Plant Microbiomes: role and interactions with the agricultural environment

Microbes inhabiting plants exhibit different life styles ranging from pathogenic to beneficial. Several recent studies have highlighted the diversity of the microorganisms inhabiting plant parts and identified the significant role of epiphytic, endophytic and rhizospheric microbes on plants well-being. One of the focus of our work is to identify the microbiome of significant crops for the Greek agriculture like olive trees and vines targeting selected emblematic indigenous varieties. Regarding olive trees we hypothesize that plant genotype (cv. Koroneiki and Chalkidikis), biogeography and season are the key determinants of the plant microbiome. The relative contribution of these factors in structuring the olive trees microbiome (rhizosphere, roots, phyllosphere, carposphere) is currently under investigation using advanced amplicon sequencing tools. In the same context we are investigating the role of microbial terroir in the production of high quality wine from local vine varieties. We study the rhizospheric, epiphytic and carposheric microbiome of selected Greek varieties (cv. Vidiano, Agiorgitiko, Asyrtiko, Moschofilero, Roditis, Sideritis) collected from different regions in Greece representing different terroirs using amplicon sequencing approaches. We further employ meta-genomic and –transcriptomic analysis in the vinification process to identify microbes from the indigenous microbiota of the grapes that drive the vinification process. This omic-driven approach will lead to the targeted isolation of these important indigenous microorganisms aiming to the development of novel fermentation processes based on the endemic microbiota for the production of high quality wines.

A second focus of our work is to study the interactions of the phyllospheric microbial community with abiotic stress conditions. Phyllosphere constitutes a harsh environment for microbes. Recent studies showed that the epiphytic bacterial and fungal community are quite diverse and carry significant functional traits like nitrogen fixation, methanol utilization and degradation of organic pollutants. The phyllosphere of cultivated plants is exposed regularly to pesticides. However little is known about the response of epiphytic microorganisms on this regular pesticide exposure. Our main research focus is to explore the response of the epiphytic microbes on pesticide exposure. Our hypothesis is that pesticide exposure would lead to changes in the epiphytic microbial community which could appear as toxicity or as acclimation towards enhanced biodegradation of the sprayed pesticides.  These interactions are explored via classic microbiological methods and amplicon sequencing analysis. Isolated epiphytes with the capacity to degrade pesticides have been isolated and their genomic context is currently determined using hybrid sequencing approaches and transcriptomics.
















  1. Karamanoli E., Thallasinos G., Karpouzas D.G., Bozapalidis A., Vokou D., Isis-Konstantinidou, E (2012) Are leaf glandular trichomes of oregano hospitable habitats for bacterial growth? Journal of Chemical Ecology 38(5): 476-485
  2. Moulas C., Petsoulas C., Rousidou C., Perruchon C., Karras P., Karpouzas D.G., (2013) The effects of systemic pesticides imidachloprid and metalaxyl on the phyllosphere of pepper plants. BIOMED Research International Volume 2013 Article ID 969750, 8 pages
  1. EXCELLENCE II, Title: Essential-oil mediated plant-microbe interactions in the Mediterranean environment: in search of a role and novel applications (ESEPIMENT), Funding Body, General Secretariat of Research and Technology, Greece, Duration 2014-2015, Coordinator: Aristotle University of Thessaloniki. Role: partner
  2. Emblematic Action Routes of Olives, Funding Body: Ministry of Education, Greece. Duration: 2018-2020, Role: partner
  3. Emblematic Action Routes of Vineyards, Funding Body: Ministry of Education, Greece. Duration: 2019-2021, Role: partner
  4. State Scholarship Foundation of Greece, Call PhD students fellowships, Title: Study of the function and diversity of the microbial community in plant phyllosphere and interactions with adjacent environmental compartments. Funding Body: State Scholarship Foundation of Greece, Duration: 2018-2020, Role: Coordinator (Benefited Student: A. Katsoula)
  5. Support of Research, Development and Innovation Projects in the Priority Sector of RIS3 – AgroFood, Region of Western Greece, Title Microbe Terroir – The role of microbial terroir in the production of high quality wine from local vine varieties. Funding Body: Region of Western Greece, Duration 2019-2021, Role: Partner (Participating organizations: Wineries Krokidas and Rouvalis, Un. Patras)




Nancy Katsoula, PhD student

Dr Myrsini Kakagianni

Maria Feka, PhD student

Dr Fotis Bekris

Elena Papadopoulou, PhD student