Genomics-based design of defined growth media for the plant pathogenXylella fastidiosa

Abstract

Based on the genetic analysis of the phytopathogen Xylella fastidiosa genome, five media with defined composition were developed and the growth abilities of this fastidious prokaryote were evaluated in liquid media and on solid plates. All media had a common salt composition and included the same amounts of glucose and vitamins but differed in their amino acid content. XDM 1 medium contained amino acids threonine, serine, glycine, alanine, aspartic acid and glutamic acid, for which complete degradation pathways occur in X. fastidiosa; XDM 2 included serine and methionine, amino acids for which biosynthetic enzymes are absent, plus asparagine and glutamine, which are abundant in the xylem sap; XDM 3 had the same composition as XDM 2 but with asparagine replaced by aspartic acid due to the presence of complete degradation pathway for aspartic acid; XDM 4 was a minimal medium with glutamine as a sole nitrogen source; XDM 5 had the same composition as XDM 4 , plus methionine. The liquid and solidified XDM 2 and XDM 3 media were the most effective for the growth of X. fastidiosa. This work opens the opportunity for the in silico design of bacterial defined media once their genome is sequenced.

Novel Antibacterial Proteins from the Microbial Communities Associated with the Sponge Cymbastela concentrica and the Green Alga Ulva australis

“…Isolation of bioactives from environmental bacteria, however, faces the limitation that many strains are recalcitrant to culturing (1,33,48,51), and this might be particularly true for obligate or facultative symbionts. To access the uncultured majority of the microbial world (43), functional metagenomic approaches that allow for the expression of environmental DNA from uncultured organisms in surrogate hosts have been developed (6,22,32,35,36,46).…”

Saprophytic growth of the alder rust fungus Melampsoridium hiratsukanum on artificial media

“…Owing to the increasing availability of sequenced rust genomes, a knowledge of genes or gene families encoding enzymes that are essential for important biochemical pathways could soon become a reality (Duplessis et al 2011). Such findings may be vital for a more accurate delineation of the nutritional requirements of rusts and thus bring about a marked improvement of current growth media, such an improvement has already occurred for other groups of obligate plant parasites (Lemos et al 2003).…”

The multi-omics promise in context: from sequence to microbial isolate

“…An early example of genome-inspired medium design was the development of a defined medium for Xylella fastidiosa, a slow-growing plant pathogen inhabiting the xylem of citrus plants (Lemos et al 2003;Almeida et al 2004;Janse & Obradovic 2010). Even though the organism had been isolated with empirical methods before (Wells et al 1987), and its genome was sequenced in 2000 (Setubal et al 2000), Lemos et al (2003) revealed that a relatively simple medium composition supported growth.…”

“…Even though the organism had been isolated with empirical methods before (Wells et al 1987), and its genome was sequenced in 2000 (Setubal et al 2000), Lemos et al (2003) revealed that a relatively simple medium composition supported growth. They prepared five minimal media that differed in amino acid composition and concentration based on the presence or absence of genes for amino acid biosynthetic pathways in the X. fastidiosa genome.…”

“…For example, despite a predicted serine auxotrophy, growth occurred in serine-free media. Potential reasons for this incongruence include incorrect gene annotation, multifunctional enzymes, unknown metabolic pathways or enzymes encoded by analogous genes (Lemos et al 2003). This example shows how a variety of genome-tailored minimal medium designs can result in improved growth rates, but advocates at the same time that currently not all metabolic capabilities of the target organisms can be predicted correctly from genomic data.…”