Biology subjects

Schloter, M.

Publications and source records attributed to Schloter, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Fragmented gut-airway microbial networks and airway Moraxella clusters in preschool wheeze

Early-life wheezing in children has been associated with microbial alterations along the gut-airway axis, yet studies simultaneously investigating bacterial communities in both compartments remain scarce. The aim of this cross-sectional exploratory pilot study (n=25) was to characterize and compare nasal and stool bacterial communities in preschool children aged 1-4 years with recurrent wheezing and healthy controls using 16S rRNA gene metabarcoding. Across participants, nasal and stool bacteriomes were highly individualized and taxonomically diverse. Overall richness, evenness, and community composition did not differ significantly between healthy children and wheezers in either compartment. However, wheezers displayed markedly higher within-group variability, particularly in nasal communities. Stratification based on microbiome similarity to healthy samples revealed increased Moraxella and reduced commensal genera including Prevotella spp. and Veillonella, along with lower richness and evenness (all p<0.001) in nasal samples with divergent bacterial communities. Stool alterations were more subtle but included trends toward reduced Bacteroides, Faecalibacterium, and Alistipes in wheezers more divergent from healthy controls. Community assembly in both compartments was largely governed by stochastic processes but accompanied by less complex and more fragmented bacterial interaction networks in wheezing children. Cross-compartment correlations were also altered, most prominently involving stool Lactococcus showing stronger and more numerous correlations with nasal taxa in wheezers than in healthy controls. Divergent wheezers exhibited distinct modular network structure and cross-compartment profiles, consistent with a differentiated microbial organization. Together, these findings suggest compartment-specific differences in microbial interaction patterns across the gut-airway axis in early-life wheezing, despite limited differences in overall community diversity. Take home messagePreschool wheezers showed fragmented gut-airway microbial networks and Moraxella-associated airway community stratification despite limited differences in overall diversity.

microbiology↗

bioRxiv2026

Vertical stratification drives additive prokaryotic diversity in beech forest floors, while site conditions shape boundary layers

The forest floor is a key interface regulating carbon and nutrient processing and transfer to the mineral soil, yet it is threatened by climate-change-driven reductions in organic layer mass. How its prokaryotic microbiome is structured across the fine-scale vertical gradient from fresh litter to mineral topsoil remains poorly resolved. We characterised prokaryotic communities across eight sequential layers spanning fresh litter, organic layers at different stages of decomposition, and mineral topsoil in three temperate beech forests using 16S rRNA gene amplicon sequencing. The decomposition stage was the dominant driver of community assembly, resulting in a strongly vertically stratified prokaryotic microbiome. While alpha diversity peaked within the fragmented litter layers, the overall high diversity of the forest floor was primarily an additive effect of vertical stratification. Site-specific effects were pronounced in the litter layer and the mineral topsoil, but diminished in the intermediate organic layers, where high local heterogeneity masked between-site differences. Redundancy analysis further showed that the environmental drivers of community structure shifted with depth, from litter quality in the upper horizons to mineral-associated properties in the mineral topsoil. At the same time, predicted 16S rRNA gene copy numbers indicate that the humified layers harbour the highest abundance of oligotrophic life strategists in the profile. By resolving the fine-scale vertical structure of the forest floor prokaryotic microbiome, our results provide a baseline for predicting how climate-change induced loss of organic layer mass threatens layer-specific communities, particularly the oligotrophic taxa in the humified layers, with consequences for the carbon turnover, tree nutrition, and nutrient cycling functions they mediate.

microbiology↗

bioRxiv2026

Longitudinal Dynamics and Site-Specific Recovery of the Human Respiratory Microbiome Following Smoking Cessation

BackgroundThe human respiratory tract harbours diverse microbial communities crucial for health, but their dynamics during environmental perturbations like smoking remain poorly understood. While smoking is a major risk factor for various diseases, its compartment-specific effects on the respiratory microbiome and potential recovery following cessation have not been fully elucidated. Here, we present a longitudinal, multi-site study of respiratory microbiome dynamics in smokers undergoing cessation, benchmarked against healthy never-smokers. MethodsUsing standardized sampling of the anterior nares, oropharynx, and bronchoalveolar lavage (BAL), combined with 16S rRNA gene amplicon sequencing and rigorous contamination controls, we characterized community composition, diversity, personalization, and microbial interactions across airway compartments. ResultsSmokers exhibited pronounced microbiome alterations: nasal richness increased, while lung richness and core taxa were reduced. Smoking-induced changes were compartment-specific and most pronounced in nose and lung. The degree of individuum-specific differences in community structure was elevated in smokers and correlated with smoking intensity and duration. Short-term cessation (6 weeks) led to minor shifts in taxa abundance but increased similarity between oropharyngeal and lung communities, whereas long-term cessation (1 year) resulted in partial restoration, particularly in lung and nasal microbiomes. Some taxa, including Haemophilus and Prevotella_7, showed persistent alterations, highlighting lasting smoking effects. Network analyses revealed that smoking disrupted microbial co-occurrence and reduced community connectivity, whereas cessation partially restored interaction networks, with dynamics differing between oropharynx and lung, reflecting different underlying ecological assembly processes. Recovery trajectories were highly individualized, with lung microbiomes influenced by deterministic processes and upper airway microbiomes shaped by stochastic factors, explaining site-specific responses and the persistence of personalized microbial signatures. ConclusionThese results provide the first time-resolved, multi-compartment characterization of respiratory microbiome recovery after smoking cessation, revealing that smoking leaves long-lasting, site-specific imprints on airway microbial communities and interactions. Our findings underscore the need for individual and compartment-specific approaches when designing microbiome-based interventions to support respiratory health.

microbiology↗

bioRxiv2026

Pseudomonas simiae-induced resistance in barley is associated with compromised JA signaling and phyllosphere microbiome responses

Interactions of plant growth-promoting rhizobacteria with plant roots can trigger induced resistance (IR) protecting above-ground tissues from disease, a process that is increasingly recognized for its potential to support sustainable crop protection strategies. Although the molecular basis of IR has been extensively studied in Arabidopsis thaliana, considerably less is known about the underlying mechanisms in cereal crops. Here, we show that Pseudomonas simae WCS417r triggers IR in barley (Hordeum vulgare), reducing the propagation of Blumeria graminis f. sp. hordei, the causative agent of barley powdery mildew. Analysis of defense-associated marker genes revealed pathogen-dependent transcriptional responses during IR: HvPATHOGENESIS-RELATED1 (HvPR1) was induced by powdery mildew but not by the bacterial pathogen Xanthomonas translucens pathovar cerealis, whereas HvPR5 responded to both pathogens, with its induction by X. translucens depending on WCS417r-IR. To improve our molecular understanding of IR, transcriptomic responses to methyl jasmonate, salicylic acid and abscisic acid were characterized and used to identify hormone-responsive genes. Notably, several jasmonate-responsive genes were suppressed during powdery mildew infection, and this suppression was more pronounced in plants undergoing IR, indicative of priming. Finally, metabarcoding of the phyllosphere microbiome demonstrated that IR was not associated with major shifts in bacterial community composition. Alpha and beta diversity remained largely unchanged, while a limited number of amplicon sequence variants differed in abundance between treatments. Together, these results show that P. simiae WCS417r induces resistance against powdery mildew in barley through priming pathogen-dependent transcriptional changes while leaving the overall phyllosphere microbiome structure largely intact.

plant biology↗

bioRxiv2025

Adaptation to a host-associated lifestyle drives convergent loss of flagellar motility in Pseudomonadota

BackgroundHost-associated bacteria must balance the benefits of motility through flagella against the offsets of energetic costs and immune surveillance. Understanding the interplay of evolutionary forces shaping this complex trait can provide insights on the dynamics and extent of within-host adaptations of flagellar assembly. We compared prevalence, redundancy, and homology of 55 known flagellar assembly genes across genomes of free-living and host-associated bacteria from a collection covering the entire Pseudomonadota phylum. ResultsWe show that the isolation of host-associated bacterial populations leads to the erosion of the flagellar regulon, driving widespread flagellum loss across lineages. This gene loss is rarely compensated by horizontal gene transfer. Moreover, host association imposes a diversifying selective pressure that acts unevenly across pathway components, resulting in greater functional heterogeneity than in free-living bacteria. ConclusionsOur results provide valuable insights into the distribution of flagellar genes in the phylum Pseudomonadota and its relation to bacterial lifestyle.

microbiology↗

bioRxiv2025

Provenance Legacies Override Species Effects in Shaping Oak Rhizosphere Microbiomes and Metabolomes

As climate change drives more frequent and intense drought-heat extremes, selecting drought-tolerant trees is crucial for future forest resilience. However, the role of tree-microbial associations for this key trait remains largely unclear. In this study, we investigated how geographic origin, species identity, and intrinsic water-use efficiency (iWUE) shape the rhizosphere microbiome and root-rhizosphere metabolome of pedunculate (Quercus robur) and sessile (Q. petraea) oaks. In a six-year common garden experiment, we analyzed trees from both species, each grown from seeds from two distinct geographic origins, the upper Rhine basin (URB) and the north-east German lowlands (NGL), differing in water availability, using 16S and ITS rRNA gene based metabarcoding and untargeted metabolomics. We found a consistent legacy effect of seed origin on the composition of the prokaryotic rhizosphere microbiome and the metabolome, whereas tree species had no significant impact. The bacterial family Pseudonocardiaceae was enriched at trees from the drier origin NGL, while Blastocatellaceae and Micromonosporaceae were positively associated with iWUE across samples. Higher iWUE was furthermore significantly correlated with lower prokaryotic diversity and shifts in {beta}-diversity, thereby linking a drought-adaptive host trait to the assembly of the belowground environment. Ellagic acid, a plant derived polyphenol associated with drought tolerance, was enriched in the drier origin NGL and linked to several prokaryotic taxa in correlation networks. The rhizosphere fungal community, however, was largely unaffected by origin or species. Solely fungal community evenness declined with increasing iWUE. Together, our findings suggest that ecotypic adaptation linked to origin can outweigh the effect of species-level traits in shaping the oak rhizosphere microbiome and metabolome. These findings emphasize that provenance-driven ecotypic adaptation can strongly influence plant-microbe interactions and underscore the need for provenance-aware selection and microbiome-informed assisted migration as strategies to strengthen forest drought resilience under global climate change.

ecology↗

bioRxiv2025

Comparison of Pairwise Samples of Endotracheal Aspirate and Bronchoalveolar Lavage for Microbial Analysis in Critically ill Patients

IntroductionBronchoalveolar lavage (BAL) is considered as gold-standard for the characterization of the lung microbiome. The aim of this study was to elucidate the applicability of less-invasive sampling by endotracheal aspirate (ETA) compared with BAL for the analysis of respiratory microorganisms in critically ill patients who required mechanical ventilation. MethodsPairwise samples of ETA and BAL obtained from mechanically ventilated patients at our intensive care units were collected anonymously for testing the accuracy of ETA compared to BAL. Bacterial community structure was assessed by a metabarcoding approach based on 16S rRNA gene sequencing in ETA and BAL samples. ResultsIn total, 13 samples of each, BAL and ETA, were collected from 13 critically ill patients. No differences between BAL and ETA were found for alpha diversity based on species richness (p=0.77), Shannon diversity (p = 0.41), Simpson index (p = 0.85) and evenness (p = 0.98). Overall, BAL and ETA samples demonstrated strong taxonomic concordance at the levels of bacterial phyla and genera but differed distinctly at the amplicon sequence variants (ASV) level. ConclusionIn an unselected cohort of mechanically ventilated patients, BAL and ETA samples exhibited profound resemblance at higher taxonomic ranks, with increasing divergence observed at finer taxonomic resolutions. Our findings may facilitate guidance towards the reliability of non-invasive ETA as a valuable approach for clinical studies investigating the lung microbiome.

microbiology↗

bioRxiv2025

Skin but not gut microbial communities in Antarctic fur seals vary with social density

Comparative studies of microbial communities occupying different body sites in wild vertebrates are scarce, but they are crucial for advancing our understanding of the ecological and evolutionary factors shaping animal microbiomes. We therefore used a "natural experiment" comprising mother-offspring pairs from two adjacent Antarctic fur seal breeding colonies that differ in social density to investigate differences between skin and gut microbial communities in relation to host-specific and environmental factors. Using 16S rRNA amplicon sequencing, we uncovered a strong influence of colony on the diversity and composition of skin but not gut microbial communities. Specifically, we observed a suppressive effect of high social density on skin microbial alpha diversity as well as an overabundance of phyla associated with diseases and bite wounds in the high-density colony. Our findings suggest that skin microbial communities may be more sensitive to external factors, whereas gut communities are more tightly regulated by the host. Overall, this study highlights the importance of considering multiple body sites and their distinct microbial communities to develop a more comprehensive understanding of the factors shaping microbial diversity and composition in marine mammals.

microbiology↗

bioRxiv2024

Nanopore- and AI-empowered metagenomic viability inference

The ability to differentiate between viable and dead microorganisms in metagenomic data is crucial for various microbial inferences, ranging from assessing ecosystem functions of environmental microbiomes to inferring the virulence of potential pathogens from metagenomic analysis. While established viability-resolved genomic approaches are labor-intensive as well as biased and lacking in sensitivity, we here introduce a new fully computational framework that leverages nanopore sequencing technology to assess microbial viability directly from freely available nanopore signal data. Our approach utilizes deep neural networks to learn features from such raw nanopore signal data that can distinguish DNA from viable and dead microorganisms in a controlled experimental setting of UV-induced Escherichia cell death. The application of explainable AI tools then allows us to pinpoint the signal patterns in the nanopore raw data that allow the model to make viability predictions at high accuracy. Using the model predictions as well as explainable AI, we show that our framework can be leveraged in a real-world application to estimate the viability of obligate intracellular Chlamydia, where traditional culture-based methods suffer from inherently high false negative rates. This application shows that our viability model captures predictive patterns in the nanopore signal that can be utilized to predict viability across taxonomic boundaries. We finally show the limits of our models generalizability through antibiotic exposure of a simple mock microbial community, where a new model specific to the killing method had to be trained to obtain accurate viability predictions. While the potential of our computational frameworks generalizability and applicability to metagenomic studies needs to be assessed in more detail, we here demonstrate for the first time the analysis of freely available nanopore signal data to infer the viability of microorganisms, with many potential applications in environmental, veterinary, and clinical settings. Author summaryMetagenomics investigates the entirety of DNA isolated from an environment or a sample to holistically understand microbial diversity in terms of known and newly discovered microorganisms and their ecosystem functions. Unlike traditional culturing of microorganisms, genomic approaches are not able to differentiate between viable and dead microorganisms since DNA might persist under different environmental circumstances. The viability of microorganisms is, however, of importance when making inferences about a microorganisms metabolic potential, a pathogens virulence, or an entire microbiomes impact on its environment. As existing viability-resolved genomic approaches are labor-intensive, expensive, and lack sensitivity, we here investigate our hypothesis if freely available nanopore sequencing signal dat that captures DNA molecule information beyond the DNA sequence might be leveraged to infer such viability. This hypothesis assumes that DNA from dead microorganisms accumulates certain damage signatures that reflect microbial viability and can be read from nanopore signal data using fully computational frameworks. We here show first evidence that such a computational framework might be feasible by training a deep model on controlled experimental data to predict viability at high accuracy, exploring what the model has learned, and using it in a real-world application by application to a bacterial species of veterinary relevance. We finally show that a specific model has to be trained to accurately predict viability after antibiotic exposure of a mock microbial community. While the generalizability of our computational framework therefore needs to be assessed in much more detail, we here demonstrate that freely available data might be usable for relevant viability inferences in environmental, veterinary, and clinical settings.

bioinformatics↗

bioRxiv2023

Air monitoring by nanopore sequencing

While the air microbiome and its diversity are essential for human health and ecosystem resilience, comprehensive air microbial diversity monitoring has remained rare, so that little is known about the air microbiomes composition, distribution, or functionality. Here we show that nanopore sequencing-based metagenomics can robustly assess the air microbiome in combination with active air sampling through liquid impingement and tailored computational analysis. We provide fast and portable laboratory and computational approaches for air microbiome profiling, which we leverage to robustly assess the taxonomic composition of the core air microbiome of a controlled greenhouse environment and of a natural outdoor environment. We show that long-read sequencing can resolve species-level annotations and specific ecosystem functions through de novo metagenomic assemblies despite the low amount of fragmented DNA used as an input for nanopore sequencing. We then apply our pipeline to assess the diversity and variability of an urban air microbiome, using Barcelona, Spain, as an example; this randomized experiment gives first insights into the presence of highly stable location-specific air microbiomes within the citys boundaries, and showcases the robust microbial assessments that can be achieved through automatable, fast, and portable nanopore sequencing technology.

molecular biology↗

bioRxiv2023

Exploring priority and year effects on plant diversity, productivity and vertical root distribution: first insights from a grassland field experiment

O_LIThe order of arrival of plant species during community assembly can affect how species interact with each other. These so-called priority effects can have strong implications for the structure and functioning of plant communities. However, the extent to which the strength, direction, and persistence of priority effects are modulated by weather conditions during plant establishment ( year effects) is not well known. C_LIO_LIHere we present the first results from a long-term field experiment (POEM: PriOrity Effects Mechanisms) initiated in 2020 in Northern Germany to test how plant functional group (PFG) order of arrival and the year of initiation of an experiment interactively affect the structure and functioning of nutrient-poor dry acidic grasslands, both above and belowground. To do this, we established the same experiment, manipulating the order of arrival of forbs, grasses and legumes on the same site, but in different years. C_LIO_LIWe found that time since establishment was a stronger driver of plant community composition than PFG order of arrival and year of initiation. These three factors interactively affected plant species diversity, with the effect of PFG order of arrival on plant species richness depending on time since establishment. Year of initiation, not PFG order of arrival, was the strongest driver of aboveground community productivity. Although we did not find any effect of PFG order of arrival on root productivity, it had a strong impact on the vertical distribution of roots. Communities where grasses were sown first rooted more shallowly than communities in which forbs or legumes were sown first. C_LIO_LISynthesis: Our results demonstrate that plant order of arrival and year effects jointly affect plant diversity and species composition, with time since establishment also playing an important role. While year effects were more important than plant order of arrival in modulating aboveground biomass production in our nutrient-poor grassland, we showed that plant order of arrival can strongly affect the vertical distribution of roots, with communities in which forbs or legumes were sown first rooting deeper than grasses-first communities. These results suggest that a deeper understanding of priority and year effects is needed to better predict restoration outcomes. C_LI

ecology↗

bioRxiv2023

A fast-slow trait continuum at the level of entire communities

Across the tree of life, organismal functional strategies form a continuum from slow-to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, the synchronization of these strategies at the entire community level is untested. We combine trait data for >2800 above-and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. Most guilds consistently respond to these drivers through both direct and trophically-mediated effects, resulting in a slow-fast axis at the level of the entire community. Fast trait communities were also associated with faster rates of whole ecosystem functioning. These findings demonstrate that slow and fast strategies can be manifested at the level of whole ecosystems, opening new avenues of ecosystem-level functional classification.

ecology↗

bioRxiv2023

Low soil moisture induces recruitment of Actinobacteria in the rhizosphere of a drought-sensitive and Rhizobiales in a drought-tolerant potato cultivar

Growing evidence suggests that soil microbes can improve plant fitness under drought. However, in potato, the worlds most important non-cereal crop, the role of the rhizosphere microbiome under drought has been poorly studied. Using a cultivation independent metabarcoding approach, we examined the rhizosphere microbiome of two potato cultivars with different drought tolerance as a function of water regime (continuous versus reduced watering) and manipulation of soil microbial diversity (i.e., natural (NSM), vs. disturbed (DSM) soil microbiome). Water regime and soil pre-treatment showed a significant interaction with bacterial community composition of the drought-sensitive (HERBST) but not the drought-resistant cultivar (MONI). Depending on the cultivar, different taxa responded to reduced watering. Under NSM conditions, these were mostly rhizobiales order representative in MONI, and Streptomyces, Glycomyces, Marmoricola, Aeromicrobium, Mycobacterium, amongst Actinobacteriota, and the root endophytic fungus Falciphora in HERBST. Under DSM conditions and reduced watering, Bradyrhizobium, Ammoniphilus, Symbiobacterium and unclassified Hydrogenedensaceae responded in the rhizosphere of MONI compared to the continuous, while in HERBST, fewer taxa of Actinobacteriota and no fungi responded to reduced vs. continuous watering. Overall, our results indicate a strong cultivar specific relationship between potato and their associated rhizosphere microbiomes under reduced soil moisture.

ecology↗

bioRxiv2022

Part-night exposure to artificial light at night has more detrimental effects on aphid colonies than fully lit nights

Artificial light at night (ALAN) threatens natural ecosystems globally. While ALAN research is increasing, little is known about how ALAN affects plants and interactions with other organisms. We explored the effects of ALAN on plant defence and plant-insect interactions using barley (Hordeum vulgare) and the English grain aphid (Sitobion avenae). Plants were exposed to full or part nights of 15-20 lux ALAN, or no ALAN control nights, to test the effects of ALAN on plant growth and defence. Although plant growth was only minimally affected by ALAN, aphid colony growth and aphid maturation were reduced significantly by ALAN treatments. Importantly, we found strong differences between full-night and part-night ALAN treatments. Contrary to our expectations, part ALAN had stronger negative effects on aphid colony growth than full ALAN. Defence-associated gene expression was affected in some cases by ALAN, but also positively correlated with aphid colony size, suggesting that the effects of ALAN on plant defences are indirect, and regulated via direct disruption of aphid colonies, rather than via ALAN-induced upregulation of defences. Mitigating ecological side effects of ALAN is a complex problem, as reducing exposure to ALAN increased its negative impact on insect herbivores.

ecology↗

bioRxiv2021

The microbiome of Lotus nodules varies with plant health in a species-specific manner

Nitrogen fixation is carried out inside nodules of legumes by symbiotic rhizobia. Rhizobia dominate the nodule microbiome, however other non-rhizobial bacteria also colonise root nodules. It is not clear whether these less abundant nodule colonisers impact nodule function. In order to investigate the relationship between the nodule microbiome and nodule function as influenced by the soil microbiome, we used a metabarcoding approach to characterise the communities inside Lotus burttii, Lotus japonicus and Lotus corniculatus nodules from plants that were either starved or healthy resulting from inoculations with different soil suspensions in a closed pot experiment. We found that the nodule microbiome of all tested Lotus species differed according to inoculum, but only that of L. burttii varied with plant health. Using a machine learning algorithm, we also found that among the many non-rhizobial bacteria inside the nodule, amplicon sequence variants that were related to Pseudomonas were the most indicative signatures of a healthy plant nodule microbiome. These results support the hypothesis that legume nodule endophytes may play a role in the overall success of root-nodule symbiosis, albeit in a plant host specific manner.

microbiology↗

bioRxiv2021

Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations

Beta-proteobacteria belonging to the genus Acidovorax have been described from various environments. Many strains can interact with a range of hosts, including humans and plants, forming neutral, beneficial or detrimental associations. In the frame of this study we investigated genomic properties of 52 bacterial strains of the genus Acidovorax, isolated from healthy roots of Lotus japonicus, with the intent of identifying traits important for effective plant-growth promotion. Based on single-strain inoculation bioassays with L. japonicus, performed in a gnotobiotic system, we could distinguish 7 robust plant-growth promoting strains from strains with no significant effects on plant-growth. We could show that the genomes of the two groups differed prominently in protein families linked to sensing and transport of organic acids, production of phytohormones, as well as resistance and production of compounds with antimicrobial properties. In a second step, we compared the genomes of the tested isolates with those of plant pathogens and free-living strains of the genus Acidovorax sourced from public repositories. Our pan-genomics comparison revealed features correlated with commensal and pathogenic lifestyle. We could show that commensals and pathogens differ mostly in their ability to use plant-derived lipids and in the type of secretion-systems being present. Most free-living Acidovorax strains did not harbour any secretion-systems. Overall, our data indicated that Acidovorax strains undergo extensive adaptations to their particular lifestyle by horizontal uptake of novel genetic information and loss of unnecessary genes.

microbiology↗

bioRxiv2021

Induced systemic resistance impacts the phyllosphere microbiome through plant-microbe-microbe interactions

Both above- and below-ground parts of plants are constantly confronted with microbes, which are main drivers for the development of plant-microbe interactions. Plant growth-promoting rhizobacteria enhance the immunity of above-ground tissues, which is known as induced systemic resistance (ISR). We show here that ISR also influences the leaf microbiome. We compared ISR triggered by the model strain Pseudomonas simiae WCS417r (WCS417) to that triggered by Bacillus thuringiensis israelensis (Bti) in Arabidopsis thaliana. In contrast to earlier findings, immunity elicited by both strains depended on salicylic acid. Both strains further relied on MYC2 for signal transduction in the plant, while WCS417-elicited ISR additionally depended on SAR-associated metabolites, including pipecolic acid. A metabarcoding approach applied to the leaf microbiome revealed a significant ISR-associated enrichment of amplicon sequence variants with predicted plant growth-promoting properties. WCS417 caused a particularly dramatic shift in the leaf microbiota with more than 50% of amplicon reads representing two bacterial species: WCS417 and Flavobacterium sp.. Co-inoculation experiments using WCS417 and At-LSPHERE Flavobacterium sp. Leaf82, suggest that the proliferation of these bacteria is influenced by both microbial and plant-derived factors. Together, our data connect systemic immunity with leaf microbiome dynamics and highlight the importance of plant- microbe-microbe interactions for plant health.

plant biology↗

bioRxiv2020

Viruses carrying genes for microbial extremotolerance are abundant and widely dispersed in the Atacama Desert hyperarid soil

Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e. DNA repair proteins, enzymes against oxidative damage, spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment. ImportanceDeserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results indicate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.

microbiology↗