Yvonne Boesch

All Publications

• Little impact of tillage system on crop yield and soil properties in a 43-years old field experiment on a clay soil in humid continental climate SOIL & TILLAGE RESEARCH Keller, T., Etana, A., Bosch, Y., Hellstedt, E., Larsbo, M., Colombi, T., Hosseinpour-Ashenaabad, R., Sjulgard, H., Arrazola-Vasquez, E., Viketoft, M., Taylor, A., Myrbeck, A., Hallin, S. 2027; 265

  View details for DOI 10.1016/j.still.2026.107403

  View details for Web of Science ID 001838260000001

• Ecology of Rozellomycota in aquatic environments with differing redox conditions FUNGAL BIOLOGY Stuer-Patowsky, K., Galindo, L., Bosch, Y., Wurzbacher, C. 2025; 129 (8)

  View details for DOI 10.1016/j.funbio.2025.101670

  View details for Web of Science ID 001604635000001

• Distribution and Environmental Drivers of Fungal Denitrifiers in Global Soils MICROBIOLOGY SPECTRUM Bosch, Y., Pold, G., Saghai, A., Karlsson, M., Jones, C. M., Hallin, S. 2023; 11 (3): e0006123

  Abstract

  The microbial process of denitrification is the primary source of the greenhouse gas nitrous oxide (N2O) from terrestrial ecosystems. Fungal denitrifiers, unlike many bacteria, lack the N2O reductase, and thereby are sources of N2O. Still, their diversity, global distribution, and environmental determinants, as well as their relative importance, compared to bacterial and archaeal denitrifiers, remain unresolved. Employing a phylogenetically informed approach to analyze 1,980 global soil and rhizosphere metagenomes for the denitrification marker gene nirK, which codes for the copper dependent nitrite reductase in denitrification, we show that fungal denitrifiers are sparse, yet cosmopolitan and that they are dominated by saprotrophs and pathogens. Few showed biome-specific distribution patterns, although members of the Fusarium oxysporum species complex, which are known to produce substantial amounts of N2O, were proportionally more abundant and diverse in the rhizosphere than in other biomes. Fungal denitrifiers were most frequently detected in croplands, but they were most abundant in forest soils when normalized to metagenome size. Nevertheless, the overwhelming dominance of bacterial and archaeal denitrifiers suggests a much lower fungal contribution to N2O emissions than was previously estimated. In relative terms, they could play a role in soils that are characterized by a high carbon to nitrogen ratio and a low pH, especially in the tundra as well as in boreal and temperate coniferous forests. Because global warming predicts the proliferation of fungal pathogens, the prevalence of potential plant pathogens among fungal denitrifiers and the cosmopolitan distribution of these organisms suggest that fungal denitrifier abundance may increase in terrestrial ecosystems. IMPORTANCE Fungal denitrifiers, in contrast to their bacterial counterparts, are a poorly studied functional group within the nitrogen cycle, even though they produce the greenhouse gas N2O. To curb soil N2O emissions, a better understanding of their ecology and distribution in soils from different ecosystems is needed. Here, we probed a massive amount of DNA sequences and corresponding soil data from a large number of samples that represented the major soil environments for a broad understanding of fungal denitrifier diversity at the global scale. We show that fungal denitrifiers are predominantly cosmopolitan saprotrophs and opportunistic pathogens. Fungal denitrifiers constituted, on average, 1% of the total denitrifier community. This suggests that earlier estimations of fungal denitrifier abundance, and, thereby, it is also likely that the contributions of fungal denitrifiers to N2O emissions have been overestimated. Nevertheless, with many fungal denitrifiers being plant pathogens, they could become increasingly relevant, as soilborne pathogenic fungi are predicted to increase with ongoing climate change.

  View details for DOI 10.1128/spectrum.00061-23

  View details for Web of Science ID 000993950400001

  View details for PubMedID 37222601

  View details for PubMedCentralID PMC10269876

• Minimizing tillage modifies fungal denitrifier communities, increases denitrification rates and enhances the genetic potential for fungal, relative to bacterial, denitrification SOIL BIOLOGY & BIOCHEMISTRY Bosch, Y., Jones, C. M., Finlay, R., Karlsson, M., Larsbo, M., Keller, T., Hallin, S. 2022; 170

  View details for DOI 10.1016/j.soilbio.2022.108718

  View details for Web of Science ID 000848016600008

• Dynamics of the Apple Fruit Microbiome after Harvest and Implications for Fruit Quality MICROORGANISMS Bosch, Y., Britt, E., Perren, S., Naef, A., Frey, J. E., Buhlmann, A. 2021; 9 (2)

  Abstract

  The contribution of the apple microbiome to the production chain of apple was so far largely unknown. Here, we describe the apple fruit microbiome and influences on its composition by parameters such as storage season, storage duration, storage technology, apple variety, and plant protection schemes. A combined culturing and metabarcoding approach revealed significant differences in the abundance, composition, and diversity of the apple fruit microbiome. We showed that relatively few genera contribute a large portion of the microbiome on fruit and that the fruit microbiome changes during the storage season depending on the storage conditions. In addition, we show that the plant protection regime has an influence on the diversity of the fruit microbiome and on the dynamics of pathogenic fungal genera during the storage season. For the genus Neofabraea, the quantitative results from the metabarcoding approach were validated with real-time PCR. In conclusion, we identified key parameters determining the composition and temporal changes of the apple fruit microbiome, and the main abiotic driving factors of microbiome diversity on apple fruit were characterized.

  View details for DOI 10.3390/microorganisms9020272

  View details for Web of Science ID 000622815900001

  View details for PubMedID 33525588

  View details for PubMedCentralID PMC7912366

• Quantitative Selection Analysis of Bacteriophage φCbK Susceptibility in <i>Caulobacter crescentus</i> JOURNAL OF MOLECULAR BIOLOGY Christen, M., Beusch, C., Boesch, Y., Cerletti, D., Flores-Tinoco, C., Del Medico, L., Tschan, F., Christen, B. 2016; 428 (2): 419-430

  Abstract

  Classical molecular genetics uses stringent selective conditions to identify mutants with distinct phenotypic responses. Mutations giving rise to less pronounced phenotypes are often missed. However, to gain systems-level insights into complex genetic interaction networks requires genome-wide assignment of quantitative phenotypic traits. In this paper, we present a quantitative selection approach coupled with transposon sequencing (QS-TnSeq) to globally identify the cellular components that orchestrate susceptibility of the cell cycle model bacterium Caulobacter crescentus toward bacteriophage φCbK infection. We found that 135 genes representing 3.30% of the Caulobacter genome exhibit significant accumulation of transposon insertions upon φCbK selection. More than 85% thereof consist of new factors not previously associated with phage φCbK susceptibility. Using hierarchical clustering of dose-dependent TnSeq datasets, we grouped these genes into functional modules that correlate with different stages of the φCbK infection process. We assign φCbK susceptibility to eight new genes that represent novel components of the pilus secretion machinery. Further, we demonstrate that, from 86 motility genes, only seven genes encoding structural and regulatory components of the flagellar hook increase phage resistance when disrupted by transposons, suggesting a link between flagellar hook assembly and pili biogenesis. In addition, we observe high recovery of Tn5 insertions within regulatory sequences of the genes encoding the essential NADH:ubiquinone oxidoreductase complex indicating that intact proton motive force is crucial for effective phage propagation. In sum, QS-TnSeq is broadly applicable to perform quantitative and genome-wide systems-genetics analysis of complex phenotypic traits.

  View details for DOI 10.1016/j.jmb.2015.11.018

  View details for Web of Science ID 000370833200003

  View details for PubMedID 26593064