Wars between microbes on roots and fruits [version 1; referees: 3 approved]

Microbes in nature often live in unfavorable conditions. To survive, they have to occupy niches close to food sources and efficiently utilize nutrients that are often present in very low concentrations. Moreover, they have to possess an arsenal of attack and defense mechanisms against competing bacteria. In this review, we will discuss strategies used by microbes to compete with each other in the rhizosphere and on fruits, with a focus on mechanisms of inter- and intra-species antagonism. Special attention will be paid to the recently discovered roles of volatile organic compounds. Several microbes with proven capabilities in the art of warfare are being applied in products used for the biological control of plant diseases, including post-harvest control of fruits and vegetables

Genome Analysis of Pseudomonas fluorescens PCL1751: A Rhizobacterium that Controls Root Diseases and Alleviates Salt Stress for Its Plant Host

Pseudomonas fluorescens PCL1751 is a rod-shaped Gram-negative bacterium isolated from the rhizosphere of a greenhouse-grown tomato plant in Uzbekistan. It controls several plant root diseases caused by Fusarium fungi through the mechanism of competition for nutrients and niches (CNN). This mechanism does not rely on the production of antibiotics, so it avoids the concerns of resistance development and is environmentally safe. Additionally, this bacterium promotes plant growth by alleviating salt stress for its plant host. To investigate the genetic mechanisms that may explain these observations, we determined the complete genome sequence of this bacterium, examined its gene content, and performed comparative genomics analysis with other Pseudomonas strains. The genome of P. fluorescens PCL1751 consisted of one circular chromosome that is 6,143,950 base-pairs (bp) in size; no plasmid was found. The annotation included 19 rRNA, 70 tRNA, and 5,534 protein-coding genes. The gene content analysis identified a large number of genes involved in chemotaxis and motility, colonization of the rhizosphere, siderophore biosynthesis, and osmoprotectant production. In contrast, the pathways involved in the biosynthesis of phytohormones or antibiotics were not found. Comparison with other Pseudomonas genomes revealed extensive variations in their genome size and gene content. The presence and absence of secretion system genes were highly variable. As expected, the synteny conservation among strains decreased as a function of phylogenetic divergence. The integration of prophages appeared to be an important driver for genome rearrangements. The whole-genome gene content analysis of this plant growth-promoting rhizobacterium (PGPR) provided some genetic explanations to its phenotypic characteristics. The extensive and versatile substrate utilization pathways, together with the presence of many genes involved in competitive root colonization, provided further support for the finding that this strain achieves biological control of pathogens through effective competition for nutrients and niches

Distribution pattern of homologous gene clusters.

<p>The maximum likelihood phylogeny was inferred from the concatenated protein alignment of 2,374 single-copy genes shared by all strains (with 783,597 aligned amino acids). All internal nodes received 100% bootstrap support based on 1,000 re-sampling and maximum likelihood inference. The numbers above each branch and proceeded by a ‘+’ sign indicate the numbers of homologous gene clusters that are uniquely present in all daughter lineages; the numbers below each branch and proceeded by a ‘-‘ sign indicate the numbers of homologous gene clusters that are uniquely absent.</p

Genome alignments.

<p>Pairwise genome alignments between <i>Pseudomonas fluorescens</i> PCL1751 and other related strains. The nucleotide (nt) and amino acid (aa) sequence similarities are calculated based on the concatenated alignment of 2,374 single-copy genes shared by all strains.</p

Secretion system gene clusters.

<p>The figure provides a visual summary of the presence (filled circles) and absence (empty circles) of genes involved in secretion systems in these genomes. Multi-copy genes are labeled by their copy number inside the filled circles.</p

Genome characteristics.

<p>Genome characteristics.</p

Selected metabolic pathways of <i>Pseudomonas fluorescens</i> PCL1751.

<p>This figure provides a visual summary of the gene content analysis described in the main text. Boxes drawn with dotted lines indicate the genes missing in the annotation.</p