Biology subjects

Colombi, E.

Publications and source records attributed to Colombi, E..

11 recordsLinked to original sources

bioRxiv2026

Drought and rewetting drive divergent microbial dynamics across soil compartments and reveal Trinickia as a key genus for soybean drought resilience

Drought conditions are projected to intensify under climate change, and engineering more resilient plant microbiomes is a promising route to supporting crop productivity. However, effectively harnessing these microbiomes depends on identifying keystone taxa and functional traits that promote plant drought tolerance. Here, we combine deep shotgun metagenomics with absolute-abundance calibration to track genome-resolved microbial dynamics across a prolonged soybean drought and rewetting cycle. Leveraging 728 high-purity metagenome-assembled genomes that capture ~83% of prokaryotic reads on average, we show that drought drives significantly greater change in community structure in the rhizosphere than in bulk soil. This was accompanied by declining taxonomic, yet rising functional diversity. While rhizosphere communities rapidly recovered within 24 hours of rewetting, bulk soil communities instead underwent a progressive post-rewetting disturbance, consistent with a Birch-effect-driven successional shift. Rhizosphere drought enrichment was dominated by a single, taxonomically underexplored genus, Trinickia, whose genomes encode a coordinated suite of osmotic-stress-tolerance, bio-fertilisation, and phytohormone/polyamine biosynthesis traits consistent with plant growth promotion. Supporting this genomic inference, Trinickia abundance strongly correlated with increased root biomass during active drought, independent of plant developmental stage. Together, these findings identify the rhizosphere as a dynamically responsive compartment during drought and rewetting, and highlight Trinickia species as genomically and phenotypically supported candidates for microbiome-based strategies to improve soybean drought resilience.

microbiology↗

bioRxiv2026

Diverse conjugative and mobilisable elements underpin key adaptive traits in Xanthomonas

Horizontal gene transfer mediated by mobile genetic elements (MGEs) is a major driver of bacterial evolution and ecological adaptation. In the plant-associated genus Xanthomonas, multiple MGEs have been implicated in virulence, host specialisation, and environmental persistence, yet MGE diversity and evolutionary dynamics across the genus remain poorly understood. Here, we performed a comparative analysis of conjugative and mobilisable plasmids, integrative and conjugative elements (ICEs), integrative and mobilisable elements (IMEs), and their cargo genes across 516 complete genomes of three major Xanthomonas species: X. campestris, X. cissicola, and X. oryzae. We identified pronounced interspecific differences, with X. cissicola and X. campestris harbouring large and diverse MGE repertoires, comprising 28.3% and 26.7% of their respective pangenomes, whereas X. oryzae contained far fewer MGEs, making up only 3.6% of the identified pangenome. These differences were associated with host defence systems, including CRISPR-Cas and restriction-modification systems, and with variation in CRISPR spacer diversity. IMEs were the most abundant MGEs across all species, encoding diverse defence systems and accessory genes. ICEs exhibited signatures of horizontal transfer within and between species, and across genera. Notably, nearly identical ICEs carrying heavy-metal resistance genes were identified in Xanthomonas and Pseudomonas aeruginosa, indicating recent transfer between genera. MGEs collectively carried genes involved in virulence, interbacterial interactions, defence against phages, and plant cell wall degradation, with several elements associated with specific pathovars. Together, our findings establish MGEs as key drivers of genome plasticity and adaptive evolution in Xanthomonas, shaped by a dynamic interplay with host defence systems.

genomics↗

bioRxiv2026

Discovery of novel antimicrobial resistance genes in food and fertiliser using a high-throughput gene capture and functional screening platform

Integrons are genetic elements that drive bacterial adaptation by capturing and expressing mobile gene cassettes. They play a key role in dissemination of antimicrobial resistance (AMR) genes, particularly in Gram-negative bacteria. In addition to known AMR determinants, integron gene cassettes carry a vast reservoir of novel genes whose functions are largely uncharacterised, making it diNicult to assess their full contribution to the resistome. Contributing to this are limitations in current sequence-based prediction methods which often lack the ability to identify unknown AMR or other adaptive genes with novel mechanisms. To address this, we developed an integron gene cassette capture system, a functional screening platform that captures environmental gene cassettes for direct phenotypic testing. Using this system, we recovered previously unknown AMR determinants while also providing insights into the prevalence of known clinical AMR genes in a range of environmental samples, including food items. Here we provide experimental data on multiple novel bleomycin resistance genes and a stress response gene conferring gentamicin and tobramycin resistance. Our sequence analysis of the captured library also highlighted the diversity of the environmental cassette pool, with 656 unique cassettes recovered, the majority of which encoded proteins with unknown functions. The cassette capture system is a powerful tool for accessing hidden elements of the resistome and discovering novel adaptive genes that may go undetected using current sequence-based approaches. Environmental implicationAntimicrobial resistance (AMR) genes are hazardous biological contaminants, yet the vast majority of environmental integron gene cassettes remain functionally uncharacterised. This study addresses this sequence-to-function gap by deploying a novel functional capture platform directly on realistic environmental matrices, including agricultural fertilisers, coastal seawater, and commercial food products. By characterising these cassettes, we uncovered hidden reservoirs of both novel and clinically established AMR genes circulating in critical exposure pathways. This work reveals the true hazardous potential of the mobile environmental resistome, validating a proactive One Health surveillance tool for monitoring emerging biological threats.

microbiology↗

bioRxiv2025

Adaptative and ancient co-evolution of integrons with Xanthomonas genomes

Integrons are genetic elements that facilitate gene acquisition. They have been extensively studied in clinical bacteria, but their evolutionary role in phytopathogens remains underexplored. Here, we analysed complete genomes of Xanthomonas species to investigate the origin, distribution, and functional dynamics of integrons in this genus. We found that 93% of genomes harboured integrons. The integron-integrase gene intI was predominantly located downstream of ilvD, indicating an ancestral acquisition of integrons, predating diversification within the genus. Phylogenetic analyses support vertical inheritance of intI, with the exception of rare horizontal gene transfer events, notably in X. arboricola. Despite their widespread presence, full-length intI genes and active integron platforms are only retained in some species, especially X. campestris, which shows high integron gene cassette variability and functional integron activity. In contrast, species such as X. cissicola and X. phaseoli exhibit widespread intI inactivation, likely occurring early in their divergence, leading to more stable cassette arrays and conserved integron-associated phenotypes. The number and diversity of genes within cassette arrays varied significantly by species and, to a lesser extent, by the ecological context of plant host cultivation. While most cassettes encoded proteins without a known function, those with annotated roles were associated with stress response mechanism, competitive exclusion, and plant-associated functions. Together, our findings demonstrate that integrons in Xanthomonas likely originated from a single ancient acquisition event, preceding genus-wide speciation, and have co-evolved with Xanthomonas pathovars as they adapted to distinct plant hosts. IMPACT STATEMENTThis study provides the first comprehensive genus-wide analysis of integron evolution and dynamics in Xanthomonas, a globally distributed and versatile plant pathogen. Integrons are genetic platforms that allow horizontal transfer of genes. They are well characterised in human pathogens where they mediate transfer of antibiotic resistance genes, but little is known about their role in plant associated bacteria. We showed that in Xanthomonas the integron platform was ancestrally acquired, yet integrons have undergone repeated lineage-specific inactivation events. Despite widespread erosion of integron activity, some species such as X. campestris maintain robust and functionally diverse integrons that continue to shape genome plasticity. Notably, high cassette diversity, combined with the presence of rare and often uncharacterized genes within these arrays (some potentially involved in environmental sensing or host interaction) suggest that integrons may serve as reservoirs of adaptive potential. Our findings reshape current views of integron function beyond antibiotic resistance and highlight their long-term role in microbial evolution, niche adaptation, and genome innovation in plant-associated bacteria. DATA SUMMARYThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Accession numbers of the genomes analysed in this manuscript are listed in Table S1.

genomics↗

bioRxiv2025

EcoFoldDB: Protein structure-guided functional profiling of ecologically relevant microbial traits at the metagenome scale

Microbial communities are fundamental to planetary health and ecosystem processes. High-throughput metagenomic sequencing has provided unprecedented insights into the structure and function of these communities. However, functionally profiling metagenomes remains constrained due to the limited sensitivity of existing sequence homology-based methods to annotate evolutionarily divergent genes. Protein structure, more conserved than sequence, and intrinsically tied to molecular function, offers a solution. Capitalising on recent breakthroughs in structural bioinformatics, we present EcoFoldDB, a database of protein structures curated for ecologically relevant microbial traits, and its companion pipeline, EcoFoldDB-annotate, which leverages Foldseek with the ProstT5 protein language model for rapid structural homology searching directly from sequence data. EcoFoldDB-annotate outperforms state-of-the-art sequence-based methods in annotating metagenomic proteins, in terms of sensitivity and precision. To demonstrate its utility and scalability, we performed structure-guided functional profiling of 32 million proteins encoded by 8,000 high-quality metagenome-assembled genomes from the global soil microbiome. EcoFoldDB-annotate could resolve the phylogenetic partitioning of important nitrogen cycling pathways, from taxonomically restricted nitrifiers to more widespread denitrifiers, as well as identifying novel, uncultivated bacterial taxa enriched in plant growth-promoting traits. We anticipate that EcoFoldDB will enable researchers to extract ecological insights from environmental genomes and metagenomes, and accelerate discoveries in microbial ecology.

microbiology↗

bioRxiv2024

Clonal expansion from standing genetic variation underpins the evolution of an emerging plant pathogen in Australia

Pathogens can evolve rapidly, leading to the emergence of novel strains that can overcome commercially deployed host plant resistance. Understanding the genetic and phenotypic diversity and population dynamics of plant pathogens is crucial to inform breeding programs targeting resistance. Tan spot, otherwise known as bacterial wilt, caused by Curtobacterium flaccumfaciens pv. flaccumfaciens, is a destructive disease of mungbean in Australia. Since the 1990s, several mungbean cultivars with partial resistance to tan spot have been released; however, cultivars initially rated as moderately resistant were later rated as moderately susceptible to tan spot. This study investigated the genetic and phenotypic diversity and temporal evolutionary dynamics of C. flaccumfaciens pv. flaccumfaciens in Australian mungbean fields. Whole-genome sequencing of 119 isolates collected from mungbean and other legumes (1986-2019) enabled analyses of pathogen evolution in Australia and in a global context. Results revealed that clonal expansion from standing genetic variation, rather than introduction of novel genotypes, has driven the evolution of this pathogen in Australia since the 1980s. Glasshouse trials confirmed the role of a plasmid in pathogenicity of C. flaccumfaciens pv. flaccumfaciens but found no significant differences in aggressiveness between clonal lineages. This study underscores the importance of understanding pathogen diversity and aggressiveness to guide breeding programs for effective and durable disease resistance and highlights the need for further studies on the competitive fitness of isolates and characterisation of private alleles linked to dominant clonal lineages. SignificanceTan spot is an increasingly significant pathogen affecting beans and mungbean worldwide, with a broad host range and quarantine importance in many countries underscoring the need for effective breeding strategies to manage the disease. Our research provides insights into genetic and phenotypic diversity of this important plant pathogen and temporal changes in its population structure in Australia, which are crucial for developing informed breeding strategies and managing the spread and impact of the disease. This work also underscores the critical need for robust, validated screening protocols and selection of aggressive, locally representative isolates for resistance breeding to ensure accurate assessment of resistance in crops for effective and durable resistance.

evolutionary biology↗

bioRxiv2024

Emergence and host range expansion of an epidemic lineage of Ralstonia solanacearum

The evolutionary processes underlying disease outbreaks remain unknown for most bacterial plant pathogens. We sequenced an outbreak of lethal wilt disease in Martinique caused by two distantly related lineages in the Ralstonia solanacearum species complex. One lineage (R. solanacearum IIB-4NPB) exhibited the broadest host range ever documented for a single lineage in the field, while the other (R. pseudosolanacearum I-18) expanded in parallel but retained specialisation on solanaceaous hosts. Phylogenomic analysis of 407 outbreak isolates shows both lineages independently disseminated from mainland populations into Martinique. We resolved fine-scale geographic patterns of genomic diversity and identified spatial hotspots of interspecies mobile element exchange, resulting in the identification of a new family of Ralstonia integrative conjugative elements (ICEs) associated with the outbreak. ICE accessory gene integration sites display striking functional specialization and differentiation despite variable gene content: each site acquires only metabolism-associated or defence-related genes, respectively. This work provides insight into the origin and genomic changes associated with an outbreak of plant disease, and highlights the role of mobile elements in driving pathogen emergence.

microbiology↗

bioRxiv2024

Bacterial metabarcoding reveals plant growth promoting members of the core Brachypodium distachyon root-associated microbiome overlooked by culture dependent techniques

Biofertilisers comprised of plant growth promoting bacteria (PGPB) present a promising sustainable alternative to synthetic fertilisers. Bacteria which consistently colonise roots of specific plants across distinct environments, known as that plants core root microbiome, are particularly promising due to their colonisation competency. However, traditional, culture-based techniques can overlook promising PGPB which do not display commonly screened for plant growth promoting traits. Although numerous studies have isolated beneficial root bacteria, few have combined bacterial metabarcoding with culture-based techniques to identify novel biofertiliser candidates. In a two-pronged approach, 16S rRNA amplicon sequencing was used to define the core root microbiome of the model cereal plant, Brachypodium distachyon, grown in four distinct soils. From 7,042 amplicon sequence variants (ASVs) detected in root fractions, only 40 ASVs were common at a prevalence of 80%. Core ASVs primarily belonged to the class Alphaproteobacteria, with the remainder comprising Actinobacteria, Bacilli, Chloroflexia, Gammaproteobacteria and Negativicutes. Secondly, B. distachyon root-associated bacterial strains were isolated from plants grown in the aforementioned soils. Of 207 root-associated isolates, 10 were identified as members of the core root microbiome, with the majority not displaying commonly screened for plant growth promoting traits. However, in a semi-hydroponic system, a core Bacillus and Rhodococcus strain significantly increased B. distachyon shoot dry weight by 32.8% and 40.0%, respectively. Additionally, two core Bacillus strains significantly increased root dry weight by 79.7 and 52.3%. This study demonstrates the potential of incorporating additional criteria afforded by culture-independent methods to screen for novel biofertiliser candidates typically overlooked by culture-dependent techniques. ImportanceBiofertilisers comprised of plant growth promoting bacteria (PGPB) present a sustainable, environmentally friendly alternative to synthetic fertilisers. The search for PGPB has historically relied on culture dependent methods to shortlist candidates by screening for plant growth promoting traits, such as N fixation or production of the plant hormone indole-3-acetic acid before conducting in planta trials. However, these screens may overlook promising bacterial strains which might promote plant growth via indeterminant mechanisms. Culture independent methods can take a snapshot of an entire microbiome without the need for culturing bacteria, allowing for additional selection criteria to be used when shortlisting PGPB. Our results show that targeting bacterial taxa which consistently colonise the roots of the model grass Brachypodium distachyon allowed for selection of bacterial isolates which were overlooked by culture-based PGPB trait screens. This result highlights the utility of combining traditional, culture-dependent methods with culture-independent techniques when searching for novel biofertiliser candidates.

microbiology↗

bioRxiv2023

Rapid dissemination of host-metabolism-manipulating transposon-like entities via integrative and conjugative elements

Integrative and conjugative elements (ICEs) are self-transmissible mobile elements that transfer functional genetic units across broad phylogenetic distances. Accessory genes shuttled by ICEs can make significant contributions to bacterial fitness, yet ICEs that carry accessory genes encoding functions other than antimicrobial resistance remain poorly characterized. Recent observation of the rapid acquisition of ICEs in a pandemic lineage of Pseudomonas syringae pv. actinidae led to investigation of the structural and functional diversity of these elements among a diverse array of P. syringae. Fifty-three unique ICE types were identified across multiple phylogroups. These ICEs display distinct evolutionary histories compared to their bacterial hosts, are highly recombinogenic, exhibit a conserved structure and are punctuated by hotspots of accessory gene integration. Many carry a 16 kb transposon-like entity (Tn6212) that shows little polymorphism indicating recent dissemination. Deletion of Tn6212 did not alter pathogen growth in planta, but mutants displayed significant fitness defects when grown on TCA cycle intermediates. These were largely attributable to a single LysR regulator. RNA-seq analysis of a set of nested Tn6212 deletions confirmed a central role of LysR in enhanced expression of more than 300 genes and down-regulation of genes controlling expression of energetically demanding loci. Together the transcriptional data indicate a major role for Tn6212 in manipulation of bacterial metabolism with primary effects on RNA degradation, protein synthesis and potential diversion of ATP to growth.

microbiology↗

bioRxiv2017

The ecological genetics of Pseudomonas syringae residing on the kiwifruit leaf surface

Interactions between commensal microbes and invading pathogens are understudied, despite their likely effects on pathogen population structure and infection processes. We describe the population structure and genetic diversity of a broad range of co-occurring Pseudomonas syringae isolated from infected and uninfected kiwifruit during an outbreak of bleeding canker disease caused by P. syringae pv. actinidiae (Psa) in New Zealand. Overall population structure was clonal and affected by ecological factors including infection status and cultivar. Most isolates are members of a new clade in phylogroup 3 (PG3a), also present on kiwifruit leaves in China and Japan. Stability of the polymorphism between pathogenic Psa and commensal P. syringae PG3a isolated from the same leaf was tested using reciprocal invasion from rare assays in vitro and in planta. P. syringae G33C (PG3a) inhibited Psa NZ54, while the presence of Psa NZ54 enhanced the growth of P. syringae G33C. This effect could not be attributed to virulence activity encoded by the Type 3 secretion system of Psa. Together our data contribute toward the development of an ecological perspective on the genetic structure of pathogen populations.\n\nORIGINALITY-SIGNIFICANT STATEMENTBacterial pathogen populations are often studied with little consideration of co-occurring microbes and yet interactions between pathogens and commensals can affect both population structure and disease progression. A fine-scale sampling of commensals present on kiwifruit leaves during an outbreak of bleeding canker disease caused by P. syringae pv. actinidiae reveals a clonal population structure. A new clade of non-pathogenic P. syringae (PG3a) appears to be associated with kiwifruit on a global scale. The presence of PG3a on kiwifruit has significant effects on the outcome of infection by P. syringae pv. actinidiae. This emphasises the value of studying the effect of co-occurring bacteria on pathogen-plant interactions.

microbiology↗

bioRxiv2016

The origin and evolution of a pandemic lineage of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae

Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa), whose emergence coincided with domestication of its host. The most recent pandemic has had a deleterious effect on kiwifruit production worldwide. In order to strengthen understanding of population structure, phylogeography and evolutionary dynamics of Psa, we sampled 746 Pseudomonas isolates from cultivated and wild kiwifruit across six provinces in China, of which 87 were Psa. Of 234 Pseudomonas isolated from wild Actinidia spp. none were identified as Psa. Genome sequencing of fifty isolates and the inclusion of an additional thirty from previous studies show that China is the origin of the recently emerged pandemic lineage. However China harbours only a fraction of global Psa diversity, with greatest diversity found in Korea and Japan. Distinct transmission events were responsible for introduction of the pandemic lineage of Psa into New Zealand, Chile and Europe. Two independent transmission events occurred between China and Korea, and two Japanese isolates from 2014 cluster with New Zealand Psa. Despite high similarity at the level of the core genome and negligible impact of within-lineage recombination, there has been substantial gene gain and loss even within the single clade from which the global pandemic arose.\n\nSIGNIFICANCE STATEMENTBleeding canker disease of kiwifruit caused by Pseudomonas syringae pv. actinidiae (Psa) has come to prominence in the last three decades. Emergence has coincided with domestication of the host plant and provides a rare opportunity to understand ecological and genetic factors affecting the evolutionary origins of Psa. Here, based on genomic analysis of an extensive set of strains sampled from China and augmented by isolates from a global sample, we show, contrary to earlier predictions, that China is not the native home of the pathogen, but is nonetheless the source of the recent global pandemic. Our data identify specific transmission events, substantial genetic diversity and point to non-agricultural plants in either Japan or Korea as home to the source population.

epidemiology↗