Biology subjects

Garbeva, P.

Publications and source records attributed to Garbeva, P..

10 recordsLinked to original sources

bioRxiv2026

Differential drought sensitivity of total and active wheat rhizosphere microbiome during rainfall reduction

Root-associated microorganisms play a pivotal role in helping plants adapt to drought stress. However, the underlying mechanisms of the rhizospheric microbiome under limiting soil moisture remain largely unresolved. Integrating total and active microbiome analyses enables a more accurate interpretation of microbial responses to climate change-associated water stress. We assessed the effect of reduced rainfall on two wheat genotypes, drought-tolerant (DT) and drought-sensitive (DS), using rainout shelters that allowed 100%, 75%, 50%, and 25% of natural precipitation to reach the crop. At the peak of the growing season, rhizosphere samples were collected for metagenomic (MG) and metatranscriptome (MT) sequencing. In parallel, rhizosphere volatile organic compounds (VOCs) were collected and analysed. Differential expression analysis of metatranscriptomic data using metagenomic abundance as a cofactor was performed by comparing all treatments to the 100% precipitation control. Our results demonstrate that particularly oxidative stress-related transcripts intensify in DS as rainfall decreases. Transcriptomic shifts primarily involved upregulation of transcripts associated with antioxidant (catalase, superoxide dismutase), heat shock proteins (Hsp10, Hsp60, DnaK/DnaJ, GroEL, GroES), as well as microbial functions related to osmoregulation, proline and glycine betaine (PutA, PutP, OpuBB), and plant growth-promoting traits such as auxin production, phosphate solubilization. Moreover, volatile organic compound (VOC) emissions differed significantly between the control and drought treatments, with higher emissions, particularly acetates, in the DS genotype than in the DT genotype. Overall, pronounced drought-induced shifts in active microbial functions and VOC emissions indicate high sensitivity and functional plasticity of the active microbiome, whereas the total microbiome remains robust under medium drought.

microbiology↗

bioRxiv2026

SynCom101: A web-based platform for the standardized design of functionally tailored synthetic microbial communities

BackgroundSynthetic microbial communities (SynComs) are essential tools for dissecting the causal mechanisms in host-microbiota interactions. To date, however, SynCom design suffers from a lack of standardization, typically oscillating between arbitrary strain selection and computational pipelines that misalign with experimental design. As microbiome research transitions toward functionally defined community systems with reproducible experimental outcomes, there is a strong need for a user-friendly platform that integrates multi-dimensional genomic and/or biological data into a standardized and tailored SynComs design. ResultsHere, we present SynCom101, a web-based platform that democratizes the design of reproducible, hypothesis-driven SynComs. SynCom101 accommodates diverse input formats including genomic annotations and laboratory-obtained phenotypic traits, allowing users to customize their design criteria with high flexibility. The platform utilizes a parsimony algorithm to ensure computational scalability for large datasets, complemented by an optional correlation-aware mode to account for microbial compatibility and co-occurrence patterns when ecological interactions among strains are available. A core innovation of SynCom101 is its suite of trait-weighting modules, which empowers researchers to strategically guide the selection algorithm toward maximal functional trait coverage, the emulation of natural community architectures, or the enrichment of positively correlated microbial assemblages to enhance community stability. We showcase the functionalities of the platform by in silico design of communities from different datasets, demonstrating its capacity to generate concise, functionally prioritized SynComs aligned with targeted design objectives. ConclusionBy providing a transparent, parameter-documented workflow, SynCom101 ensures that community design is no longer a "black box" but a reproducible scientific record. This platform establishes a necessary standard for in silico community assembly, facilitating the transition from descriptive microbiome studies toward high-throughput, predictive functional screening and cross-study comparability. AvailabilitySynCom101 can be accessed via the web interface (https://syncom101.bioinformatics.nl/). The datasets used for case studies are available on Zenodo (https://doi.org/10.5281/zenodo.18310451). The source code is available at Git (https://git.wur.nl/jiayi.jing/syncom101).

bioinformatics↗

bioRxiv2026

Reconstructing plant beneficial bacterial consortia by integrating dilution-to-extinction microbiome perturbation with genome-resolved synthetic ecology

Across the biosphere, microbiomes play essential roles in shaping the health of their host. One notable example of such a microbiome-associated phenotype is disease-suppressive soils, where susceptible plant hosts enrich and activate specific rhizosphere microbial consortia for protection against fungal root pathogens. However, identifying and reconstructing microbial consortia responsible for host protection remains challenging, given the inherent taxonomic and functional complexity of microbiomes. Here, we integrated metagenomic profiling of disease-suppressive microbiomes perturbed by dilution-to-extinction (DTE) with comprehensive culturing and synthetic ecology to identify the key bacterial taxa conferring suppressiveness to the fungal wheat pathogen Fusarium culmorum. Metagenomics of wheat rhizosphere samples along the DTE trajectory revealed bacterial taxa and functions associated with the disease-suppressive phenotype. Crosslinking these DTE metagenome data with a genome-sequenced collection of 336 rhizobacterial isolates from the suppressive soil allowed the reconstruction of synthetic communities (SynComs) of 11 de-replicated strains negatively associated with disease severity. Upon re-introduction in sterilized suppressive soils, this SynCom consistently reproduced the disease-suppressive phenotype. Paired time-series metagenomics and metatranscriptomics of the SynComs pinpointed candidate biosynthetic gene clusters, including a novel non-alpha poly-amino-acid (NAPAA) gene cluster from Arthrobacter, upregulated in presence of F. culmorum. Chemically synthesized NAPAA variants {varepsilon}-poly-L-lysine and {delta}-poly-L-ornithine significantly inhibited F. culmorum hyphal growth. Collectively, our work establishes a transformative strategy for reconstructing microbial consortia that recapitulates beneficial microbiome-associated phenotypes in plant and animal kingdoms.

microbiology↗

bioRxiv2026

Pseudomonas volatiles shape the root transcriptome and microbiome to promote plant growth under drought

O_LIVolatile organic compounds (VOCs) emitted by soil bacteria influence interactions with other soil microbes and with plant roots. While their potential as plant-growth promoters is well recognized, their role in promoting plant resilience to abiotic stress and the underlying molecular mechanisms remains poorly understood. Here, we investigate the role of Pseudomonas VOCs in enhancing plant resilience to drought stress. C_LIO_LIArabidopsis thaliana plants were exposed to VOCs emitted by Pseudomonas strains under both control and osmotic-stress conditions. VOC exposure generally enhanced plant growth, and this effect was even more pronounced under both drought and salt stress. Transcriptomic analysis revealed that VOC exposure modulates key stress-responsive pathways, including those related to abscisic acid biosynthesis and signalling, sugar transport, iron uptake, aliphatic glucosinolate biosynthesis, and plant defences. Using Arabidopsis mutants, we identified abscisic acid and aliphatic glucosinolates as important components in mediating the plant response to VOCs. SWEET11/12 sugar transporters and ABA signaling genes were downregulated by VOCs exposure, in order to allow for a positive regulation of lateral root numbers (in case of SWEET genes) and plant growth in general under drought stress. In summary, using metabolomics, transcriptomics and functional analysis, we showed a negative cross-talk between the effects of VOCs on plant growth and glucosinolate production, whereas a positive interaction was observed between the biosynthesis of coumarins and VOCs. C_LIO_LINotably, VOCs also improved drought tolerance in soil-grown Brassica oleracea plants. We showed that VOC treatment altered the root-associated microbiome under drought, leading to a community composition more similar to that of well-watered plants. C_LIO_LIOur results show that Pseudomonas emitted VOCs can promote plant growth under drought conditions, linked to root transcriptional reprogramming and direct or indirect microbiome modulation. C_LI

plant biology↗

bioRxiv2024

Linking microbial community structure with function using functional amplicon sequencing of the NRPS genes around wheat roots during drought stress

Secondary metabolites are bioactive compounds, diverse in structure with versatile ecological functions including key roles in mediating interactions between microorganisms and plants. Importantly, these compounds can promote the colonization of plant surfaces, such as roots, or modulate root exudates to enhance microbial recruitment and establishment. However, owing to the vast diversity of secondary metabolites, their importance in plant root colonization and in particular under stress conditions such as drought, remains unclear. To determine the involvement in root colonization of some of these secondary metabolites, we used amplicon sequencing targeting the adenylation domain of the NRPSs and the 16S rRNA gene from the rhizoplane of wheat grown in soil under normal and drought stress conditions. Results showed that drought transiently affected the bacterial community composition and the NRPS composition in the rhizoplane. We observed that drought selected for distinct groups of siderophores from different taxonomical groups, enriching for Streptomyces and depleting Pseudomonas siderophores. In addition, drought enriched Pseudomonas-derived NRPS genes encoding viscosin, a cyclic lipopeptide with biosurfactant properties, indicating that compounds linked to motility and colonization provide a competitive advantage during rhizoplane colonization under drought stress condition. This observation was experimentally confirmed using the viscosin producing P. fluorescens SBW25 and its viscosin-deficient mutant. A higher abundance of SBW25 colonized the roots under drought stress conditions compared to the viscosin-deficient mutant. In summary, our work demonstrates the potential for amplicon sequencing of NRPS genes coupled with in planta experiments to elucidate the importance of secondary metabolites in root colonization. ImportanceTo harness beneficial plant-microbe interactions for improved plant resilience, we need to advance our understanding of key factors required for successful root colonization. Bacterial produced secondary metabolites are important in plant-microbe interactions, and thus, targeting these genes generate new knowledge that is essential for leveraging bacteria for sustainable agriculture. We used amplicon sequencing of the NRPS A domain on the rhizoplane of wheat exposed to drought stress to identify important secondary metabolites in plant-microbe interactions during drought. We show that the siderophores respond differently to drought stress depending on taxonomic affiliation and that the potential to synthesize viscosin increases root colonization. Importantly, this study demonstrates the potential of amplicon sequencing of NRPS genes to reveal specific secondary metabolites involved in root colonization, particularly in relation to drought stress, and highlights how the resolution provided by this approach can link specific compounds to a specific stress condition in a soil system.

microbiology↗

bioRxiv2023

Enhanced niche colonisation and competition during bacterial adaptation to a fungus

Bacterial-fungal interactions (BFIs) influence microbial community performance of most ecosystems and elicit specific microbial behaviours, including stimulating specialised metabolite production. Using a simple BFI system encompassing the Gram-positive bacterium Bacillus subtilis and the black mould fungus Aspergillus niger, we established a co-culture experimental evolution method to investigate bacterial adaptation to the presence of a fungus. In the evolving populations, B. subtilis was rapidly selected for enhanced production of the lipopeptide surfactin and accelerated surface spreading ability, leading to inhibition of fungal expansion and acidification of the environment. These phenotypes were explained by specific mutations in the DegS-DegU two-component system. In the presence of surfactin, fungal hyphae exhibited bulging cells with delocalised secretory vesicles and RlmA-dependent cell wall stress induction. Increased surfactin production typically enhances the competitive success of bacteria against fungi, which likely explains the primary adaption path in the presence of A. niger. Significance statementExperimental evolution and co-cultivation of different microbes are important and useful techniques for discovering new traits and unravelling cryptic regulatory connections. We combined these methods by evolving the Gram-positive bacterium Bacillus subtilis in the presence of the black mould fungus Aspergillus niger that were previously shown to engage in an intricate and physical interaction. Both are ubiquitous, environmentally and industrially relevant model microbes in the colonisation of rhizo- and endosphere and in the production of enzymes. Our results demonstrate how laboratory adaptation can be exploited to improve biocontrol properties of bacteria.

microbiology↗

bioRxiv2021

Do size and shape matter? Exploring the interactions and the metabolome of the soil isolate Hylemonella gracilis

Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 m. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far no study investigated if such bacteria exist in terrestrial environments like e.g. soil. Here, we isolated soil bacteria that passed through a 0.1 m filter, by applying a novel isolation and culturing approach. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. A set of co-culture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The co-culture assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact. Our study indicates that bacteria are present in the soil that can pass through a 0.1 m filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, are able to induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities. ImportanceAnalysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 m. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments e.g. soil. By applying a novel isolation method, we show that such bacteria also exist in soil. The isolated bacteria was identified as Hylemonella gracilis. Co-culture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when co-cultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1 m filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.

microbiology↗

bioRxiv2020

Nitrapyrin has far reaching effects on the soil microbial community structure, composition, diversity and functions

Nitrapyrin is one of the most common nitrification inhibitors that are used to retain N in the ammonia form in soil to improve crop yields and quality. Whereas the inhibitory effect of nitrapyrin is supposedly specific to ammonia oxidizers, in view of the keystone role of this group in soils, nitrapyrin could have far-reaching impacts. Here, we tested the hypothesis that nitrapyrin leads to large shifts in soil microbial community structure, composition, diversity and functions, beyond its effect on ammonia-oxidizers. To test this hypothesis, we set-up a field experiment where wheat (Triticum aestivum cv. AC Walton) was fertilized with ammonium nitrate (NH4NO3) and supplemented or not with nitrapyrin. Rhizosphere and bulk soils were sampled twice, DNA was extracted, the 16S rRNA gene and ITS region were amplified and sequenced to follow shifts in archaeal, bacterial and fungal community structure, composition and diversity. To assess microbial functions, several genes involved in the nitrogen cycle were quantified by real-time qPCR and volatile organic compounds (VOCs) were trapped in the rhizosphere at the moment of sampling. As expected, sampling date and plant compartment had overwhelming effects on the microbial communities. However, within these strong effects, we found statistically significant effects of nitrapyrin on the relative abundance of Thaumarchaeota, Proteobacteria, Nitrospirae and Basidiomycota, and on several genera. Nitrapyrin also significantly affected bacterial and fungal community structure, and the abundance of all the N-cycle gene tested, but always in interaction with sampling date. In contrast, nitrapyrin had no significant effect on the emission of VOCs, where only sampling date significantly influenced the profiles observed. Our results point out far-reaching effects of nitrapyrin on soil and plant associated microbial communities, well beyond its predicted direct effect on ammonia-oxidizers. In the longer term, these shifts might counteract the positive effect of nitrapyrin on crop nutrition and greenhouse gas emissions.

microbiology↗

bioRxiv2018

Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces

Soil-inhabiting streptomycetes are Natures medicine makers, producing over half of all known antibiotics and many other bioactive natural products. However, these bacteria also produce many volatile compounds, and research into these molecules and their role in soil ecology is rapidly gaining momentum. Here we show that streptomycetes have the ability to kill bacteria over long distances via air-borne antibiosis. Our research shows that streptomycetes do so by producing surprisingly high amounts of the low-cost volatile antimicrobial ammonia, which travels over long distances and antagonises both Gram-positive and Gram-negative bacteria. Glycine is required as precursor to produce ammonia, and inactivation of the glycine cleavage system annihilated air-borne antibiosis. As a resistance strategy, E. coli cells acquired mutations resulting in reduced expression of the porin master regulator OmpR and its cognate kinase EnvZ, which was just enough to allow them to survive. We further show that ammonia enhances the activity of the more costly canonical antibiotics, suggesting that streptomycetes adopt a low-cost strategy to sensitize competitors for antibiosis over longer distances.

microbiology↗

bioRxiv2018

LAESI mass spectrometry imaging as a tool to differentiate the root metabolome of native and range-expanding plant species

Our understanding of chemical diversity in biological samples has greatly improved through recent advances in mass spectrometry (MS). MS-based-imaging (MSI) techniques have further enhanced this by providing spatial information on the distribution of metabolites and their relative abundance.\n\nThis study aims to employ laser-assisted electrospray ionization (LAESI) MSI as a tool to profile and compare the root metabolome of two pairs of native and range expanding plant species.\n\nIt has been proposed that successful range-expanding plant species, like introduced exotic invaders, have a novel, or a more diverse secondary chemistry. Although some tests have been made using aboveground plant materials, tests using root materials are rare. We tested the hypothesis that range-expanding plants possess more diverse root chemistries than native plant species.\n\nTo examine the root chemistry of the selected plant species, LAESI-MSI was performed in positive ion mode and data was acquired in a mass range of m/z 50-1200 with a spatial resolution of 100 {micro}m. The acquired data was analyzed using in-house scripts, and differences in the spatial profiles were studied for discriminatory mass features. The results revealed clear differences in the metabolite profiles amongst and within both pairs of congeneric plant species, in the form of distinct metabolic fingerprints. The use of ambient conditions and the fact that no sample preparation was required, established LAESI-MSI as an ideal technique for untargeted metabolomics and for direct correlation of the acquired data to the underlying metabolomic complexity present in intact plant samples.

ecology↗