Ecology and Genomic Insights into Plant-Pathogenic and Plant-Nonpathogenic Endophytes

Abstract

Plants are colonized on their surfaces and in the rhizosphere and phyllosphere by a multitude of different microorganisms and are inhabited internally by endophytes. Most endophytes act as commensals without any known effect on their plant host, but multiple bacteria and fungi establish a mutualistic relationship with plants, and some act as pathogens. The outcome of these plant-microbe interactions depends on biotic and abiotic environmental factors and on the genotype of the host and the interacting microorganism. In addition, endophytic microbiota and the manifold interactions between members, including pathogens, have a profound influence on the function of the system plant and the development of pathobiomes. In this review, we elaborate on the differences and similarities between nonpathogenic and pathogenic endophytes in terms of host plant response, colonization strategy, and genome content. We furthermore discuss environmental effects and biotic interactions within plant microbiota that influence pathogenesis and the pathobiome.

On plant defense signaling networks and early land plant evolution

“…Microorganisms are not only beneficial to plants and algae – they can exploit their hosts as (facultative) phytopathogens [39]. For example, several bacterial and fungal genera or species complexes include mutualistic, pathogenic and endophytic species [39].…”

“…For example, several bacterial and fungal genera or species complexes include mutualistic, pathogenic and endophytic species [39]. Such microbe-host relationships can in fact switch between neutral, beneficial and detrimental in response to, for example, environmental factors [40,41].…”

Linking ecology and plant pathology to unravel the importance of soil-borne fungal pathogens in species-rich grasslands

“…Some of these non-pathogenic strains can even act as antagonists of pathogenic strains (Mandeel and Baker 1991). Furthermore, it is becoming more apparent that plantpathogenic fungi can also display an endophytic lifestyle (Brader et al 2017), i.e. colonization without causing disease (Rodriguez et al 2009).…”

“…This process is plant species and genotype specific, but is also influenced by environmental factors such as soil type and temperature (Brader et al 2017;Philippot et al 2013;Schlemper et al 2017). The bacterial rhizobiome is a dynamic microbial network that affects pathogen invasiveness, infection and severity (Chapelle et al 2016;Raaijmakers et al 2009).…”

The potential of plant microbiota in reducing postharvest food loss

“…Moreover, a clear distinction between plant‐beneficial or harmful microorganisms is not always possible (Hentschel et al ., 2000). The outcome of plant–microbe interactions depends on biotic and abiotic environmental factors but also the manifold interactions between members of the plant microbiota, including pathogens, strongly influence the phenotype of plant–microbe interactions (Brader et al ., 2017). Often disease outbreak in plants correlates with shifts in the microbiome composition, resulting in a microbial dysbiosis and a response of specific microbes, which can act as antagonists or synergists towards plant pathogens (Berg et al ., 2017).…”