Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

Abstract

One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only 'passengers' with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as 'gatekeepers' to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage 'priming' plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.

Keywords: biocontrol bacteria; endophytic bacteria; plant defense signaling; plant growth promotion; plant microbiome.

FIGURE 1

Schematic representation of the bacterial distribution and colonization patterns in the endosphere of a plant root. The emerging sites of lateral roots are among the hotspots of bacterial colonization. Arrows represent the translocation of bacteria inside the xylem and phloem. Endophytic bacteria may engage in different life styles as depicted by different colored ovals. This illustration was inspired by studies of Compant et al. (2005, 2008) and Glaeser et al. (2016).

FIGURE 2

Schematic representation of bacterial colonization patterns in a leaf. The picture shown on the left demonstrates that the presence of bacteria has been detected in the leaf petiole, midrib and veins. The picture shown on the right is a magnified leaf cross-section, which demonstrates that endophytic bacteria may not only colonize the apoplast but are also present intracellularly. Endophytic bacteria are believed to be able to ascend from roots to leaf via the vascular tissues of xylem and phloem.

FIGURE 3

Schematic representation summarizing typical properties that may be employed by endophytic bacteria to cope with the plant’s immune system. Genes encoding secretion systems including T2SS, T5SS, and T6SS are normally detected in high copy numbers in endophytic bacteria. The rare presence of T3SS and T4SS that generally elicit significant plant defense, and the production of scavenging enzymes of endophytic bacteria may have contributed to their successfully colonization in plants.

FIGURE 4

Activation of SA, JA, and ET signaling pathways by exogenous treatments suppresses the colonization of particular bacterial inoculants in the root endosphere. In contrast, defense signaling effects on the plant endosphere-associated microbiome could be small and variable (Iniguez et al., 2005; Miché et al., 2006; Kniskern et al., 2007; Lebeis et al., 2015), but a reduced bacterial diversity has been observed in the roots of wheat seedlings upon activation of JA signaling (Liu et al., 2017).

FIGURE 5

Schematic representation summarizing plant growth promoting traits (PGPTs) of endophytic bacteria. Some endophytic bacteria are able to improve plant growth by reducing the synthesis of stress ethylene in plants, producing growth-promoting phytohormones and providing plants with macro- and/or micro- nutrients such as phosphate, nitrogen and Fe³⁺. Endophytic bacteria can also benefit plants indirectly by suppressing the growth and reproduction of phytopathogens via multi-antagonistic effects, including quenching quorum sensing (QS), competing for nutrients, producing cell-wall degrading products and antimicrobial compounds. In this graph, arrows denote plant-bacteria interactions and ‘⊥’ indicates inhibition. IAA, indoleacetic acid; ACC, 1 aminocyclopropane-1-carboxylic acid; GAs, gibberellins; CK, cytokinin, EPS, extracellular polymeric substance; LPS, lipopolysaccharide; αkb, α-ketobutyrate.

FIGURE 6

Visualization of endophytic bacteria-induced systemic resistance (ISR). The right half of this illustration presents the elicitation of plant-primed conditions by endophytic bacteria. Endophytic bacteria-mediated ISR may be modulated by either one or combined signaling cascades of SA, JA, and ET in an endophytic bacteria-dependent manner. Some beneficial effects may include changes in root architecture relative to uninoculated plants as shown by the left half of the plant.