Thomas Oberhänsli

Compost is a valuable amendment for soil and potting substrate when it comes to suppressing soilborne pathogens. However, the effectiveness of different composts varies and cannot 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 7 commercial compost producers to analyze the association of their bacterial and fungal communities with suppressive activity in three plant-pathogen systems: cress- Globisporangium ultimum , cucumber- G . 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 physicochemical properties, microbial activity, or the alpha- and beta-diversity of composts’ bacterial and fungal communities. Instead, microbial composition was largely shaped by producer-specific composting conditions and maturation processes, which were not necessarily linked to suppressive activity. A more nuanced comparison between the most and least suppressive composts revealed bacterial and a 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. IMPORTANCE: Soilborne diseases are a major yield-limiting factor in agricultural crop production worldwide, particularly in seedling cultivation. Their control remains a significant challenge and still largely relies on chemical fumigation of soils and steam sterilization of potting substrates. While chemical fumigants are increasingly criticized for their negative environmental impact, sterilization practices, in general, disrupt beneficial microbial communities, 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 effectiveness and the lack of reliable tools to identify effective composts. This study provides a comprehensive abiotic and biotic characterization of compost, enabling a detailed analysis 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.

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

We investigated microRNAs (miRNAs) as potential prognostic biomarkers for equine sarcoid (ES) disease. In a breed-, age-, and sex-matched case-controlled study involving 45 ES-affected and 15 control horses, we assessed the diagnostic, prognostic, and theragnostic value of 3 miRNAs (eca-miR-127, eca-miR-379, eca-miR-432) in horses treated with European mistletoe ( Viscum album ) extract versus placebo. Whole-blood miRNA concentrations were measured using reverse-transcription quantitative real-time PCR (RT-qPCR) at 3 different times. We found that eca-miR-432 expression was lower in ES-affected (median = −1.93; 95% CI: −2.03 to −.86) compared to control (median = −1.71; 95% CI: −1.92 to −1.6) horses ( p = 0.03, r = 0.3; 95% CI: 0.024–0.57) with a median difference of −1.93 versus −1.71, respectively. The ROC curve analysis indicated an area under the curve of 0.71 (95% CI: 0.51–0.84; p = 0.005) with a sensitivity of 74% (95% CI: 61–88%) and a specificity of 73% (95% CI: 39–94%) to diagnose ES. However, none of the miRNAs evaluated had prognostic potential or significant changes in expression following treatment. Additionally, miRNA expression was not influenced by breed, sex, or season. Although whole-blood eca-miR-432 had moderate diagnostic potential for ES, identifying prognostic miRNA biomarkers for ES remains a challenge.

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. Importance: Soilborne 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.

Apple blotch (AB) is a major disease of apple in Asia and recently emerged in Europe and the United States. It is caused by the fungus Diplocarpon coronariae (formerly Marssonina coronaria; teleomorph: Diplocarpon mali) and leads to severe defoliation of apple trees in late summer, resulting in reduced yield and fruit quality. To develop effective disease management strategies, a sound knowledge of the pathogen's biology is crucial. Data on the early phase of disease development are scarce: No data on spore dispersal in Europe are available. We developed a highly sensitive TaqMan qPCR method to quantify D. coronariae conidia in spore trap samples. We monitored temporal and spatial dispersal of conidia of D. coronariae and the progress of AB in spring and early summer in an extensively managed apple orchard in Switzerland in 2019 and 2020. Our results show that D. coronariae overwinters in leaf litter, and spore dispersal and primary infections occur in late April and early May. We provide the first results describing early-season dispersal of conidia of D. coronariae, which, combined with the observed disease progress, helps to understand the disease dynamics and will be a basis for improved disease forecast models. Using the new qPCR method, we detected D. coronariae in buds, on bark, and on fruit mummies, suggesting that several apple tissues might serve as overwintering habitats for the fungus, in addition to fallen leaves. [ ] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Didymella pinodella is the major pathogen of the pea root rot complex in Europe. This wide host range pathogen often asymptomatically colonizes its hosts, making the control strategies challenging. We developed a real-time PCR assay for the detection and quantification of D. pinodella based on the TEF-1 alpha gene sequence alignments. The assay was tested for specificity on a 54-isolate panel representing 35 fungal species and further validated in symptomatic and asymptomatic pea and wheat roots from greenhouse tests. The assay was highly consistent across separate qPCR reactions and had a quantification/detection limit of 3.1 pg of target DNA per reaction in plant tissue. Cross-reactions were observed with DNA extracts of five Didymella species. The risk of cross contamination, however, is low as the non-targets have not been associated with pea previously and they were amplified with at least 1000-fold lower sensitivity. Greenhouse inoculation tests revealed a high correlation between the pathogen DNA quantities in pea roots and pea root rot severity and biomass reduction. The assay also detected D. pinodella in asymptomatic wheat roots, which, despite the absence of visible root rot symptoms, caused wheat biomass reduction. This study provides new insights into the complex life style of D. pinodella and can assist in better understanding the pathogen survival and spread in the environment.

White lupin (Lupinus albus) represents an important legume crop in Europe and other parts of the world due to its high protein content and potential for low-input agriculture. However, most cultivars are susceptible to anthracnose caused by Colletotrichum lupini, a seed- and air-borne fungal pathogen that causes severe yield losses. The aim of this work was to develop a C. lupini-specific quantitative real-time TaqMan PCR assay that allows for quick and reliable detection and quantification of the pathogen in infected seed and plant material. Quantification of C. lupini DNA in dry seeds allowed us to distinguish infected and certified (non-infected) seed batches with DNA loads corresponding to the disease score index and yield of the mother plants. Additionally, C. lupini DNA could be detected in infected lupin shoots and close to the infection site, thereby allowing us to study the disease cycle of this hemibiotrophic pathogen. This qPCR assay provides a useful diagnostic tool to determine anthracnose infection levels of white lupin seeds and will facilitate the use of seed health assessments as a strategy to reduce the primary infection source and spread of this disease.

Background: Apple blotch (AB) caused by Diplocarpon coronariae (Dc) has been established in Europe since 2010. AB is a serious apple disease, mostly in low input orchards and in cider production areas in Northern Italy, Switzerland, Austria and Germany. However, the epidemiology and population genetic structure of this pathogen is unknown. Methods: We developed twelve Dc-specific microsatellite markers and screened DNA of both pure fungal isolates and infected apple leaves. The marker data of 313 European samples of Dc were compared to Dc isolates from Asia (n = 7) and the USA (n = 3). Results: We found 31 distinct multilocus genotypes (MLGs) in European samples, and seven additional MLGs in the Asian and USA samples. The European samples had the typical genetic signature of a recently introduced species including high clonality, a low number of private alleles and one dominant MLG across all the sampling sites. All European MLGs were genetically distant from those MLGs of Asian and USA origin. Based on the lack of linkage disequilibrium observed, there is evidence that Dc undergoes regular cycles of sexual recombination in the European population, although the sexual stage (apothecia) has not been observed in Europe. Conclusions: The twelve newly developed SSR markers reported here provide a useful tool to characterize the population genetic diversity and structure of Dc in Europe. Our study supports the hypothesis that Dc is a recently introduced pathogen in Europe, but of currently unknown origin. Dc has a large effective population size during field epidemics, so we believe that the pathogen has substantial evolutionary potential. Application of the SSR markers to large-scale and diverse Dc samples will help to better understand the epidemiology of AB, which has become a global apple disease, and will help guide effective mitigation strategies based on disease management and resistance breeding.