CV

RESEARCH ACTIVITIES

Since Oct 2019

Junior group Leader (CR1)

Centre national de la rechereche scientifique (CNRS)

UMR CNRS Ecologie Microbienne, Université Lyon 1, Villeurbanne, France.

Oct 2017-Sep 2019

Assistant Professor position

Dept. Microbial interactions in plant ecosystems (Chair : E. Kemen), Center for plant molecular biology, University of Tübingen, Germany.

Dec 2016- Sep 2017

Post Doc position

E. Kemen Lab, Max Planck Institute for Plant Breeding Research, Cologne, Germany.

Topic: Temporal profiles of microbial networks associated to Arabidopsis thalianaleaves. (Project leader: E. Kemen)

Mar 2013- Jul 2016

Post Doc position

M. Bucher Lab, University of Cologne, Cologne, Germany.

Cluster of Excellence on Plant Sciences (CEPLAS)

Plant Fellows fellowship (FP7-COFUND-Marie Curie Actions)

Topic: Structural and functional characterization of the Arabis alpina fungalmicrobiome. (Project leader: M. Bucher)

PhD student I. Fabianská co-supervision

Topic: The role of the molecular network controlling phosphate homeostasis, in structuring Arabidopsis fungal microbiome. Co-advisors: Juliana Almario and Marcel Bucher.

Sep 2009 – Dec 2012

Ph.D. Microbial Ecology

UMR CNRS Ecologie Microbienne, Université Lyon 1, Villeurbanne, France.

PhD grant from the French ministry for higher education and research

Topic: Functional relationship between the plant-protecting activity of 2,4‑diacetylphloroglucinol-producing Pseudomonas in the rhizosphere, and soil suppressiveness to black root-rot disease of tobacco. Advisors: Daniel Muller and Yvan Moënne-Loccoz

SCIENTIFIC EXPERTISE

Microbiology

Bacterial and fungal cultures. Nucleic acids (DNA and RNA) extraction and purification from pure cultures, roots and soil. Staining methods, fluorescence microscopy and confocal laser scanning microscopy (CLSM) to study bacteria and fungi in roots. Recovery and culture of fungal endophytes from plant roots. Fungal transformation.

Molecular biology

PCR, real-time PCR and RT real-time PCR, primer design and in vitro transcription. Bacterial transformation and use of reporter gene systems (gfp, inaZ, lacZ) in comple environments (soil, roots). Multiplexing techniques for high-throughput sequencing.

Microbial diversity

Terminal fragment length polymorphism (tRFLP), fungal and bacterial Automated Ribosomal Intergenic Spacer Analysis (ARISA), bacterial 16S rRNA microarray, fungal ITS2 Illumina sequencing. Knowledge of bacterial and fungal systematics.

Plant sciences

Plant growth in vitro and in soil and plant sampling in nature. Rhizosphere and root-endosphere sampling. Plant elemental composition analysis (Ionome) by ICP-MS. Extraction and detection of metabolites from the rhizosphere (HPLC-UV and mass spectrometry).

In vitro and gnotobiotic systems to study plant-microbe interactions. Fungus-mediated radioactive phosphate (³³P) transport to plants in compartmentalized systems as used in mycorrhizal research.

Biostatistics

Descriptive statistics, hypothesis testing with parametric and non-parametric tests. Data transformation and normalization methods. Multivariate analysis (PCA, NMDS, Clustering, Co-inertia analyses, Mantel test, etc.). Use of R environment, ADE4 and Vegan packages.

Bioinformatics

Comparative genomics, phylogenetic and functional sequence analyses (Muscle, MAFFT, PhyML, MrBayes and Figtree software).

Paired-end amplicon sequencing analysis for the study of bacterial, fungal and protist diversity. Analysis of complex microbial networks in temporal studies (Mothur, Qiime, cytoscape, sparCC, eLSA).

Image analysis

Image analysis of microarray hybridization using GenePix software and of microscopy images using ImageJ software.

Languages

Spanish (first language), French and English (fluent) and German (beginner level).

SCIENTIFIC TALKS

INTERNATIONAL MEETINGS

Almario, J., Wunder, J., Coupland, G., Bucher, M. Depicting the Arabis alpina fungal microbiome. 4^thRhizosphere meeting. Maastricht, The Netherlands, June 2015.

Almario, J., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y. Effect of clay mineralogy on iron bioavailability and rhizosphere expression of 2,4‑diacetylphloroglucinol biosynthetic genes in biocontrol Pseudomonas protegens. 14^th International Symposium on Microbial Ecology ISME14. Copenhagen, Denmark, August 2012.

Almario, J., Moënne-Loccoz, Y., Muller, D. Monitoring natural populations of 2,4‑diacetylphloroglucinol-producing Pseudomonas spp. in tobacco black root-rot suppressive and conducive soils through a new real-time PCR method. 10^th Plant-Bacteria Interactions Meeting, Aussois, France, January 2012

NATIONAL/REGIONAL/LOCAL MEETINGS

Almario, J., Jeena, G., Wunder, J., Langen, G., Zuccaro, A., Coupland, G., Bucher, M. 2017. The root fungal microbiota of non-mycorrhizal Arabis alpina and its contribution to plant P acquisition (Invited talk). CEPLAS internal symposium, Colgne, Germany, October 2017.

Almario, J., Jeena, G., Wunder, J., Langen, G., Zuccaro, A., Coupland, G., Bucher, M. 2017. The root fungal microbiota of non-mycorrhizal Arabis alpina and its contribution to plant P acquisition (Invited talk). NIOO-KNAW, Wageningen, The Netherlands, October 2016.

Almario, J., Wunder, J., Coupland, G., Bucher, M. Arabis alpina fungal microbiome. Arabis meeting. Zurich, Switzerland, April 2013.

Almario, J. Understanding disease suppressive soils (Invited talk). Meeting of the Swiss Society for Phytiatry and the Swiss Society of Agronomy. Zollikofen, Switzerland, March 2013.

Almario, J., Prigent-Combaret, C., Muller, D., Moënne-Loccoz, Y. Effect of clay mineralogy on the plant-protecting activity of Pseudomonas in the rhizosphere. 2^nd meeting of Ph.D. students in Ecology, Evolution, Microbiology and Modeling, Villeurbanne, France, March 2012 (Best communication prize).

TEACHING EXPERIENCE

Practical lab internship: March 2013 - 2016

Teaching assistant: Oct 2009 - Sept 2011

COURSES

- Plant-microbe interactions (practical laboratory internship)

1 month, 3 students, 1^st year Master of Biology.

University of Cologne, Cologne, Germany.

- General Microbiology (practical laboratory course)

2 x 40 hours, 3^rd year Bachelor of pharmacy

Université Lyon 1, Villeurbanne, France

- Bacteriology and antibiotics (practical laboratory course)

16.5 hours, 4^th year Bachelor of pharmacy

Université Lyon 1, Villeurbanne, France

- Plant Biology (practical laboratory course)

18 hours, 1^st year Bachelor of Biology

Université Lyon 1, Villeurbanne, France