Affiliation:
1. Joint Institute for Computational Sciences, University of Tennessee, Knoxville, Tennessee, USA
2. Molecular Microbiology and Genomics Consultants, Zotzenheim, Germany
3. Biosciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee, USA
Abstract
ABSTRACT
The
Pseudomonas
genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000
Pseudomonas
genomes, including 21
Pseudomonas
strains isolated from the roots of native
Populus deltoides
(eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All
Pseudomonas aeruginosa
genomes clustered together, and these were clearly distinct from other
Pseudomonas
species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of
Pseudomonas fluorescens
were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21
Populus
-associated isolates formed three distinct subgroups within the major
P. fluorescens
group, supported by pathway profile analysis, while two isolates were more closely related to
Pseudomonas chlororaphis
and
Pseudomonas putida
. Genes specific to
Populus
-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from
P. fluorescens
, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing
Pseudomonas
strains for use to promote growth and increase disease resistance in plants.
Funder
U.S. Department of Energy
Publisher
American Society for Microbiology
Subject
Ecology,Applied Microbiology and Biotechnology,Food Science,Biotechnology