Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates

Abstract

BackgroundPlant root exudates have been shown to play an important role in mediating interactions between plant growth-promoting rhizobacteria (PGPR) and their host plants. Most investigations were performed on Gram-negative rhizobacteria, while much less is known about Gram-positive rhizobacteria. To elucidate early responses of PGPR to root exudates, we investigated changes in the transcriptome of a Gram-positive PGPR to plant root exudates.ResultsBacillus amyloliquefaciens FZB42 is a well-studied Gram-positive PGPR. To obtain a comprehensive overview of FZB42 gene expression in response to maize root exudates, microarray experiments were performed. A total of 302 genes representing 8.2% of the FZB42 transcriptome showed significantly altered expression levels in the presence of root exudates. The majority of the genes (261) was up-regulated after incubation of FZB42 with root exudates, whereas only 41 genes were down-regulated. Several groups of the genes which were strongly induced by the root exudates are involved in metabolic pathways relating to nutrient utilization, bacterial chemotaxis and motility, and non-ribosomal synthesis of antimicrobial peptides and polyketides.ConclusionsHere we present a transcriptome analysis of the root-colonizing bacterium Bacillus amyloliquefaciens FZB42 in response to maize root exudates. The 302 genes identified as being differentially transcribed are proposed to be involved in interactions of Gram-positive bacteria with plants.

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

“…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).…”

Gene Deletions Resulting in Increased Nitrogen Release by Azotobacter vinelandii: Application of a Novel Nitrogen Biosensor

“…Biological assimilation of nutrients in addition to timed-release of nitrogen compounds would mitigate issues associated with agricultural residue runoff from excessive application of industrial fertilizers, leading to eutrophication of nearby water supplies and streams. Both higher land plants and microalgae are known to produce extracellular carbon as a potential source of fixed carbon to support beneficial heterotrophs that make up part of the rhizosphere (5,(12)(13)(14)(15).…”

Biotic Interactions in the Rhizosphere: A Diverse Cooperative Enterprise for Plant Productivity

“…They show that transcript-based cloning is a valid approach for cloning genes and that this method does not require the construction of a genetic map. This approach also could be used to study plant productivity and rhizosphere dynamics, as was done in some recent reports (Fan et al, 2012;Alavi et al, 2013;Carvalhais et al, 2013). Other important genes discovered with transcriptomics are the nodule Cys-rich antimicrobial peptides (NCR) genes.…”

“…In the rhizosphere of pea, R. leguminosarum expressed genes related to bacterial metabolism and Nod factor synthesis, while in the presence of the alfalfa rhizosphere, the genes involved in lignin breakdown and metabolite transporters were up-regulated (Ramachandran et al, 2011). Studies on the gram-positive rhizobacterium B. amyloliquefaciens in response to root exudates from maize revealed that 8.2% of the bacterial transcriptome was altered in the presence of these exudates (Fan et al, 2012). The majority of the altered genes were upregulated, and most of them are involved in nutrient utilization, bacterial chemotaxis and motility, and antimicrobial peptides.…”