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Factors Structuring the Epiphytic Archaeal and Fungal Communities in a Semi-arid Mediterranean Ecosystem


The phyllosphere microbiome exerts a strong effect on plants’ productivity, and its composition is determined by various factors. To date, most phyllosphere studies have focused on bacteria, while fungi and especially archaea have been overlooked. We studied the effects of plant host and season on the abundance and diversity of the epiphytic archaeal and fungal communities in a typical semi-arid Mediterranean ecosystem. We collected leaves in two largely contrasting seasons (summer and winter) from eight perennial species of varying attributes which could be grouped into the following: (i) high-canopy, evergreen sclerophyllοus shrubs with leathery leaves, and low-canopy, either semi-deciduous shrubs or non-woody perennials with non-leathery leaves, and (ii) aromatic and non-aromatic plants. We determined the abundance of epiphytic Crenarchaea, total fungi, Alternaria and Cladosporium (main airborne fungi) via q-PCR and the structure of the epiphytic archaeal and fungal communities via amplicon sequencing. We observed a strong seasonal effect with all microbial groups examined showing higher abundance in summer. Plant host and season were equally important determinants of the composition of the fungal community consisted mostly of Ascomycota, with Hypocreales dominating in winter and Capnodiales and Pleosporales in summer. In contrast, the archaeal community showed plant host driven patterns dominated by the Soil Crenarchaeotic Group (SCG) and Aenigmarchaeota. Plant habit and aromatic nature exhibited filtering effects only on the epiphytic fungal communities. Our study provides a first in-depth analysis of the key determinants shaping the phyllosphere archaeal and fungal communities of a semi-arid Mediterranean ecosystem.

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Data Availability

All relevant nucleic acids data have been submitted to relevant databases (see manuscript). All other data generated and/or analysed during the current study are available from the corresponding author on reasonable request.

Code Availability

Not applicable.


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This work was supported by (a) the project “ESEPMINENT” implemented under the “ARISTEIA” Action of the “OPERATIONAL PROGRAMME EDUCATION AND LIFELONG LEARNING” and is co-funded by the European Social Fund (ESF) and National Resources and (b) matching funds of the IAPP-FP7-MC project LOVE-TO-HATE provided by the General Secretariat of Research and Technology. A. Katsoula is supported by a PhD scholarship from the State Scholarship Foundation of Greece with resources of the EP “Development of Human Resources, Education and Life-long Learning 2014-2020” and co-funded by the European Social Fund and the Greek State.

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Correspondence to D. Vokou or D. G. Karpouzas.

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Katsoula, A., Vasileiadis, S., Karamanoli, K. et al. Factors Structuring the Epiphytic Archaeal and Fungal Communities in a Semi-arid Mediterranean Ecosystem. Microb Ecol 82, 638–651 (2021).

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  • Phyllosphere
  • Fungal communities
  • Archaeal communities
  • Season
  • Plant host
  • Semi-arid ecosystems