Biology subjects

Floerl, L.

Publications and source records attributed to Floerl, L..

4 recordsLinked to original sources

bioRxiv2025

Interaction of Environment and Vineyard Management Effects Shape Microbial Functionality, Terroir, and Grape Qualities

Vineyards are complex agroecological systems, with geographically distinct microbial communities playing a central role in mediating vine health, grape quality, and ultimately local wine characteristics (terroir). However, the extent to which environmental factors and vineyard management practices interact to shape these microbial communities and their functions remains poorly understood. We implemented a multidisciplinary citizen science collaboration together with winegrowers to sample 19 Pinot Noir vineyards across two distinct Swiss regions (N=38 samples). This allowed us to evaluate how a combination of environmental conditions and management practices (such as cover cropping and fungicide use) collectively impact soil and grape microbiomes, soil enzymatic activities, nutrient concentration in leaves, and grape chemistry. Regional differences were the primary drivers of variation, but multivariate analysis revealed a distinct, secondary influence from management practices on soil and berries. Berry quality was linked to functional soil properties, including microbial activity, which were further associated with key fermentative yeasts likely involved in wine fermentation. These findings highlight the interconnected nature of environmental, microbial, and agronomic factors in grapevine systems and offer novel insights into functional aspects of microbial terroir.

microbiology↗

bioRxiv2025

Grape Expectations: Disentangling Environmental Drivers of Microbiome Establishment in Winegrowing Ecosystems

Microbial communities play an integral role in agricultural systems, where their composition and function are shaped by environmental factors and interactions with the plant host. In viticulture and winemaking, the resulting distinct microbial biogeographic patterns influence wine characteristics - a well-established concept termed microbial terroir. Yet, due to the complexity of interactions, the specific environmental drivers shaping these microbiomes remain poorly understood. We conducted a multi-year, large-scale survey (N = 680 samples) of Swiss vineyards (N = 95 sites), following a subset (N = 12, within 2.46 km) longitudinally over 3 years. We integrate microbiome (bacterial and fungal marker-gene sequencing), untargeted metabolomics (GC-MS and LC-MS/MS), environmental monitoring, and sensory data to disentangle abiotic factors influencing community assembly and interactions in vineyards and in wine fermentations. Results show that topography and climate collectively structure microbial communities, yet exhibit distinct influences on soil- and plant-associated microbiomes. Berry-associated fungal communities exhibit the strongest site-specific imprint, enabling machine-learning-based prediction of even subtle microclimatic differences. Climatic factors and berry chemistry exhibit an inverse relationship, selectively favoring either Hanseniaspora sp. or Saccharomyces cerevisiae - each correlating with distinct metabolite and aroma profiles. Additionally, plant stress-response metabolites were associated with shifts in microbial composition and fermentation outcomes. By integrating multi-omics and machine learning approaches, this study enhances our understanding of microbial biogeography and its role in winegrowing. Our findings highlight the need for further research on microbial transmission, vineyard management, and implications for wine quality, offering a foundation for a more precise, science-driven approach to terroir expression. Graphical AbstractWe sampled a total of 95 vineyards, with longitudinal sampling of 12 over three years, controlling for cultivar while capturing variations in topography, soil properties, and microclimate. Data collected in vineyards further included berry chemistry, vineyard management, and phenology. We sequenced microbial communities in both vineyard and fermentation samples, and the wines were additionally analysed with three different untargeted metabolomics approaches. Supervised and unsupervised modeling revealed spatio-temporal variability, the influence of environmental factors on microbial communities, and their impact on wine characteristics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/652874v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1ccb855org.highwire.dtl.DTLVardef@15a13f2org.highwire.dtl.DTLVardef@d39455org.highwire.dtl.DTLVardef@af8c29_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

The Genetic Basis of Microbiome Recruitment in Grapevine and its Association with Fermentative and Pathogenic Taxa

O_LIWhile grapevine is an exceptional perennial model for studying host-microbiome interactions, the host genomes role in microbiome assembly is often masked by environmental factors. This research provides a first insight into the genetic mechanisms shaping berry-associated microbial communities. C_LIO_LIUsing QTL mapping in a newly established population of 140 F1-progeny grapevine genotypes in a complete random block design, we were able to control abiotic effects and investigate how the host genome influences grape berry-associated bacterial and fungal communities. C_LIO_LIWe identify significant associations between various microorganisms and the grape genome, including pathogenic fungi such as Botrytis spp. and fermentative yeasts such as Saccharomyces cerevisiae. Many of these taxa map to the same genetic loci associated with plant immune responses, suggesting that specific genetic loci broadly influence microbial community assembly in fruits. C_LIO_LIOur findings demonstrate that grapevine genetics significantly shape the microbiome, even under varying environmental conditions; moreover, that broad, rather than known symbiont-specific mechanisms control microbial colonization of fruit, revealing an emergent "domino" effect with implications for plant-fungal-bacterial interactions. We provide a framework for understanding genotype-microbiome interactions in perennial plants, enabling future targeted experiments to establish causal relationships in microbiome recruitment and offer a potential avenue for breeding programs advancing sustainable viticulture. C_LI

microbiology↗

bioRxiv2020

Development of genetic tools for the thermophilic filamentous fungus Thermoascus aurantiacus

BackgroundFungal enzymes are vital for industrial biotechnology, including the conversion of plant biomass to biofuels and bio-based chemicals. In recent years, there is increasing interest in using enzymes from thermophilic fungi, which often have higher reaction rates and thermal tolerance compared to currently used fungal enzymes. The thermophilic filamentous fungus Thermoascus aurantiacus produces large amounts of highly thermostable plant cell wall degrading enzymes. However, no genetic tools have yet been developed for this fungus, which prevents strain engineering efforts. The goal of this study was to develop strain engineering tools such as a transformation system, a CRISPR/Cas9 gene editing system and a sexual crossing protocol to improve enzyme production. ResultsHere we report Agrobacterium tumefaciens-mediated transformation (ATMT) of T. aurantiacus using the hph marker gene, conferring resistance to hygromycin B. The newly developed transformation protocol was optimized and used to integrate an expression cassette of the transcriptional xylanase regulator xlnR, which led to up to 500% increased xylanase activity. Furthermore, a CRISPR/Cas9 gene editing system was established in this fungus, and two different gRNAs were tested to delete the pyrG orthologue with 10% and 35% deletion efficiency, respectively. Lastly, a sexual crossing protocol was established using a hygromycin B- and a 5-fluororotic acid-resistant parent strain. Crossing and isolation of progeny on selective media was completed in a week. ConclusionThe genetic tools developed for T. aurantiacus can now be used individually or in combination to further improve thermostable enzyme production by this fungus.

microbiology↗