Biology subjects

Croll, D.

Publications and source records attributed to Croll, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Comparative analyses reveal rapid turnover and emergence of transitory 3D genome architectures in the fungal kingdom

The three-dimensional architecture of genomes plays major roles in biological processes such as gene expression and DNA replication. The architecture of genomes has evolved substantially with distinct 3D genome shapes being identified in different lineages. The factors driving the evolution of genome architectures have primarily been assessed in animals and plants, yet large parts of the tree of life remain poorly explored. Fungi offer excellent models to assess the evolution of 3D genome architecture in a phylogenetic context given rapid genome size changes and chromosomal sequence turnover. Here, we analyzed chromosome conformation data (Hi-C) of 55 fungal species with completely assembled genomes. We identified ten species with Rabl, one species with chromosome territories and ten with a novel, intermediate chromosomal architecture, where centromeres and telomeres are at opposites in the nucleus (Rabl-like) but with a distinct 3D organization. This "bean" shape likely evolved several times independently. The discovery of a genome with a chromosome territories conformation was unexpected, as this was thought to be associated with condensin II subunits in the animal kingdom. We investigated whether 3D conformations correlated with genome size and repeat content using phylogenetic independent contrasts, however we found no genomic feature to be significantly associated with changes in genome architecture. Overall, we report the first large-scale comparison of 3D genome architecture in the fungal kingdom and identify a novel "bean" configuration. SignificanceThree-dimensional genome architecture strongly influences gene regulation, yet little is known about 3D genome architecture in an organismal group that has adapted to nearly all ecosystems on our planet, Fungi. We reconstructed 3D genome architectures from 55 fungal species covering three different phyla and demonstrate that most species do not conform to the existing definitions of 3D architectures. We identified the first case of Chromosome Territories in the Fungal Kingdom and a previously undescribed organization that we label "bean-shaped", and show that some fungal species do not conform to the canonical 3D-architecture categories of the animal and plant kingdoms. The diversity of genome architectures observed in the study could reflect the diverse gene regulatory mechanisms known from Fungi and marks the beginning of mapping out 3D genome organizations in this diverse clade. Further research in this area will uncover the diverse strategies employed by Fungi in light of their rapid adaptation.

evolutionary biology↗

bioRxiv2026

DNA damage drives a unique, Alzheimer's disease-relevant senescent state in neurons

Alzheimers disease (AD) shares molecular hallmarks with the canonical drivers of cellular senescence. Senescent cells have also been shown to accumulate in the brain with age, yet the mechanisms linking AD pathology to the accumulation of senescent cells in the brain remain unclear. Here, we demonstrate that DNA damage in patient-derived directly induced neurons (iNs) drives a senescent-like cell state with relevance to AD. DNA damage-induced senescent iNs show significant transcriptional concordance with human AD neurons and a weighted gene co-expression network analysis (WGCNA) uncovers candidate regulators associated with the senescent-like state in neurons. Direct comparison of iNs to the original patient fibroblasts reveals striking cell-type specific senescence signatures following DNA damage. iNs adopt a p21-associated senescent-like state characterized by a senescence-associated secretory phenotype (SASP) and predicted activation of NF-{kappa}1. In contrast, fibroblasts develop a p16-associated senescent state lacking a SASP phenotype and show a predicted repression of NF-{kappa}1. Early responses to DNA damage further reveal divergent DNA damage response (DDR), with neurons exhibiting higher accumulation of damage lesions relative to fibroblasts. Together, these findings demonstrate that DNA damage drives a unique senescent-like neuronal state that models molecular features of AD, while also revealing fundamental cell-type specific differences in senescent-like phenotypes and DDR.

cell biology↗

bioRxiv2026

Downregulation is the dominant effect of new regulatory mutations in a fungal pathogen

Well-tuned gene regulation is essential for an organisms survival. However, the origin and predominant effects of regulatory mutations remain poorly understood outside of model organisms. Here, we analyzed a large panel of genome sequencing data of the major fungal wheat pathogen Zymoseptoria tritici to recapitulate the evolutionary history of cis-regulatory mutations. We found that new mutations predominantly cause downregulation of the associated genes. The dominance of downregulation is reinforced for mutations occurring closest to the coding sequence and downstream. Mutations causing the strongest downregulation segregate at high frequencies in populations despite their recent origin. This suggests that selection may have played a role in their rapid increase since speciation. Overall, our study highlights the power of mapping populations combined with genomic surveys to unravel fundamental patterns of regulatory evolution.

genetics↗

bioRxiv2025

A conserved fungal transcription factor domain drives protein-protein interactions and necrotrophic effector-mediated virulence in Parastagonospora nodorum

The fungal pathogen Parastagonospora nodorum utilises necrotrophic effectors (NEs) to cause chlorosis and necrosis on wheat. NE expression is mediated by an assortment of transcription factors (TF), the most well-characterised of which is PnPf2. Orthologues of PnPf2 regulate virulence in phytopathogenic fungi across the Ascomycete fungal lineage, yet their protein architecture remains functionally uncharacterised. These orthologues are characterised by the archetypal N-terminal Zn2Cys6 zinc-finger DNA-binding domain (DBD), a conserved yet poorly characterised middle-homology region (MHR) and a C-terminal disordered region. We investigated the role of each of the three domains through PnPf2 truncation mutants in situ. This revealed the conserved MHR of PnPf2 is required for the development of disease symptoms on wheat, but also that the C-terminal disordered region in-part modulates NE expression. Domain-interaction analysis through yeast-2-hybrid (Y2H) screening reveals PnPf2 forms a homodimer mediated by the MHR, indicating its importance mediating protein-protein interactions. Using the MHR as a bait in library-scale protein-protein interaction Y2H assays, we identified the COP9-signalosome protein PnCsn6 as a key interaction partner. PnCsn6 is essential for disease symptoms during P. nodorum infection on wheat, including NE expression. Our study presents the first domain-level functional investigation this virulence-regulating TF orthologue, the results of which underpin the essential role of the MHR in driving protein-protein interactions and effector regulation. It also reveals an essential protein-signalling pathway with which PnPf2 directly interacts and shares regulatory control of virulence.

molecular biology↗

bioRxiv2025

Uncovering senescent fibroblast heterogeneity connects DNA damage response to idiopathic pulmonary fibrosis

Cellular senescence is a largely heterogeneous state of cell stress that deleteriously accumulates with age. Many types of heterogeneity in senescence have been described; however, cellular senescence within the same cell type has only started to be documented. Here, we show primary, human lung fibroblasts from donors who are healthy or diagnosed with idiopathic pulmonary fibrosis (IPF) exhibit a subtle form of heterogeneity over time after DNA damage. Moreover, senescent IPF lung fibroblasts display a dysregulated transcriptional-protein DNA damage response (DDR). Weighted gene correlation network analysis (WGCNA) reveals unique and known targets linking senescent IPF lung fibroblast heterogeneity to genes associated with DNA damage and repair, cytokine and chemokine responses, and extracellular matrix (ECM) signaling. We combine our healthy and IPF senescent gene expression signatures to develop a novel gene set of senescence-associated genes that identify disease-relevant cells in human single-cell RNA-seq (scRNA-seq) data. Collectively, our results uncover human-relevant senescence signatures, highlight IPF-specific DDR, cytokine and chemokine, and ECM targets, and expand our understanding of how a dysregulated DDR contributes to senescent cell heterogeneity in IPF.

cell biology↗

bioRxiv2025

MycoMobilome: A community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom

Transposable elements (TEs) are found in nearly all eukaryotic genomes. Despite significant advances in the sequencing of genomes, TE resources remain sparse, leading to a lack of traceability, reproducibility, and duplication of effort when annotating TEs. Here, we focus on the fungal kingdom and present MycoMobilome, a non-redundant database of TE consensus sequences systematically curated using a set of 4,309 genomes covering all major clades. The initial database contains 276,641 consensus sequences after filtering to remove putative host genes and low-quality consensus sequences. We provide a consistent naming convention to surface information on the confidence in the classification including potential conflicting ORF functions, along with metadata to enable evaluation of TEs of interest and to determine whether further curation work is required on a case-by-case basis. Finally, we provide guidelines for community contributions, and encourage researchers to deposit new or curated sequences, which will be incorporated into future MycoMobilome releases.

genomics↗

bioRxiv2025

Intra-population variability in genome-wide repressive histone marks underpins differential gene expression in a fungal wheat pathogen

Epigenetic modifications influence the expression of phenotypic traits by modulating gene expression and responses to environmental cues. In plant pathogens, the expression of virulence-associated genes such as effectors and gene clusters encoding the production of secondary metabolites are known to be regulated by epigenetic modifications. Modulating epigenetic patterns of such genes is considered a key adaptation for pathogens to successfully attack hosts. Gene expression variation within pathogen species are regulated by extensive cis- regulatory polymorphism and insertion activities of transposable elements. However, whether pathogens vary in epigenetic profiles among members of the same species remains largely unexplored. Here, we focus on the major fungal wheat pathogen Zymoseptoria tritici and establish histone methylation profiles for 45 isolates of an extensively characterized wheat field population. We analyzed the facultative heterochromatin mark H3K27me3, a histone methylation that is thought to regulate effector and gene cluster loci in the genome. H3K27m3 coverage was increased in transposable element rich regions, with newly inserted long-terminal repeat retrotransposons contributing to epigenetic variation among pathogen genotypes. Overall, nearly 20% of all genes showed within-population variation in H3K27me3 marks, which likely contributes to the substantial within-population variation in gene expression. Effector candidate genes and members of gene clusters showed higher than average variation in repressive histone marks among isolates. Taken together, our study provides among the first insights into intra-species epigenetic variation of a fungal pathogen. Such population-level variation in histone methylation patterns opens avenues to recapitulate epigenetic mechanisms of pathogen adaptation.

genomics↗

bioRxiv2025

High-resolution microbial network analysis defines biocontrol consortia in the wheat phyllosphere

Plant-associated microbiomes comprise diverse microbial species that coexist and interact, influencing community structure and host plant health. However, our understanding of these interactions in field conditions and at strain-resolution remains limited. This hinders the development of effective biocontrol applications, as laboratory findings often fail to translate to field settings due to insufficient insights into in situ interaction network structures. This study addresses this limitation by employing taxon-specific high-resolution amplicons to resolve a cross-kingdom co-occurrence network within the wheat phyllosphere microbiome. We performed in-depth monitoring of strains from the hub genus Pseudomonas, revealing a high degree of strain-specificity of Pseudomonas interactions both within and across kingdoms. Through negative interaction modelling, we identified a consortium of ten biocontrol taxa with the potential to suppress seven fungal pathogens in field conditions. Additional stabilizer strains were found to likely enhance persistence. We validated the strain-specific interactions of Pseudomonas with the major fungal pathogen Zymoseptoria tritici using co-inoculation experiments with genotypes retrieved from the same field. Consistent with our prediction, we identified a P. poae isolate as the most antagonistic towards the pathogen both in vitro and in planta. Our study demonstrates that taxon-specific high-resolution network inference can effectively map microbial interaction networks and predict strain-specific interaction patterns of biocontrol genotypes with high persistence under field conditions. Our novel approach supports the design of more effective and sustainable biocontrol strategies.

microbiology↗

bioRxiv2025

Massive proliferation of retrotransposons contributes to genome size expansion in species of the Pseudocercospora genus

Genome size expansions are common among eukaryotic lineages. Enlarged genomes can be bioenergetically demanding, and active mobile elements can trigger chromosomal rearrangements and loss of gene function. What triggers genome size expansions remains largely unexplored in many biological clades, particularly within the fungal kingdom. Activation of large transposable elements (TEs), such as long-terminal repeats (LTRs), is a common contributor. Yet the mechanisms of LTR activation remain poorly understood. Here, we focus on the fungal genus Pseudocercospora and closely related species with known variation in genome size. In using an assembly-free approach, we found that TE content is highly variable among species, with species-specific retrotransposon families being the main drivers of independent genome expansions. We further focussed on the two species with the most expanded genomes and reference-quality genomes, P. fijiensis and P. ulei. We found that the P. ulei genome is compartmentalized, with highly variable TE densities among chromosomal regions, and a striking reduction in pathogenicity-associated genes. Overall, our study indicates that species of Pseudocercospora originally had reduced genome sizes, and genome expansions are species-specific, driven by heterogeneous sets of TE families. Furthermore, we found that in the species with the most expanded genome, TE activity might not have ceased yet as indicated by resequencing data analysis of six strains from diverse locations in Colombia. We discuss what might have caused TE activation and subsequent proliferation in the genus, including stress conditions and host adaptation. Surveys of clades with highly dynamic genome sizes are crucial for the investigation of causal factors driving long-term TE dynamics.

genomics↗

bioRxiv2025

A pangenomics-enabled platform for the high-throughput discovery of antifungal resistance factors in crop pathogens

The rise of antifungal resistance is a global challenge for both human health and food security, because resistance emergence easily outpaces the antifungal development pipeline. Furthermore, resistance arises often in parallel and through alternative mechanisms creating challenges to predict emergence. In agriculture, where vast areas are sprayed by diverse cocktails, antifungal resistance gains are particularly complex. Despite broad efforts, knowledge of resistance mechanisms is often limited to model genotypes and empirical evidence from the field is lacking. Here, we define and validate a high- throughput pipeline for antifungal resistance discovery informed by emerging resistance gains at continental scale. We analyzed a thousand-genome European diversity panel of the major wheat pathogen Zymoseptoria tritici and assessed resistance levels against over 29 fungicides covering all major classes. We optimized high-throughput phenotyping assays to comprehensively capture emerging resistance phenotypes. Pangenome-informed genotyping techniques revealed a total of 2192 genes associated with antifungal resistance. This expands by an order of magnitude the current knowledge and establishes a refined atlas of resistance mutations. We generated mutants to recapitulate several of the discovered resistance factors. Hence, our approach captures in-field resistance gains across Europe for all major fungicide classes and can define exact molecular targets. Broad knowledge of resistance gains will guide more sustainable fungicide development pipelines.

microbiology↗

bioRxiv2025

A new molecular seed assay to predict Ustilago nuda field infection levels

Seed health tests are performed to prevent sowing untreated seeds with problematic pathogen levels. The detection of internal seedborne pathogens like Ustilago nuda, causing loose smut in barley (Hordeum vulgare), is challenging because symptoms only appear when teliospores replace barley inflorescences and smutted ears develop. Currently, U. nuda seed infection levels are determined from the visual inspections of extracted embryos or fields of plants used for seed production, both of which are laborious and can be unreliable. To improve U. nuda detection, we developed a multiplex qPCR method targeting U. nuda and H. vulgare DNA. Naturally infected seed lots were tested using this qPCR method and the visual analysis of embryos. We grew the same seed lots in the field over two seasons and used the observed smutted ears as the reference infection level. The qPCR results, U. nuda DNA normalized to H. vulgare DNA, better correlated with observed field infections than the number of infected embryos. Our qPCR method more accurately distinguished seed lots with infections above and below the field tolerance threshold. It offers a reliable alternative to the visual analysis of extracted embryos. The integration of our qPCR method with field observations can enhance U. nuda management and reduce unnecessary prophylactic seed treatments, thereby bolstering integrated pest management strategies.

plant biology↗

bioRxiv2025

Transposable elements create distinct genomic niches for effector evolution among Magnaporthe oryzae lineages

Plant-pathogen interactions are characterized by evolutionary arms races. At the molecular level, fungal effectors can target important plant functions, while plants evolve to improve effector recognition. Rapid evolution in genes encoding effectors can be facilitated by transposable elements (TEs). In Magnaporthe oryzae, the causal agent of blast disease in several cereals and grasses, TEs play important roles in chromosomal evolution as well as the gain or loss of effector genes in host specialized lineages. However, a global understanding of TE dynamics driving effector evolution at population scale and across lineages is lacking. Here, we focus on 16 AVR effector loci assessed across a global sampling of 11 reference genomes and 447 newly generated draft genome assemblies across all major M. oryzae lineages and outgroups. We classified each effector based on evidence for duplication, deletion and translocation processes among lineages. Next, we determined AVR gain and loss dynamics across lineages allowing for a broad categorization of effector dynamics. Each AVR was integrated in a distinct genomic niche determined by the TE activity profile contributing to the diversification at the locus. We quantified TE contributions to effector niches and found that TE identity helped diversify AVR loci. We used the large genomic dataset to recapitulate the evolution of the rice blast AVR1-CO39 locus. Taken together, our work demonstrates how TE dynamics are an integral component of M. oryzae effector evolution, likely facilitating escape from host recognition. In-depth tracking of effector loci is a valuable tool to predict the durability of host resistance.

microbiology↗

bioRxiv2025

Corn rust population genomics reveals a cryptic virulent group and adaptive effectorome

Understanding the population structure of pathogens and the genetic determinants driving virulence gains is crucial for managing epidemic plant diseases. Puccinia polysora, a giga-scale fungal pathogen causing southern corn rust, has posed significant threat to global food security recently. Traditionally, P. polysora was considered clonal with minimal genetic variation. However, our population genomic and transcriptomic studies conducted in China, the emerging epicentre of the disease, have challenged this view. By adopting variant analyses appropriate to the dikaryotic nature of the pathogen, we discovered an unexpectedly clear population structure with six distinct groups. A cryptic group exhibits high virulence, facilitated by group-specific variation, and diversification of effectors. Although the Chinese population of P. polysora is predominantly asexual, internuclear exchange on some chromosomes have introduced recombination signals. The comprehensive pan-effectorome analyses revealed substantial presence/absence variation and alternative splicing events on effectors, shaping a highly adaptive effector repertoire in P. polysora. In conclusion, our findings highlight the tandem mapping on exploring clear genetic structure of dikaryotic species and reported the emergence of a virulent group and an adaptive effectorome of P. polysora. Effective containment strategies must be flexible to counter the threats posed by the unexpectedly dynamic evolution of this pathogen.

molecular biology↗

bioRxiv2025

Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen

Transposable elements (TEs) can drive the evolution of host-pathogen interactions and gains in antimicrobial resistance. However, how adaptive TEs arise in populations and historical contingencies affect TE dynamics remains unknown. Fungal pathogens in agriculture provide unique frameworks to address such questions due to the availability of spatially explicit sampling and well- characterized niche conditions. We characterised TE evolutionary dynamics using an extensive intraspecies sampling of 1,953 genomes across the global distribution range of the major fungal wheat pathogen Zymoseptoria tritici. Employing a pangenomic approach, we characterise genomic diversity and benchmark methods to robustly infer TE insertion polymorphism, before systematically assessing TEs as a source of adaptive variation. We annotated [~]3.2 million TE loci among genomes, finding substantial variation in TE content within and among populations. TE activity surged during the pathogens expansion from its centre of origin in the Middle East, with unique TE activity profiles arising in derived populations. TE-mediated adaptation emerged from distinct waves of TE mobilization. The highest rates of TE activity were observed over timescales as short as 25 years. 45 TE loci showing local adaptation signatures within 1kb of 49 host genes were identified, with adaptive TE insertions likely related to adaptation to antifungals and the plant host environment. This work highlights the power of vast genomic datasets to unravel intraspecies TE invasion histories and pinpoint factors likely driving recent adaptation. This argues for a shift in focus to incorporate deep population-level TE activity surveys in our pursuit to uncover the molecular drivers of adaptive evolution.

genomics↗

bioRxiv2025

A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen

Fungicide resistance in crop pathogens poses severe challenges to sustainable agriculture. Demethylation inhibitors (DMIs) are critical for controlling crop diseases but face rapid resistance gains in the field. Even though the main molecular basis of resistance is well established, field surveys have repeatedly revealed alternative resistance mechanisms. The European continent in particular has seen rapid and heterogeneous gains in azole resistance in the past decades. Here, we establish a large genome panel to dissect the genetic architecture of emerging resistance in the major wheat pathogen Zymoseptoria tritici. The European diversity panel spans 15 sampling years and 27 countries for a total of 1394 sequenced and phenotyped strains. Using two complementary assays to quantify resistance levels of each strain, we captured fine-grained shifts in DMI resistance over space and time. We conducted genome-wide association studies based on a comprehensive set of genotyping approaches for six DMIs. We mapped a total of 21,220 genetic variants and 158 genes linked to resistance. The substantial scope in genetic mechanisms underpinning DMI resistance significantly expands our mechanistic understanding how continent-wide resistance arises in fungal pathogens over time. Diversification of the Cyp51 coding sequence was particularly striking with new resistant haplotypes emerging with complex configurations and geographic patterns. This study provides expansive new insights into fungicide resistance gains of crop pathogens relevant for future resistance management strategies.

microbiology↗

bioRxiv2025

Wheat infection by Fusarium graminearum species complex members is facilitated by a transcriptionally conserved non-ribosomal peptide synthetase gene cluster

Biosynthetic gene clusters (BGCs) are often found in fungal pathogens and encode secondary (or specialized) metabolites that play crucial roles in host and niche adaptation. However, the regulatory dynamics and functions of these BGCs during host infection remain largely unknown. To address this gap, we employed interspecies comparative transcriptomics to identify BGCs involved in host-pathogen interactions mediated by the Fusarium graminearum species complex (FGSC). We conducted joint transcriptomic and metabolomic analyses during wheat infection and in vitro experiments with five members of the FGSC to understand gene regulation during host infection. Our findings revealed that expression regulation was predominantly species-specific, but we also identified a set of shared upregulated genes that were common to all five FGSC species showing enrichment for metabolic and pathogenicity-associated functions. We focused on jointly upregulated BGC during infection and identified a NRPS-like gene cluster named SM3. The cluster was highly conserved within FGSC and shared by the more distant F. sambucinum species complex. We show that inactivation of the BGC core gene significantly impairs F. graminearum sensu stricto (s.s.) spore production, reduces fungal spread and Fusarium Head Blight symptoms on wheat kernels. Our results highlight that comparative infection transcriptomes can reveal conserved metabolic functions mediating the host infection process of a plant pathogen.

microbiology↗

bioRxiv2025

A systematic screen for genetic factors underpinning transposon defense systems across the fungal kingdom

Fungal genome sizes exhibit more than a 100-fold variation, largely driven by the expansion of repetitive sequences such as transposable elements (TEs). Silencing mechanisms targeting TEs at the epigenetic or transcript level have independently evolved in many lineages. In fungi, repeat-induced point mutation (RIP) targets TEs by recognizing repetitive sequences and inducing mutagenesis. However, the prevalence of RIP across the fungal kingdom and the fidelity of the canonical C-to-T mutation signatures remain unclear. In this study, we address these gaps by tracking shifts in genome architecture across the fungal kingdom. We find that a striking [~]30-fold increase in genome size within a clade of leotiomycetes is associated with the absence of several RIP-related genes, suggesting a relaxation of genome defense mechanisms during this expansion. To track the impact of genome defenses, we designed a quantitative screen for RIP-like mutation signatures. The phylum of ascomycetes was unique in showing enrichment in mutation signatures in non-coding and repetitive sequences, consistent with a phylogenetically restricted occurrence of RIP-like genome defense systems. Then, we performed a phylogeny-aware association study to identify gene functions associated with RIP-like mutation signatures. We identified a zinc-finger protein as the strongest candidate underpinning a novel mechanism of genome defenses. Our findings reveal the multifaceted drivers of genome defense systems and their close ties to genome size evolution in fungi, highlighting how proximate molecular mechanisms can shape genome evolution on deep phylogenetic scales.

evolutionary biology↗

bioRxiv2024

Rapid and In-situ Detection of Biological Agents via Near-Infrared Spectroscopy and Cloud-Powered Neural Networks

The contagious nature of certain biological agents and the difficulty in treating infections render them a significant threat to public health and safety. In situations involving chemical, biological, radiological, and nuclear (CBRN) agents, effective detection is of paramount importance to prevent the undetected spread of these agents and enable swift and targeted responses tailored to the specific threat. Although portable detection tools are effective for chemical and nuclear detection, current biological detection methods face several challenges, including limited mobility, extended processing times, and varying accuracy. In the context of biological threats, where agents such as anthrax can be rapidly dispersed due to environmental factors and human activities, rapid detection is of paramount importance. It is imperative to develop field-applicable detection devices that are highly selective, capable of differentiating between biological and non-biological agents, as well as benign and harmful microorganisms. This study examines the potential of near-infrared (NIR) spectroscopy in conjunction with machine learning as a rapid in-situ biological detection method. The objective is to distinguish between biological agents and common white powders that are used as confounding agents in suspect letters. The non-pathogenic surrogates employed are safe and representative of typical biological warfare agents. The near-infrared (NIR) spectra of lyophilized bacterial and fungal surrogates, along with common white powders, were subjected to analysis and processing through the application of principal component analysis (PCA) and hierarchical clustering analysis (HCA). This resulted in the successful classification of the samples into distinct groups. The classification model demonstrated high accuracy in its prediction, thereby emphasizing the potential of the method for field detection of solid biological agents. These promising results suggest that NIR spectroscopy combined with machine learning could be further investigated as a rapid in-situ tool for biological detection in CBRN contexts.

microbiology↗