, where 93% of the vOTUs could not be assigned to a known family. Viromes were dominated by Caudoviricetes and unclassified lineages and were extremely heterogeneous: no vOTU occurred in more than 8.3% of samples. Season, but not sampling year, structured virome composition (family-level PERMANOVA R2 = 0.050, p = 0.001; year p = 0.08), and within-site turnover between spring and autumn exceeded turnover between years. Bray-Curtis ordination linked virome structure weakly to pH, dissolved organic carbon, conductivity, nitrate-N and dissolved oxygen (envfit R2 [≤] 0.066), while threshold indicator taxa analysis (TITAN) identified vOTUs with abrupt change points along alkalinity, dissolved oxygen, nitrate-N and temperature gradients. Predicted host associations were concentrated in Pseudomonodota, Cyanobacteriota and Bacteroidota, with Microcoleus, Chamaesiphon and Flavobacterium among the dominant host genera. Virus-host networks were modular, and module abundances correlated with water quality variables (dissolved oxygen, pH, nitrate etc.), suggesting that environmental filtering acts partly through host ecology. Predicted virus-host associations formed a sparse network organised around a few highly connected viral lineages. Functional profiling showed that the biofilm virome was dominated by nucleotide metabolism, DNA methylation, phosphate-stress, glycan-modification and photosynthesis-related AMGs, with nrdA/nrdB ribonucleotide reductase as the dominant AMG signal. Few vOTUs (1.2%) were detected as proviruses, although provirus fractions were higher in selected host-linked lineages. Collectively, these results show that river biofilm viromes are seasonally structured ecological communities whose composition, host associations and metabolic potential reflect the physicochemical and biological state of rivers. We propose that biofilm viromes provide a complementary layer of information for understanding river health, microbial ecology and the propagation of anthropogenic pressures in freshwater systems.

microbiology↗

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↗

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↗

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↗

bioRxiv2024

Fetal programming by the maternal microbiome of offspring behavior, and DNA methylation and gene expression within the hippocampus

BackgroundThe microorganisms colonizing the gastrointestinal tract of animals, collectively referred to as the gut microbiome, affect numerous host behaviors dependent on the central nervous system (CNS). Studies comparing germ-free mice to normally colonized mice have demonstrated influences of the microbiome on anxiety-related behaviors, voluntary activity, and gene expression in the CNS. Additionally, there is epidemiologic evidence supporting an intergenerational influence of the maternal microbiome on neurodevelopment of offspring and behavior later in life. There is limited experimental evidence however directly linking the maternal microbiome to long-term neurodevelopmental outcomes, or knowledge regarding mechanisms responsible for such effects. ResultsHere we show that that the maternal microbiome has a dominant influence on several offspring phenotypes including anxiety-related behavior, voluntary activity, and body weight. Adverse outcomes in offspring were associated with features of the maternal microbiome including bile salt hydrolase activity gene expression (bsh), abundance of certain bile acids, and hepatic expression of Slc10a1. In cross-foster experiments, offspring resembled their birth dam phenotypically, despite faithful colonization in the postnatal period with the surrogate dam microbiome. Genome-wide methylation analysis of hippocampal DNA identified microbiome- associated differences in methylation of 196 loci in total, 176 of which show conserved profiles between mother and offspring. Further, single-cell transcriptional analysis revealed accompanying differences in expression of several differentially methylated genes within certain hippocampal cell clusters, and vascular expression of genes associated with bile acid transport. Inferred cell-to-cell communication in the hippocampus based on coordinated ligand-receptor expression revealed differences in expression of neuropeptides associated with satiety. ConclusionsCollectively, these data provide proof-of-principle that the maternal gut microbiome has a dominant influence on the neurodevelopment underlying certain offspring behaviors and activities, and selectively affects genome methylation and gene expression in the offspring CNS in conjunction with that neurodevelopment.

microbiology↗

bioRxiv2023

The response to ketogenic diet in colorectal cancer is mediated by lasting functional alterations of the gut microbiome

Colorectal cancer (CRC) patients have been shown to possess an altered gut microbiome. Diet is a well-established modulator of the microbiome, and thus, dietary interventions might have a beneficial effect on CRC. An attenuating effect of the ketogenic diet (KD) on CRC cell growth has been previously observed, however the role of the gut microbiome in driving this effect remains unknown. Here, we describe a reduced colonic tumor burden upon KD consumption in a CRC mouse model with a humanized microbiome. Importantly, we demonstrate a causal relationship through microbiome transplantation into germ-free mice, whereby alterations in the gut microbiota were maintained in the absence of continued selective pressure from the KD. Specifically, we identify a shift toward bacterial species that produce stearic acid in ketogenic conditions, whereas consumers were depleted, resulting in elevated levels of free stearate in the gut lumen. This microbial product demonstrated tumor-suppressing properties by inducing apoptosis in cancer cells and decreasing colonic Th17 immune cell populations. Taken together, the beneficial effects of the KD are mediated through alterations in the gut microbiome, including, among others, increased stearic acid production, which in turn significantly reduces intestinal tumor growth.

cancer biology↗

bioRxiv2023

Functional assignment of gut-specific archaeal proteins in the human gut microbiome

The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as IBD and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.

microbiology↗

bioRxiv2023

Cross-domain interactions induce community stability to benthic biofilms in proglacial streams

Cross-domain interactions are an integral part of the success of complex biofilms in natural environments. Here, we report on cross-domain interactions in biofilms of streams draining proglacial floodplains in the Swiss Alps. These streams, as a consequence of the retreat of glaciers, are characterized by multiple environmental gradients and stability that depend on the time since deglaciation. We estimate co-occurrence of prokaryotic and eukaryotic communities along this gradient and show that key community members have disproportionate effects on the stability of co-occurrence networks. The topology of the networks was similar independent of environmental gradients and stability. However, network stability was higher in the streams draining proglacial terrain that was more recently deglaciated. We find that both pro- and eukaryotes are central to the stability of these networks, which fragment upon the removal of both pro- and eukaryotic taxa. These keyplayers are not always abundant, suggesting an underlying functional component to their contributions. Thus, we show that there is a key role played by individual taxa in determining microbial community stability of glacier-fed streams.

microbiology↗

bioRxiv2023

Shift from a Simplified to Complex Gut Microbiota Reduces Adenoma Burden in a Preclinical Rat Model of Colon Cancer

Specific bacterial taxa in the gastrointestinal tract have been strongly associated with cases of colorectal cancer (CRC) cancer in familial adenomatous polyposis and spontaneous disease cases in humans. This has been recapitulated in animal models of CRC with positive correlations with many commensals and pathogens. However, many of these studies are performed either in germ-free animals or employ an antibiotic regime, overlooking the complex interactions of the commensals within the colon. To simplify the challenges associated with the complexity of the microbiota in the GI tract we established the Pirc rat model of colon cancer on an Altered Schaedler Flora (ASF) gut microbiota (GM), maintained in a barrier room. To elucidate the role of the simplified (ASF) and conventional GMs on disease susceptibility, We conventionalized ASF Pirc littermates. We found that the conventionalized F1 rats had increased microbial diversity and decreased colonic adenoma multiplicity. Our findings show that the complexity and the interactions of the GM community and not a Firmicutes to Bacteroidetes ratio are an important factor affecting disease susceptibility.

microbiology↗

bioRxiv2022

Altered infective competence of the human gut microbiome in COVID-19

ObjectivesInfections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. DesignWe used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group. ResultsWe found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19 positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19 positive individuals compared to healthy controls. ConclusionOur analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients.

microbiology↗

bioRxiv2022

Multi-omics analysis of mouse fecal microbiome reveals supplier-dependent functional differences and novel metagenome-assembled genomes

Host genetics, sex, and other within-source factors have been associated with characteristic effects on the fecal microbiome in mice, however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes in particular confer differences in disease susceptibility in models of inflammatory conditions, as well as baseline behavior and body morphology. However, current knowledge regarding the compositional differences between suppliers is based on 16S rRNA amplicon sequencing data, and functional differences between these communities remain poorly defined. Here, we applied a meta-omic (metagenomic and metatranscriptomic) approach to biomolecules (DNA/RNA) extracted from murine fecal samples representative of two large U.S. suppliers of research mice, which differ in composition, and influence baseline physiology and behavior as well as disease severity in mouse models of intestinal disease. We reconstructed high-quality metagenome-assembled genomes (MAGs), frequently containing genomic content unique to each supplier. These differences were observed both within pangenomes of dominant taxa as well as the epibiont Saccharimonadaceae. Additionally, transcriptional activity and pathway analyses revealed key functional differences between the metagenomes associated with each supplier, including differences in carbohydrate enzyme activity and dissimilatory sulfate reduction by sulfate-reducing bacteria (SRB). These data provide a detailed characterization of the baseline differences in the fecal metagenome of laboratory mice from two U.S. commercial suppliers suggesting that these functional differences are influenced by differences in the initial inoculum of colony founders, as well as additional taxa gained during growth of the production colony.

microbiology↗

bioRxiv2022

Biofilm competency of Desulfovibrio vulgaris Hildenborough facilitates colonization in the gut and represses adenoma development in a rat model of colon cancer

Human epidemiological and animal model studies have shown that the presence of colon cancer is associated with certain microbiota. Previous human colon cancer case-control reports and our preclinical model studies identify several bacterial taxa correlating with the suppression of tumor growth. This includes a sulfate-reducing bacteria from the genus Desulfovibrio, which correlates with fewer tumors and decreased phenotype penetrance as early as 1 month of age in rats. However, other studies have shown that Desulfovibrio spp. are decreased in relative abundance in healthy patient controls. To address this disparity we treated PIRC rats, a model of human familial colon cancer that harbored a complex gut microbiota, with biofilm-forming and biofilm-deficient strains of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH). We found that the biofilm-forming DvH strain could stably colonize the rat colon, with the bacteria detected even at 3.5 months post treatment. The biofilm-deficient DvH mutant only transiently colonized the rat colon and was no longer detected in fecal samples one-week post treatment. The colonic adenoma burden at four months of age was significantly reduced in rats colonized with the biofilm- forming DvH compared to those treated with the biofilm-deficient DvH. We found a differential shift in the endogenous gut microbiota (GM) structure over time, with a notable increase in known mucin degraders in the buffer-treated control and biofilm-deficient DvH treated groups. These latter groups of rats also showed a higher level of expression of MUC2 in the colon, which encodes for the sulfonated mucin 2 expressed primarily in the gut and trachea. We also detected more dissolved sulfide in the feces from rats treated with either buffer or biofilm-deficient DvH compared to rats colonized with the biofilm-competent DvH. We found that the in vitro biofilm- forming capacity of DvH enabled in vivo engraftment of this bacterium within a complex GM population, altering the bacterial composition, and significantly reducing tumor burden in PIRC rats.

microbiology↗

bioRxiv2021

Glacier-fed stream biofilms harbour diverse resistomes and biosynthetic gene clusters

BackgroundAntimicrobial resistance (AMR) is a universal phenomenon whose origins lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. However, the ecological and evolutionary processes shaping AMR need to be better understood in view of better antimicrobial stewardship. Resolving antibiotic biosynthetic pathways, including biosynthetic gene clusters (BGCs), and corresponding antimicrobial resistance genes (ARGs) may therefore help in understanding the inherent mechanisms. However, to study these phenomena, it is crucial to examine the origins of AMR in pristine environments with limited anthropogenic influences. In this context, epilithic biofilms residing in glacier-fed streams (GFSs) are an excellent model system to study diverse, intra- and inter-domain, ecological crosstalk. ResultsWe assessed the resistomes of epilithic biofilms from GFSs across the Southern Alps (New Zealand) and the Caucasus (Russia) and observed that both bacteria and eukaryotes encoded twenty-nine distinct AMR categories. Of these, beta-lactam, aminoglycoside, and multidrug resistance were both abundant and taxonomically distributed in most of the bacterial and eukaryotic phyla. AMR-encoding phyla included Bacteroidota and Proteobacteria among the bacteria, alongside Ochrophyta (algae) among the eukaryotes. Additionally, BGCs involved in the production of antibacterial compounds were identified across all phyla in the epilithic biofilms. Furthermore, we found that several bacterial genera (Flavobacterium, Polaromonas, etc.) including representatives of the superphylum Patescibacteria encode both ARGs and BGCs within close proximity of each other, thereby demonstrating their capacity to simultaneously influence and compete within the microbial community. ConclusionsOur findings highlight the presence and abundance of AMR in epilithic biofilms within GFSs. Additionally, we identify their role in the complex intra- and inter-domain competition and the underlying mechanisms influencing microbial survival in GFS epilithic biofilms. We demonstrate that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. We also find that the taxonomic affiliation of the AMR and the BGCs are congruent. Importantly, our findings allow for understanding how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Importantly, these observations may be generalizable and potentially extended to other environments which may be more or less impacted by human activity.

microbiology↗