Higher organisms evolved in the omnipresence of microbes, which could be of pathogenic or symbiotic nature. A framework of response patterns evolved which is known as innate immunity. A major part of this response is the recognition of microbial-associated molecular patterns (MAMP) such as chitin or lipochitooligosaccharides, peptidoglycan, lipopolysaccharides or flagellum structures, and the initiation of efficient plant defence reactions (Janeway and Medzhitov, 2002; Jones and Dangl, 2006). However, there are many plant-associated endophytic bacteria known, which are living within plants without triggering persistent and apparent defence responses or visibly do not harm the plant. In some cases, even a stimulation of plant growth due to the presence of specific players within the plant microbiome was reported (Turner et al., 2013). It is now generally accepted, that plant performance and activities can only be characterized and understood completely, if the “holobiont,” the plant plus the intimately associated microbiota, is considered (Zilber-Rosenberg and Rosenberg, 2008). The evolutionary advantage of an integrated holobiontic system is characterized by a much better adaptability and flexibility towards rapidly changing adverse environmental conditions. It is still mostly unknown, which particular plant genetic loci are controlling the interactions with the plant microbiome and which signals are steering this cooperativity. Mutualistic microbes are able to overcome or short-circuit plant defence responses to enable successful colonization of the host (Zamioudis and Pieterse, 2012; Alqueres et al., 2013). Beneficial associations with microbes other than mycorhiza or Rhizobia are also controlled by systemically regulated or autoregulated processes on top of the basic innate immunity response. The induction of systemic immunity responses like ISR (induced systemic resistance) by some beneficial rhizosphere bacteria or the SAR (systemic acquired resistance) response provoked by pathogens are results of multiple response cascades employed by the plant host to respond to microbial and other environmental interactions. However, the entire response network is by far not yet revealed. For example, bacteria-induced plant responses resulting in improved resistance towards pathogens can also be due to the perception of secondary metabolites, like the surfactin lipopeptide, produced by certain biocontrol Bacilli (Garcia-Gutiérrez et al., 2013) or volatile compounds of plant-associated microbes (Yi et al., 2010). The biocontrol activity of microbial inoculants is probably due to multiple effects of their secondary metabolites to achieve direct inhibition of the pathogenic counterpart as well as an increase of systemic resistance of the plant host.
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