BACKGROUND : Soil microorganisms are key determinants of soil fertility and plant health. Soil phytopathogenic fungi
are one of the most important causes of crop losses worldwide. Microbial biocontrol agents have been extensively
studied as alternatives for controlling phytopathogenic soil microorganisms, but molecular interactions between
them have mainly been characterised in dual cultures, without taking into account the soil microbial community.
We used an RNA sequencing approach to elucidate the molecular interplay of a soil microbial community in
response to a plant pathogen and its biocontrol agent, in order to examine the molecular patterns activated by the
RESULTS : A simplified soil microcosm containing 11 soil microorganisms was incubated with a plant root pathogen
(Armillaria mellea) and its biocontrol agent (Trichoderma atroviride) for 24 h under controlled conditions. More than
46 million paired-end reads were obtained for each replicate and 28,309 differentially expressed genes were
identified in total. Pathway analysis revealed complex adaptations of soil microorganisms to the harsh conditions of
the soil matrix and to reciprocal microbial competition/cooperation relationships. Both the phytopathogen and its
biocontrol agent were specifically recognised by the simplified soil microcosm: defence reaction mechanisms and
neutral adaptation processes were activated in response to competitive (T. atroviride) or non-competitive (A. mellea)
microorganisms, respectively. Moreover, activation of resistance mechanisms dominated in the simplified soil
microcosm in the presence of both A. mellea and T. atroviride. Biocontrol processes of T. atroviride were already
activated during incubation in the simplified soil microcosm, possibly to occupy niches in a competitive ecosystem,
and they were not further enhanced by the introduction of A. mellea.
CONCLUSIONS : This work represents an additional step towards understanding molecular interactions between plant
pathogens and biocontrol agents within a soil ecosystem. Global transcriptional analysis of the simplified soil
microcosm revealed complex metabolic adaptation in the soil environment and specific responses to antagonistic
or neutral intruders.