Understanding and exploiting plant beneficial microbes

Abstract

After a century of incremental research, technological advances, coupled with a need for sustainable crop yield increases, have reinvigorated the study of beneficial plant-microbe interactions with attention focused on how microbiomes alter plant phenotypes. We review recent advances in plant microbiome research, and describe potential applications for increasing crop productivity. The phylogenetic diversity of plant microbiomes is increasingly well characterized, and their functional diversity is becoming more accessible. Large culture collections are available for controlled experimentation, with more to come. Genetic resources are being brought to bear on questions of microbiome function. We expect that microbial amendments of varying complexities will expose rules governing beneficial plant-microbe interactions contributing to plant growth promotion and disease resistance, enabling more sustainable agriculture.

Figure 1

The number of articles about bacterial plant growth promotion per year per thousand plant-related papers, found in the PubMed database, using the search term (("plant development"[MeSH Terms] OR ("plant"[All Fields] AND "development"[All Fields]) OR "plant development"[All Fields] OR ("plant"[All Fields] AND "growth"[All Fields]) OR "plant growth"[All Fields]) AND promoting[All Fields] AND ("microbiology"[Subheading] OR "microbiology"[All Fields] OR "bacteria"[All Fields] OR "bacteria"[MeSH Terms])) OR (("plant development"[MeSH Terms] OR ("plant"[All Fields] AND "development"[All Fields]) OR "plant development"[All Fields] OR ("plant"[All Fields] AND "growth"[All Fields]) OR "plant growth"[All Fields]) AND promoting[All Fields] AND rhizobacteria[All Fields]).

Figure 2. Diversity of genome-sequenced plant associated bacterial isolates from Arabidopsis and Populus currently available on IMG/JGI

An approximately-maximum-likelihood phylogenetic tree of 831 plant-associated bacteria isolated from Arabidopsis thaliana roots (blue and green bars) and shoots (red bars); and Populus deltoides roots (yellow bars). Tree branches are colored by Phylum. Purple: Firmicutes, Blue: Actinobacteria, Yellow: Bacteroidetes, Pink: Deinococcus-thermus and Orange: Proteobacteria. The tree was constructed using a concatenated filtered alignment of 31 single copy genes [97]. The genome assemblies of each of the three different sequencing projects can be accessed via the IMG/JGI portal by using the following project IDs: “Genome sequencing of Arabidopsis leaf and root microbiota representing the majority of bacterial species in their natural communities.” A. thaliana. Max Planck Cologne and ETH Zurich “Plant associated metagenomes-Microbial community diversity and host control of community assembly across model and emerging plant ecological genomics systems.” A. thaliana. University of North Carolina “Populus root and rhizosphere microbial communities from Tennessee, USA” – P. deltoides The tree can be visualized and downloaded on iTOL [98] using the following link: http://itol.embl.de/tree/1522317731415721485965060 or via the user Understanding_the_plant_microbiome_COPB.