Adaptation of Rhizobium leguminosarumto pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics

Abstract

BackgroundThe rhizosphere is the microbe-rich zone around plant roots and is a key determinant of the biosphere's productivity. Comparative transcriptomics was used to investigate general and plant-specific adaptations during rhizosphere colonization. Rhizobium leguminosarum biovar viciae was grown in the rhizospheres of pea (its legume nodulation host), alfalfa (a non-host legume) and sugar beet (non-legume). Gene expression data were compared to metabolic and transportome maps to understand adaptation to the rhizosphere.ResultsCarbon metabolism was dominated by organic acids, with a strong bias towards aromatic amino acids, C1 and C2 compounds. This was confirmed by induction of the glyoxylate cycle required for C2 metabolism and gluconeogenesis in all rhizospheres. Gluconeogenesis is repressed in R. leguminosarum by sugars, suggesting that although numerous sugar and putative complex carbohydrate transport systems are induced in the rhizosphere, they are less important carbon sources than organic acids. A common core of rhizosphere-induced genes was identified, of which 66% are of unknown function. Many genes were induced in the rhizosphere of the legumes, but not sugar beet, and several were plant specific. The plasmid pRL8 can be considered pea rhizosphere specific, enabling adaptation of R. leguminosarum to its host. Mutation of many of the up-regulated genes reduced competitiveness for pea rhizosphere colonization, while two genes specifically up-regulated in the pea rhizosphere reduced colonization of the pea but not alfalfa rhizosphere.ConclusionsComparative transcriptome analysis has enabled differentiation between factors conserved across plants for rhizosphere colonization as well as identification of exquisite specific adaptation to host plants.

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

“…Several studies have addressed the transcriptomics of the rhizosphere (Diehn and Relman, 2001;Mark et al, 2005;Matilla et al, 2007;Ramachandran et al, 2011), but always using a controlled approach with a single bacterium, one or a few plants in sterile substrates or purified root exudates. In this study, we used a metatranscriptomic approach and assessed the whole microbial community associated with willow roots growing in non-sterile soil from a contaminated site.…”

“…The overall increase in the expression of phosphoenolpyruvate carboxykinase (involved in the rate-controlling step of glucose synthesis; repressed by sugars) and CUT1 transport gene (involved in the transport of oligosaccharides) expression in the rhizosphere and the high expression of organic acid uptake and utilization genes in the contaminated rhizosphere suggest that simple sugars are not the main bacterial carbon source in the rhizosphere of willows. Organic acids were previously reported as the main source of carbon in the rhizosphere of many plants, including poplar (Jones, 1998;Lugtenberg et al, 2001;Naik et al, 2009;Ramachandran et al, 2011).…”

“…Biofilm formation is an essential feature of rhizosphere colonization (Lugtenberg et al, 2001;Ramey et al, 2004) and bacteria living in biofilms have increased resistance to environmental stresses (Costerton et al, 1999;Hogan and Kolter, 2002). Consequently, genes related to biofilm formation were reported to be over-expressed during rhizosphere colonization, and their inactivation led to reduced fitness (Matilla et al, 2007;Ramachandran et al, 2011;Fan et al, 2012). Some of the genes included in the quorum sensing and biofilm formation category (for example, N-acyl homoserine lactone synthetase) are also involved in plant-microbe communication, as N-acyl homoserine lactone will induce plants to release root exudates (Mathesius et al, 2003).…”

Shining a light on the dark world of plant root–microbe interactions

“…There are obviously a large range of Arabidopsis mutants that could be tested in this way, including those involved in immune signaling (18) and root secretion such as ABC exporters (19). The alternative approach will be to use bacteria labeled with inducible fluorescent, luminescent (e.g., lux) (20)(21)(22), or FRET biosensors (23) to monitor root secretion and the bacterial response to roots.…”

Application effects of biofertilizers on blackleg disease and the development of potato plants

“…Nascimento et al (2013) found better effectiveness of biofertilizers in relation to chemical fungicides to control anthracnose in tomato. Several studies have found satisfactory effects in disease control with the use of biofertilizers in plants such as watermelon, cucumber, pepper, peas and others (Murphy et al 2003;Barra et al, 2009;Ling et al 2011;Ramachandran et al 2011;Aravindi et al 2009). …”