Biology subjects

Gindro, K.

Publications and source records attributed to Gindro, K..

8 recordsLinked to original sources

bioRxiv2026

Long-Term Dynamics of Esca Disease in Western Switzerland

Agroscope conducted a long-term survey to assess the incidence of esca disease in Western Switzerland between 2001 and 2022 and to characterize its temporal dynamics. This study has four main objectives: (1) to provide a rare and particularly valuable long-term dataset documenting the incidence of esca over more than two decades; (2) to identify potentially important climatic drivers using a recent model-independent variable importance algorithm that quantifies the strength of their association with esca incidence; (3) to develop predictive models of esca incidence using climatic covariates derived from microclimatic weather data; and (4) to investigate the relationship between water balance and regionally aggregated esca incidence. The climatic variables identified by the variable importance algorithm as being most strongly associated with esca incidence at the plot level were primarily related to water balance. The predictive analysis showed that model performance at the plot level was limited. Consistent with previous studies, analysis of the variables contributing to model predictions did not allow us to identify a single factor, or set of factors, that could reliably predict esca incidence. At the regional scale, however, water balance and seasonal vapor pressure deficit (VPD) were strongly associated with esca incidence across years, with drier regions generally showing lower disease incidence. Finally, addressing the initial question that motivated this long-term survey, we observed a slight decreasing trend in esca incidence over the study period. This trend coincided with increasingly dry conditions in Western Switzerland and may therefore be partly associated with changes in regional water balance in the context of climate change. All the datasets and analyses presented here are made available and reproducible.

plant biology↗

bioRxiv2025

Phyllosphere microbiome-based biocontrol solution against the filamentous pathogens Botrytis cinerea and Plasmopara viticola in grapevine

Plants harbor different microbial communities in their different organs. This difference is due to the various conditions to which the different parts of the plant are subjected. Consequently, the phyllosphere microbiota can differ strongly from root-associated communities. We hypothesize that the grapevine phyllosphere is a valuable source of biocontrol bacteria, whose adaptation to the aerial plant environment may enable them to reach their full protective potential against foliar pathogens. In previous work, we isolated phyllosphere bacteria and showed that many strains were very effective against such pathogens in vitro, inhibiting their mycelial and spore development. This work investigates the biocontrol ability of these phyllosphere bacteria in leaf disc assays against two foliar pathogens: Botrytis cinerea (gray mold) and Plasmopara viticola (downy mildew). Our results show that 40 strains out of 46 affected at least one pathogen by altering their spore physiology and/or reducing disease progression. Among these strains, 27 strains could impact both pathogens and 20 were also capable of stimulating plant defenses. Because bacterial consortia might perform better than single strains, we also compared the protection conferred by individual bacteria and associations of up to three strains. When combined, bacteria showed improved efficacy in vitro against B. cinerea and in planta against P. viticola, resulting in a much stronger protection than that obtained by the application of the strains alone. These data suggest that phyllosphere bacteria could be a promising tool to help winegrowers manage grapevine diseases by providing an effective and sustainable protection of their crops.

plant biology↗

bioRxiv2024

Revisiting sour rot of grapevine through disease-associated microbiomes: a tripartite co-infection?

Sour rot in grapevines is thought to result from berry infection by yeasts, acetic acid bacteria and vinegar flies. To better characterize the role of each of the actors involved in sour rot expression, we conducted experiments involving the isolation of 1593 fungi and bacteria to understand the composition and dynamics of the microbiomes associated with healthy berries, diseased berries and insect vectors. As some grape clusters became symptomatic for sour rot in the absence of acetic acid bacteria, the latter might not necessarily be needed for disease expression. Similar to other yeast genera, the yeast genus Geotrichum is here also reported for the first time to be able to initiate sour rot in grapes, however, this finding has to be confirmed by further studies. By allowing or denying the access of insect vectors to intact or artificially wounded grapes we could emphasize that they accelerate the expression of the disease when berries are injured. Moreover, the microbial communities identified on native vinegar flies (Drosophila spp.) and the introduced Drosophila suzukii were similar and yeast dominated. This highlights the key role of these insect vectors in the transmission of microorganisms inflicting sour rot to wounded berries. Finally, our data also suggest that sour rot and grey mould can coexist in a vineyard at an advanced stage of grape decomposition, which runs counter to recent studies that emphasize the supremacy of sour rot over grey mould. IMPORTANCEThis study sheds new light on the complex interactions between microbiomes, insect vectors and physical factors favoring the development of sour rot. While previous studies suggested that acetic acid bacteria were mandatory for sour rot expression our results suggest that grape sour rot could also result solely from yeast infection. Moreover, native vinegar flies and the introduced D. suzukii host and vectorize a similar microbial community to injured berries in vineyards and their presence accelerates the infection process and consequently the expression of sour rot.

pathology↗

bioRxiv2024

Discovery of anti-infective compounds against Mycobacterium marinum after biotransformation of simple natural stilbene scaffolds by a fungal secretome

This study evaluated the efficacy of a high-throughput Dictyostelium discoideum - Mycobacterium marinum Dd-Mm infection system by first benchmarking it against a set of antibiotics and second in screening a library of natural product (NP) derivatives for anti-infective activity against intracellular Mycobacterium marinum (Mm). The study observed no activity of pyrazinamide against Mm, consistent with known resistance patterns, and confirmed other antibiotics, such as rifampicin and bedaquiline, with activity below defined antibacterial susceptibility breakpoints. From screening a small library of NP derivatives, trans-{delta}-viniferins emerged as promising anti-infective scaffolds, particularly two compounds which exhibited an anti-infective activity on Mm during infection but not on Mm in broth, 17 with an IC50 of 18.1 {micro}M, and 19 with an IC50 of 9 {micro}M). Subsequent exploration via halogenation and structure-activity relationship (SAR) studies led to the identification of derivatives with improved selectivity and potency. The observed anti-infective phenotype may involve mechanisms such as blocking mycobacterial virulence factors or boosting host defense. Furthermore, the study highlights the potential of natural product-inspired derivatization approaches for drug discovery and underscores the utility of the Dd-Mm infection system in identifying novel anti-infective compounds. IMPORTANCEThis study underscores the significance of leveraging natural product-inspired approaches and innovative infection models in search for novel anti-infective compounds. By benchmarking and employing high-throughput Dictyostelium discoideum-Mycobacterium marinum infection system on a small, focused library of natural product derivatives, the study identified trans-{delta}-viniferins as promising anti-infective scaffolds against Mycobacterium marinum, opening potential therapeutic avenues for combating tuberculosis. The findings highlight the value of exploring nature-inspired chemistry for drug discovery and addressing global health challenges.

microbiology↗

bioRxiv2024

Landscape-scale endophytic community analyses in replicated grapevine stands reveal that dieback disease is not caused by specific fungal communities

Tree diebacks are complex and multi-factorial diseases with suspected biotic and abiotic components. Microbiome effects on plant health are challenging to assess due to the complexity of fungal and bacterial communities. Grapevine wood dieback is the main threat to sustainable production worldwide and no causality with microbial species has been established. Here, we aimed to test the hypothesis that grapevine esca disease progression has reproducible drivers in the fungal species community. For this, we analyzed a set of 21 vineyards planted simultaneously with a single susceptible cultivar to provide replication at the landscape scale. We sampled a total of 496 plants across vineyards in two different years to perform deep amplicon sequencing analyses of the fungal communities inhabiting grapevine trunks. The communities were highly diverse with a total of 4,129 amplified sequence variants assigned to 697 distinct species. Individual plants varied in fungal community composition depending on the year of sampling, vineyard location, and disease status. However, we detect no specific fungal species driving symptom development across the vineyards contrary to long-standing expectations. Our study shows how landscape-scale replicated field surveys allow for powerful hypothesis-testing for complex dieback disease drivers and prioritize future research towards additional factors.

microbiology↗

bioRxiv2023

New viruses of Cladosporium sp. expand considerably the taxonomic structure of Gammapartitivirus genus

Despite the fact that Cladosporium sp. are ubiquitous fungi, their viromes have been little studied. By analysing a collection of Cladosporium fungi, two new partitiviruses named Cladosporium cladosporioides partitivirus 1 (CcPV1) and Cladosporium cladosporioides partitivirus 2 (CcPV2) co-infecting a strain of Cladosporium cladosporioides were identified. Their complete genome consists in two monocistronic dsRNA segments (RNA1 and RNA2) with a high percentage of pairwise identity on 5 and 3 end. The RNA dependant RNA polymerase (RdRp) of both viruses and the capsid protein (CP) of CcPV1 display the classic characteristics required for their assignment to the Gammapartitivirus genus. In contrast, CcPV2 RNA2 encodes for a 41 KDa CP that is unusually small with a low percentage of amino acid identity as compared to CPs of other viruses classified in this genus. This sequence was used to annotate fifteen similar viral sequences with unconfirmed function. The phylogeny of the CP was highly consistent with the phylogeny of their corresponding RdRp, supporting the organization of gammapartitiviruses into three distinct clades despite stretching the current demarcation criteria.

microbiology↗

bioRxiv2023

A systemic approach allows to identify the pedoclimatic conditions most critical in the susceptibility of a grapevine cultivar to esca/Botryosphaeria dieback

Esca and/or Botryosphaeria dieback (esca-BD) are two of the most destructive grapevine trunk diseases in the world, disease complex which remains poorly understood. As some vine cultivars show highly variable susceptibility to esca-BD, we designed a four-year experiment to identify which environmental factors influence the expression of the disease. We collected epidemiological and physiological data once a year for four consecutive years in 19 vineyard plots located in four wine-growing regions of Western Switzerland. We compared these data with climatic data obtained from weather stations for these same plots for four years and over the long term. We also estimated the soil water holding capacity of each plot. Confounding factors were minimal because all vineyards were planted in 2003 with the same cultivar and all plants grafted in the same nursery with genetically homogeneous grafting material. Principal component and regression analyses of combined epidemiological, biotic and pedoclimatic data identified a positive correlation between soil water retention capacity and plant mortality due to esca-BD. These analyses also showed that leaf disease symptoms and apoplexy are more frequent when cold, wet periods are followed - or alternate with - hot, dry periods, and that apoplexy occurs more frequently when weather conditions change abruptly (cold, wet May followed by a hot June) and deviate significantly from long-term climatic conditions. Regression analyses show that the soil water holding capacity impacts less the disease expression when the climate is warm and dry, both at the regional and at year-specific levels. Having identified the most important environmental factors towards expression of esca-BD, this study allows recommendations to be given to the winegrowers for the cultivar studied but can also be used as a model to identify the environmental factors that influence the expression of fungal diseases in other grapevine cultivars, other grapevine trunk diseases and even in other woody plants.

plant biology↗

bioRxiv2022

Quantifying trade-offs in the choice of ribosomal barcoding markers for fungal amplicon sequencing: a case study on the grapevine trunk mycobiome

The evolution of sequencing technology and multiplexing has rapidly expanded our ability to characterize fungal diversity in the environment. However, obtaining an unbiased assessment of the fungal community using ribosomal markers remains challenging. Longer amplicons were shown to improve taxonomic resolution and resolve ambiguities by reducing the risk of spurious operational taxonomic units. We examined the implications of barcoding strategies by amplifying and sequencing two ribosomal DNA fragments. We analyzed the performance of the full internal transcribed spacer (ITS) and a longer fragment including also a part of the 28S replicated on 60 grapevine trunk core samples. Grapevine trunks harbor highly diverse fungal communities with implications for disease development. Using identical handling, amplification and sequencing procedures, we obtained higher sequencing depths for the shorter ITS amplicon. Despite the more limited access to polymorphism, the overall diversity in amplified sequence variants was higher for the shorter ITS amplicon. We detected no meaningful bias in the phylogenetic composition due to the amplicon choice across analyzed samples. Despite the increased resolution of the longer ITS-28S amplicon, the higher and more consistent yields of the shorter amplicons produced a clearer resolution of the fungal community of grapevine stem samples. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals.

microbiology↗