Biology subjects

Flury, P.

Publications and source records attributed to Flury, P..

3 recordsLinked to original sources

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

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

Zymoseptoria tritici suppresses the host immune response and facilitates the success of avirulent strains in mixed infections

Plants interact with a plethora of pathogenic microorganisms in nature. Pathogen-plant interaction experiments focus mainly on single-strain infections, typically ignoring the complexity of multi-strain infections even though mixed infections are common and critical for the infection outcome. The wheat pathogen Zymoseptoria tritici forms highly diverse fungal populations in which several pathogen strains often colonize the same leaf. Despite the importance of mixed infections, the mechanisms governing interactions between a mixture of pathogen strains within a plant host remain largely unexplored. Here we demonstrate that avirulent pathogen strains benefit from being in mixed infections with virulent strains. We show that virulent strains suppress the wheat immune response, allowing the avirulent strain to colonize the apoplast and to reproduce. Our experiments indicate that virulent strains in mixed infections can challenge the plant immune system both locally and systemically, providing a mechanistic explanation for the persistence of avirulent pathogen strains in fields planted to resistant host plants.

plant biology↗