Biology subjects

Raaijmakers, J. M.

Publications and source records attributed to Raaijmakers, J. M..

13 recordsLinked to original sources

bioRxiv2026

Plant-associated Streptomyces detoxify the mycotoxin fusaric acid by amino acid conjugation

Streptomycetes are prevalent members of soil and plant microbiomes, yet how they cope with toxins produced by root-infecting fungal pathogens remains poorly understood. Plant pathogenic Fusarium species produce the mycotoxin fusaric acid (FA) that contributes to virulence and perturbs rhizosphere microbiome dynamics. Here, we show that root-colonising Streptomyces sp. ATMOS43 neutralizes FA through amino acid conjugation. Metabolomics revealed the formation of single amino acid and dipeptidyl conjugates of FA, with FA-Ser as a major conjugate that lacked detectable toxicity in in vitro and in planta assays. Proteomics and physiological analyses revealed that FA toxicity involves, in part, zinc chelation, which is abolished upon conjugation of FA to Ser. Co-cultivation experiments further showed that Streptomyces sp. ATMOS43 restores growth of FA-sensitive streptomycetes, indicating that conjugation can mitigate the impact of FA on plant microbiome assembly. Together, our findings show that plant-associated streptomycetes can protect plants by directly inhibiting Fusarium growth and by neutralizing its toxic virulence factor FA.

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↗

bioRxiv2025

Antifungal biosynthesis by root-associated Streptomyces and Pseudomonas is elicited upon plant colonization

Plants are colonized by a diverse microbiome, with microorganisms residing inside and outside of plant tissues. Plants can harness the protective traits of their microbial inhabitants to ward off insect pests and fungal pathogens. However, current understanding of the role of commensal interactions on activating the desired microbial genomic traits remains limited. Here we show that biosynthesis of the antifungal 2,5-dihydro-L-phenylalanine (DHP) by the endophytic Streptomyces sp. PG2 is strongly induced upon colonization of Arabidopsis thaliana. DHP production protects the plant from infection by the fungal root pathogen Rhizoctonia solani, both in vitro and in vivo.. We identified the DHP biosynthetic gene cluster (BGC) and showed that heterologous expression of the BGC in the DHP non-producer Streptomyces coelicolor also conferred plant-inducible DHP production. The BGC was also found in plant-associated Gram-negative bacteria, and in Pseudomonas syringae FF5 we again observed strongly enhanced DHP production upon plant colonization. An ecology-inspired elicitor screen showed that L-valine and brassinosteroid hormones elicit DHP biosynthesis in the plant-beneficial Streptomyces sp. PG2, while L-valine also elicited DHP biosynthesis in S. coelicolor. In vivo experiments confirmed the stimulation of antifungal activity in Streptomyces sp. PG2 by L-valine, while brassinolide mutant plants showed reduced DHP induction. Conversely, neither L-valine nor brassinolide elicited the expression of the DHP BGC in the pathogenic P. syringae, revealing important divergence in the responses to plant signaling, which may reflect selectivity in how endosymbionts and pathogens respond to host cues. Collectively, our data demonstrate that plant colonization can elicit the biosynthetic potential of root-associated microbes, thereby enhancing plant resilience.

microbiology↗

bioRxiv2025

Predicting Rhizosphere Competence Related Catabolic Gene Clusters in plant-associated bacteria with RhizoSMASH

Plants release a substantial fraction of their photosynthesized carbon into the rhizosphere as root exudates, a mix of chemically diverse compounds that drive microbiome assembly. Deciphering how plants modulate the composition and activities of rhizosphere microbiota through root exudates is challenging, as no dedicated computational methods exist to systematically identify microbial root exudate catabolic pathways. Here we used and integrated published information on catabolic genes in bacterial taxa that contribute to their rhizosphere competence. We developed the RhizoSMASH algorithm for genome-synteny-based annotation of rhizosphere-competence-related catabolic gene clusters (rCGCs) in bacteria by means of a set of 58 knowledge-based logic detection rules carefully curated through sequence similarity network analysis. Our analysis revealed large heterogeneity of rCGC prevalence both across and within plant-associated bacterial taxa, indicating extensive niche specialization. Furthermore, we validated that the presence or absence of rCGCs in bacterial genomes reflects their catabolic capacity and is predictive for their rhizosphere competence by aligning rhizoSMASH results with paired genome/metabolome datasets of rhizobacterial taxa. RhizoSMASH provides an extensible framework for studying rhizosphere bacterial catabolism, allowing targeted selection of beneficial bacterial taxa for microbiome-assisted breeding approaches for sustainable agriculture.

bioinformatics↗

bioRxiv2024

Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks

The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.

microbiology↗

bioRxiv2023

Reciprocal interactions between the sorghum root microbiome and the parasitic weed Striga hermonthica

The soil microbiome plays a crucial role in protecting plants against various pests and pathogens. However, its impact on interactions between plants and parasitic weeds, such as Striga hermonthica, is poorly understood. In this study, sorghum plants susceptible to Striga were grown in 22 different field soils infested with parasite seeds. Significant variations in Striga infections were observed among the soils. When the most Striga-suppressive soil was gamma-irradiated, there was a significant increase in Striga attachments, highlighting the importance of the soil microbiome in disrupting parasite infection. In the presence of the soil microbiome, the Striga-susceptible sorghum plants performed similarly to three Striga-resistant genotypes. This effect was lost when the soil microbiome was eliminated by gamma-irradiation. Subsequent analysis revealed that Striga substantially affected the sorghum rhizosphere microbiome and that both the sorghum rhizosphere mycobiome and bacteriome composition significantly correlated with Striga attachment. Interestingly, certain fungal species in the sorghum rhizosphere mycobiome were only detected when Striga seeds were present. Further investigation showed that these fungal taxa originated from the Striga seeds and are known sorghum pathogens, suggesting a potential partnership between Striga and fungal pathogens to invade their shared host. Overall, our study demonstrated that the soil microbiome influences Striga infection and sorghum performance in a genotype-dependent manner, and the microbiome of Striga seeds affects the composition of the sorghum rhizosphere microbiome.

ecology↗

bioRxiv2022

The plant stress hormone jasmonic acid evokes defensive responses in streptomycetes

Actinobacteria are prevalent in the rhizosphere and phyllosphere of diverse plant species where they help to enhance tolerance of plants against biotic and abiotic stresses. Here, we show that the plant hormones jasmonic acid (JA) and methyljasmonate (MeJA) alter growth, development and specialized metabolism of Streptomyces. Challenge of Streptomyces coelicolor with JA or MeJA led to strongly enhanced production of the polyketide antibiotic actinorhodin. JA is toxic to Streptomycetaceae, whereby members of the genus Streptacidiphilus are generally more sensitive than streptomycetes. As a defensive response, extensive amino acid conjugation of JA was observed; the most prevalent conjugation was with glutamine (Gln), while conjugates with Val, Tyr, Phe and Leu/Ile were identified after longer exposure to JA. Synthetic JA conjugates failed to activate antibiotic production and had strongly reduced toxicity, strongly suggesting that conjugation inactivates JA and serves to detoxify the hormone. Thus, for the first time we provide evidence that plant hormones modulate growth, development and secondary metabolism of streptomycetes, whereby amino acid conjugation serves as a defense strategy by the bacteria to circumvent plant hormone toxicity. IMPORTANCEMicroorganisms that live on or inside plants greatly influence plant health. Streptomycetes are considered to have an important role in defense against plant diseases, but the mechanisms through which they protect plants are currently not fully understood. It has been suggested that streptomycetes respond to changes in the plants physiology, among others by producing protective molecules; however, little is known of the signal transduction from plant to bacterium. We here demonstrate that the plant hormones jasmonic acid (JA) and methyljasmonate (MeJA) directly influence the life cycle of streptomycetes by modulating antibiotic synthesis and promoting faster development. Moreover, the plant hormones specifically stimulate the synthesis of the polyketide antibiotic actinorhodin in Streptomyces coelicolor. Jasmonic acid is then modified in the cell by amino acid conjugation, which reduces the bioactivity of the hormone and thus quenches the signal. To the best of our knowledge, this has not been reported previously. Collectively, these results suggest a relationship between plant physiological changes and the response of streptomycetes in multiple ways.

microbiology↗

bioRxiv2022

The soil microbiome reduces Striga infection of sorghum by modulation of host-derived signaling molecules and root development

Sorghum bicolor is one of the most important cereals in the world and a staple crop for smallholder famers in sub-Saharan Africa. However approximately 20% of sorghum yield is annually lost on the African continent due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies often show an inconsistent to low efficacy. Hence, novel and integrated approaches are needed as an alternative strategy. Here, we demonstrate that the soil microbiome suppresses Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation, and depletion of haustorium inducing factors (HIFs), root exudate compounds that are critical for the initial stages of Striga infection. We further identify microbial taxa associated with reduced Striga infection with concomitant changes in root cellular anatomy and differentiation as well as HIF degradation. Our study describes novel microbiome-mediated mechanisms of Striga suppression, encompassing repression of haustorium formation and induction of physical barriers in the host root tissue. These findings open new avenues to broaden the effectiveness of Striga management practices.

plant biology↗

bioRxiv2021

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, 16S amplicon and metagenomic features of the rhizosphere microbiome were mapped as quantitative traits of a recombinant inbred line population of a cross between wild and domesticated tomato. Gene content analysis of prioritized tomato QTLs suggested a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31-Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the aquaporin SlTIP2.3. Within metagenome-assembled genomes of the rhizobacterial lineages Streptomyces and Cellvibrio, we identified microbial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associated with either modern or wild tomato QTLs. Integrating microbiomics and quantitative plant genetics pinpointed putative plant and reciprocal microbial traits underlying microbiome assembly, thereby providing the first step towards plant-microbiome breeding programs.

microbiology↗

bioRxiv2021

TbasCO: Trait-based Comparative 'Omics Identifies Ecosystem-Level and Niche-Differentiating Adaptations of an Engineered Microbiome

A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while 14 genomes containing the high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by 11 genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for revealing hidden metabolic versatility when investigating genomic data alone by assigning trait-attributes through genome-resolved time-series metatranscriptomics.

genomics↗

bioRxiv2019

Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes

One of the fundamental tenets of biology is that the phenotype of an organism (Y) is determined by its genotype (G), the environment (E) and their interaction (GE). Quantitative phenotypes can then be modeled as Y=G+E+GE+e, where e is the biological variance. This simple and tractable model has long served as the basis for studies investigating the heritability of traits and decomposing the variability in fitness. Increasingly, the importance of microbe interactions on organismal phenotypes is being recognized, but it is currently unclear what the relative contribution of microbiomes to a given host phenotype is and how this translates into the traditional GE model. Here we address this fundamental question and propose an expansion of the original model, referred to as GEM, which explicitly incorporates the contribution of the microbiome (M) to the host phenotype, while maintaining the simplicity and tractability of the original GE model. We show that by keeping host, environment and microbiome as separate but interacting variables, the GEM model can capture the nuanced ecological interactions between these variables. Finally, we demonstrate with an in vitro experiment how the GEM model can be used to statistically disentangle the relative contributions of each component on specific host phenotypes.

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↗