Biology subjects

Maurhofer, M.

Publications and source records attributed to Maurhofer, M..

5 recordsLinked to original sources

bioRxiv2026

The insect- and plant-associated lifestyles of Pseudomonas protegens CHA0 are preserved following serial passage through insect larvae

The plant-beneficial bacterium Pseudomonas protegens CHA0 (CHA0) is widely studied for the biological control of soil-borne plant diseases. Beyond its root-colonising capabilities, CHA0 can also infect and kill insect larvae and thus exhibits a multi-host lifestyle shared with other plant- and insect-colonising bacteria. To better understand the robustness of this multi-host lifestyle, we subjected CHA0 to ten consecutive passages through larvae of the pest insect Plutella xylostella via repeated cycles of insect colonisation and killing forcing it into an insect-only lifestyle. Overall, serial passaging did not result in consistent changes in insect killing speed, larval or root colonisation, plant protection efficiency, microbial antagonism or in vitro growth. This suggests that its multi-host lifestyle was conserved following serial passage. Nonetheless, a few independently passaged lines showed an increase in larval killing speed, which in one case might be linked to choline uptake. To disentangle changes specific to the insect host from those arising due to the experimental system itself, we conducted parallel serial passages through the same system while omitting the insect host. In some of these lines, exposure to the background of the system led to changes in microbial antagonism and in in vitro growth, which likely are associated with mutations in regions encoding for regulatory systems. Our findings indicate that P. protegens CHA0 remains phenotypically stable in complex environments such as an insect host, suggesting that the multi-host lifestyle might also be conserved when applied in the field and supporting CHA0s potential for reliable biocontrol performance against both plant diseases and insect pests. Author summaryControlling insect pests with living organisms, known as biological control, offers an environmentally friendly alternative to chemical pesticides. The plant-beneficial bacterium Pseudomonas protegens CHA0 is a promising biocontrol candidate that not only colonizes plant roots but also infects and kills certain insect larvae. This ability to colonize different hosts appears to be a conserved trait also observed in other bacteria. To better understand the robustness of this multi-host lifestyle, we repeatedly exposed CHA0 to larvae of the insect pest Plutella xylostella and assessed the resulting physiological and genetic changes. Surprisingly, after ten cycles, CHA0 largely retained its insect-killing and plant-protective traits. Although a few populations showed minor changes, including slightly faster insect killing and traits associated with aspects of the experimental system, these changes were limited in scope. Overall, our findings suggest that P. protegens CHA0 does not change rapidly in complex environments such as an insect host, supporting its potential for reliable biocontrol performance in the field.

microbiology↗

bioRxiv2025

Microbial community analyses of composts are influenced by particle size fraction and DNA extraction method

Composting plays a key role in sustainable agriculture by converting organic waste into a valuable soil conditioner. The process is driven by complex microbial communities, whose characterization is essential for optimizing the composting process and compost quality. Molecular techniques such as amplicon sequencing are commonly used for this purpose. However, sampling procedures and DNA extraction methods, key steps in the sequencing workflow, vary often across studies, challenging comparability. We investigated two aspects of sampling preparation that may influence compost microbial analyses. For DNA extraction, often fine fractions (<2 mm) are used. However, compost has a heterogeneous structure, including coarse particles. To assess the effect of particle size, we separately sequenced bacterial and fungal communities of the fine (0-2 mm) and coarse (2-10 mm) fractions of three composts. In addition, DNA was extracted using a carboxyl affinity-based magnetic method and a silanol affinity-based filter method to evaluate the impact of the extraction technique. We found that the coarse fraction had higher bacterial richness and a distinct bacterial and fungal community structure compared to the fine fraction. DNA extraction method also influenced bacterial community profiles, with the magnetic bead method improving coverage, particularly for Bacillota. Although the effects of particle size and extraction method were small compared to general diversity among composts, we recommend including coarse particles in sequencing analyses and using standardized DNA extraction protocols, especially for studies aiming at high-resolution community analyses. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/682543v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1cd1b77org.highwire.dtl.DTLVardef@c64c9corg.highwire.dtl.DTLVardef@cfb5f6org.highwire.dtl.DTLVardef@b350df_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

High-resolution microbial network analysis defines biocontrol consortia in the wheat phyllosphere

Plant-associated microbiomes comprise diverse microbial species that coexist and interact, influencing community structure and host plant health. However, our understanding of these interactions in field conditions and at strain-resolution remains limited. This hinders the development of effective biocontrol applications, as laboratory findings often fail to translate to field settings due to insufficient insights into in situ interaction network structures. This study addresses this limitation by employing taxon-specific high-resolution amplicons to resolve a cross-kingdom co-occurrence network within the wheat phyllosphere microbiome. We performed in-depth monitoring of strains from the hub genus Pseudomonas, revealing a high degree of strain-specificity of Pseudomonas interactions both within and across kingdoms. Through negative interaction modelling, we identified a consortium of ten biocontrol taxa with the potential to suppress seven fungal pathogens in field conditions. Additional stabilizer strains were found to likely enhance persistence. We validated the strain-specific interactions of Pseudomonas with the major fungal pathogen Zymoseptoria tritici using co-inoculation experiments with genotypes retrieved from the same field. Consistent with our prediction, we identified a P. poae isolate as the most antagonistic towards the pathogen both in vitro and in planta. Our study demonstrates that taxon-specific high-resolution network inference can effectively map microbial interaction networks and predict strain-specific interaction patterns of biocontrol genotypes with high persistence under field conditions. Our novel approach supports the design of more effective and sustainable biocontrol strategies.

microbiology↗

bioRxiv2025

Comprehensive analysis of 37 composts: microbial indicators for soilborne disease suppression in three plant-pathogen systems

Compost is a valuable amendment for soil and potting substrate when it comes to sup-pressing soilborne pathogens. However, the effectiveness of different composts varies and can not yet be predicted. Microbial communities in compost play a key role in disease suppression, and therefore their composition or specific taxa may serve as indicators of suppressive composts. In this study, we investigated 37 composts from seven commercial compost producers to analyze the association of their bacterial and fungal communi-ties with suppressive activity in three plant-pathogen systems: cress-Globisporangium ultimum, cucumber-Globisporangium ultimum and cucumber-Rhizoctonia solani. Our results underscore that compost suppressiveness is primarily pathogen-specific and, to a lesser extent, host-plant-specific. Suppressiveness was not correlated with physico-chemical properties, microbial activity, or the alpha-and beta-diversity of composts bac-terial and fungal communities. Instead, microbial composition was largely shaped by producer-specific composting conditions and maturation processes, which were not nec-essarily linked to suppressive activity. A more nuanced comparison between the most and least suppressive composts revealed bacterial and few fungal taxa as potential indicators of suppressiveness for each plant-pathogen system. Notably, for G. ultimum-suppression, bacteria from the genera Luteimonas, Sphingopyxis, and Algoriphagus and for R. solani bacteria belonging to the phylum Actinomycetota emerged as promising candidates. ImportanceSoilborne diseases are a major yield-limiting factor in agricultural crop production world-wide, particularly in seedling cultivation. Their control remains a significant challenge and still largely relies on chemical fumigation of soils and steam sterilization of pot-ting substrates. While chemical fumigants are increasingly criticized for their negative environmental impact, sterilization practices in general disrupt beneficial microbial com-munities, making substrates more susceptible to pathogen (re)-infestation. Amending soil or potting substrate with disease-suppressive compost offers a promising alternative. However, the targeted use of compost for plant protection is hindered by variable effec-tiveness and the lack of reliable tools to identify effective composts. This study provides a comprehensive abiotic and biotic characterization of compost, enabling a detailed anal-ysis of the properties associated with suppressiveness. The identification of bacterial and fungal taxa indicative of disease-suppressive composts lays the groundwork for targeted isolation of microorganisms and functional studies, with the ultimate aim of predicting and optimizing compost-mediated disease suppression.

molecular biology↗

bioRxiv2023

High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific amplicons and long-read sequence

High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Here, we developed and validated a pipeline for designing, multiplexing, and sequencing highly polymorphic taxon-specific long-read amplicons. We focused on the wheat microbiome as a proof-of-principle and demonstrate unprecedented resolution for the wheat-associated Pseudomonas microbiome and the ubiquitous fungal pathogen Zymoseptoria tritici. We achieved an order of magnitude higher phylogenetic resolution compared to existing ribosomal amplicons. The designed amplicons accurately capture species and strain diversity outperforming full-length 16S and ITS amplicons. Furthermore, we tracked microbial communities in the wheat phyllosphere across time and space to establish fine-grained species and strain-specific dynamics. To expand the utility of our approach, we generated pangenome-informed amplicon templates for additional key bacterial and fungal genera. Pangenome-informed microbiome profiling enables the tracking of microbial community dynamics in complex environments and overcomes limitations in phylogenetic resolution.

microbiology↗