Structure and Functions of the Bacterial Microbiota of Plants

Abstract

Plants host distinct bacterial communities on and inside various plant organs, of which those associated with roots and the leaf surface are best characterized. The phylogenetic composition of these communities is defined by relatively few bacterial phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. A synthesis of available data suggests a two-step selection process by which the bacterial microbiota of roots is differentiated from the surrounding soil biome. Rhizodeposition appears to fuel an initial substrate-driven community shift in the rhizosphere, which converges with host genotype-dependent fine-tuning of microbiota profiles in the selection of root endophyte assemblages. Substrate-driven selection also underlies the establishment of phyllosphere communities but takes place solely at the immediate leaf surface. Both the leaf and root microbiota contain bacteria that provide indirect pathogen protection, but root microbiota members appear to serve additional host functions through the acquisition of nutrients from soil for plant growth. Thus, the plant microbiota emerges as a fundamental trait that includes mutualism enabled through diverse biochemical mechanisms, as revealed by studies on plant growth-promoting and plant health-promoting bacteria.

Antibiotic resistance genes in manure-amended soil and vegetables at harvest

“…Endophytes have been found to be closely related to human pathogens or opportunistic human pathoges [51], which could trigger potential threat to human health. Phyllosphere, normally referring to the aerial leaf surfaces, is a special niche harboring diverse species of microbes, especially bacteria [52]. Therefore, vegetables grown in manureamended soil, particularly that are eaten raw or only subjected to minimal processing before consumption, could serve as vehicles for expanding the pool of antibiotic resistance available to bacteria (pathogens or otherwise) [47].…”

Assembly of seed-associated microbial communities within and across successive plant generations

“…Community assembly processes could be divided into four main forces: dispersal, diversification, ecological drift and selection (Nemergut et al 2013). Recently, many research groups have investigated the importance of selection in determining community assembly in the rhizosphere and the phyllosphere (Bulgarelli et al 2013;Müller et al, 2016). For instance, it has been shown that selection by the environment (e.g.…”

Microbiome and the future for food and nutrient security

“…There is significant evidence to suggest that ecological functions performed by the phytomicrobiome extend a plant's ability to adapt to different environmental conditions and changes (Bulgarelli et al ., 2013), which is of primary significance for the plant's fitness considering their sessile lifestyles. However, traditional crop breeding programmes do not consider key components of crop fitness, i.e.…”