Microorganisms have always been a source of secondary metabolites used for the benefit of
human kind. Many of the antibiotics used against pathogens originate from bacteria and fungi. Other
metabolites produced by microorganisms are being used in the industry. Using microorganisms and
their products for the control of pathogens in agriculture is not new. Some bacterial and fungal
biocontrol agents (BCAs) or their secondary metabolites are registered for the control of plant disease
in organic or conventional farming. The use of endophytes as BCAs and as the source of secondary
metabolites is not common yet. We have been looking for endophytes in trees with the aim of
discovering those with antibiotic activity able to affect tree pathogens and especially systemic ones.
The involvement of woody tissue, large plants and long life cycle makes it difficult to suppress
systemic fungal diseases, by using chemical and cultural methods. The idea of combining the
endophytes ability to develop systemically in trees, to produce and secret biologically active secondary
metabolites and to suppress systemic pathogens of trees is a logical approach. Recognizing and
characterizing those secondary metabolites will enable us to exploit and use it in large scale for the
control of plant pathogens in fruit trees. In the last few years, we have isolated and tested over a
thousand endophytes from different trees in Israel, many of them with biological activity against plant
pathogens. Some were found to secrete secondary metabolites with a wide range of inhibition against a
diversity of pathogens while others were specific to certain pathogens. A very unique endophyte that
we have isolated was found to emit active volatiles that may be used in the control of pathogens in
postharvest and storage of fruit, vegetables and seeds. Molecular identification of active endophytic
fungi by rDNA 5.8S ITS region and actin and β-tubulin gene sequencing was performed.