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...-related genes (ppGpp metabolism and oxidative stress) were upregulated in these bacterial families. We postulate that the invading pathogenic fungus induces, directly or via the plant, stress responses in the rhizobacterial community that lead to shifts in microbiome composition and to activation of antagonistic traits that restrict pathogen infection. The ISME Journal (2016) 10, 265–268; doi:10.1038/ismej.2015.82; published online 29 May 2015 Suppressive soils have been described for various soilborne pathogens and occur worldwide (Mazzola, 2007; Mendes et al., 2011; Berendsen et al., 2012; Mendes et al., 2013). Disease suppressiveness to soilborne fungal pathogens is in many cases microbial in origin and develops in the field after several disease outbreaks (Mazzola, 2007). Hence, interactions between the fungal pathogen, the plant and the rhizosphere microbiome are key elements in shaping a plant-protective microbiome. To date, however, the responsible microbes and the underlying mechanisms are largely unknown. To understand how pathogen invasion affects the composition and activities of rhizobacterial communities, we sequenced metagenomic DNA and RNA of the rhizosphere microbiome of sugar beet se...

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...sch, 2009). Opportunistic pathogens in the vegetable microbiome Plants, especially their endospheres and rhizospheres are important reservoirs for emerging opportunistic pathogens (Berg et al., 2005; =-=Mendes et al., 2013-=-). The number of documented outbreaks of human infections associated with the consumption of raw vegetables has increased in recent years (Buck et al., 2003). Diverse human pathogens are able to colon...

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...rdieva et al. 2008). The majority of soil bacteria can be found in biofilms on roots, litter and soil particles (Burmølle et al. 2007). One of the most complex ecosystems on earth is the rhizosphere (=-=Mendes et al. 2013-=-), where root exudates influence the microbial habitat to yield bacterial cell numbers of 108 cells per gram of fresh root (Berg et al. 2002). Furthermore, more than 95% of the short roots of most ter...

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...cally fixed carbon into the root–soilsinterface [83], which can influence the microbial activity and diversity, thereby enhancing seedsgermination rates, nutrient uptake, plant growth and development =-=[82,84]-=-. Recent studies have shownsthat plants actively recruit disease-suppressive microbes that can protect the host from various infectionssthrough the production specific molecules, such as nonribosomal ...

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...ound in many species of this group, together with plant-pathogenic species such as Pseudomonas savastanoi or Pseudomonas syringae as well as human nosocomial pathogens such as Pseudomonas aeruginosa (=-=Mendes et al. 2013-=-). Several species of the genus Pseudomonas have been reported to be present in potato (Solanum tuberosum L.) tissues (Berg et al., 2005; Krechel et al., 2002; Sturz & Matheson, 1996), most of them re...