Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella

Abstract

Investigation of the evolutionary relationships between related bacterial species and genera with a variety of lifestyles have gained popularity in recent years. For analysing the evolution of specific traits, however, a robust phylogeny is essential. In this study we examined the evolutionary relationships among the closely related genera Erwinia, Tatumella and Pantoea, and also attempted to resolve the species relationships within Pantoea. To accomplish this, we used the whole genome sequence data for 35 different strains belonging to these three genera, as well as nine outgroup taxa. Multigene datasets consisting of the 1039 genes shared by these 44 strains were then generated and subjected to maximum likelihood phylogenetic analyses, after which the results were compared to those using conventional multi-locus sequence analysis (MLSA) and ribosomal MLSA (rMLSA) approaches. The robustness of the respective phylogenies was then explored by considering the factors typically responsible for destabilizing phylogenetic trees. We found that the nucleotide datasets employed in the MLSA, rMLSA and 1039-gene datasets contained significant levels of homoplasy, substitution saturation and differential codon usage, all of which likely gave rise to the observed lineage specific rate heterogeneity. The effects of these factors were much less pronounced in the amino acid dataset for the 1039 genes, which allowed reconstruction of a fully supported and resolved phylogeny. The robustness of this amino acid tree was also supported by different subsets of the 1039 genes. In contrast to the smaller datasets (MLSA and rMLSA), the 1039 amino acid tree was also not as sensitive to long-branch attraction. The robust and well-supported evolutionary hypothesis for the three genera, which confidently resolved their various inter- and intrageneric relationships, represents a valuable resource for future studies. It will form the basis for studies aiming to understand the forces driving the divergence and maintenance of lineages, species and biological traits in this important group of bacteria.

Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost

“…Strikingly, out of 219 clinical strains, only two (0.91%) belong to the S. marcescens UENF-22GI clade, suggesting that strains from this group rarely cause opportunistic (mostly nosocomial) infections, as observed with those from more distant clades. A similar approach has been recently used to better define the phylogenetic structure of the Pantoea genus [ 53 ].…”

Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria

“…Therefore, more reliable approaches for phylogenetic inference were sought to obtain better resolved trees. This led to the use of multiple locus sequence analyses (MLSA) (Gevers et al, 2005 ; Konstantinidis and Tiedje, 2007 ; Glaeser and Kämpfer, 2015 ), ribosomal MLSA (Bennett et al, 2012 ) and more recently core genome phylogenies (Bennett et al, 2012 ; Chan et al, 2012 ; Rahman et al, 2015 ; Schwartz et al, 2015 ; Palmer et al, 2017 ). These approaches, especially those based on large numbers of core genes, provide robust evolutionary hypotheses that seems to be resilient to most known phylogenetic errors (Beukes et al, 2017 ; Palmer et al, 2017 ) and have recently formed the foundation of taxonomic decisions, particularly in problematic taxa (Zhang et al, 2011 ; Bennett et al, 2012 ; Chan et al, 2012 ; Richards et al, 2014 ; Ormeno-Orrillo et al, 2015 ; Rahman et al, 2015 ).…”

“…In this study, we explored the possibility of linking biological characters to higher-level taxonomic groups in bacteria by making use of whole genome sequence information. For this purpose we used the genus Pantoea for which genome sequences of 21 species were available (Hong et al, 2012 ; Kamber et al, 2012 ; Wan et al, 2015 ; Palmer et al, 2017 ). These were chosen to span the diversity of the genus, which includes plant pathogens ( P. agglomerans, P. ananatis, P. stewartii amongst others; Coutinho and Venter, 2009 ) and species that affect humans ( P. brenneri, P. conspicua, P. eucrina , and P. septica; Walterson and Stavrinides, 2015 ), as well as species that have been isolated from insects, fungal fruiting bodies and environmental samples (Walterson and Stavrinides, 2015 ; Ma et al, 2016 ; Palmer et al, 2016 ; Rong et al, 2016 ).…”

“…Overall the members of this genus appear to be highly adaptable to changing environments and may act opportunistically when in contact with potential eukaryotic hosts (Coutinho and Venter, 2009 ; De Maayer et al, 2012b , 2014 ; Walterson and Stavrinides, 2015 ). From a phylogenetic perspective, Pantoea and its sister taxon, Tatumella , are nested within the Enterobacteriaceae where they are closely related to Erwinia (Glaeser and Kämpfer, 2015 ; Palmer et al, 2017 ). Pantoea further separates into four well-supported lineages, viz .…”

“…indologenes ), P. rodasii (containing P. rodasii, P. rwandensis , and Pantoea sp. GM01) and P. dispersa (containing P. dispersa, P. eucrina and P. wallisii ) lineages (Palmer et al, 2017 ). Other than a limited set of general biological traits (e.g., colony and cell morphology, respiration status, growth temperature), characters that potentially define Pantoea and its lineages have never been identified.…”