Biology subjects

Tetu, S. G.

Publications and source records attributed to Tetu, S. G..

15 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

Revegetation following grazing cessation drives sequential shifts in soil microbial functions and life-history strategies over decadal time scales

Revegetation is a key strategy for restoring degraded lands globally. While this process can reshape belowground microbial communities, the extent to which such changes restore soil ecosystem functions, and whether different microbial traits recover synchronously or on distinct timescales remains less clear. Understanding this is essential for evaluating restoration success, as different microbial traits underpin distinct ecosystem services, from carbon storage to plant growth promotion, and the sequence in which these are restored can inform restoration targets and provide meaningful indicators of long-term ecological recovery. To address this, we applied deep metagenomic sequencing to characterise soil microbial responses following revegetation (spanning 1-31 years prior to sampling) on grazing agricultural lands. We find that revegetation following grazing cessation drove significant and sequential shifts in dominant microbial functions and life-history strategies. Functional changes occurred in distinct phases: an early, rapid restructuring of core soil health processes, detectable as early as three years, including enrichment of nutrient retention and carbon fixation pathways, followed by a more gradual development of plant growth-promoting traits as the plant community matures. Genome-resolved analyses of nearly 500 metagenome-assembled genomes revealed a fundamental shift in dominant microbial life history strategies: from a resource-scavenging and stress tolerance profile in grazing soils to strategies that prioritise biosynthesis and growth yields in revegetated soils. These lifestyle shifts have important implications for enhancing the microbial biomass and carbon sink potential of soils. Together, these findings show that microbial functional shifts following revegetation are temporally structured - informing expectations for when key restoration targets may be achieved, and providing a practical framework for monitoring ecosystem recovery.

microbiology↗

bioRxiv2025

A genome-wide approach uncovers the suite of genes important for swarming motility in the biocontrol bacteria Pseudomonas protegens Pf-5

Motility is a crucial bacterial trait, important for competitive success in many contexts. Plant growth promoting rhizobacteria, such as Pseudomonas protegens Pf-5, can protect agricultural crops against disease, relying on motility to access and colonize the plant rhizosphere. Swarming motility is the multicellular movement of bacteria powered by rotating flagella across a semi-solid surface which allows bacteria to move rapidly, search for and acquire food, avoid toxic substances, and colonize new niches. Here we performed genome-wide investigations, using transposon-directed insertion site sequencing (TraDIS) to identify 136 genes involved in P. protegens Pf-5 swarming motility. This method identified flagella biosynthesis, assembly, structure and regulatory genes, as expected. We also identified an additional suite of genes important for swarming, including chemotaxis, c-di-GMP turnover, cell division, peptidoglycan turnover, lipopolysaccharide biosynthesis, metabolism of thiamine (vitamin B1) and transport of pyoverdine. Overall, this study increases our understanding of pseudomonad motility and expands the breadth of lifestyles and habitats examined in relation to swarming motility. Understanding the genetic basis of swarming motility in biocontrol bacteria is important for successful application of these important plant growth promoting microbes in agricultural settings.

genomics↗

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

Agriculture alters protein evolution of nitrogen cycling genes in soil bacteria at a global scale

Humans are the worlds greatest evolutionary force. Yet, our impacts on the evolution of Earths microbiomes and their biogeochemical processes remain poorly understood. Notably, the overlooked potential for the intensive use of agricultural fertiliser to drive evolutionary changes in soil nutrient cycling genes warrants urgent attention. Here, analysing >2,500 soil metagenomes from across the globe, we identify increased rates of diversifying positive selection on genes involved in the reduction of nitrate (a key component of nitrogen fertilisers) in agricultural, but not natural land systems. Altered selection on genes encoding the respiratory nitrate reductase were specific to Burkholderiales, a major group of denitrifying bacteria. We provide evidence that agriculture is driving evolution of protein regions implicated in substrate access to the enzymes active site, possibly resulting in increased rates of nitrate reduction. We hypothesise that increasing substrate turnover would be evolutionarily advantageous under excess nitrate availability, ultimately enhancing growth rates despite potential enzymatic trade-offs. As Burkholderiales are dominant denitrifiers globally, such evolutionary consequences of agriculture on this lineage could have cascading ecological impacts. These findings indicate that anthropogenic selection can alter protein-level evolution of vital microbial biogeochemical processes.

microbiology↗

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

Seed banking alters native seed microbiome composition and function relative to natural populations

O_LISeed banks are a vital resource for preserving plant species diversity globally. However, seedling establishment and survival rates from banked seeds can be poor. Despite a growing appreciation for the role of seed microbiota in supporting seed quality and plant health, our understanding of the effects of conventional seed banking processes on seed microbiomes remains limited. C_LIO_LIWe investigated the composition and functional potential of the epiphytic seed microbiome of a native plant species using both 16S rRNA gene sequencing and culture-based approaches. C_LIO_LIComparing the bacterial community composition of freshly collected seeds and those sourced from seed banking organisations, we found stored seeds hosted significantly less diverse bacterial populations, with substantial reductions in both low-abundance taxa and some core community members identified in unstored seeds. Bacteria with key plant growth promoting traits including IAA production, ACC deaminase activity, phosphate solubilisation, siderophore activity, and nitrogen fixation were identified in seed epiphytic communities, but these beneficial traits were less prevalent in stored seed compared to fresh seeds. C_LIO_LIOverall, these results suggest that epiphytic seed microbiomes may undergo significant changes during the storage process, selecting for bacteria tolerant to storage conditions, and potentially reducing the population of plant-growth promoting bacteria on seeds. C_LI

microbiology↗

bioRxiv2023

Stratified microbial communities in Australia's only anchialine cave are taxonomically novel and drive chemotrophic energy production via coupled nitrogen-sulphur cycling

BackgroundAnchialine environments, in which oceanic water mixes with freshwater in coastal aquifers, are characterised by stratified water columns with complex physicochemical profiles. These environments, also known as subterranean estuaries, support an abundance of endemic macro and microorganisms. There is now growing interest in characterising the metabolisms of anchialine microbial communities, which is essential for understanding how complex ecosystems are supported in extreme environments, and assessing their vulnerability to environmental change. However, the diversity of metabolic strategies that are utilised in anchialine ecosystems remains poorly understood. ResultsHere, we employ shotgun metagenomics to elucidate the key microorganisms and their dominant metabolisms along a physicochemical profile in Bundera Sinkhole, the only known continental subterranean estuary in the Southern Hemisphere. Genome-resolved metagenomics suggests that the communities are largely represented by novel taxonomic lineages, with 75% of metagenome-assembled genomes assigned to entirely new or uncharacterised families. These diverse and novel taxa displayed depth-dependent metabolisms, reflecting distinct phases along dissolved oxygen and salinity gradients. In particular, the communities appear to drive nutrient feedback loops involving nitrification, nitrate ammonification, and sulphate cycling. Genomic analysis of the most highly abundant members in this system suggests that an important source of chemotrophic energy is generated via the metabolic coupling of nitrogen and sulphur cycling. ConclusionThese findings substantially contribute to our understanding of the novel and specialised microbial communities in anchialine ecosystems, and highlight key chemosynthetic pathways that appear to be important in these energy-limited environments. Such knowledge is essential for the conservation of anchialine ecosystems, and sheds light on adaptive processes in extreme environments.

microbiology↗

bioRxiv2023

Plastic Leachate Exposure Drives Antibiotic Resistance and Virulence in Marine Bacterial Communities

Plastic pollution is a serious global problem, with more than 12 million tonnes of plastic waste entering the oceans every year. Plastic debris can have considerable impacts on microbial community structure and functions in marine environments, and has been associated with an enrichment in pathogenic bacteria and antimicrobial resistance (AMR) genes. However, our understanding of these impacts is largely restricted to microbial assemblages on plastic surfaces. It is therefore unclear whether these effects are driven by the surface properties of plastics, providing an additional niche for certain microbes residing in biofilms, and/or chemicals leached from plastics, the effects of which could extend to surrounding planktonic bacteria. Here, we examine the effects of polyvinyl chloride (PVC) plastic leachate exposure on the relative abundance of genes associated with bacterial pathogenicity and AMR within a seawater microcosm community. We show that PVC leachate, in the absence of plastic surfaces, drives an enrichment in AMR and virulence genes. In particular, leachate exposure significantly enriches AMR genes that confer multidrug, aminoglycoside and peptide antibiotic resistance. Additionally, enrichment of genes involved in the extracellular secretion of virulence proteins was observed among pathogens of marine organisms. This study provides the first evidence that chemicals leached from plastic particles alone can enrich genes related to microbial pathogenesis within a bacterial community, expanding our knowledge of the environmental impacts of plastic pollution with potential consequences for human and ecosystem health.

microbiology↗

bioRxiv2023

Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-PCR technology

Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbour class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation and concatenation polymerase chain reaction) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multi-gene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts towards hotspots of class 1 integron-mediated dissemination of AMR. SynopsisWe present a novel single-cell genomic surveillance technology for identifying environmental bacterial hosts of a class of mobile genetic elements that are linked to anthropogenic pollution and contribute to the dissemination of antimicrobial resistance.

microbiology↗

bioRxiv2023

Identifying the suite of genes central to swimming in the biocontrol bacteria Pseudomonas protegens Pf-5

Swimming motility is a key bacterial trait, important to success in many niches, including assisting in colonization of host surfaces. Biocontrol bacteria, such as Pseudomonas protegens Pf-5 are increasingly being used as an agricultural tool to control crop diseases, where motility is a factor in successful colonization of the plant rhizosphere. Swimming motility has been studied in a range of bacteria and typically involves a suite of flagella and chemotaxis genes, however the specific gene set employed for both regulation and biogenesis can differ substantially between organisms. Here we used transposon directed insertion site sequencing (TraDIS), a genome-wide approach, to identify 249 genes involved in P. protegens Pf-5 swimming motility. As expected, flagella and chemotaxis genes comprised a large proportion of these genes. However we also identified a suite of additional genes important for swimming, including genes related to peptidoglycan turnover, O-antigen biosynthesis, cell division, signal transduction, c-di-GMP turnover and phosphate transport, along with 27 conserved hypothetical proteins. Experimental gene knockout mutants and TraDIS data together suggest that defects in the Pst phosphate transporter lead to enhanced swimming motility. Overall, this study expands our knowledge of pseudomonad motility and highlights the utility of a TraDIS-based approach for systematically analyzing the functions of thousands of genes. This work sets a foundation for understanding how swimming motility may be related to the inconsistency in biocontrol bacteria effectiveness and reliability in the field. ImportanceBiocontrol bacteria, such as Pseudomonas protegens Pf-5 are increasingly being used as an agricultural tool to control crop diseases, and motility is a key factor in their successful colonization of plant surfaces. Here we use a high-throughput approach to identify the suite of genes important for swimming motility in P. protegens Pf-5. These included flagella and chemotaxis genes, as well as a variety of cell surface, cell division and signalling genes. We also show that defects in the Pst phosphate transporter lead to enhanced swimming motility, a hitherto unreported link between phosphate transport and swimming motility. Understanding the genetic basis of swimming motility enhances our knowledge of key processes in biocontrol bacteria that are needed to ensure their competitive success. This will contribute to developing strategies to increase the utility of biocontrol bacteria in agricultural settings to prevent crop losses.

genomics↗

bioRxiv2022

Discovery of integrons in Archaea: platforms for cross-domain gene transfer

Horizontal gene transfer between different domains of life is increasingly being recognised as an important driver of evolution, with the potential to provide the recipient with new gene functionality and assist niche adaptation1-3. However, the molecular mechanisms underlying the integration of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria via site-specific DNA recombination4-7. Integrons, however, have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here we show that integrons are also present among diverse phyla within the domain Archaea. Further, we provide experimental evidence that integron-mediated recombination can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a new mechanism that can facilitate horizontal gene transfer between the two domains of prokaryotes, which has important implications for prokaryotic evolution in both clinical and environmental contexts.

microbiology↗

bioRxiv2021

Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities

Integrons are bacterial genetic elements that can integrate mobile gene cassettes. They are mostly known for spreading antibiotic resistance cassettes among human pathogens. However, beyond clinical settings, gene cassettes encode an extraordinarily diverse range of functions important for bacterial adaptation. The recovery and sequencing of cassettes has promising applications, including: surveillance of clinically important genes, particularly antibiotic resistance determinants; investigating the functional diversity of integron-carrying bacteria; and novel enzyme discovery. Although gene cassettes can be directly recovered using PCR, there are no standardised methods for their amplification and, importantly, for validating sequences as genuine integron gene cassettes. Here, we present reproducible methods for the PCR amplification, sequence processing, and validation of gene cassette amplicons from complex communities. We describe two different PCR assays that either amplify cassettes together with integron integrases, or gene cassettes together within cassette arrays. We compare the use of Nanopore and Illumina sequencing, and present bioinformatic pipelines that filter sequences to ensure that they represent amplicons from genuine integrons. Using a diverse set of environmental DNAs, we show that our approach can consistently recover thousands of unique cassettes per sample and up to hundreds of different integron integrases. Recovered cassettes confer a wide range of functions, including antibiotic resistance, with as many as 300 resistance cassettes found in a single sample. In particular, we show that class 1 integrons appear to be collecting and concentrating antibiotic resistance genes out of the broader diversity of cassette functions. The methods described here can be applied to any environmental or clinical microbiome sample.

microbiology↗

bioRxiv2020

Elucidating essential genes in plant-associated Pseudomonas protegens Pf-5 using transposon insertion sequencing

Gene essentiality studies have been performed on numerous bacterial pathogens, but essential gene sets have been determined for only a few plant-associated bacteria. Pseudomonas protegens Pf-5 is a plant-commensal, biocontrol bacteria that can control disease-causing pathogens on a wide range of crops. Work on Pf-5 has mostly focused on secondary metabolism and biocontrol genes, but genome-wide approaches such as high-throughput transposon mutagenesis have not yet been used in this species. Here we generated a dense P. protegens Pf-5 transposon mutant library and used transposon-directed insertion site sequencing (TraDIS) to identify 446 genes essential for growth on rich media. Genes required for fundamental cellular machinery were enriched in the essential gene set, while genes related to nutrient biosynthesis, stress responses and transport were under-represented. Comparison of the essential gene sets of Pf-5 and P. aeruginosa PA14, an opportunistic human pathogen, provides insight into the biological processes important for their different lifestyles. Key differences include cytochrome c biogenesis, formation of periplasmic disulfide bonds, lipid biosynthesis, ribonuclease activity, lipopolysaccharides and cell surface structures. Comparison of the Pf-5 in silico predicted and in vitro determined essential gene sets highlighted the essential cellular functions that are over- and underestimated by each method. Expanding essentiality studies into bacteria with a range of lifestyles can improve our understanding of the biological processes important for survival and growth in different environmental niches. ImportanceEssential genes are those crucial for survival or normal growth rates in an organism. Essential gene sets have been identified in numerous bacterial pathogens, but only a few plant-associated bacteria. Employing genome-wide approaches, such as transposon insertion sequencing, allows for the concurrent analysis of all genes of a bacterial species and rapid determination of essential gene sets. We have used transposon insertion sequencing to systematically analyze thousands of Pseudomonas protegens Pf-5 genes and gain insights into gene functions and interactions that are not readily available using traditional methods. Comparing Pf-5 essential genes with those of P. aeruginosa PA14, an opportunistic human pathogen, provides insight into differences in gene essentiality which may be linked to their different lifestyles.

genomics↗