Publications

Check out my ORCiD page for my full and most updated list of publications.

Verdon, V., Malard, L., Collart, F., Adde, A., Yashiro E., Lara Pandi, E., Mod, H., Singer, D., Niculita-Hirzel, H., Guex, N., Guisan, A. (2024) Can we accurately predict the distribution of soil microorganism presence and relative abundance? Ecography https://doi.org/10.1111/ecog.07086

Møller, K.V.M., Wesseltoft, J.L., Malarzarte, R., Kousgaard, S.J., Nielsen, H.L., Yashiro, E., Olsen, A. (2023) Usage of cultured human fecal microbiota for colonization of Caenorhabditis elegans to study host-microbe interaction. Applied Microbiology https://doi.org/10.3390/applmicrobiol3040078

Seppey, C.V.W., Lara, E., Broennimann, O., Guisan, A., Malard, L., Singer, D., Yashiro, E., Fournier, B. (2023) Land use change decreases soil protist diversity in alpine meadowsLandscape structure is a key driver of soil protist diversity in meadows in the Swiss Alps. Landscape Ecology 38:949-965

Yashiro, E. and Ørsted, M., Hoffmann, A.A., Kristensen, T.N. (2022) Population bottlenecks constrain microbiome diversity and host genetic variation impeding fitness. PLOS Genetics 18(5): e1010206 https://doi.org/10.1371/journal.pgen.1010206
Note: Shared first authorship

Malard, L.A., Mod, H.K., Guex, N., Broennimann, O., Yashiro, E., Lara, E., Mitchell, E.A.D., Niculita-Hirzel, H., Guisan, A. (2022) Comparative analysis of diversity and environmental niches of soil bacterial, archaeal, fungal, and protist communities reveal niche divergences along environmental gradients in the Alps. Soil Biology and Biochemistry 169:108674

Mazel, F., Malard, L., Niculita-Hirzel, H., Yashiro, E., Mod, H.K., Mitchell, E.A.D., Singer, D., Buri, A., Pinto, E., Guex, N., Lara, E., Guisan, A. (2021) Soil protist function varies with elevation in the Swiss Alps. Environmental Microbiology https:/doi.org/10.1111.1462-2920.15686

Jiang, C., McIlroy, S.J., Qi, R., Petriglieri, F., Yashiro, E., Kondrotaite, Z., Nielsen. P.H. (2021) Identification of microorganisms responsible for foam formation in mesophilic anaerobic digesters treating surplus activated sludge. Water Research 191:116779

Pertoldi, C., Schmidt, J.B., Thomsen, P.M., Nielsen, L.B., de Jonge, N., Iacolina, L., Muro, F., Nielsen, K.T., Pagh, S., Lauridsen, T.L., Andersen, L.H., Yashiro, E., Lukassen, M.B., Nielsen, J.L., Elmeros, M., Bruhn, D. (2021) Comparing DNA metabarcoding with faecal analysis for diet determination of the Eurasian otter (Lutra lutra) in Vejlerne, Denmark. Mammal Research 66(1):115-122

Jiang, C., Peces, M., Andersen, M.H., Kucheryavskiy, S., Nierychlo, M., Yashiro, E., Andersen, K.S., Kirkegaard, R.H., Hao, L., Høgh, J., Hansen, A.A., Dueholm, M.S., Nielsen, P.H. (2021) Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbiome structure and key drivers. Water Research 193:116871

Mod, H., Buri, A., Yashiro, E., Guex, N., Malard, L., Pinto-Figueroa, E, Pagni, M., Niculita-Hirzel, H., van der Meer, J.R., Guisan, A. (2021) Predicting spatial patterns of soil bacteria under current and future environmental conditions. ISME Journal https://doi.org/10.1038/s41396-021-00947-5

Mod, H.K., Scherrer, D., Di Cola, V., Broennimann, O., Blandenier, Q., Breiner, F., Buri, A., Goudet, J., Lara, E., Mitchell, E., Niculita-Hirzel, H., Pagni, M., Pellissier, L., Pinto-Figueroa., E., Sanders, I., Schmidt, B., Seppey, C., Singer, D., Ursenbacher, S., van der Meer, J.R., Yashiro, E., Guisan, A.(2020) Greater climate control on above- than belowground communities. Global Change Biology 26(12):6715-6728 Note: The authors are listed in alphabetical order except for the 1st and co-last authors.

Dueholm, M.S., Andersen, K.S., McIlroy, S.J., Kristensen, J., Yashiro, E., Karst, S.M., Albertsen, M., Nielsen, P.H. (2020) Generation of comprehensive ecosystem-specific reference databases with species-level resolution by high-throughput full-length 16S rRNA gene sequencing and automated taxonomy assignment (AutoTax). mBio. 11:e01557-20

Buri, A., Grand, S., Yashiro, E., Adatte, T., Spangenberg, J.E., Pinto-Figueroa, E., Verrecchia, E., Guisan, A. (2020) What are the most crucial soil variables for predicting the distribution of mountain plant species? A comprehensive study in the Swiss Alps. Journal of Biogeography 47(5):1143-1153

Seppey, C.V.W., Broennimann, O., Buri, A., Yashiro, E., Pinto, E., Singer, D., Blandenier, Q., Mitchell, E.A.D., Niculita-Hirzel, H., Guisan, A., Lara, E. (2019) Soil protist diversity in the Swiss western Alps is better predicted by topo-climatic than by edaphic variables. Journal of Biogeography 47(4): 866-878

Rasmussen, S.L., Yashiro, E., Sverrisdóttirx, E., Nielsen, K.L., Lukassen, M.B., Nielsen, J.L., Asp, T., Pertoldi, C. (2019) Genomic characterization of a Danish population of the European hedgehog (Erinaceus europaeus). Genetics and Biodversity 3(2): 78-86

Yashiro, E., Savova-Bianchi D., Niculita-Hirzel, H. (2019) Major Differences in the Diversity of Mycobiomes Associated with Wheat Processing and Domestic Environments: Significant Findings from High-Throughput Sequencing of Fungal Barcode ITS1 International Journal of Environmental Research and Public Health 16(13): 2335

Pinto-Figueroa, E., Seddon, E., Yashiro, E., Buri, A., Niculita-Hirzel, H., van der Meer, J.R., Guisan, A. (2019) Archaeorhizomycetes spatial distribution in soils along wide elevational and environmental gradients reveal co-abundance patterns with other fungal saprobes and potential weathering capabilities. Frontiers in Microbiology 10:656. doi: 10.3389/fmicb.2019.00656

Erkosar, B., Yashiro, E., Zajitschek, F., Friberg, U., Maklakov, A.A., van der Meer., J.R., Kawecki, T.J. (2018) Host diet mediates a negative relationship between abundance and diversity of Drosophila gut microbiota. Ecology and Evolution 8(18):9491-9502

Yashiro, E., Pinto-Figueroa, E., Buri, A., Spangenberg, J.E., Adatte, T., Niculita-Hirzel, H., Guisan, A., van der Meer, J.R. (2018) Meta-scale mountain grassland observations uncover commonalities as well as specific interactions among plant and non-rhizosphere soil bacterial communities. Scientific Reports 8:5757

Buri, A., Cianfrani, C., Pinto, E., Yashiro, E., Guisan, A. & Pradervand, J.-N. (2017) Soil factors improve predictions of plant species distribution in a mountain environment. Progress in Physical Geography 41(6):703-722
Note: The authors are listed in alphabetical order except for the 1st and co-last authors.

Mohamad, R., Maynaud, G., Le Quéré, Vidal, C., Klonowska, A., Yashiro, E., Cleyet-Marel, J.-C., Brunel., B. (2017) Ancient heavy metal contamination in soils as a driver of tolerant Anthyllis vulneraria rhizobial communities. Applied and Environmental Microbiology 83(2): e01735-16

Yashiro, E., Pinto-Figueroa, E., Buri, A., Spangenberg, J., Adatte, T., Niculita-Hirzel, H., Guisan, A., van der Meer, J.R. (2016) Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps. Applied and Environmental Microbiology 82(21): 6303-6316

Maynaud, G., Brunel, B., Yashiro, E., Mergeay, M., Cleyet-Marel, J-C., Le-Quéré, A. (2014) CadA of Mesorhizobium metallidurans isolated from a zinc-rich mining soil is a PIB-2-type ATPase involved in cadmium and zinc resistance. Research in Microbiology 165:175-189

Yashiro, E., McManus, P.S. (2012) Effect of streptomycin treatment on bacterial community structure in the apple phyllosphere. PloS One 7(5): e37131

Yavitt, J.B., Yashiro, E., Cadillo-Quiroz, H., Zinder, S.H. (2012) Methanogen diversity and community composition in peatlands of the central to northern Appalachian mountain region, North America. Biogeochemistry 109: 117-131

Yashiro, E., Spear, R.N., McManus, P.S. (2011) Culture-dependent and culture-independent assessment of bacteria in the apple phylloplane. Journal of Applied Microbiology 110(5): 1284-1296

Yashiro, E., Spear, R., Clinton-Cirocco, K., McManus, P. (2008) Assessment of bacteria from apple leaves by culture-dependent and culture-indpendent methods. Phytopathology 98:S177

Cadillo-Quiroz, H., Yashiro, E., Yavitt, J.B., Zinder, S.H. (2008) Characterization of the Archaeal Community in a Minerotrophic Fen and Terminal Restriction Fragment Length Polymorphism-Directed Isolation of a Novel Hydrogenotrophic Methanogen. Applied and Environmental Microbiology 74(7): 2059-2068

Bräuer, S.L., Cadillo-Quiroz, H., Yashiro, E., Yavitt, J.B., Zinder, S.H. (2006) Isolation of a Novel Acidiphilic Methanogen from an Acidic Peat Bog. Nature 442: 192-194

Bräuer, S.L., Yashiro, E., Ueno, N.G., Yavitt, J.B., Zinder, S.H. (2006) Characterization of Acid-Tolerant H2/CO2-Utilizing Methanogenic Enrichment Cultures from an Acidic Peat Bog in New York State. FEMS Microbiology Ecology 57: 206-216

Cadillo-Quiroz, H., Bräuer, S., Yashiro, E., Sun, C., Yavitt, J., Zinder, S. (2006) Vertical Profiles of Methanogenesis and Methanogens in Two Contrasting Acidic Peatlands in Central New York State, USA. Environmental Microbiology 8(8): 1428-1440

Book chapters

Guisan A., Broennimann O., Buri A., Cianfrani C., D’Amen M., Di Cola V., Fernandes R., Gray S., Mateo R.G., Pinto E., Pradervand J.-N., Scherrer D., von Däniken I., Yashiro E., Vittoz, P. (2019) Climate change impact on mountain biodiversity. Climate change & Biodiversity chapt. 17 p.221-233, ed. Tom Lovejoy & Lee Hannah. ISBN: 9780300206111 Note: The authors are listed in alphabetical order except for the 1st and last authors.

Acknowledgements

Kuntke, F., de Jonge, N., Hesselsøse, M., Nielsen, J. (2019) Stream water quality assessment by metabarcoding of invertebrates. Ecological Indicators https://doi.org/10.1016/j.ecolind.2019.105982
Contribution: Contributed ideas and discussion.

Sentchilo, V., Mayer, A.P., Guy, L., Miyazaki, R., Tringe, S.G., Barry, K., Malfatti, S., Goessmann, A., Robinson-Rechavi, M., van der Meer, J.R. (2013) Community-wide plasmid gene mobilization and selection. ISME Journal doi: 10.1038/ismej.2013.13
Contribution: Wrote scripts to analyze data.

Shade, A., Hogan, C.S., Klimowicz, A.K., Linske, M., McManus, P.S., Handelsman, J. (2012) Culturing captures members of the soil rare biosphere. Environmental Microbiology 14(9): 2247-2252
Contribution: Contributed ideas and comments on the earlier stages of the work

Cadillo-Quiroz, H., Yavitt, J.B., Zinder, S.H., Thies, J.E. (2010). Diversity and Community Structure of Archaea inhabiting the rhizoplane of two contrasting plants from an acidic bog. Microbial Ecology 59:757-767.
Contribution: Contributed ideas and comments.

Kajila, M.K., Andreeva, O., Gilbreath, M.T., Paskewitz, S.M. (2010). Characterization of expression, activity and role in antibacterial immunity of Anopheles gambiae lysozyme c-1. Comparative Biochemistry and Physiology 155(2): 201-209.
Contribution: Helped with sequence analysis.

Miché, L., Moulin, L., Chaintreuil, C., Contreras-Jimenez, J.L., Munive-Hernández, J-A., Villegas-Hernandez, M.D.C., Crozier, F., Béna, G. (2009). Diversity analyses of Aeschynomene symbionts in Tropical Africa and Central America reveal that nod-independent stem nodulation is not restricted to photosynthetic bradyrhizobia. Environmental Microbiology 12(8):2152-2164.
Contribution: Assistance with manuscript correction.