Biology subjects

Schlaeppi, K.

Publications and source records attributed to Schlaeppi, K..

16 recordsLinked to original sources

bioRxiv2026

ZeaMiC: a Publicly Available Culture Collection of Maize Root-Associated Bacteria

Plant-associated microbiota are composed of hundreds of microbial species. For many of them, little is known about their individual functions and even less is known about their emergent community-level traits. While culture-independent methods provide valuable insights into the composition, diversity, and functional potential of plant-associated microbiota, culture-dependent methods are essential for reductionist lines of inquiry into the roles of individual species and their interactions within a community. Here, we present ZeaMiC, a publicly available culture collection of root-associated bacteria from Zea mays (maize). This resource comprises 88 isolates obtained from diverse soils and several maize genotypes, with live cultures available through DSMZ (German Collection of Microorganisms and Cell Cultures) both as single stocks and as cost-effective bundles (https://www.dsmz.de/collection/catalogue/microorganisms/microbiota/zeamic). To maximize relevance, isolates were selected to be representative of maize root-associated microbiomes in the Corn Belt of the United States, based on abundance-occupancy patterns from previously published root microbiome data, phylogenetic diversity, and literature-based evidence of functional importance. Whole-genome sequencing and annotation revealed genes associated with root colonization, plant growth promotion, and nutrient cycling, including functions such as chemotaxis, biofilm formation, secretion systems, hormone modulation, and phosphate solubilization. This collection serves as a community resource for future mechanistic studies of plant-microbe and microbe-microbe interactions, filling the gap in our understanding of the ecological interactions in plant microbiomes.

microbiology↗

bioRxiv2026

Paralleled Dynamics of Arabidopsis Root Exudation and SynCom Assembly in a Controlled Environment

Plant roots host defined microbial communities that differ from those found in the surrounding soil and these communities shift dynamically in response to plant development and environmental changes. Whilst it is widely accepted that root exudates play a key role in the assembly and dynamics of root-associated microbial communities, the underlying mechanisms are not well understood. This is partly due to a lack of controlled experimental systems that monitor both exudate- and microbiome-dynamics simultaneously. Here, we compared two microcosm systems commonly used in either root microbiome (clay particle-based) or root exudate studies (glass bead-based) for their suitability to simultaneously monitor both aspects. We evaluated these systems based on plant performance, bacterial growth, and time-resolved community and exudate profiling. In both systems, we reveal an exudate effect, characterised by higher bacterial diversity and Pseudomonas abundances in proximity to plant roots. While clay particles impeded exudate recovery, even when plants were removed from microcosms for exudate collection, the glass bead set-up allowed us to uncover dynamic exudate shifts during bacterial community establishment. This highlighted a transient increase of glucosinolates upon root colonisation by initially dominant Pseudomonas species. Overall, the comparison proved only the glass bead-based semi-hydroponic system to be suitable for the paralleled study of exudate and root microbiome dynamics.

plant biology↗

bioRxiv2026

Soil iron drives beneficial maize microbiome feedbacks inrotations with wheat

BackgroundPlants change their surrounding soil microbiome by root exudates and such conditioned microbiomes impact the performance of the present as well as the next plant generation as for example in crop rotations. The big challenge is that such microbiome feedbacks are highly context-dependent, i.e. they vary in strength and direction dependent on the local soil environment - of which the driving factor(s) remain unknown. Including maize in crop rotations involves benzoxazinoids (BXs), which are exuded from roots and alter the soil microbiome, which in turn affects growth and defence of the following crop. ResultsHere, we grew wild-type and BX-depleted maize in the field to differentially condition their soil microbiome and we found varying feedbacks on wheat performance dependent on the local physicochemical soil parameters. Using multivariate, correlation and modelling approaches and including additional data from two previous field experiments, we identified plant-available (PA) iron to explain BX-dependent microbiome feedbacks on wheat. The BX-conditioned soil microbiome caused wheat to grow taller at low levels of soil PA-iron but smaller at high levels. This finding was generalized testing these maize microbiome feedbacks on the model plant Arabidopsis thaliana using soil batches containing different levels of iron. Consistent with wheat, a significant inverse relationship between soil PA-iron levels and plant growth was found. This relationship was experimentally validated with Arabidopsis grown at low levels of soil iron where iron supplementation abolished the beneficial feedback of the BX-conditioned soil microbiome. ConclusionTogether these findings revealed that beneficial microbiome feedbacks occur at low levels of plant-available iron, i.e. when plants grow in a suboptimal soil, but they are lost when plants are nutritionally well supported. These results underscore the importance of iron availability in soil for beneficial microbial feedbacks on plant growth and predict agronomic benefits of incorporating maize in crop rotations on low iron soils.

microbiology↗

bioRxiv2025

Synthetic communities of maize root bacteria interact and redirect benzoxazinoid metabolization

Plant roots are colonised by diverse microbial communities. These communities are shaped by root exudates including plant specialized metabolites. Benzoxazinoids are such secreted compounds of maize. Individual microbes differ in their ability to tolerate and metabolize antimicrobial benzoxazinoids. To investigate how these traits combine in a community, we designed two synthetic communities of maize root bacteria that share six common strains and differ in their ability to metabolize benzoxazinoids based on the seventh strain. We exposed both communities to the benzoxazinoid MBOA (6-methoxybenzoxazolin-2(3H)-one) and found that the metabolizing community did not degrade MBOA to its aminophenoxazinone, as observed for individual strains, but as a community they formed the corresponding acetamide. MBOA shaped differential compositions of both communities and increased the fraction of MBOA-tolerant strains. The benzoxazinoid metabolizing community showed a higher tolerance to MBOA and was able to utilize MBOA as their sole carbon source for growth. Hence, bacterial interaction results in alternative benzoxazinoid metabolization and increases community performance in presence of these antimicrobial compounds. Future work is needed to uncover the genetics of this metabolic interaction and ecological consequences for the bacterial community and the host plant. ImportanceWe investigated how maize root bacteria - alone or in community - tolerate and metabolize antimicrobial compounds of their host plant. We found the capacity to metabolize such a compound to impact bacterial community size and structure and most importantly, to beneeit community eitness. We also found that interacting bacteria redirected the metabolisation of the antimicrobial compound to an alternative degradation product. Our work highlights the need to study the team work of microbes to uncover their community traits to ultimately understand the ecological consequences for the bacterial community and eventually the host plant.

microbiology↗

bioRxiv2025

A TNL receptor mediates microbiome feedbacks in Arabidopsis

Plant performance depends on the soil microbiome. While microbiome feedbacks are well documented, the mechanisms by which plants perceive and mediate these feedbacks remain unclear. We established a framework using two distinct microbiomes in the same soil, where one led to enhanced growth of the Arabidopsis thaliana accession Col-0. Screening 410 accessions revealed substantial variation in growth feedbacks, which we used for genome-wide association mapping. We identified the immune receptor Mediator of Microbiome Feedback 1 (MMF1) as a candidate gene involved in microbiota feedbacks. Characterisation in the reference accession Col-0 revealed that mmf1 mutants lost the beneficial growth feedback, had an altered root bacterial community, and failed to induce a defence-related transcriptional response observed in wild-type plants. The discovery of MMF1 implies that integration of microbial signals optimises host microbiome composition and immune status to enhance growth.

plant biology↗

bioRxiv2024

Benzoxazinoid-mediated microbiome feedbacks enhance Arabidopsis growth and defense

O_LIPlants modulate their surrounding microbiome via root exudates and such conditioned soil microbiomes feed back on the performance of the next generation of plants. How plants perceive altered soil microbiomes and modulate their performance in response to such microbiome feedbacks however remains largely unknown. C_LIO_LIAs tool to condition contrasting microbiomes in soil, we made use of two maize lines, which differ in their ability to exude benzoxazinoids. Based on these differentially conditioned soil microbiomes we have established a model system with Arabidopsis thaliana (Arabidopsis) to investigate the mechanisms of microbiome feedbacks. C_LIO_LIArabidopsis plants responding to the benzoxazinoid-conditioned soil microbiome grew better and were developmentally more advanced. Further, these plants harboured differential root bacterial communities, showed enhanced defence signatures in transcriptomes of their shoots and they were more resistant to the fungal pathogen Botrytis cinerea. C_LIO_LIIntriguingly, Arabidopsis responded with both improved growth and enhanced defence to the benzoxazinoid-conditioned soil microbiome, and we found that this simultaneous increase of growth and defence was mediated by priming of the defences. Further advancing our basic understanding how plants respond to soil microbiomes and mediate their feedbacks is particularly important for the goal to improve crops so they can benefit from their soil microbiome. C_LI

plant biology↗

bioRxiv2024

Time-resolved, integrated multi-omic analysis reveals central role of amino acid pathways for defense responses in Arabidopsis thaliana

Plants respond to biotic stresses by altering gene expression and metabolism. However, how fast different tissues respond to microbial presence, and how similar these responses are is mostly unresolved. Here, we treat Arabidopsis thaliana with elicitors and investigate time-resolved changes in shoot, root, and root-derived (exudate) metabolite profiles. We find that root responses precede shoots and that first metabolite changes take place after 1.5 h and persist for 3 d. Exudates respond within 4 h (earliest timepoint available) to elicitor presence. This response diminishes when plants are pulse-treated but persists for continuously treated plants. Defense compounds such as phenylpropanoids increase after 1.5-4 h. Amino acids were iden6fied as central players in defense: they increase after 1.5 h in shoots, roots, and exudates. Transcriptome analysis at 4 h and 1 d and integrated, multi-omic analysis of transcription and metabolome suggest that aromatic and aliphatic amino acids are central players in defense responses. As their transcriptional and metabolite increases are fast and persisting over days for most amino acids, we propose amino acids as early indicators for biotic stress monitoring.

plant biology↗

bioRxiv2024

Component specific responses of the microbiomes to common chemical stressors in the human food chain

Along a food chain, microbiomes occur in each component and often contribute to the functioning or the health of their host or environment. One Health emphasizes the connectivity of each components health. Chemical stress typically causes dysbiotic microbiomes, but it remains unclear whether chemical stressors consistently affect the microbiomes along food chain components. Here, we systematically challenged a model food chain, including water, sediments, soil, plants, and animals, with three chemical stresses consisting of arsenic (a toxic trace element), benzoxazinoids (an abundant bioactive plant metabolites), and terbuthylazine (an herbicide typically found along a human food chain). The analysis of 1,064 microbiome profiles for commonalities and differences in their stress responses indicated that chemical stressors decreased microbiome diversity in soil and animal, but not in the other microbiomes. In response to stress, all food chain communities strongly shifted in their composition, generally becoming compositionally more similar to each other. In addition, we observed stochastic effects in host-associated communities (plant, animal). Dysbiotic microbiomes were characterized by different sets of bacteria, which responded specifically to the three chemical stressors. Microbial co-occurrence patterns significantly shifted with either decreased (water, sediment, plant, animal) or increased (soil) network sparsity and numbers of keystone taxa following stress treatments. This suggested major re-distribution of the roles that specific taxa may have, with the community stability of plant and animal microbiomes being the most affected by chemical stresses. Overall, we observed stress- and component-specific responses to chemical stressors in microbiomes along the model food chain, which could have implications on food chain health.

microbiology↗

bioRxiv2023

The lactonase BxdA mediates metabolic adaptation of maize root bacteria to benzoxazinoids

Root exudates contain secondary metabolites that affect the plants root microbiome. How microbes cope with these bioactive compounds, and how this ability shapes root microbiomes remain largely unknown. We investigated how maize root bacteria metabolise benzoxazinoids, the main specialised metabolites of maize. Diverse and abundant bacteria metabolised the major compound (6-methoxy-benzoxazolin-2-one, MBOA) in the maize rhizosphere to 2-amino-7-methoxyphenoxazin-3-one (AMPO). By contrast, bacteria isolated from Arabidopsis, which does not produce benzoxazinoids, were unable to metabolise MBOA. Among Microbacteria strains, this differential metabolisation allowed to identify a conserved gene cluster containing the lactonase bxdA. BxdA converts MBOA to AMPO in vitro and we show that this capacity provided bacteria a growth benefit under carbon-limiting conditions. Together these results reveal that maize root bacteria - through BxdA - are metabolically adapted to the benzoxazinoids of their host. We propose that metabolic adaptation to plant-specialised compounds shapes root bacterial communities across the plant kingdom.

microbiology↗

bioRxiv2023

Bacterial tolerance to host-exuded specialized metabolites structures the maize root microbiome

Plants exude specialized metabolites from their roots and these compounds are known to structure the root microbiome. However, the underlying mechanisms are poorly understood. We established a representative collection of maize root bacteria and tested their tolerance against benzoxazinoids, the dominant specialized and bioactive metabolites in the root exudates of maize plants. In vitro experiments revealed that benzoxazinoids inhibited bacterial growth in a strain- and compound-dependent manner. Tolerance against these selective antimicrobial compounds depended on bacterial cell wall structure. Further, we found that native root bacteria isolated from maize tolerated the benzoxazinoids better compared to non-host Arabidopsis bacteria. This finding suggests the adaptation of the root bacteria to the specialized metabolites of their host plant. Bacterial tolerance to 6-methoxy-benzoxazolin-2-one (MBOA), the most abundant and selective antimicrobial metabolite in the maize rhizosphere, correlated significantly with the abundance of these bacteria on benzoxazinoid-exuding maize roots. Thus, strain-dependent tolerance to benzoxazinoids largely explained the abundance pattern of bacteria on maize roots. Abundant bacteria generally tolerated MBOA, while low abundant root microbiome members were sensitive to this compound. Our findings reveal that tolerance to plant specialized metabolites is an important competence determinant for root colonization. We propose that bacterial tolerance to plant-secreted antimicrobial compounds is an underlying mechanism determining the structure of host-specific microbial communities. Significance StatementDiverse microbial communities colonize plant roots. They feed on carbon rich root exudates which contain a diverse mix of chemicals including primary and specialized metabolites. Here we show that specialized metabolites act as selective antibiotics to shape the root bacterial communities. By growing single isolates of maize root bacteria in the presence of benzoxazinoids in vitro, we find that the strains differ greatly in their tolerance to benzoxazinoids. Their different levels of tolerance largely explained their abundance on benzoxazinoid-exuding roots. Our work shows how plant specialized metabolites act to shape the maize root microbial community and thus deepened our mechanistic understanding of how plants shape their microbiome.

microbiology↗

bioRxiv2023

Soil chemical and microbial gradients determine accumulation of root exuded secondary metabolites and plant-soil feedbacks in the field

IntroductionHarnessing positive plant-soil feedbacks via crop rotations is a promising strategy for sustainable agriculture. Plants can influence soil properties including microbes by exuding specialized metabolites. However, the effects are often context dependent and variable. If and how local soil heterogeneity may explain this variation is unknown. Benzoxazinoids are specialized metabolites that are released in high quantities by cereals such as wheat and maize. Benzoxazinoids can alter rhizosphere microbiota and the performance of plants subsequently growing in the exposed soils and are thus an excellent model to study agriculturally relevant plant-soil feedbacks in the field, and to assess how soil factors affect their outcome. Materials & methodsTo understand the importance of local variation in soil properties on benzoxazinoid-mediated plant-soil feedbacks, we conditioned plots with wild-type maize and benzoxazinoid-deficient bx1 mutant plants in a grid pattern across an arable field. We then grew winter wheat across the entire field in the following season. We determined accumulation of benzoxazinoids, root-associated microbial communities, abiotic soil properties and wheat performance in each plot. We also determined benzoxazinoid conversion dynamics in a labelling experiment under controlled conditions, and then assessed associations between soil chemical variation and benzoxazinoid-mediated plant-soil feedbacks. ResultsAcross the field, we detected a marked gradient in soil chemical and microbial community composition. This gradient resulted in significant differences in benzoxazinoid accumulation. These differences were explained by differential benzoxazinoid degradation rather than exudation. Benzoxazinoid exudation modulated alpha diversity of root and rhizosphere bacteria and fungi during maize growth, but not during subsequent wheat growth, while the chemical fingerprint of benzoxazinoid accumulation persisted. Averaged across the field, we detected no significant feedback effects of benzoxazinoid conditioning on wheat performance and defence, apart from a transient decrease in biomass during vegetative growth. Closer analysis however, revealed pronounced feedback effects along the chemical and microbial gradient of the field, with effects gradually changing from negative to positive along the gradient. ConclusionOverall, this study revealed that plant-soil feedbacks differ in strength and direction within a field, and that this variation can be explained by standing chemical and microbial gradients, which strongly affect benzoxazinoid accumulation in the soil. Understanding within-field soil heterogeneity is crucial for the future exploitation of plant-soil feedbacks in sustainable precision agriculture.

plant biology↗

bioRxiv2022

Plant secondary metabolite-dependent plant-soil feedbacks can improve crop yield in the field

Plant secondary metabolites that are released into the rhizosphere alter biotic and abiotic soil properties, which in turn affect the performance of other plants. How such plant-soil feedbacks affect agricultural productivity and food quality in crop rotations is unknown. Here, we assessed the impact of maize benzoxazinoids on the performance, yield and food quality of three winter wheat varieties in a two-year field experiment. Following maize cultivation, we detected benzoxazinoid-dependent chemical and microbial fingerprints in the soil. The chemical fingerprint was still visible during wheat growth, while the microbial fingerprint was no longer detected. Benzoxazinoid soil conditioning by wild-type maize led to increased wheat emergence, tillering, growth and biomass compared to soil conditioning by bx1 mutant plants. Weed cover remained unaffected, while insect damage decreased in a subset of varieties. Wheat yield was increased by over 4% without a reduction in grain quality across varieties. This improvement was directly associated with increased germination and tillering. Taken together, our experiments demonstrate that plant secondary metabolites can increase yield via plant-soil feedbacks under agronomically realistic conditions. If this phenomenon holds across different soils and environmental conditions, optimizing plant root exudation could be a powerful, genetically tractable strategy to enhance crop yields without additional inputs.

plant biology↗

bioRxiv2021

Soil composition and plant genotype determine benzoxazinoid-mediated plant-soil feedbacks in cereals

Plant-soil feedbacks refer to effects on plants that are mediated by soil modifications caused by the previous plant generation. Maize conditions the surrounding soil by secretion of root exudates including benzoxazinoids (BXs), a class of bioactive secondary metabolites. Previous work found that a BX- conditioned soil microbiota enhances insect resistance while reducing biomass in the next generation of maize plants. Whether these BX-mediated and microbially driven feedbacks are conserved across different soils and response species is unknown. We found the BX-feedbacks on maize growth and insect resistance conserved between two arable soils, but absent in a more fertile grassland soil, suggesting a soil-type dependence of BX feedbacks. We demonstrated that wheat also responded to BX-feedbacks. While the negative growth response to BX-conditioning was conserved in both cereals, insect resistance showed opposite patterns, with an increase in maize and a decrease in wheat. Wheat pathogen resistance was not affected. Finally and consistent with maize, we found the BX-feedbacks to be cultivar specific. Taken together, BX- feedbacks affected cereal growth and resistance in a soil and genotype dependent manner. Cultivar-specificity of BX-feedbacks is a key finding, as it hides the potential to optimize crops that avoid negative plant-soil feedbacks in rotations.

plant biology↗

bioRxiv2020

Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field

BackgroundPlants influence their root and rhizosphere microbial communities through the secretion of root exudates. However, how specific classes of root exudate compounds impact the assembly of these root-associated microbiotas is not well understood. Maize roots secrete benzoxazinoids (BXs), a class of indole-derived defense compounds, and thereby impact the assembly of their microbiota. Here, we investigated the broader impacts of BX exudation on root and rhizosphere microbiotas of adult maize plants grown under natural conditions at different field locations in Europe and the US. We examined the microbiotas of BX-producing and multiple BX-defective lines in two genetic backgrounds across three soil types. ResultsOur analysis showed that the secretion of BXs affected community composition of rhizosphere and root microbiota, with the most pronounced effects observed for root fungi. The impact of the two genetic backgrounds was weaker than that of the presence or absence of BXs, suggesting that BX exudation is a key trait by which maize structures its associated microbiota. BX-producing plants were not consistently enriching microbial lineages across the three soil types. Instead, BX exudation consistently depleted Flavobacteriaceae and Comamonadaceae, and enriched various plant pathogenic fungi in the roots. ConclusionsThese findings reveal that BXs have a selective impact on root and rhizosphere microbiota composition across different field locations. Taken together, this study identifies the BX pathway as an interesting breeding target to manipulate plant-microbiome interactions.

plant biology↗

bioRxiv2019

Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework

The "One Health" framework emphasizes the ecological relationships between soil, plant, animal and human health. Microbiomes play important roles in these relationships, as they modify the health and performance of the different compartments and influence the transfer of energy, matter and chemicals between them. Standardized methods to characterize microbiomes along food chains are, however, currently lacking. To address this methodological gap, we evaluated the performance of DNA extractions kits and commonly recommended primer pairs targeting different hypervariable regions (V3-V4, V4, V5-V6, V5-V6-V7) of the 16S rRNA gene, on microbiome samples along a model food chain, including soils, maize roots, cattle rumen, and cattle and human faeces. We also included faeces from gnotobiotic mice colonized with defined bacterial taxa and mock communities to confirm the robustness of our molecular and bioinformatic approaches on these defined low microbial diversity samples. Based on Amplicon Sequence Variants, the primer pair 515F-806R led to the highest estimates of species richness and diversity in all sample types and offered maximum diversity coverage of reference databases in in silico primer analysis. The influence of the DNA extraction kits was negligible compared to the influence of the choice of primer pairs. Comparing microbiomes using 515F-806R revealed that soil and root samples have the highest estimates of species richness and inter-sample variation. Species richness decreased gradually along the food chain, with the lowest richness observed in human faeces. Primer pair choice directly influenced the estimation of community changes (beta diversity) within and across compartments and may give rise to preferential detection of specific taxa. This work demonstrates why a standardized approach is necessary to analyse microbiomes within and between source compartments along food chains in the context of the One Health framework.

microbiology↗

bioRxiv2018

SPECIES-SPECIFIC ROOT MICROBIOTA DYNAMICS IN RESPONSE TO PLANT-AVAILABLE PHOSPHORUS

O_LIPhosphorus (P) is a limiting element for plant growth. Several root microbes, including arbuscular mycorrhizal fungi (AMF), have the capacity to improve plant nutrition and their abundance is known to depend on P fertility. However, how complex root-associated bacterial and fungal communities respond to changes in P availability remains ill-defined.\nC_LIO_LIWe manipulated the availability of soil P in pots and compared the root microbiota of non-mycorrhizal Arabidopsis with mycorrhizal Petunia plants. Root bacteria and fungi were profiled using ribosomal operon gene fragment sequencing, we searched for P sensitive microbes and tested whether a P sensitive core microbiome could be identified.\nC_LIO_LIRoot microbiota composition varied substantially by P availability. A P sensitive core microbiome was not identified as different bacterial and fungal groups responded to low-P conditions in Arabidopsis and Petunia. P sensitive microbes included Mortierellomycotina in Arabidopsis, while these were AMF and their symbiotic endobacteria in Petunia. Of note, their P-dependent root colonization was reliably quantified by sequencing.\nC_LIO_LIThe species-specific root microbiota dynamics suggest that Arabidopsis and Petunia evolved different microbial associations under the selection pressure of low P availability. This implies that the development of microbial products that improve P availability requires the consideration of host-species specificity.\nC_LI

plant biology↗