Plants microbiome: its role and its 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 emblematic crops for Greek agriculture like olive trees and vines. Our hypothesis is that the microbiome of olives and vines is composed of a core microbiome of microrganisms which have developed specific interactions with the plant host while the rest of it is shaped by the plant itself (variety) and the edaphoclimatic conditions. In this frame selected endemic varieties  of olive trees (Koroneiki, Chalkidikis) and vines have been selected and the rhizospheric, endophytic, epiphytic and carposheric microbiome will be determined using amplicon sequencing approaches. In addition the role of microbiome in downstream processing like wine production or spoilage will be assessed 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 adaptation. The latter could lead to the establishment of a fraction of the epiphytic microbiota which is able to rapidly degrade pesticides.  These interactions we explore via classic microbiological methods and amplicon sequencing analysis.




  1. ARISTEIA II,Essential-oil mediated plant-microbe interactions in the Mediterranean environment: in search of a role and novel applications(ESEPIMENT), Funding: General Secretariat of Research and Technology, Greece, Duration 2014-2015,
  2. EMBLEMATIC ACTION "THE CHARIOTS OF OLIVES". Funding: Ministry of Education, Greece, Duration 2018-2020
  3. 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, Benefited Student: A. Katsoula

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  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


- Nancy Katsoula, PhD student